@article {pmid42098757,
year = {2026},
author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J},
title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42098757},
issn = {1674-9782},
support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; },
abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.

RESULTS: Fifty‑six lactating Holstein cows (28 high‑yield cows, HY; 28 low‑yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high‑yield control (HCON), high‑yield SIF (HSIF), low‑yield control (LCON), and low‑yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.

CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.},
}

@article {pmid42098796,
year = {2026},
author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V},
title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42098796},
issn = {2049-2618},
support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Università e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; },
mesh = {Humans ; Female ; *Microbiota/genetics ; *Vulva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; *RNA, Messenger/genetics ; Vagina/microbiology ; *Host Microbial Interactions/genetics ; *RNA-Seq/methods ; Transcriptome ; },
abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.

RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.

CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.},
}

Humans
Female
*Microbiota/genetics
*Vulva/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
*RNA, Messenger/genetics
Vagina/microbiology
*Host Microbial Interactions/genetics
*RNA-Seq/methods
Transcriptome

@article {pmid42098798,
year = {2026},
author = {Evens, KC and Bakke, I and Bohannan, BJM},
title = {Aquaculture facility-specific microbiota shape the zebrafish gut microbiome.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00573-6},
pmid = {42098798},
issn = {2524-4671},
abstract = {BACKGROUND: Environmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.

RESULTS: We compared water and zebrafish gut microbiomes across five aquaculture facilities two in the United States and three in Norway- using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity analyses revealed significant clustering by sample type, facility, and geographic location, with facility identity explaining the largest proportion of compositional variance. Multivariate dispersion also differed significantly across facilities, indicating that observed compositional differences reflect both shifts in community composition and differences in within-facility variability. Each facility harbored a distinct microbial community in both water and fish gut samples, with geographic location further structuring community composition between Oregon and Norwegian facilities. Similarity Percentage analysis identified key taxa driving facility differences, including Cetobacterium, Vibrio, and Aeromonas in fish gut microbiomes and Pseudomonas and Rheinheimera in tank water. Microbial source tracking using FEAST revealed that facility-level tank water contributed measurably to fish gut microbiome composition in most facilities, though unknown sources dominated estimates across all facilities (71-99%) and the strength of fish-water microbiome association varied substantially across facilities.

CONCLUSIONS: This study demonstrates that zebrafish aquaculture facilities harbor unique microbial communities shaped by both environmental and geographic factors. While tank water microbiomes show associations with zebrafish gut microbiome composition, the dominant contribution of unknown sources to gut microbiome composition suggests that factors beyond the immediate tank water environment- including diet, host physiology, and other facility-specific conditions- are primary drivers of gut microbiome variation. The strength of this association varied considerably across facilities and appeared related to fish domestication history, a pattern that warrants direct experimental investigation. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration, unaccounted variation in environmental microbiota may affect microbiome composition and reduce cross-study reproducibility. Moving forward, standardized reporting of environmental conditions and microbial composition across facilities will be critical for strengthening reproducibility and interpretation in zebrafish microbiome research.},
}

@article {pmid42098855,
year = {2026},
author = {Sattayawat, P and Promubon, K and Sripinta, K and Chunguaongsuk, W and Juntama, C and Noirungsee, N and Panya, A and Disayathanoowat, T},
title = {Proof-of-concept engineering of Escherichia coli expressing a bee-derived cytochrome P450 monooxygenase for thiamethoxam detoxification.},
journal = {Journal of biological engineering},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13036-026-00686-1},
pmid = {42098855},
issn = {1754-1611},
abstract = {Bees are unintentionally exposed to pesticides applied to control other insect pests. Although bees possess endogenous detoxification mechanisms, their efficiency may not always be sufficient. To this end, the use of probiotics that can assist in pesticide detoxification may offer an additional layer of protection. In this study, we engineered Escherichia coli BL21(DE3) to heterologously express the bee-derived cytochrome P450 monooxygenase (CYP450), CYP9Q1, from Apis mellifera as a proof-of-concept microbial platform for thiamethoxam biotransformation and future microbiome-assisted pesticide detoxification strategies. We first assessed the toxicity of thiamethoxam, a systemic insecticide, on E. coli, which showed obvious impaired growth at relatively high concentrations (5 and 10 g/L). Subsequently, we computationally modeled the 3D structure and modified the CYP450 to improve its solubility when expressed in E. coli. Molecular docking of the CYP450 and thiamethoxam was also performed to confirm their potential interaction. pRSFDuet-1 plasmid was used to carry the modified CYP450 gene for expression in E. coli and the induction condition was optimized, with 0.5 mM isopropyl 𝛽-D-1-thiogalactopyranoside (IPTG) yielding the most favorable expression level. A whole-cell detoxification assay subsequently showed reduced concentrations of thiamethoxam after 46 h of biocatalytic activity, as monitored by High-Performance Liquid Chromatography (HPLC). Liquid Chromatography-Mass Spectrometry (LC-MS) analysis further revealed the presence of desnitro thiamethoxam corresponding to m/z 247.04105 confirming enzymatic transformation of thiamethoxam. To our knowledge, this study provides the first demonstration of bee CYP9Q1 heterologous expression in E. coli for whole-cell thiamethoxam biotransformation, highlighting its potential as a platform for developing probiotic or gut microbiome-based detoxification strategies to support bee pesticide tolerance.},
}

@article {pmid42098876,
year = {2026},
author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B},
title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02406-9},
pmid = {42098876},
issn = {2049-2618},
support = {2023YFD2000703//National Key R&D Program of China/ ; 2023YFD2000701//National Key R&D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.

RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150 kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20 g/kg dry matter) decreased daily CH4 emissions by ~ 8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.

CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.},
}

@article {pmid42098920,
year = {2026},
author = {Zhang, H and Ni, T and Zha, X and Elsabagh, M and Wang, M},
title = {The Involvement of Gut Microbiota and Their Key Metabolites in Regulating Fetal Development via the Gut-Placental Axis.},
journal = {Cellular reprogramming},
volume = {},
number = {},
pages = {21524971261450000},
doi = {10.1177/21524971261450000},
pmid = {42098920},
issn = {2152-4998},
abstract = {The gut is the organ with the largest number of microorganisms in the organism, and host-microbe interactions allow the host to shape the composition of the microbiome and thus its numbers and diversity. The gut microbiome is integral to the facilitation of vital host functions that have a direct impact on the overall health of the host. This paper aims to present a thorough overview of the composition and function of the gut microbiome and its main metabolites (such as lipopolysaccharides, short-chain fatty acids, and bile acids), as well as their key roles and mechanisms in fetal development. The theme highlights the significance of the gut microbiome in fetal development, and the paper aims to establish their relationship and importance in a systematic manner. In the latter portion of the article, an analysis is presented regarding the proposed mechanism of the gut-placental axis, with an effort to outline strategies for regulating maternal gut microbiology in order to enhance fetal growth and development. By delving into this subject matter extensively, we aim to enhance comprehension of the correlation between maternal gut microbes and fetal development. This can contribute to safeguarding the mother's health, enhancing the survival and well-being of the fetus, and carrying significance for both human and animal reproduction. Furthermore, it can provide valuable insights for future research and clinical practices.},
}

@article {pmid42099162,
year = {2026},
author = {Kurmi, S and Shirodkar, S and Parab, SB and Doshi, G},
title = {A Multimodal Framework for Alzheimer's Prevention: Diet, Exercise, Fasting, Sleep, and Gut Microbiota.},
journal = {Current Alzheimer research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672050467997260323164241},
pmid = {42099162},
issn = {1875-5828},
abstract = {Alzheimer's Disease (AD) and related dementias arise from a multifactorial interplay of genetic susceptibility, metabolic dysfunction, neuroinflammation, and lifestyle determinants. With limited disease-modifying pharmacotherapies, lifestyle interventions have emerged as compelling, evidence-based avenues for prevention and early management. This review integrates mechanistic, translational, and clinical insights on major modifiable behaviours, physical activity, diet, intermittent fasting, sleep regulation, and gut-microbiome-based approaches that collectively shape cognitive ageing. Aerobic, anaerobic, and resistance exercises exert neuroprotective effects by activating BDNF-TrkB signalling, enhancing hippocampal neurogenesis, improving synaptic plasticity, and stimulating peripheral myokines (CTSB, IGF-1, GPLD1) that cross the blood-brain barrier to support neuronal resilience. Dietary interventions such as the Mediterranean, Mediterranean- DASH Intervention for Neurodegenerative Delay (MIND), and ketogenic diets mitigate AD pathology by reducing oxidative stress, inhibiting Aβ deposition, improving mitochondrial efficiency, and modulating APOE4-linked metabolic vulnerability. Intermittent fasting induces a metabolic shift toward ketone utilisation, activates autophagy pathways (AMPK, SIRT3, Nrf2), remodels the gut microbiome, and promotes angiogenesis through GDF11 signalling. The gut-brain axis contributes to cognitive health through microbial metabolites, such as Short-Chain Fatty Acids (SCFAs), tryptophan derivatives, modulation of neuroinflammation, and enhanced neuronal survival. Meanwhile, sleep quality, particularly slow-wave sleep, optimises glymphatic clearance and prevents the pathological accumulation of Aβ and tau. Collectively, the evidence suggests that multidomain lifestyle approaches offer synergistic benefits that exceed those of individual interventions, representing promising strategies for delaying cognitive decline. However, gaps remain regarding dose-response relationships, personalised protocols for APOE4 carriers, and long-term validation in diverse populations. Strengthening these research directions is crucial for integrating lifestyle medicine into preventive neurology and public health frameworks.},
}

@article {pmid42099164,
year = {2026},
author = {Nayak, RK and Mohapatra, SR and Sahoo, SK and Sahu, SK and Chowdhury, B and Banu, Z and Das, NR},
title = {Gut Microbiota Dysbiosis in Alzheimer's Disease and Possible Therapeutic Options.},
journal = {Current Alzheimer research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672050448298260303052535},
pmid = {42099164},
issn = {1875-5828},
abstract = {Human microbiota consists of trillions of microbial cells dominated by bacteria, which live in the human body, while the term microbiome refers to the collective genetic material of microorganisms. Among them, the gut microbiota has emerged as pivotal, producing its own metabolites, neurotransmitter precursors, and immune mediators that affect brain development and function. These signals function via the complex, bidirectional Gut-Brain Axis (GBA). This is a communication network that connects the gastrointestinal tract to the central nervous system. This axis plays an important role in the regulation of gastrointestinal homeostasis, neurodevelopment, emotional regulation, and cognitive processes. Increasing evidence suggests that microbial dysbiosis within the gastrointestinal tract is involved in the pathogenesis and progression of several neurological and neurodegenerative disorders, including mood disorders, schizophrenia, autism spectrum disorder, Alzheimer's Disease (AD), Parkinson's Disease (PD), and Huntington's Disease. These insights have opened new therapeutic possibilities, and multiple microbiota-targeted interventions, such as dietary modification, prebiotics, probiotics, postbiotics, psychobiotics, antibiotics, and Fecal Microbiota Transplantation (FMT), are now being explored for their therapeutic value, especially in Alzheimer's disease.},
}

@article {pmid42099232,
year = {2026},
author = {Song, J and Cui, H and Yang, P and Xu, Y and Liu, Y and Zhang, G and Liu, Y and Tian, A and Che, J and Sun, H and Zhang, Z},
title = {Gut microbiota and its metabolites: Key factors of drug resistance in the treatment of advanced prostate cancer (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {1},
pages = {},
doi = {10.3892/mmr.2026.13900},
pmid = {42099232},
issn = {1791-3004},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; *Prostatic Neoplasms/metabolism/drug therapy/microbiology/pathology/therapy ; *Drug Resistance, Neoplasm ; Antineoplastic Agents/therapeutic use/pharmacology ; Animals ; },
abstract = {Prostate cancer (PCa) is a leading cause of cancer‑related deaths among men, and its incidence is increasing worldwide. Current treatments include androgen deprivation therapy, surgery, radiotherapy, chemotherapy and immunotherapy, among others. Surgical treatment has a less effective therapeutic effect in patients with advanced PCa. However, drug‑based treatments often lead to the development of drug resistance, highlighting the need to adopt new treatment strategies. The present review summarizes the role of gut microbiota and its metabolites in the treatment resistance of advanced PCa, potential microbiome‑targeted therapies and future research directions, for developing novel therapeutic approaches to overcome drug resistance and improve prognosis.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
*Prostatic Neoplasms/metabolism/drug therapy/microbiology/pathology/therapy
*Drug Resistance, Neoplasm
Antineoplastic Agents/therapeutic use/pharmacology
Animals

@article {pmid42099457,
year = {2026},
author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y},
title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70123},
pmid = {42099457},
issn = {2770-596X},
abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.},
}

@article {pmid42099459,
year = {2026},
author = {Bai, D and Fang, O and Li, C and Cai, B and Tan, X and Jiang, M and Gan, B and Fu, J and Gao, Y and Wang, Y and Liu, YX},
title = {Accu16S/AccuITS: Accurate and broadly applicable amplicon sequencing for absolute microbiome quantification.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70116},
pmid = {42099459},
issn = {2770-596X},
abstract = {Traditional 16S rRNA gene and Internal Transcribed Spacer region amplicon sequencing provides only relative abundance, often leading to biased ecological interpretations. To overcome this limitation, we developed Accu16S/AccuITS, an absolute quantification method for bacterial and fungal amplicons based on synthetic internal spike-in DNA with known copy numbers. By adding internal standards prior to Polymerase Chain Reaction and sequencing, absolute microbial abundances can be calculated using standard curve regression. Accu16S/AccuITS exhibits sensitivity and consistency comparable to quantitative Polymerase Chain Reaction and is applicable to diverse sample types. A single sequencing run simultaneously yields relative abundance, total absolute abundance, and taxon-specific absolute abundance. Case studies across diverse ecosystems demonstrate that absolute quantification provides ecologically and functionally meaningful insights beyond those obtained from relative abundance analyses.},
}

@article {pmid42099462,
year = {2026},
author = {Zhang, C and Du, Y and Wu, M and Li, C and Jiang, R and Qi, E and Li, S and Yi, X and Chu, B and Feng, S and Zhou, H},
title = {Spinal cord injury induces acute microbiome shock and system-wide transcriptomic reprogramming.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70128},
pmid = {42099462},
issn = {2770-596X},
abstract = {This study investigates the systemic consequences of spinal cord injury (SCI), with a particular focus on alterations in the gut microbiome and multi-organ transcriptomic responses. We identify a rapid and severe disruption of the gut microbiota-termed "microbiome shock"-that emerges within 12 h post-SCI and persists before gradually resolving by 5 days post-injury. To support further research in this field, we established an open-access resource, the Spinal Cord Injury Gut Microbiome and Multi-Organ Gene Expression Atlas (SCIGAMA).},
}

@article {pmid42099557,
year = {2026},
author = {Cui, G and Wang, X and Hong, W and Chen, Z and Kang, Y},
title = {Beyond antibiotics: Multidimensional interventions and coordinated governance against ESKAPE resistance.},
journal = {Biosafety and health},
volume = {8},
number = {2},
pages = {81-85},
pmid = {42099557},
issn = {2590-0536},
abstract = {ESKAPE, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. pose a significant global health threat due to their extensive drug resistance and rapid evolutionary capacity. This article advocates a paradigm shift from conventional antibiotic warfare to "ecological co-management", integrating four innovative strategies plus an overarching framework: (1) microbiome-based interventions using probiotics, phages, and niche modulation; (2) a One Health 2.0 framework that incorporates wastewater surveillance and artificial intelligence (AI)-driven stewardship; (3) evolutionary constraint methods including anti-virulence agents and clustered regularly interspaced short palindromic repeats (CRISPR)-based targeting; (4) metabolic pathway intervention and antimetabolite therapy such as biotin biosynthesis inhibition; and (5) the establishment of a clinical translation and risk management system for innovative antimicrobial strategies. These multidimensional efforts aim to disrupt resistance transmission, restore antibiotic susceptibility, and promote sustainable pathogen control through ecological and systems-level integration.},
}

@article {pmid42099577,
year = {2026},
author = {Penton, CR and Vadakattu, G},
title = {The root rhizosphere as a functional analog to the gut microbiome: Cases for microbial symbiosis and dysbiosis in parallel contexts.},
journal = {PNAS nexus},
volume = {5},
number = {5},
pages = {pgag132},
pmid = {42099577},
issn = {2752-6542},
abstract = {Microbiomes associated with both the human gut and plant root rhizosphere are essential for the maintenance of host health and function as holobionts where both the host and microbiome operate as an integrated unit. Though substantial differences exist in both host biology and environment, these systems share functional parallels: both are enriched by host-derived nutrients, undergo successional shifts during development, and maintain core microbiomes that are taxonomically variable yet functionally redundant. Central to both systems is the balance that is maintained where beneficial microbes regulate nutrient cycling, modulate host immune response, and suppress pathogens in the presence of biotic and abiotic influences that may serve to disrupt this equilibrium. When dysbiosis occurs, there is a disruption in the composition and/or function of the associated microbiome and a loss of beneficial functional guilds, which results in a reduction in host fitness. These shared dynamics underscore dysbiosis as a cross-kingdom pathology that may be treated with similar interventions. Probiotics and prebiotics mirror microbial inoculants and organic amendments; synbiotics incorporate both biotic and abiotic factors, while fecal and soil microbiome transplants represent parallel strategies to restore a beneficial microbiome. By framing dysbiosis within a "One Health" perspective and illustrating the connectedness between human and plant health, this review advocates for microbial stewardship as a unifying strategy to mitigate disease, enhance resilience, and ensure sustainable health across both systems.},
}

@article {pmid42099587,
year = {2026},
author = {Xie, X and Chen, X and Wang, Z and Chen, Y and Li, J},
title = {The role of gut microbiota-immune-endocrine crosstalk in the pathogenesis of osteoporosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1813653},
pmid = {42099587},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Osteoporosis/immunology/metabolism/microbiology/etiology ; Animals ; Dysbiosis/immunology ; *Endocrine System/immunology/metabolism ; Female ; Bone and Bones/metabolism/immunology ; },
abstract = {Osteoporosis (OP) is a common metabolic bone disorder characterized by decreased bone mass and deterioration of bone microarchitecture that result in increased bone fragility and fracture risk, especially in postmenopausal women and older adults. The gut microbiota-immune-endocrine axis has recently emerged as an important regulator of bone homeostasis, but its mechanistic role in OP pathogenesis remains incompletely understood. This review synthesizes current evidence on how gut dysbiosis, immune dysregulation, and endocrine changes interact to promote bone loss. Clinical and preclinical studies indicate that gut dysbiosis in OP is characterized by reduced microbial diversity and an increased Firmicutes/Bacteroidetes ratio, leading to altered levels of key microbial metabolites-such as decreased short-chain fatty acids (SCFAs) that normally promote bone formation, and increased lipopolysaccharide (LPS) that drives inflammation. Immune changes include chronic low-grade inflammation with elevated pro-inflammatory cytokines [e.g., tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6)] and an imbalanced T-cell profile skewed toward osteoclastogenic T helper 17 (Th17) over anti-osteoclastogenic regulatory T (Treg) cells, which together favor bone resorption. Endocrine factors further modulate this gut-bone crosstalk: estrogen deficiency (in postmenopausal OP) promotes gut dysbiosis and Th17 expansion; excess glucocorticoids compromise the gut barrier and induce dysbiosis; gut-derived incretin hormones [e.g., glucagon-like peptide-1 (GLP-1) and peptide YY (PYY)] are influenced by microbial metabolites like butyrate; and parathyroid hormone (PTH) effects on bone are both regulated by and dependent on the gut microbiota. Overall, OP can be viewed as a multi-system disorder involving an interplay among the gut microbiome, the immune system, and the endocrine system. This integrated perspective on the "gut-bone axis" suggests that interventions targeting the gut microbiota (probiotics, prebiotics, etc.) could complement traditional therapies for OP. Enhancing skeletal health may require a multidisciplinary approach that considers gut microbial status, immune function, and hormonal milieu in tandem.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Osteoporosis/immunology/metabolism/microbiology/etiology
Animals
Dysbiosis/immunology
*Endocrine System/immunology/metabolism
Female
Bone and Bones/metabolism/immunology

@article {pmid42099620,
year = {2026},
author = {Mo, M and Chen, L and Wang, Y and Lin, X and Li, H and Chen, B and Yuan, J and Tao, E},
title = {The gut-lung axis in childhood asthma: from early-life programming to microbiome-informed precision medicine-a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1814901},
pmid = {42099620},
issn = {1664-3224},
mesh = {Humans ; *Asthma/microbiology/immunology/etiology/therapy ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; *Lung/immunology/microbiology ; Child ; Dysbiosis ; },
abstract = {The gut-lung axis links early-life microbial programming to long-term respiratory health, offering a pivotal framework for understanding childhood asthma pathogenesis. This review synthesizes current evidence on how disruptions in microbial-immune crosstalk during critical developmental windows shape asthma susceptibility. Perinatal determinants-including maternal diet, delivery mode, antibiotic exposure, and breastfeeding-establish gut microbial communities that educate the developing immune system. Distinguishing itself from recent reviews, this review offers three novel contributions: (i) an integrated multi-omics framework linking early-life microbial maturation trajectories to specific asthma endotypes; (ii) a systematic synthesis of the molecular mechanisms by which microbial metabolites-including short-chain fatty acids, tryptophan derivatives, and bile acids-orchestrate gut-lung immune crosstalk; and (iii) a clinically actionable precision medicine algorithm that translates multi-omics profiling into personalized risk prediction, endotype-driven therapy selection, and targeted preventive strategies. Dysbiosis, characterized by delayed microbial maturation and depletion of short-chain fatty acid-producing taxa, compromises epithelial barrier integrity and skews immune homeostasis toward pro-allergic type-2 responses. Microbial metabolites, particularly short-chain fatty acids (acetate, propionate, butyrate) and tryptophan derivatives (indole-3-lactic acid, indole-3-propionic acid), serve as key molecular mediators that regulate regulatory T cells differentiation, reinforce mucosal barriers, and modulate distal airway inflammation. Microbial signatures correlate with specific asthma endotypes, offering opportunities for patient stratification. We critically evaluate emerging microbiome-targeted interventions-including strain-specific probiotics, prebiotics, postbiotics, and fecal microbiota transplantation-highlighting both therapeutic promise and the need for rigorous, well-powered clinical trials. Integrating multi-omics microbial profiling with host genetics and clinical phenotyping holds potential for microbiome-informed precision medicine, enabling personalized risk prediction, endotype-driven therapy selection, and novel preventive strategies targeting the gut-lung axis from the earliest stages of life.},
}

Humans
*Asthma/microbiology/immunology/etiology/therapy
*Gastrointestinal Microbiome/immunology
Precision Medicine
*Lung/immunology/microbiology
Child
Dysbiosis

@article {pmid42099642,
year = {2026},
author = {Li, J and Chen, H and Zhou, Y and Sun, L and Xing, Y and Sun, Y and Yang, Y and Shi, Y},
title = {Angel or demon? The dual role of branched-chain amino acids in chronic inflammatory and injury-related diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1778455},
pmid = {42099642},
issn = {1664-3224},
mesh = {Humans ; *Amino Acids, Branched-Chain/metabolism ; Animals ; *Inflammation/metabolism ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Signal Transduction ; Diabetes Mellitus, Type 2/metabolism ; Chronic Disease ; },
abstract = {Branched-chain amino acids (BCAAs)-leucine, isoleucine, and valine-are essential nutrients that exhibit context-dependent, paradoxical effects on human health, with mTORC1 (mechanistic target of rapamycin complex 1) signaling serving as a central mechanistic node through which physiological BCAA concentrations support anabolism and repair while chronic pathological elevation drives metabolic and inflammatory injury. While their anabolic properties in promoting muscle protein synthesis, modulating immune responses, and conferring hepatoprotection are well-documented, accumulating evidence demonstrates that chronically elevated circulating BCAA concentrations are strongly associated with the pathogenesis and progression of metabolic, inflammatory, and injury-related diseases, including insulin resistance, type 2 diabetes mellitus (T2DM), cardiovascular disease (CVD), metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD), and certain malignancies. This biological duality is mechanistically rooted in a network of interconnected pathological processes, in which BCAA-mediated modulation of mTORC1 signaling-already introduced above-represents one central hub operating alongside impaired catabolic flux, accumulation of branched-chain α-keto acids (BCKAs) and branched-chain acylcarnitines, mitochondrial redox imbalance, and cellular stress pathway activation. Physiological BCAA concentrations support anabolic processes and cellular repair, whereas chronic pathological elevation is associated with mTORC1 hyperactivation alongside impaired BCKDH-mediated catabolic flux, accumulation of branched-chain α-keto acids (BCKAs) and branched-chain acylcarnitines, mitochondrial redox imbalance, and activation of cellular stress pathways-collectively contributing to disrupted metabolic homeostasis, amplified inflammatory cascades, and mitochondrial dysfunction. The ultimate biological impact of BCAAs is not intrinsic to these amino acids but rather is determined by a complex interplay of factors including: dosage and duration of exposure, individual metabolic status (particularly insulin sensitivity and mitochondrial oxidative capacity), specific disease context, and genetic polymorphisms affecting BCAA metabolism alongside gut microbiome composition. This review comprehensively synthesizes current understanding of BCAA biology and advocates for a paradigm shift toward precision nutrition approaches. Evidence supports therapeutic BCAA supplementation in hypercatabolic conditions such as sarcopenia and hepatic cirrhosis, while suggesting potential adverse metabolic consequences in insulin-resistant or obese individuals. Future nutritional and therapeutic strategies should transition from universal dietary recommendations to personalized interventions based on comprehensive metabolic phenotyping and genetic profiling, thereby optimizing BCAA intake for individual health trajectories and providing novel preventive and therapeutic opportunities for chronic disease management.},
}

Humans
*Amino Acids, Branched-Chain/metabolism
Animals
*Inflammation/metabolism
Mechanistic Target of Rapamycin Complex 1/metabolism
Signal Transduction
Diabetes Mellitus, Type 2/metabolism
Chronic Disease

@article {pmid42099660,
year = {2026},
author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF},
title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.},
journal = {BJUI compass},
volume = {7},
number = {5},
pages = {e70186},
pmid = {42099660},
issn = {2688-4526},
abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.

SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12 weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.

RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p = 0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p = 0.001), Bray-Curtis (p = 0.008), and nonweighted UniFrac metrics (p = 0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p = 0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p = 0.043) but not of treatment response.

CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.},
}

@article {pmid42099859,
year = {2026},
author = {Hwang, I and Seo, M},
title = {Complex food matrices reveal microbiota-nutrient balance interactions that modulate gut microbiome diversity in vitro.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101423},
pmid = {42099859},
issn = {2665-9271},
abstract = {Diet-microbiome relationships are often evaluated using isolated nutrients, yet microbes encounter complex food matrices in which nutrient accessibility and baseline microbial community context jointly shape gut fermentation outcomes. This study integrated an in vitro digestion and gut fermentation to examine the nutrient-baseline microbiota interaction to modulate community diversity. Nutrient-defined matrix classes were grouped using free saccharides, free amino acids, and free fatty acids content in food digesta. Two machine learning models-a classification model that predicted nutrient-defined matrix class from genus-level relative abundance changes (0-12 h) and regression models that predicted α-diversity change using nutrient and baseline (0 h) community features-were developed. SHAP-based feature attribution revealed that three nutrient-defined matrix classes exhibited distinct microbial response signatures (Turicibacter/Alistipes/Staphylococcus-centered), suggesting post-digestion nutrient associations with gut microbial restructuring patterns. However, α-diversity shifts within the same nutrient class were bidirectional, and inclusion of baseline microbiota features improved model performance for predicting diversity change from R[2] = 0.34 to R[2] = 0.72, consistent with a role for baseline-nutrient interactions. Fermented food matrices further illustrated that food-associated microbial contexts can modify restructuring trajectories beyond nutrient profiles. Overall, these findings propose that diversity outcomes during fermentation may depend on baseline-conditioned responses to bioaccessible nutrients, highlighting a matrix-specific but context-dependent diet-microbiome effects.},
}

@article {pmid42099956,
year = {2026},
author = {Vigneron, M and Halary, S and Crochemore, S and Plaisance, L and Parthuisot, N and Bettarel, Y},
title = {Uncovering leaf and root microbiomes of mangrove trees in French Guiana.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1782119},
pmid = {42099956},
issn = {2813-4338},
abstract = {Microorganisms are now widely acknowledged as essential contributors to the health and resilience of coastal environments. Yet, mangrove ecosystems, despite offering numerous ecological and economic services, remain relatively overlooked in microbial research. In this study, we examined the bacteriome of the rhizosphere and the phyllosphere of two mangrove tree species: Avicennia germinans and Rhizophora mangle. Both species were sampled along the banks of the Sinnamary estuary in French Guiana. Our results revealed notable differences in microbiome composition between the two organs and between the two tree species. On average, only 0.3% of ASVs were shared between the leaves and roots and 2.2% between A. germinans and R. mangle. The taxonomic differences were characterized mainly by the significant presence of Rhodothermia and Bacteroidia in the leaves and Cyanobacteria and Planctomycetia in the roots. Furthermore, our results showed that the root microbiome of both species was only weakly influenced by the surrounding water and sediment, with an average of less than 0.7% of ASVs shared. Finally, our study indicates a strong specificity in the bacterial communities of both the phyllosphere and rhizosphere and also raises questions regarding the near absence of Gammaproteobacteria in both the leaves and roots, which remain to be elucidated.},
}

@article {pmid42099957,
year = {2026},
author = {Alali, MA and Shori, AB},
title = {Understanding the human gut microbiome: from composition to disease association.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1717288},
pmid = {42099957},
issn = {2813-4338},
abstract = {The human gut microbiota is critical for regulating host metabolism, immune responses, epithelial integrity, and systemic homeostasis, and disturbance has been linked to metabolic, inflammatory, and immune-mediated illnesses. Despite significant advances in microbiome research, the interpretation of gut microbiota-disease relationships is still limited by an overreliance on taxonomic profiling and observational study designs, which frequently overlook functional, strain-level, and mechanistic aspects of host-microbiota interactions. Growing research suggests that microbial functional capacity, metabolic activity, and ecological features such as resilience and functional redundancy are better markers of gut health than compositional measurements alone. Nonetheless, significant inter-individual variability, methodological heterogeneity, and dependence on fecal-based analysis continue to limit reproducibility and causal inference across studies. This review integrates current evidence on gut microbiota composition, functional features, and important influencing variables, while emphasizing mechanistic linkages between microbial dysbiosis and major human illnesses, filling significant conceptual gaps in modern microbiome research.},
}

@article {pmid42099988,
year = {2026},
author = {Minhajuddin, F and Colgan, SP and Cartwright, IM},
title = {Impact of Neutrophils on the Tissue Microenvironment During Intestinal Inflammation.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {540855},
pmid = {42099988},
issn = {1178-7031},
abstract = {Neutrophils (polymorphonuclear leukocytes, PMN) are abundant innate immune cells that rapidly accumulate at mucosal surfaces during inflammation. While their antimicrobial functions are essential for host defense, sustained PMN activation profoundly alters the tissue microenvironment, driving epithelial barrier disruption, ECM remodeling, metabolic imbalance, and microbiome dysbiosis. In chronic inflammatory diseases such as inflammatory bowel disease (IBD), these processes contribute to persistent tissue injury and therapeutic resistance. In this review, we synthesize evidence from human mucosal biopsies, experimental models of intestinal inflammation, and emerging single-cell, spatial, and metabolic approaches to define how PMN shape the inflamed mucosal microenvironment. We highlight mechanisms governing PMN recruitment, retention, and survival; effector programs including reactive oxygen species production, protease release, and PMN extracellular trap formation; and bidirectional crosstalk with epithelial, stromal, and immune cell compartments. We further discuss how PMN-driven metabolic and microbiome alterations reinforce chronic inflammation and influence responses to biologic therapy. Collectively, these insights reframe PMN as context-dependent regulators of mucosal pathology and repair and identify PMN-centered pathways as promising targets for precision therapies aimed at restoring barrier function and promoting durable inflammatory resolution.},
}

@article {pmid42100045,
year = {2026},
author = {Panwar, N and Stewart, JE and Ibarra Caballero, JR and Szczepaniec, A},
title = {Characterizing fungal community shifts associated with Amauromyza karli Hendel (Diptera: Agromyzidae) infestation in quinoa.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1741091},
pmid = {42100045},
issn = {1664-462X},
abstract = {INTRODUCTION: Fungal communities are central elements of phytobiomes, yet their roles in mediating plant-insect interactions remain poorly understood. Here, we addressed this knowledge gap in quinoa, which has recently suffered significant losses due to a stem-boring pest.

METHODS: We used culture-based isolation from stems and amplicon-based profiling of rhizosphere soils to characterize quinoa-associated fungi across six site-year combinations in Colorado and to relate community patterns to abundance of stem-boring fly Amauromyza karli Hendel (Diptera: Agromyzidae).

RESULTS: Eighteen stem endophytes dominated by Ascomycota were isolated. Soil sequencing resolved 23 core amplicon sequence variants detected across all site-years; the core was primarily Ascomycota, with Fusarium spp., Alternaria spp., and Plectosphaerella spp. comprising over half of relative abundance of the entire community. Alpha diversity (richness, Shannon, inverse Simpson) differed significantly among site-years, and beta-diversity analyses revealed clustering by site and year. Abundance of adult A. karli was correlated positively with soil fungal richness and Shannon diversity and was also significantly associated with differences in community composition. Indicator and differential-abundance analyses identified taxa linked to low fly abundance (e.g., Cladosporium herbarum, Alternaria spp.) versus high abundance (e.g., Fusarium solani, Microdochium spp.). Fusarium spp., and Alternaria spp. were more prevalent in fields with high larval abundance, whereas antagonistic endophytes such as Gibellulopsis piscis and Heydenia spp. dominated in low-abundance fields.

DISCUSSION: These results indicated that community composition impacted pest pressure, with pathogenic fungi coinciding with higher fly abundance and entomopathogenic fungi enriched where larval pressure was lower. These findings identify candidate taxa for microbiome-informed integrated pest management and underscore the potential of site-specific practices (e.g., intercrops, organic amendments) to foster fungal communities that enhance quinoa resilience.},
}

@article {pmid42100046,
year = {2026},
author = {Li, X and Zhao, D and Zhao, J and Li, C and Deng, W and Gao, S and Chen, G and Hu, H},
title = {Response of Morus alba L. to cadmium stress with potential for restoration: physiological and microbiological perspectives.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1795556},
pmid = {42100046},
issn = {1664-462X},
abstract = {Cadmium (Cd) contamination threatens plant productivity and the stability of soil ecosystems. However, the mechanisms by which woody plants tolerate Cd stress remain incompletely understood. In this study, one-year-old Morus alba L. saplings were exposed to a gradient of Cd concentrations to investigate plant physiological responses, metal allocation patterns, cellular ultrastructure, and rhizosphere microbial communities. Increasing Cd concentrations progressively reduced plant growth, nutrient status, pigment content, and photosynthetic performance, while oxidative stress and membrane damage increased. In contrast, low Cd exposure induced a mild hormetic response, characterized by enhanced antioxidant activity, osmotic regulation, and a temporary increase in photosynthetic capacity. Bioaccumulation indices together with ultrastructural observations revealed a dose-dependent change in Cd handling. Under lower Cd exposure, Cd was more readily translocated to shoots, whereas higher Cd levels promoted root sequestration and intracellular compartmentalization. Despite Cd treatment, rhizosphere bacterial α-diversity remained relatively stable, although several Cd-tolerant taxa increased in relative abundance. Overall, these results demonstrate the tolerance capacity of M. alba to Cd stress and highlight its potential for the phytoremediation of mildly to moderately Cd-contaminated soils.},
}

@article {pmid42100057,
year = {2026},
author = {Gimignani, G and Borello, A and Panetta, C and Lucchetti, L and Caorsi, R and Gattorno, M and Conforti, A},
title = {Age-Related Microbiota Signatures in Inflammatory Diseases: Comparative Insights into Paediatric and Adult Crohn's Disease, Ulcerative Colitis, and Spondyloarthritis.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {1},
pages = {146-155},
pmid = {42100057},
issn = {2529-198X},
abstract = {OBJECTIVES: The study investigated the relationship among the human microbiota in the development and progression of inflammatory bowel diseases (IBD), specifically Crohn's Disease (CD) and Ulcerative Colitis (UC), as well as Spondyloarthritis (SpA), comparing paediatric and adult populations.

METHODS: The research elaborated the distinct characteristics and impacts of CD, UC, and SpA across age groups. It further explored the developmental stages of the paediatric microbiota, identifying factors like delivery method, feeding, and antibiotics as critical influencers. It examined specific dysbiosis patterns in paediatric IBD and SpA associated to disease activity. Subsequently, it addressed the adult microbiota's stability and variations due to diet, lifestyle, and medications, detailing microbial alterations in adult CD, UC, and SpA.

RESULTS: A comparative analysis underscores age-related differences in microbiota composition, clinical manifestations, and treatment responses, indicating greater yet weaker microbial populations in adults. In paediatric patients, there was a marked decrease in Faecalibacterium prausnitzii and other bacteria responsible for producing short-chain fatty acids. In contrast, adults tended to show a more persistent form of dysbiosis and lower microbiome resilience. These disparities in microbial and metabolic phenotypes were strongly associated with the activity of the disease and the response to the treatment, which suggests the potential of microbiota-based biomarkers to create age-specific diagnostic and therapeutic approaches.

CONCLUSION: This research found that microbiota play a great role in the inflammatory diseases and they can be of great use in the current treatments as well as serve as a biomarker. The new targeted therapies underscored the necessity of patient specific microbiome studies to enhance diagnostics and therapies of these disorders throughout the lifespan.},
}

@article {pmid42100141,
year = {2026},
author = {Doyle, WJ and Schumacher, SM and Gates, MR and Sofaly, N and Angelo, E and Hedelius, H and Johnson, DR and Wells, J and Perlmutter, M and Caradonna, K and Ochoa-Repáraz, J},
title = {Sexual dimorphism in the colonic microbiome and host's transcriptomics profiles of a murine model of multiple sclerosis.},
journal = {Clinical immunology communications},
volume = {9},
number = {},
pages = {102-114},
pmid = {42100141},
issn = {2772-6134},
support = {P20 GM148321/GM/NIGMS NIH HHS/United States ; R15 NS107743/NS/NINDS NIH HHS/United States ; },
abstract = {BACKGROUND: Multiple Sclerosis is a chronic autoimmune disease that attacks the myelin sheath in the central nervous system, with a higher prevalence among female patients. We and others have documented significant changes in microbial taxa in response to the induction of active experimental autoimmune encephalomyelitis (EAE), an MS model.

OBJECTIVE: To evaluate sex as a biological variable in both the host and colonic microenvironment during active EAE.

METHODS: We conducted colonic transcriptomics and microbiota analysis of colonic fecal content in male and female EAE C57BL/6 J mice and controls at the time of disease induction, pre-onset, and peak disease.

RESULTS: Analysis showed significant sex-specific differences in colonic gene expression during EAE. As disease severity increased, the profiles of colon microbiome and transcriptomics became less distinct.

CONCLUSIONS: Our results suggest early changes in colonic inflammatory pathways, with notable differences between males and females associated with microbiota alterations triggered by disease induction.},
}

@article {pmid42100225,
year = {2026},
author = {Tang, Q and Qiu, D and Wen, C and Bu, Z and Huang, Y and Zou, C and Wu, H and Chen, F and Liu, L and Li, Z and Xie, X and Huang, H and Gan, K and Liu, Y},
title = {Effects of dietary rumen-degradable protein on growth performance, nitrogen metabolism, and rumen microbiome in dairy buffalo heifers.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1806578},
pmid = {42100225},
issn = {2297-1769},
abstract = {INTRODUCTION: Buffaloes are globally important dairy animals, but their low feed nitrogen utilization efficiency and excessive dietary rumen-degradable protein (RDP) results in aggravated nitrogen pollution and high breeding costs. Studies on the optimal RDP levels for 7-10-month-old dairy buffalo heifers remain scarce, limiting precise nutritional management.

MATERIALS AND METHODS: Dairy buffalo heifers (n = 36, 7-10-month-old, 193.39 ± 4.10 kg) were selected, and randomly assigned to six groups (n = 6 heifers/group, with one heifer in each replicate; Dietary RDP: 60.85-88.90 g/kg). The 73-day trial (15-day adaptation) included measurements of growth performance, nitrogen metabolism, serum indices, rumen parameters, and microbiome (16S rRNA/ITS sequencing).

RESULTS: (1) No differences in initial/final body weight or dry matter intake were found among the groups (p > 0.05). The low-RDP group (LP-1, 67.31 g/kg) had the highest average daily gain (0.79 kg/d) and lowest feed-to-gain ratio (7.88) (p < 0.05). (2) With a decrease in dietary RDP levels, intake nitrogen (IN), urinary nitrogen (UN), digested nitrogen, and UN /IN efficiency decreased (p < 0.05). The low-RDP group (LP-1) had the highest retention nitrogen/IN efficiency (32.31%) (p < 0.05). (3) The serum total protein and urea levels decreased with decreasing dietary RDP levels (lowest in LP-2: 64.52 g/L and 5.15 mmol/L, p < 0.05), with no differences in liver or kidney function or glucose-lipid metabolism (p > 0.05). (4) LP-1 had the highest rumen total volatile fatty acids, acetate, and butyrate levels (p < 0.05), while rumen pH and NH3-N decreased with RDP (p < 0.05). (5) Dietary RDP levels significantly altered the rumen microbial structure. Pichia in LP-1 was 28.81-fold and 39.68-fold higher than in HP-1 and MP-1 groups, respectively (p < 0.05), along with the presence of group-specific taxa.

DISCUSSION: An optimal dietary RDP level for 7-10-month-old dairy buffalo heifers was 67.31 g/kg, which improved the ADG and nitrogen utilization efficiency without compromising health, while also altering the rumen microbial structure. Therefore, when formulating diets for buffaloes, it is advisable to consider to note only meet the DCP requirements but also appropriately regulate the dietary RDP levels.},
}

@article {pmid42100351,
year = {2026},
author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z},
title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100600},
pmid = {42100351},
issn = {2666-5174},
abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.},
}

@article {pmid42100398,
year = {2026},
author = {Akintola, A and Dareng, EO and Adebamowo, SN and , and Adebamowo, CA},
title = {Impact of educational intervention on the uptake of self-sampling for HPV test-based cervical cancer screening.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1810950},
pmid = {42100398},
issn = {2234-943X},
abstract = {BACKGROUND: Self-sampling for HPV testing is increasingly adopted for cervical cancer screening globally, including in Sub-Saharan Africa. However, concerns remain regarding women's willingness and ability to collect samples and the effectiveness of educational interventions. Although prior studies in Africa and Nigeria have examined acceptability and barriers, there is limited evidence on whether structured educational interventions can modify women's attitudes toward HPV self-sampling in routine screening contexts. We evaluated the effect of a structured educational intervention on women's attitudes toward self-sampling and, secondarily, explored baseline correlates of willingness to self-sample among Nigerian women.

METHODS: We conducted a single-group pre-post quasi-experimental study nested within the African Collaborative Center for Microbiome and Genomics (ACCME) prospective cohort study in central Nigeria. A total of 220 eligible women undergoing cervical cancer screening were enrolled. Baseline measurements were obtained prior to the intervention. The standardized educational intervention, delivered by trained research staff, included brochures, leaflets, an instructional video, verbal instructions, and hands-on familiarization with the Evalyn[®] self-sampling brush. Participants subsequently performed self-sampling privately at participating screening facilities. Post-intervention measurements were collected immediately after the educational session and procedure. Samples were analyzed using DEIA/LIPA HPV assays.

RESULTS: Most participants were married (63.2%), belonged to the middle socioeconomic group (69.5%), had prior knowledge of cervical cancer (61.8%), and had never undergone screening (89.5%). At baseline, 91.8% were willing to self-sample. The intervention significantly improved mean attitude scores from 42.6 (SD 8.3) to 50.8 (SD 9.8) (p<0.001). Among women unwilling to self-sample, 50.0% (9/18) were in the lower SES group compared with 12.9% (26/202) among willing participants (p<0.001). In exploratory analyses, younger age (OR 0.95, 95% CI 0.90-1.00), cervical cancer knowledge (OR 1.42, 95% CI 1.00-1.99), middle SES (OR 3.69, 95% CI 1.07-12.66), and pre-intervention attitude (OR 0.89, 95% CI 0.81-0.99) were associated with willingness.

CONCLUSIONS: A structured educational intervention significantly improved attitudes toward HPV self-sampling. Baseline willingness was high, and exploratory analysis indicate that younger age, better knowledge, and middle SES are associated with willingness. These findings support context-specific educational strategies to optimize HPV self-sampling uptake in Nigeria and similar low-resource settings.},
}

@article {pmid42100420,
year = {2026},
author = {Zhang, J and Zhi, J and Li, J and Li, L and Zhang, S and Niu, J and Wang, W},
title = {Gut microbiome restructuring in laryngeal squamous cell carcinoma identifies stable microbial biomarkers with diagnostic potential.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1788705},
pmid = {42100420},
issn = {2234-943X},
abstract = {BACKGROUND: Alterations in the gut microbiota have been reported in various malignancies, but its role in laryngeal squamous cell carcinoma (LSCC) remains unclear.

METHODS: This retrospective study included 101 patients undergoing laryngeal surgery (46 benign, 55 malignant). Preoperative fecal samples were collected and subjected to 5R 16S rRNA sequencing. Sequencing data were processed using DADA2 and QIIME2, followed by α/β diversity analysis, differential abundance detection (Wilcoxon test, LEfSe, random forest), and LASSO regression. Functional pathway differences were inferred using PICRUSt2.

RESULTS: There were no significant differences in α diversity metrics between groups, whereas β diversity analysis revealed significant separation between Benign and LSCC (PERMANOVA, P<0.01). Distinct community composition differences were observed: Malignant cases showed enrichment of genera such as Streptococcus and Lactobacillus, while Benign cases exhibited enrichment of genera including Bacteroides and Lachnospira. Multimethod integration identified 17 core bacterial genera, which were further refined via LASSO regression to select a stable set of genera (e.g., Streptococcus, Eubacterium, Lachnospira) capable of reliably distinguishing benign from malignant cases. The logistic regression model based on stable genera demonstrated excellent diagnostic performance (AUC > 0.8), particularly in distinguishing benign from LateLSCC. Functional prediction revealed pathway imbalances: malignant cases showed enrichment in cell wall and amino acid synthesis pathways, while benign cases favored vitamin and steroid metabolism pathways.

CONCLUSION: LSCC patients exhibit structural remodeling of their gut microbiota, characterized by distinct taxonomic and functional alterations. Stable microbial signatures holding potential as a foundation for the future development of non-invasive diagnostic and staging biomarkers, though their clinical translation necessitates further large-scale validation.},
}

@article {pmid42100577,
year = {2026},
author = {Chen, H and Chen, Y and Liu, Y and Chen, C},
title = {Oral microbiota and urinary system diseases: from mechanistic insights to clinical implications-a comprehensive review.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1803961},
pmid = {42100577},
issn = {2673-4915},
abstract = {The human oral microbiome has attracted considerable attention due to its role in oral health and potential implications for systemic diseases. Oral microbes provide real-time insights into health and disease status, making them valuable for early disease risk stratification and treatment outcome prediction. Accumulating evidence indicates that oral microbiota contribute to the pathogenesis of urinary system diseases. Notably, in pediatric populations, the oral microbiome-shaped by age, feeding patterns, and immune maturation-may modulate susceptibility to renal-related systemic conditions; clinical observations specifically link untreated early childhood caries to an increased risk of Henoch-Schönlein purpura nephritis (HSPN). This review critically appraises the existing literature to clarify the nature and magnitude of the association between the oral microbiome and urinary system diseases, including chronic kidney disease, urolithiasis, benign prostatic hyperplasia, and urologic cancers, as well as pediatric HSPN. We also analyze the potential mechanisms through which the oral microbiota are involved in the pathogenesis and progression of these relevant diseases, and explore its potential implications for the prevention, diagnosis, and management of urinary system disorders.},
}

@article {pmid42100652,
year = {2026},
author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C},
title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799729},
pmid = {42100652},
issn = {2235-2988},
mesh = {Animals ; *Probiotics/administration & dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; },
abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.

METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 μg/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1×10⁸ CFU/day) and high (1×10⁹ CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.

RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6±6.8 to 512.4±48.9 U/L), AST (78.3±9.5 to 684.7±62.1 U/L), and plasma ammonia (38.9±5.2 to 128.6±14.3 μmol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7±41.6 U/L (low dose) and 248.9±32.4 U/L (high dose). Ammonia levels decreased to 86.4±9.7 μmol/L and 59.8±7.6 μmol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8±4.2 to 63.9±6.4 mM), lower ammonia (8.9±1.1 to 3.7±0.5 mM), improved intestinal barrier integrity (TEER: 462±38 to 721±44 Ω·cm²), and reduced TNF-α (214.6±22.8 to 74.9±12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.},
}

Animals
*Probiotics/administration & dosage
Rats, Wistar
Male
Metagenomics
Rats
Feces/microbiology/chemistry
Disease Models, Animal
*Gastrointestinal Microbiome
*Liver Failure
Cytokines
Ammonia/blood
Dysbiosis
Galactosamine

@article {pmid42100658,
year = {2026},
author = {Wu, J and Lu, Y and Zheng, Z and Zheng, J and Fu, Q},
title = {A primary study: high-throughput sequencing analysis of amniotic fluid microbiota in 50 high-risk pregnant women during the second trimester.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1748232},
pmid = {42100658},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology ; *Pregnancy Trimester, Second ; High-Throughput Nucleotide Sequencing ; Adult ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Amniocentesis ; *Pregnancy, High-Risk ; Gestational Age ; DNA, Bacterial/genetics ; Maternal Age ; },
abstract = {OBJECTIVE: Whether bacteria exist in the pregnancy uterus without pathological infection has long been a controversial topic. Through this study, we aim to determine whether characteristic amniotic fluid microbiota exists in the uterus of high-risk pregnant women during the second trimester.

METHODS: This study recruited high-risk pregnant women in the second trimester from September 1, 2024, to August 30, 2025, and recorded their age and gestational age. Amniotic fluid samples were obtained through amniocentesis under strictly sterile conditions, and 16S rRNA high-throughput sequencing was performed on the samples. The inclusion criteria mainly consisted of: advanced maternal age, non-invasive prenatal test results indicating chromosomal abnormalities, abnormal fetal ultrasound findings, history of adverse pregnancy outcomes, and high-risk Down syndrome screening results.

RESULTS: This study included a total of 50 high-risk pregnant women who underwent amniocentesis. The results showed that bacteria were present in all amniotic fluid samples, primarily composed of Actinobacteriota and Proteobacteria. There was no difference in amniotic fluid microbiota diversity between pregnant women under 35 years old and those 35 years or older; however, the abundances of Cutibacterium and Leifsonia differed between the two groups. A slight difference in microbiota diversity was observed between women with gestational ages below 20 weeks and those at 20 weeks or above, but no significant difference was found in microbial composition between the two groups.

CONCLUSION: There was bacterial DNA in amniotic fluid of high-risk pregnant women in the second trimester, with Actinobacteriota and Proteobacteria being the predominant phyla, showing limited correlation with maternal age or gestational age. This study provided evidence for the presence of microorganisms in amniotic fluid during pregnancy and might offer some preliminary data for future research related to eugenics and reproductive health.},
}

Humans
Female
Pregnancy
*Amniotic Fluid/microbiology
*Pregnancy Trimester, Second
High-Throughput Nucleotide Sequencing
Adult
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Amniocentesis
*Pregnancy, High-Risk
Gestational Age
DNA, Bacterial/genetics
Maternal Age

@article {pmid42100662,
year = {2026},
author = {Ding, X and Fan, L and Ma, X and Li, J and Qian, P and Qiu, N and Xu, L and Yue, J},
title = {Alterations of the skin microbiome in HIV infection with pruritus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1749838},
pmid = {42100662},
issn = {2235-2988},
mesh = {Humans ; *Pruritus/microbiology/etiology ; *HIV Infections/complications/microbiology ; *Skin/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Adult ; Male ; Female ; Middle Aged ; Interleukin-10/blood ; Bacteria/classification/genetics/isolation & purification ; Cytokines/blood ; Interleukin-6/blood ; DNA, Bacterial/genetics ; Skin Microbiome ; },
abstract = {INTRODUCTION: Pruritus is one of the main common symptoms of human immunodeficiency virus (HIV) infection. Skin changes caused by scratching, or the absence of skin findings despite ongoing pruritus, impact patients' quality of life. With cutaneous HIV infection, pruritus is continuous, though it is unknown whether HIV infection affects the skin microbiota to cause pruritus.

METHODS: The skin microbiomes and plasma of HIV infection with pruritus, HIV and healthy were investigated in this study. Swabs were taken from four body sites and the composition of the microbiome at those sites was assessed using 16S rRNA amplification. Cytokines(interleukins 10 and 6) in plasma were detected by enzyme-linked immunosorbent assay.

RESULTS: The skin microbiome in the pruritus group was characterized by a significant depletion of protective commensals, specifically Cutibacterium and the Burkholderia-Caballeronia-Paraburkholderia. Conversely, opportunistic microbiome, including Prevotella and Leptotrichia, were markedly enriched and identified as key microbial signatures by Random Forest analysis. Correlation analysis revealed that the loss of protective commensals was positively associated with anti-inflammatory IL-10 levels, while the expansion of opportunistic pathogens was linked to elevated pro-inflammatory IL-6, indicating a microbial-driven immune imbalance.

CONCLUSIONS: The results reveal that skin microbiota collapse and the loss of inherent anti-inflammatory defenses are pivotal features of HIV infection with pruritus.},
}

Humans
*Pruritus/microbiology/etiology
*HIV Infections/complications/microbiology
*Skin/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Adult
Male
Female
Middle Aged
Interleukin-10/blood
Bacteria/classification/genetics/isolation & purification
Cytokines/blood
Interleukin-6/blood
DNA, Bacterial/genetics
Skin Microbiome

@article {pmid42100688,
year = {2026},
author = {Yadav, J and Gehlot, P and Soni, P and Jain, T},
title = {Plant microbiome engineering: from inoculation to genome editing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781381},
pmid = {42100688},
issn = {1664-302X},
abstract = {Plant-associated microbiomes are central to crop productivity, nutrient efficiency, and stress resilience, yet conventional microbiome manipulation strategies, largely based on microbial inoculation and agronomic management, often suffer from inconsistent field performance and limited persistence. Although several recent reviews have discussed CRISPR-mediated plant-microbe engineering and synthetic microbial community (SynCom) design separately, few reviews integrate genome editing, ecological stability of microbiomes, and climate-resilient agricultural applications within a unified conceptual framework. Recent advances in molecular biotechnology are transforming this landscape by enabling precision engineering of plant-microbe interactions at genetic, metabolic, and community levels. In particular, synthetic biology tools including CRISPR/Cas genome editing, RNA interference, and synthetic microbial communities (SynComs), now allow targeted modification of plant traits governing microbial recruitment, microbial pathways underpinning nutrient cycling and stress tolerance, and community-level functional complementarity. This review integrates molecular genetics, microbial ecology, and systems-level microbiome design to frame the plant and its microbiome as an engineerable holobiont. We integrate insights from genome editing in plants and microbes, omics-guided SynCom design, climate-resilience mechanisms, and emerging AI-assisted decision frameworks, including machine learning and ecological modeling approaches used to analyze multi-omics datasets, and predict plant-microbiome interactions across experimental and field-based studies. Importantly, we critically assess limitations related to ecological stability, trait trade-offs, biosafety, and regulatory challenges that constrain large-scale deployment. By bridging genome-enabled microbiome manipulation with ecological design principles, this review proposes an integrative framework for climate-smart microbiome engineering and identifies key research priorities required to transition from empirical inoculation toward predictive, sustainable, and socially responsible agricultural biotechnology.},
}

@article {pmid42100690,
year = {2026},
author = {Gao, Q and Xiong, M and Zhou, S and Lu, J and Ren, B and Peng, Q and Zeng, M and Song, H},
title = {Gut microbiota and uveitis: exploring novel mechanisms of inflammatory ocular diseases via the gut-eye axis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1749111},
pmid = {42100690},
issn = {1664-302X},
abstract = {Uveitis is an inflammatory ocular condition that primarily affects young adults and is often associated with systemic and autoimmune disorders. This disease primarily affects intraocular structures such as the iris, ciliary body, and choroid. Clinically, it manifests through a series of symptoms, including eye redness, pain, and blurred vision, which significantly impact the quality of life for patients worldwide. Recently, the role of gut microbiota (GM) in the immune regulation and pathogenesis of inflammatory diseases has garnered significant scientific interest. This study aimed to investigate the potential association between GM and uveitis, with the objective of demonstrating novel mechanisms underlying inflammatory ocular diseases through the emerging concept of the "gut-eye axis." Current research suggests that gut dysbiosis may influence the immune status of distal organs via various pathways, including molecular mimicry, modulation by microbial metabolites, disruption of intestinal immune homeostasis, and compromise of the intestinal mucosal barrier. Building on these mechanisms, we further explored innovative therapeutic strategies targeting GM and its metabolites, including probiotics, prebiotics, antibiotics, immunomodulators, phage therapy, fecal microbiota transplantation, and dietary interventions. This review systematically examined the association between GM dysbiosis and uveitis pathogenesis, offering new insights and directions for future research in this emerging field and establishing a theoretical foundation for developing targeted therapies based on the modulation of the microbiome.},
}

@article {pmid42100694,
year = {2026},
author = {Yu, C and Wang, M and Zhao, M and Zhang, S and Cao, M and Liu, Z and Jiang, J and Zhang, Y and Pan, Y and Zhao, X},
title = {Root-associated bacterial community dynamics and assembly mechanisms in healthy and root rot-infected soybeans.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1789440},
pmid = {42100694},
issn = {1664-302X},
abstract = {INTRODUCTION: Soybean root rot, a devastating soil-borne disease, severely limits global soybean yield and quality. Traditional control measures cause environmental pollution and have regional limitations. Root-associated microbiomes are vital for plant health, but most studies use relative abundance sequencing that distorts actual microbial quantities. This study used absolute quantitative high-throughput sequencing to clarify soil chemical properties and bacterial community assembly in healthy and diseased soybeans, laying a theoretical foundation for microbiome-based root rot management.

METHODS: Samples were collected from bulk soil, and the endosphere, rhizoplane, rhizosphere of healthy and diseased soybeans in black soil fields of Heilongjiang. Soil chemical properties, including pH, soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK), were determined. Absolute quantitative sequencing of bacterial 16S rRNA V4-V5 region was performed, combined with qPCR for absolute abundance calibration. Bioinformatics analyses included α/β diversity, co-occurrence network, community assembly (βNTI & RCbray), random forest and correlation analysis to identify key taxa and their relationships with environmental factors.

RESULTS: Root rot significantly reduced rhizosphere SOC (by 29.13%), TN (8.57%), AN (24.18%), AP (18.86%), while increased AK (12.82%) and pH. However, the contents of certain bacterial taxa at the genus levels showed significant differences in both absolute and relative abundances. The bacterial co-occurrence network indicate that the interaction in the healthy soybean (H) group was more complex than that in the diseased soybean (S) group. Specifically, 1 module hub and 21 connectors were identified in the H group, whereas 55 connectors were detected in the S group. Community assembly in both the H and S groups was governed by deterministic processes, with homogeneous selection primarily observed in the S group. Random forest and correlation heatmap analyses revealed ASV115 (Candidatus Koribacter) in H group was positively correlated with SOC, pH and AN; ASV16 (Streptomyces), ASV42 (Agrobacterium) and ASV46 (Mesorhizobium) were keystones in S group.

DISCUSSION: Root rot destroyed rhizosphere nutrient balance and reshaped bacterial community structure, reducing network complexity. Absolute quantification effectively compensated for the defects of relative abundance, accurately reflecting community changes. These findings clarify the microecological mechanism of soybean root rot, supporting the development of biocontrol strategies targeting rhizosphere microbiome for sustainable soybean production.},
}

@article {pmid42100703,
year = {2026},
author = {Liu, L and Liang, G and Gao, H and Xing, S and Wang, K and Zhou, X and Huang, X and Li, C},
title = {Integrated transcriptome-microbiome analysis reveals a host-microbe interplay associated with insecticide resistance in Aedes albopictus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1788609},
pmid = {42100703},
issn = {1664-302X},
abstract = {INTRODUCTION: Aedes albopictus is the primary vector of major arboviral diseases such as dengue fever, chikungunya fever, and Zika virus disease, and its control is highly dependent on chemical insecticides. However, the long-term use of pyrethroid insecticides has led to the development of insecticide resistance in Ae. albopictus, which severely undermines the efficacy of vector control programs.

METHODS: Ae. albopictus populations were collected from five sites in Guangdong and Hainan provinces, China. Beta-cypermethrin resistance levels were determined via bioassays, with resistance ratios at the median lethal concentration (RR50) calculated. Target-site resistance was evaluated via kdr mutation detection in the voltage-gated sodium channel (VGSC) gene. Transcriptome sequencing identified differentially expressed genes (DEGs), and 16S rRNA sequencing characterized gut microbiome alterations. Correlation analysis and Cedecea neteri dietary supplementation assays verified the role of gut microbiota in resistance.

RESULTS: The results showed that all four populations (except the CP population) exhibited varying degrees of resistance to beta-cypermethrin, with resistance ratios at the median lethal concentration (RR50) ranging from 2.84 to 29.18. Detection of kdr mutations revealed three mutations (F1534C, F1534L, F1534S) at codon 1534 of the voltage-gated sodium channel (VGSC) gene in all field populations, with mutation frequencies ranging from 49.4% to 100.0%, and a low-frequency V1016G mutation at codon 1016. Transcriptome analysis identified a total of 2,566 commonly upregulated genes and 994 commonly downregulated genes across the resistant populations. Gut microbiome analysis revealed a significant alteration in the intestinal microbial community structure of resistant populations; specifically, the relative abundance of the genus Cedecea differed significantly between resistant and susceptible populations and correlated strongly with the expression of most differentially expressed genes. Furthermore, dietary supplementation with Cedecea neteri significantly increased the survival rate of Ae. albopictus exposed to β-cypermethrin (73.86% vs 40.00%; P < 0.0001).

DISCUSSION: From the perspectives of target-site mutations, gene expression regulation, and gut microbe interactions, this study providing a foundation for further studies on resistance mechanisms in Ae. albopictus, thereby providing a theoretical foundation for further dissection of resistance mechanisms and optimization of vector control strategies.},
}

@article {pmid42098513,
year = {2026},
author = {Wang, L and Zhou, J and Wei, W and George, TS and Feng, G},
title = {Deciphering bacterial community composition and function at critical interfaces of plant-arbuscular mycorrhizal fungi-bacterial holobiont.},
journal = {Mycorrhiza},
volume = {36},
number = {3},
pages = {},
pmid = {42098513},
issn = {1432-1890},
support = {32401431//National Natural Science Foundation of China/ ; 32272807//National Natural Science Foundation of China/ ; GZB20230852//Postdoctoral Fellowship Program of CPSF/ ; 2023M743792//China Postdoctoral Science Foundation/ ; 31711530217//National Nature Fund and Royal Society Joint Project/ ; },
mesh = {*Mycorrhizae/physiology ; *Soil Microbiology ; *Bacteria/classification/genetics ; *Microbiota ; Plant Roots/microbiology ; *Zea mays/microbiology ; Phylogeny ; Rhizosphere ; Symbiosis ; },
abstract = {Arbuscular mycorrhizal (AM) fungi connect plant roots and soil bacteria, forming a cross-kingdom holobiont driven by plant-derived carbon flux and soil-derived nutrient flux. This holobiont encompasses not only roots and rhizosphere but also interfaces expanded by slender AM fungal hyphae. Our understanding of the microbiomes across these interconnected interfaces remains limited and fragmented. We used a split-root microcosm to inoculate the same maize root system with three AM fungal species, establishing a simplified holobiont. Amplicon sequencing, Biolog-ECO plates, and [13]CO2 labelling revealed the bacterial diversity and community-level physiological profiles (CLPPs). Bacterial communities colonizing non-mycorrhizal roots, mycorrhizal roots, and hyphae exhibited distinct structures and CLPPs. AM fungal species significantly influenced these bacterial communities, particularly in the mycorrhizosphere and hyphosphere, where notable changes occurred in key nutrient-cycling groups, such as phosphate solubilizers and nitrogen fixers. The diversity of the hyphosphere microbiome was closely aligned with fungal phylogeny. Additionally, a stable core microbiome persisted across all interfaces within the plant-AM fungi-bacterial holobiont, with key taxa such as Pseudomonas and Bacillus harboring the P-mobilizing genes encoding quinoprotein glucose dehydrogenase (gcd) and β-propeller phytase (bpp), highlighting their functional importance in nutrient cycling. Our study provides a comprehensive and precise hyphal-scale characterization of microbial communities across key interfaces, offering detailed insights into plant-microbial dynamics driving nutrient cycling and ecosystem functioning.},
}

*Mycorrhizae/physiology
*Soil Microbiology
*Bacteria/classification/genetics
*Microbiota
Plant Roots/microbiology
*Zea mays/microbiology
Phylogeny
Rhizosphere
Symbiosis

@article {pmid42090762,
year = {2026},
author = {Barnabei, G and Destri, D and Franco-Benito, M and Cebrian-Aldana, M and Mishra, A and Gil-Guerrero, S and Castilla-Alcantara, JC and Velasco-Arroyo, B and Barros-Garcia, R and Di Mambro, R and Bertelloni, N and Di Gregorio, S},
title = {Region-specific patterns of soil bacterial communities' adaptation to hexachlorocyclohexane contamination.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142224},
doi = {10.1016/j.jhazmat.2026.142224},
pmid = {42090762},
issn = {1873-3336},
abstract = {Hexachlorocyclohexane (HCH) is a persistent organochlorine pollutant whose attenuation at former production sites relies on microbial degradation. The canonical lin pathway, predominantly associated with Sphingomonadaceae, is considered the main aerobic route for HCH transformation, yet its environmental distribution remains limited. We investigated soil bacterial communities and enrichment-derived bacterial consortia from three historically contaminated sites in Germany, Italy, and Spain using HCH depletion assays, 16S rDNA metabarcoding, and functional inference, based on a curated BIOSYSMOdb dataset developed by the BIOSYSMO project. Based on the ASL-level functional inference, the Spanish samples uniquely encoded a complete lin pathway restricted to Sphingobium sp., whereas German and Italian communities harboured respectively partial (LinB-C) or single-step (LinB) modules. Despite these differences, efficient depletion of all HCH isomers occurred across all enrichment cultures. Core-microbiome and differential-abundance analyses identified several non-Sphingomonadaceae taxa, including Stenotrophomonas, Pseudomonas, Achromobacter, Pseudolabrys, and Cupriavidus, which consistently increased during selective enrichment and likely contribute to HCH depletion. Overall, our findings suggest that effective HCH degradation is not restricted to the canonical lin pathway nor to Sphingomonadaceae but it might be mediated also by diverse soil bacteria via alternative lin-independent mechanisms. These results broaden the known ecological and functional landscape of HCH biodegradation and support the exploration of non-Sphingomonadaceae taxa for bioremediation of legacy lindane-contaminated sites.},
}

@article {pmid42090907,
year = {2026},
author = {Su, X and Li, A and Liu, J and Guo, Y and Yu, H and Yu, J and Wang, R and Garza, DR and Qu, J and Wen, B and Liu, B},
title = {From microbes to molecules: Gut microbiota as a prerequisite threshold determinant for cancer immunotherapy efficacy.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128539},
doi = {10.1016/j.micres.2026.128539},
pmid = {42090907},
issn = {1618-0623},
abstract = {Cancer immunotherapy, represented by immune checkpoint inhibitors, adoptive cell therapy, and cancer vaccines, has revolutionized the clinical management of multiple malignant tumors, yet profound interindividual heterogeneity in treatment response and widespread primary/acquired resistance remain the most critical bottlenecks restricting its long-term clinical benefits. Accumulating preclinical and clinical evidence has unequivocally established the gut microbiota as a pivotal regulator of host anti-tumor immune responses. However, the vast majority of existing studies and reviews frame the gut microbiota as a mere adjuvant enhancer of immunotherapy efficacy, focusing solely on its role in boosting the upper limit of treatment effects, while neglecting its more fundamental role as a prerequisite for establishing a responsive immune baseline. In this review, we propose a unifying, evidence-based original core hypothesis: the gut microbiota is not merely an enhancer of cancer immunotherapy efficacy, but an indispensable prerequisite condition that sets the minimal baseline threshold for therapeutic responsiveness-a central thesis that distinguishes this review from previous descriptive work. Guided by this hypothesis, we systematically dissect the taxonomic and functional characteristics of threshold-determining gut microbiota, and clarify that microbial metabolites (e.g., short-chain fatty acids, bile acids, tryptophan derivatives) act as core molecular mediators translating microbial signals into host immune activation, which is critical for establishing the baseline efficacy threshold required for effective immunotherapy. We further perform a critical synthesis of clinical data from prospective cohorts, randomized controlled trials, and microbiota intervention studies, validating that threshold-based microbial signatures serve as non-invasive predictive biomarkers for immunotherapy outcomes, and propose mechanism-driven translational strategies targeting the gut microbiota (e.g., fecal microbiota transplantation, probiotic supplementation, dietary modulation) to reset the impaired immunotherapy efficacy threshold. This review provides a novel theoretical framework for understanding the microbiota-immunotherapy axis, which not only deepens the mechanistic insight into microbial metabolite-mediated immune regulation, but also facilitates the development of microbiota-guided personalized cancer immunotherapy and the overcoming of primary treatment resistance.},
}

@article {pmid42090982,
year = {2026},
author = {Ghanam, AR and Gatermann, S and Juckel, G},
title = {Reduced gut microbiome alpha diversity associates with depressive symptom severity and somatic symptom burden in major depression.},
journal = {Journal of psychiatric research},
volume = {199},
number = {},
pages = {237-242},
doi = {10.1016/j.jpsychires.2026.04.022},
pmid = {42090982},
issn = {1879-1379},
abstract = {OBJECTIVE: Alteration in gut microbiome have been increasingly linked to many psychiatric disorders inclusive depression. However, findings regarding microbiome diversity in depression remain inconsistent. Differences in depression subtypes, particularly the somatic versus affective symptoms profiles may partly explain this heterogeneity in previous results.

METHODS: This cross-sectional study included 31 Participants diagnosed with major depressive disorder. The participants divided into two groups by severity of depression (BDI-II >34 vs. <34) and severity of somatic symptoms of depression (somatic dimension vs. cognitive-affective dimension of BDI-II). Fecal samples were collected, and 16S rRNA gene sequencing of the V3/V4 region was performed on an Illumina platform to profile the gut microbiome. Amplicon Sequence Variants (ASVs) were used to analyze microbial alpha diversity, including ACE, Chao1 and Shannon.

RESULTS: Participants with higher depressive severity showed significantly reduced gut microbiome alpha diversity compared to lower depressive state (ACE; p = 0.019, Chao1; p = 0.019, and Shannon; p = 0.053). Across the total sample, BDI-II total score correlated negatively with alpha diversity significantly for ACE (r = -0.435, p = 0.015), Chao1 (r = -0.435, p = 0.015) and Shannon (r = -0.376, p = 0.037). While the somatic dimension of the BDI-II showed significant negative correlation with all tested alpha diversity indices, no significant correlations were detected between gut microbiome alpha diversity and the cognitive-affective dimension. Shannon diversity further correlated negatively with HDRS-17 scores (p = 0.033).

CONCLUSION: In conclusion, the results show that a lower diversity of gut microbiota alpha is linked to more severe depressive symptoms, specifically the somatic aspect of depression. These results emphasize the importance of considering somatic symptom profiles in microbiome research and point to the gut-brain axis as a potential target for future therapeutic interventions.},
}

@article {pmid42091112,
year = {2026},
author = {Gao, S and Zhao, W and Jiang, J and Guan, X and Pan, Y and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Zhao, D and Mi, R and Zhou, Z},
title = {Bottom Grinding Increases the Phototrophic Bacteria While Reduces Bacterial Community Stability in Sea Cucumber Cultural Ponds.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70357},
pmid = {42091112},
issn = {1758-2229},
support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//undamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2025JCX1008//undamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; },
mesh = {*Ponds/microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; *Sea Cucumbers/microbiology/growth & development ; *Aquaculture/methods ; Phototrophic Processes ; Geologic Sediments/microbiology ; Water Microbiology ; },
abstract = {Bottom grinding (BG), which suspends the anaerobic microorganisms deposited at the bottom of the pond through aeration, is a common practice in sea cucumber aquaculture for maintaining water quality. However, little is known about the effects of BG on the environmental microbiome. This study investigated differences in bacterial communities from three niches (surface water, bottom water and sediments) of culture ponds with and without BG operations. Only minor changes in sediment bacterial communities were observed between BG-treated and control ponds. In contrast, the composition of the bacterial communities in the water was also significantly altered by the BG operation, with an increase in Cyanobacteria and a decrease in Proteobacteria. Additionally, functional prediction revealed increased phototrophy and decreased chemoheterotrophy in aquatic bacterial communities following BG treatment. Co-occurrence network analysis revealed that bacterial communities in all three niches were more complex but unstable with BG treatment compared to without, indicating some remedial operations for farming practice. Analysis of community assembly mechanisms showed increased stochastic assembly of bacterial communities in all three niches induced by BG treatment. Overall, this study revealed the effects of BG operation on the bacterial communities in culture ponds, providing insights into the ongoing evolution of farming techniques.},
}

*Ponds/microbiology
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota
*Sea Cucumbers/microbiology/growth & development
*Aquaculture/methods
Phototrophic Processes
Geologic Sediments/microbiology
Water Microbiology

@article {pmid42091350,
year = {2026},
author = {Monday, L and Krishna, A and Chopra, T},
title = {Prevention and Control of Clostridioides difficile Infection for the Infectious Diseases Clinician.},
journal = {Infectious disease clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idc.2026.02.009},
pmid = {42091350},
issn = {1557-9824},
abstract = {This article highlights the challenges of preventing Clostridioides difficile infection (CDI) in health care settings. It emphasizes a multifaceted approach including hand hygiene, contact precautions, environmental cleaning, and antimicrobial stewardship. Diagnostic stewardship, using combined testing algorithms and electronic alerts, helps reduce unnecessary testing and misdiagnosis. Emerging strategies like microbiome restoration, vaccines, and monoclonal antibodies are under active investigation. When CDI rates remain high despite standard measures, additional interventions such as sporicidal disinfectants and no-touch technologies may be necessary. Overall, a comprehensive, adaptive approach is essential to effectively reduce CDI incidence and improve patient outcomes.},
}

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48529-9},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

@article {pmid42092044,
year = {2026},
author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E},
title = {CCMRI: a classification and curated database of climate change-related microbiome studies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51914-z},
pmid = {42092044},
issn = {2045-2322},
support = {2772//Hellenic Foundation for Research and Innovation/ ; },
abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.},
}

@article {pmid42092115,
year = {2026},
author = {Xu, W and Yuan, X and Cao, J and Cui, X and Fu, K and Wang, G and Ling, N and Yin, Y and Shi, Q and Shi, Z},
title = {Trichoderma-based fertilizer enhances quality of Elymus breviaristatus silage via microbial and metabolic modulation.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10028-y},
pmid = {42092115},
issn = {2399-3642},
abstract = {Elymus breviaristatus is an important alpine forage, there is limited information regarding its potential use as silage and how fertilizer treatments affect the ensiling process in this forage crop. Here, we investigated how organic fertilizer (M), nitrogen-phosphorus-potassium fertilizer (NPK), and Trichoderma harzianum fertilizer (B) affect Elymus breviaristatus silage quality (30 days and 60 days ensiling) via microbiome and metabolome analyses. Before ensiling, plant height and chlorophyll content increased by 29.93% and 39.72%, respectively, in the B group. After 60 days of ensiling, the M group had reduced crude protein and elevated butyric acid, the NPK group had higher ammonia nitrogen and butyric acid, and the B group had increased crude protein and lactic acid. These quality shifts correlated with microbial and metabolic changes. In the M group, alpha-linolenic acid metabolism was downregulated and Alternaria enriched, while the NPK group had enhanced flavone biosynthesis and a reduced level of Lactiplantibacillus. The B group had enhanced glycine, serine, and threonine metabolism, and displayed the most complex microbial networks along with increased levels of Lactiplantibacillus and Aspergillus. Overall, these results demonstrate that Trichoderma-based fertilization enhances silage quality by promoting accumulation of beneficial microbes and increasing flux through specific metabolic pathways, potentially offering a sustainable strategy for alpine forage improvement.},
}

@article {pmid42092154,
year = {2026},
author = {Yu, XA and Strachan, CR and Herbold, CW and Lang, M and Gasche, C and Makristathis, A and Segata, N and Pollak, S and Tett, A and Polz, MF},
title = {Genome-wide sweeps create ecological units in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42092154},
issn = {1476-4687},
abstract = {The human gut microbiome is shaped by diverse selective forces that originate from host and environmental factors and it substantially influences health and disease. Whereas the association of microbial lineages with various health conditions has been shown at different taxonomic levels[1-5], the extent to which unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations remains poorly understood. Here we show that genome-wide selective sweeps are a pervasive mechanism that differentiates bacteria in the microbiome. This mechanism leads to population structures akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others in its niche followed by rediversification, and they manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes. Indeed, we show that genome-wide sweeps originate under a wide range of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest that sweep clusters can spread globally within decades and that this process has occurred throughout human history. Sweep clusters are associated with different host conditions-such as age, colorectal cancer, inflammatory bowel diseases and type 2 diabetes-as an indication of their ecological differentiation. Our results reveal an evolutionary mechanism for the observation of stably inherited strains with differential associations and provide a theoretical foundation for analysing adaptation among microbial populations.},
}

@article {pmid42092264,
year = {2026},
author = {Vargas-Robles, D and Santos Agrait, JL and Suárez-Pérez, J and Vázquez, F and Dominicci-Maura, A and Sariol, CA and Zorrilla, C and Romaguera, J and Godoy-Vitorino, F},
title = {Oral Microbiome Resilience During SARS-CoV-2 Infection and Diversity Shifts After COVID-19 Vaccination in a Hispanic Population.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70310},
pmid = {42092264},
issn = {2045-8827},
support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54GM133807/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; U01CA260541/CA/NCI NIH HHS/United States ; COVID-19 RAPID GRANT #2020-00269//Puerto Rico Science, Technology and Research Trust/ ; P20 GM103475/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/prevention & control/microbiology/immunology/virology ; *Microbiota ; Hispanic or Latino ; Female ; Male ; SARS-CoV-2 ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; *Mouth/microbiology ; *COVID-19 Vaccines/administration & dosage/immunology ; Longitudinal Studies ; Vaccination ; Bacteria/classification/genetics/isolation & purification ; Aged ; White ; },
abstract = {The relationship between SARS-CoV-2 infection and the oral microbiome remains poorly understood, particularly in the Hispanic population. Oral samples from 62 individuals (38 SARS-CoV-2 positive, 24 negative) were analyzed using 16S rRNA sequencing, comparing diversity and taxa by infection and symptoms. Longitudinal data from 11 participants assessed microbiome changes as the infection resolved over time. To assess the impact of vaccination, we further examined 68 consistently SARS-CoV-2-negative individuals with paired samples collected before and after vaccination. SARS-CoV-2 infection was not significantly associated with alpha diversity, while beta diversity showed a non-significant but marginal trend (p = 0.051). Prevotella nanceiensis was consistently depleted in infected individuals, even after excluding recent antibiotic users, suggesting a reproducible association with infection status rather than a diagnostic marker. Among infected participants, mucosa-related symptoms were associated with lower Veillonella parvula abundance. Longitudinal data revealed stable microbiome profiles with slightly reduced variance in alpha diversity following viral clearance. In contrast, COVID-19 vaccination in consistently negative individuals was associated with significant increases in Shannon (p = 0.050) and Simpson diversity (p = 0.017), indicating greater evenness without expansion of richness. Beta diversity analyses showed vaccination-related shifts in community composition (PERMANOVA p = 0.026), with increases in Treponema, Campylobacter, Oribacterium, and Selenomonas, and a decrease in Haemophilus. The oral microbiome of Hispanics with mild SARS-CoV-2 infection appeared resilient, with only subtle taxonomic alterations. In contrast, COVID-19 vaccination was associated with short-term increases in diversity and compositional shifts, highlighting its influence on oral microbial ecology.},
}

Humans
*COVID-19/prevention & control/microbiology/immunology/virology
*Microbiota
Hispanic or Latino
Female
Male
SARS-CoV-2
RNA, Ribosomal, 16S/genetics
Middle Aged
Adult
*Mouth/microbiology
*COVID-19 Vaccines/administration & dosage/immunology
Longitudinal Studies
Vaccination
Bacteria/classification/genetics/isolation & purification
Aged
White

@article {pmid42092273,
year = {2026},
author = {Wang, N and Li, X and Wang, L and Zhu, Z and Gu, M and Zou, K and Zhang, J},
title = {Global Trends in Postoperative Sepsis After Pancreatoduodenectomy: A Bibliometric Analysis.},
journal = {The Journal of surgical research},
volume = {323},
number = {},
pages = {48-57},
doi = {10.1016/j.jss.2026.04.010},
pmid = {42092273},
issn = {1095-8673},
abstract = {INTRODUCTION: Postoperative sepsis after pancreatoduodenectomy (PSPD) remains a major determinant of morbidity and mortality. Although extensive clinical studies have explored its risk factors and management, the global research landscape and evolving priorities of PSPD have not been systematically characterized.

METHODS: Publications related to PSPD from 1980 to July 2025 were retrieved from the Web of Science Core Collection. CiteSpace, VOSviewer, and R-based bibliometrix were used to analyze publication trends, collaborative networks, influential journals and references, research hotspots, and emerging trends.

RESULTS: A total of 297 studies were included. Global PSPD research has grown steadily over the past 45 years, with rapid acceleration since 2020. The United States, Japan, Germany, Italy, and China were the leading contributors, supported by high-output institutions such as the University of Verona, Vita-Salute San Raffaele University, and Mayo Clinic. Research hotspots centered on risk stratification, surgical technique optimization, prevention of postoperative pancreatic fistula, and perioperative infection control. Emerging frontiers include surgical site infection prevention, microbiome-gut barrier and bacterial translocation mechanisms, precision risk prediction using machine learning models, and individualized perioperative strategies.

CONCLUSIONS: Global PSPD research has evolved from descriptive clinical studies toward mechanistic, predictive, and precision-oriented investigations. Future progress will likely depend on integrating surgical innovation with microbiological, immunological, and data-driven approaches to enable earlier identification and targeted prevention of PSPD.},
}

@article {pmid42092351,
year = {2026},
author = {Dohlman, AB and Mjelle, R and Wood, HM and Jiang, K and Shumate, A and Lee, I and Piccinno, G and Serna, G and Yakubu, AR and Nuciforo, P and Quirke, P and Huttenhower, C and Segata, N and Meyerson, M},
title = {Biodiversity and biogeography of the multi-kingdom cancer microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.04.015},
pmid = {42092351},
issn = {1097-4172},
abstract = {Microorganisms represent an important component of the tumor microenvironment, but conflicting reports have left the extent of microbial prevalence across cancer types unclear, necessitating more robust methods for characterizing tumor-associated microbiomes. We built and benchmarked a host-subtraction and classification pipeline to identify microbiota in whole-genome sequencing data and applied it to 16,369 high-depth tumor whole genomes from the UK 100,000 Genomes Project. After decontamination, microbial signatures were indistinguishable from the background in most cancer types. However, in orodigestive tumors, we detected multi-kingdom polymicrobial communities, including bacteria, fungi, viruses, archaea, and, in some cases, Trichomonas, a protozoan parasite. These communities varied by tumor site and subtype, with increased microbial colonization of microsatellite-instable and polymerase ε (POLE)/polymerase δ (POLD1)-mutated tumors, supported by a correlation between microbial load and tumor mutation burden observed across orodigestive cancers. This analysis helps to resolve pan-cancer microbial structure and links the tumor microbiome to host phenotype and tumor genomic context.},
}

@article {pmid42092466,
year = {2026},
author = {Gavini, CK and Raux, L and Labouèbe, G and Gornick, E and Mc Hugh, S and Elshareif, N and Calcutt, NA and Di Summa, PG and Gorostidi, F and Vonaesch, P and Mansuy-Aubert, V},
title = {A gut-adipose-nerve axis mediates inulin protection against Western diet-induced somatosensory dysfunction.},
journal = {Brain, behavior, and immunity},
volume = {137},
number = {},
pages = {106795},
doi = {10.1016/j.bbi.2026.106795},
pmid = {42092466},
issn = {1090-2139},
abstract = {Westernized diets (WDs)-high in fat and sugar and low in fiber-produce somatosensory deficits, chronic pain, and neuropathy, yet the mechanisms linking diet to peripheral nervous system (PNS) pathology remain incompletely defined. Emerging evidence implicates gut-derived metabolites in sensory homeostasis; for example, fecal microbiota transplantation (FMT) from lean donors to WD fed mice reduces hypersensitivity and attenuates PNS inflammation potentially via modifying short chain fatty acid (SCFA) levels, although FMT outcomes are variable. We therefore tested whether targeted modulation of the gut microbiota with fermentable complex carbohydrates (inulin) producing SCFA could reproducibly improve somatosensory function in WD-fed mice. Using an integrated pipeline-behavioral and physiological assays, peripheral nerve electrophysiology, and molecular and immune profiling-we show that inulin improved thermal and mechanical sensory function indirectly by improving metabolic health and remodeling immune cells in adipose tissue depots. Interestingly, in separate genetic experiments we found that deletion of the SCFA receptor FFAR2 (GPR43) in myeloid cells altered thermal sensitivity and adipose inflammatory gene expression, indicating that immune SCFA sensing can modulate pain-related behavior. These findings identify mechanisms by which dietary fiber indirectly preserves PNS function through effects on adiposity and systemic inflammation and provide a tractable alternative to FMT for mitigating WD-associated sensory neuropathy.},
}

@article {pmid42092549,
year = {2026},
author = {Wester, RJ and Samera, GJ and Walcott, JR and Williams, R and Atkins, G and McCarthy, GC and Baillie, LL and Adams, PJ},
title = {Molecular surveillance of Mycoplasmopsis bovis across dairy farms in Western Canada and 16s microbiome assessment in pneumonic calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28245},
pmid = {42092549},
issn = {1525-3198},
abstract = {Mycoplasmopsis bovis (M. bovis) is an important bacterial pathogen that severely impacts the Canadian dairy industry and has been linked to bovine respiratory disease (BRD), a complex that includes pneumonia, as well as mastitis, otitis media, and arthritis. Despite its clinical relevance, limited data exists on its prevalence in Western Canadian dairy herds, and its role within the microbiome in the context of pneumonia remains unclear. This study aimed to determine the prevalence of M. bovis in British Columbia and Alberta and to assess microbial shifts in pneumonic calves to investigate its potential role in BRD. A total of 60 farms were screened for M. bovis using qPCR on bulk tank milk (BTM) and swab samples. M. bovis DNA was detected in 20% of screened farms. However, there were notable differences in detection between swab and BTM samples, highlighting the importance of considering both sample types in surveillance initiatives. Additionally, 82 swab samples from calves in a single herd were analyzed using 16S rRNA sequencing to compare microbial communities across clinical groups. Microbial diversity, differential abundance (ANCOM-BC2), and taxa correlations (SECOM) were assessed. M. bovis presence was not significantly associated with clinical status, although calves with pneumonia exhibited significantly altered microbial diversity compared with healthy calves. M. bovis abundance was significantly enriched, and several commensal taxa were significantly depleted in the pneumonic microbiome. M. bovis abundance was also inversely correlated with some of these taxa, supporting a role in dysbiosis. Overall, these findings suggest that M. bovis is associated with dysbiosis within the respiratory microbiota and may contribute to BRD pathogenesis under conditions of microbial disruption.},
}

@article {pmid42092559,
year = {2026},
author = {Niu, Y and Wang, C and Nie, C and Wu, Y and Huang, R and Zhang, W},
title = {Integrated multi-omics reveals that replacing corn silage with triticale silage improves milk quality via rumen microbiome-metabolome crosstalk in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28155},
pmid = {42092559},
issn = {1525-3198},
abstract = {The objective of this study was to evaluate the effects of replacing corn silage with triticale (× Triticosecale Wittmack) silage on lactation performance, milk fatty acid profile, and rumen microbiome-metabolome interactions in dairy cows. In this study, 27 mid-lactation dairy cows were used in replicated 3 × 3 Latin squares with 3 28-d periods and 3 treatments, in which 0, 25, or 50% of the corn silage (DM basis) was replaced with triticale silage. Replacing 25% of corn silage maintained DMI and milk yield, whereas 50% replacement reduced both variables. Diets containing triticale silage lowered SCC and increased the proportion of oleic acid in milk fat. The 50% replacement further increased the proportions of linoleic acid (LA), α-linolenic acid (ALA), and milk protein concentration. In the rumen, the 50% replacement increased pH and NH3-N concentration, and triticale diets increased the proportions of ALA and several C18:1 and C18:2 biohydrogenation intermediates, resulting in a greater UFA proportion and a lower SFA: UFA ratio in rumen fluid. Metataxonomic analysis revealed higher relative abundances of Butyrivibrio_A, Ruminococcus_E, and Prevotella in triticale diets, whereas metabolomic profiling indicated enrichment of pathways related to LA, ALA, and amino acid metabolism. Correlation analysis associated Butyrivibrio_A and Ruminococcus_E with LA oxidation products and amino acid derivatives, indicating the involvement of rumen microbiome-metabolome interactions in shaping the milk UFA responses. Overall, partial replacement of corn silage with triticale silage improved the milk fatty acid profile and udder health indicators without compromising performance at 25% inclusion, indicating that winter triticale is a promising component of forage systems.},
}

@article {pmid42092564,
year = {2026},
author = {Freund, L and Ramirez Leal, B and Hsu, CL},
title = {Impact of alcohol on gut microbial metabolism and the gut-liver-brain axis.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {134},
number = {},
pages = {44-53},
doi = {10.1016/j.alcohol.2026.04.009},
pmid = {42092564},
issn = {1873-6823},
abstract = {The gut microbiome includes a large and diverse microbial community that plays a central role in host health, supported by an extensive genomic repertoire that is distinct from and complementary to mammalian enzymatic pathways. Alcohol consumption disrupts this ecosystem, inducing microbial dysbiosis and altering functional interactions between the host and its gut bacteria that can lead to systemic effects. In this review, we examine how alcohol affects gut bacteria, and how these changes impair essential bacterial functions, including short-chain fatty acid production, mucin metabolism, biofilm formation, and bile acid metabolism, that support intestinal, liver, and brain health. We further describe how certain gut bacteria tolerate or produce ethanol, and how these traits contribute to the systemic harms associated with alcohol-induced dysbiosis. Finally, we highlight therapeutic strategies aimed at targeting ethanol-tolerant or ethanol-producing bacteria as potential avenues for preventing or mitigating intestinal inflammation, liver injury, and other metabolic disorders.},
}

@article {pmid42092736,
year = {2026},
author = {Prasad, B},
title = {Predicting Pharmacokinetic Variability and Drug Interaction Risk Using Omics-Based Biomarkers.},
journal = {Clinical and translational science},
volume = {19},
number = {5},
pages = {e70591},
pmid = {42092736},
issn = {1752-8062},
support = {R01 HD081299/HD/NICHD NIH HHS/United States ; //National Institutes of Health (NIH)/ ; },
mesh = {Humans ; Drug Interactions/genetics ; *Biomarkers/analysis ; Pharmacogenetics/methods ; *Pharmacokinetics ; Precision Medicine/methods ; Risk Assessment/methods ; },
abstract = {Interindividual variability in drug pharmacokinetics and susceptibility to drug-drug interactions remain major barriers in precision dosing, particularly for narrow therapeutic index drugs. While genetic factors contribute, much variability arises from dynamic influences such as physiology, disease, age, diet, microbiome, and concomitant medications. Conventional approaches provide limited retrospective insight. Emerging phenotypic biomarkers offer a proactive, mechanism-based strategy to quantify variability, improve exposure prediction, assess drug interaction risk, and individualize dosing beyond pharmacogenomics.},
}

Humans
Drug Interactions/genetics
*Biomarkers/analysis
Pharmacogenetics/methods
*Pharmacokinetics
Precision Medicine/methods
Risk Assessment/methods

@article {pmid42092753,
year = {2026},
author = {Palanisamy, M and Babalola, OO and Ramalingam, S},
title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42092753},
issn = {2730-6844},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; },
abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.

DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.},
}

*Salvia officinalis/microbiology
*Plant Leaves/microbiology
*Metagenomics
*Endophytes/genetics/classification
*Microbiota
*Metagenome
Bacteria/genetics/classification
Fungi/genetics

@article {pmid42092798,
year = {2026},
author = {Liu, J and He, S and Zhang, H and Mai, H and Li, X and Liang, H and Cui, P and Lan, L and Liao, W and Huang, Q and Ning, H and Li, Z and Liang, Y and Yang, X and Huang, J},
title = {Machine learning-driven clinical decision support for liver cirrhosis: a gut microbiome-based web prediction model with explainable AI integration.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-04890-7},
pmid = {42092798},
issn = {1471-230X},
support = {82160385//National Natural Science Foundation of China/ ; 82273694//National Natural Science Foundation of China/ ; 2024GXNSFBA010104//Natural Science Foundation of Guangxi Zhuang AutonomousRegion/ ; 2023GXNSFDA026036//Natural Science Foundation of Guangxi Zhuang AutonomousRegion/ ; GXJKKJ2025ZC004//Science and Technology Project for Disease Control and Prevention of Guangxi Zhuang Autonomous Region/ ; },
abstract = {BACKGROUND: Liver cirrhosis (LC) is a chronic liver disease with global prevalence. Current diagnostic methods for LC still face limitations in safety and accessibility. We aimed to develop an interpretable machine learning (ML) prediction model for LC using gut microbes and deploy it as a web-based clinical decision support tool.

METHODS: Data were retrieved from PubMed and BioProject databases. Bioinformatics re-analysis and discriminant analysis effect size (LEfSe) analysis was conducted to preliminarily identify key genera associated with LC. Further feature selection was performed using Least Absolute Shrinkage and Selection Operator (LASSO) regression. The independent datasets were combined to form an integrated dataset, which was then subjected to five-fold cross-validation and leave-one-dataset-out (LODO) analysis. Model performance was evaluated using metrics such as the area under the receiver operating characteristic curve (AUC), and the optimal model was selected. The decision mechanism of the optimal model was interpreted using SHapley Additive exPlanations (SHAP), and the model was deployed as a web application using the Streamlit framework.

RESULTS: We ultimately included 11 datasets related to LC. The genera Veillonella, Lachnospira, Romboutsia, Akkermansia, Erysipelatoclostridium, Prevotella, UCG.005, and Streptococcus were identified as key predictors distinguishing LC patients from healthy controls. The Random Forest (RF) model demonstrated the best predictive performance (AUC in five-fold cross-validation: 0.875, 95% CI: 0.823-0.905; AUC in LODO analysis: 0.793, 95% CI: 0.702-0.940) and was deployed as an online LC prediction tool.

CONCLUSION: The interpretable RF model, along with its web-based implementation, has the potential to provide decision support for healthcare professionals and shows promise as a valuable auxiliary tool for LC screening and early clinical intervention.},
}

@article {pmid42093056,
year = {2026},
author = {Itoh, H and Shimoji, H and Nakane, D and Jang, S and Kikuchi, Y},
title = {Soil pH as an external filter shaping stink bug-Burkholderia gut symbiosis.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42093056},
issn = {2049-2618},
support = {19K15724//Japan Society for the Promotion of Science/ ; 22H05065//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Symbiosis ; *Burkholderia/physiology/isolation & purification/genetics/classification ; *Soil/chemistry ; Hydrogen-Ion Concentration ; *Soil Microbiology ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; },
abstract = {BACKGROUND: Many animals and plants establish intimate symbiotic relationships with specific microorganisms acquired from the environment. Given the immense diversity of environmental microbiomes, selecting appropriate partners from such a vast microbial pool poses a critical challenge for host organisms. To meet this challenge, hosts have evolved sophisticated internal partner-choice mechanisms that ensure stable associations with beneficial microbes. However, because these symbionts primarily inhabit external environments, environmental conditions themselves are also expected to influence the establishment of symbiosis. Despite this expectation, the mechanistic role of external environmental filters in shaping the intended symbiosis remains largely unexplored. Focusing on stink bugs, which acquire their symbiotic bacteria from soil each generation, we investigated how soil properties influence the establishment of gut symbiosis in terrestrial insects.

RESULTS: Microbiome analyses confirmed that Burkholderia sensu lato overwhelmingly dominates a specific gut organ in six stink bug species from the superfamilies Coreoidea and Lygaeoidea, including serious agricultural pests (relative abundance ranging from 74.5 to 100%). Rearing experiments with isolated Burkholderia revealed that insects were strictly dependent on this symbiont; failure to acquire it from soil severely reduced host growth and reproduction, indicating that the availability of symbionts from soil can represent an ecological constraint. Field surveys identified patches of exceptionally high stink bug density in weedy fields with soil pH < 7.0, whereas such aggregations were absent in fields with pH ≥ 7.0. Laboratory experiments with collected field soils showed that the abundance of Burkholderia in soils was negatively correlated with soil pH, and stink bugs readily acquired their symbionts from soils with pH < 7.0 but rarely from soils with pH ≥ 7.0. Experimental manipulations of soil pH followed by rearing experiments confirmed that increasing soil pH to 7-8 markedly suppressed symbiont acquisition by the host, likely by impairing symbiont growth and motility.

CONCLUSIONS: We demonstrate that, beyond host-intrinsic mechanisms, a soil chemical property can act as an externally filter that constrains symbiont acquisition prior to colonization inside the host in a stink bug-Burkholderia symbiosis. This finding highlights how local environmental conditions can shape the assembly of environmentally acquired insect-microbe symbioses. Video Abstract.},
}

Animals
*Symbiosis
*Burkholderia/physiology/isolation & purification/genetics/classification
*Soil/chemistry
Hydrogen-Ion Concentration
*Soil Microbiology
*Gastrointestinal Microbiome
*Heteroptera/microbiology

@article {pmid42093248,
year = {2026},
author = {Durkin, ES and La Luz Maldonado, A and Keiser, CN},
title = {Exploring microbiome diversity between behavioural strategies in a facultatively parasitic mite.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1017/S0031182026102121},
pmid = {42093248},
issn = {1469-8161},
}

@article {pmid42093578,
year = {2026},
author = {Alcamán-Arias, ME and Ramos-Tapia, I and Fuentes, F and Bastías, R and Manzano, CA and Plaza, N and Higuera, G and Araneda, D and Troncoso, M and Ugalde, JA and Vergara, K},
title = {Atmospheric Dispersal and Local Drivers Shape Snow and Air Microbial Communities in the Western Antarctic Peninsula.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70316},
doi = {10.1111/1462-2920.70316},
pmid = {42093578},
issn = {1462-2920},
support = {11200413//ANID/FONDECYT/INACH/ ; 1523A0002//ANID/FONDAP/ ; ATE220061//ANID ANILLO/ ; 1221209//ANID/FONDECYT/ ; },
mesh = {Antarctic Regions ; *Microbiota ; *Snow/microbiology ; RNA, Ribosomal, 16S/genetics ; *Air Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; },
abstract = {Microbial communities in Antarctica's snow and atmosphere are critical for nutrient cycling and are highly sensitive to environmental change. We characterised the bacterial composition, diversity, and co-occurrence network structure of surface snow and airborne microbiomes from two contrasting bays along the Western Antarctic Peninsula (WAP): Arturo Prat Base (APB; Chile Bay, Greenwich Island) and Yelcho Base (YB; South Bay, Doumer Island), sampled during consecutive austral summers (2022-2023). Surface snow and air samples were analysed using 16S rRNA gene sequencing, diversity indices, and network analyses to evaluate spatial and interannual dynamics. Proteobacteria and Bacteroidota dominated both environments, but community structures differed between sites: APB showed stronger local and anthropogenic signals near logistic stations, whereas YB reflected more stable deposition regimes and distant atmospheric inputs. Airborne communities displayed limited interannual variation and high compositional similarity between sites, consistent with atmospheric seeding by polar air masses. Co-occurrence networks revealed denser, more structured interactions within snow communities, with keystone taxa linking snow and air, sustaining deposition-resuspension dynamics. These findings highlight that long-range atmospheric transport and local conditions shape Antarctic microbial dynamics, providing insights for forecasting microbiome responses and assessing airborne health risks amid human activity and climate change in polar regions.},
}

Antarctic Regions
*Microbiota
*Snow/microbiology
RNA, Ribosomal, 16S/genetics
*Air Microbiology
*Bacteria/classification/genetics/isolation & purification
Biodiversity

@article {pmid42093609,
year = {2026},
author = {Harberts, A and Fondevila, MF and Kreimeyer, H and Miwa, T and Lang, S and Demir, M and Schnabl, B},
title = {Faecal Cathepsin B and S Are Associated With Liver Disease Severity and Adiposity in MASLD.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {6},
pages = {e70663},
doi = {10.1111/liv.70663},
pmid = {42093609},
issn = {1478-3231},
support = {R01 AA24726/NH/NIH HHS/United States ; R01 AA031710/NH/NIH HHS/United States ; R37 AA020703/NH/NIH HHS/United States ; P30 DK120515/NH/NIH HHS/United States ; },
mesh = {Humans ; *Cathepsin B/analysis/metabolism ; Female ; Male ; Middle Aged ; *Feces/chemistry ; Gastrointestinal Microbiome ; Severity of Illness Index ; *Adiposity ; Case-Control Studies ; *Cathepsins/analysis/metabolism ; Adult ; *Fatty Liver/metabolism ; Aged ; },
abstract = {BACKGROUND & AIMS: Dysregulation of hepatic cathepsins contributes to metabolic dysfunction-associated steatotic liver disease (MASLD) by promoting inflammation, apoptosis, and fibrosis. However, the role of intestinal cathepsins in MASLD has not been investigated. Given the central role of the gut-liver axis in disease progression, this represents an important knowledge gap.

METHODS: Faecal cathepsin B and S activity was measured in 95 patients with MASLD and 18 healthy controls. Cathepsin activity was correlated with liver disease severity, metabolic parameters, and gut microbiome composition.

RESULTS: Faecal cathepsin B and S activity was higher in patients with MASLD than in healthy controls. Cathepsin B activity was further increased in patients with metabolic dysfunction-associated steatohepatitis. Cathepsin B and S activity correlated with serum transaminases and hepatic steatosis, while cathepsin B activity was additionally associated with liver stiffness. Cathepsin B and S activity correlated with adiposity but showed no associations with other metabolic dysfunction-related parameters. Moreover, gut microbiome composition differed between patients with low vs. high faecal cathepsin B or S activity, respectively.

CONCLUSION: Increased faecal cathepsin B and S activity is associated with liver disease severity and adiposity in MASLD and is linked to alterations of the gut microbiome, suggesting a potential role of intestinal cathepsins in gut-liver axis dysfunction.},
}

Humans
*Cathepsin B/analysis/metabolism
Female
Male
Middle Aged
*Feces/chemistry
Gastrointestinal Microbiome
Severity of Illness Index
*Adiposity
Case-Control Studies
*Cathepsins/analysis/metabolism
Adult
*Fatty Liver/metabolism
Aged

@article {pmid42093690,
year = {2026},
author = {Liao, J and Cui, Y and Wang, Y and Zeng, X and Chen, T and Xiang, Y and Wang, D},
title = {Comparative analysis of the rhizosphere microbiome and transcriptome in clubroot-susceptible and resistant rapeseed (Brassica napus).},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1729220},
pmid = {42093690},
issn = {1664-462X},
abstract = {Clubroot disease, caused by Plasmodiophora brassica, severely threatens the rapeseed industry in China, with an annual affected area exceeding 667000 hectares. To elucidate the mechanisms in clubroot resistance, we compared the differences in soil physicochemical properties, rhizosphere microbiome, and transcriptomic responses between a susceptible variety, HYZ62 (disease index 54.86), and a resistant variety, HYZ5R (disease index 17.05), following P. brassicae infection. The results showed that the electrical conductivity of HYZ5R (R) was 1.73 and 1.57 times that of HYZ62 (S) in the inoculated and uninoculated treatments, respectively. Compared to the 17.18% decrease in alkali-hydrolysable nitrogen content in HYZ62 (S) after inoculation, its content in HYZ5R (R) showed no significant difference. The rhizosphere microbial community significantly differed between HYZ5R (R) and HYZ62 (S), with HYZ5R (R) exhibiting higher relative abundances of several microbial genera, such as Burkholderia-Caballeronia-Paraburkholderia, Humibacter, Dyella, and Trichoderma. Although Bacillus had a significantly higher relative abundance in the rhizosphere of uninoculated HYZ62 (S), its relative abundance decreased by 30.36% after infection. Transcriptome analysis revealed that, compared to HYZ62 (S), the expression of pattern-triggered immunity-related genes, such as CML, WRKY, and PR1, was higher in HYZ5R (R) and was more strongly induced upon inoculation. Effector-triggered immunity-related genes, such as RIN4, RPS5, and HSP90, were consistently expressed at higher levels. In contrast, HYZ62 (S) showed a broad suppression of defense-related gene expression after inoculation. Furthermore, although P. brassicae infection generally suppressed defense-related secondary metabolic pathways, including phenylpropanoid biosynthesis, the expression levels of multiple genes in this pathway remained higher in HYZ5R (R). Together, these results suggest that the higher relative abundances of specific microbial taxa in the rhizosphere and the high expression of defense-related genes are associated with the clubroot resistance in HYZ5R (R).},
}

@article {pmid42093732,
year = {2026},
author = {Shen, Z and Xing, X and Rong, K and Geng, Z and Yang, N and Xu, L and Ge, H and Sang, W},
title = {Short-Term Longitudinal Analysis of Gut Microbiota Dynamics During Anti-CD19 CAR-T Cell Therapy in Diffuse Large B-Cell Lymphoma Patients.},
journal = {Blood and lymphatic cancer : targets and therapy},
volume = {16},
number = {},
pages = {598958},
pmid = {42093732},
issn = {1179-9889},
abstract = {PURPOSE: Alterations in gut microbiota may influence immune response and treatment outcomes in patients with diffuse large B-cell lymphoma (DLBCL). However, the dynamics during anti-CD19 CAR-T cell therapy remain unclear.

METHODS: We conducted a short-term longitudinal microbiome analysis in DLBCL patients (n=12) undergoing CAR-T cell therapy targeting CD19. Stool samples were collected at baseline, 1 week, and 2 weeks post-infusion. 16S rRNA gene sequencing was used to assess microbial diversity, taxonomic composition, and functional pathways. Correlation analyses were then conducted between microbial taxa and inflammatory biomarkers.

RESULTS: Alpha diversity indices showed no statistically significant differences across time points. Beta diversity analysis revealed distinct clustering between baseline and week 1 samples in sPLS-DA, although PERMANOVA did not reach statistical significance. At the phylum level, Bacteroidota abundance significantly increased at week 2 compared with baseline (P = 0.008), accompanied by a marked reduction in the Firmicutes/Bacteroidota ratio. Genus-level heatmap and LEfSe analysis identified enrichment of Parabacteroides, and Prevotella at week 2, whereas baseline samples were enriched in Clostridium sensu stricto 13 and Fusobacterium. Functional prediction indicated that lipoic acid metabolism pathways were significantly upregulated at weeks 1 and 2 compared with baseline (both P < 0.05). Correlation analysis demonstrated that specific bacterial taxa, including Parabacteroides and Prevotella, were positively associated with lymphocyte counts and inversely correlated with C-reactive protein levels.

CONCLUSION: Gut microbiota alterations following CAR-T infusion, characterized by increased Bacteroidota abundance, specific taxonomic shifts, and enhanced lipoic acid metabolism, may provide early microbial signatures for monitoring immune modulation in DLBCL patients.},
}

@article {pmid42093801,
year = {2026},
author = {Busmail, H and Weerakoon, S and Mandefro, BT and Sundara, SV and Lu, X and Avula, S and Mohammed, L},
title = {Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Systematic Review of Efficacy and Safety.},
journal = {Cureus},
volume = {18},
number = {4},
pages = {e106453},
pmid = {42093801},
issn = {2168-8184},
abstract = {Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory condition of the gastrointestinal tract associated with immune dysregulation and alterations in the gut microbiota. Growing evidence suggests that intestinal microbial dysbiosis plays an important role in disease pathogenesis, prompting interest in microbiome-targeted therapies, such as fecal microbiota transplantation (FMT). This systematic review aimed to evaluate the efficacy and safety of FMT in adult patients with IBD. A comprehensive literature search was conducted in PubMed, Embase, Scopus, and the Cochrane Library for studies published between 2020 and 2025 using keywords related to "fecal microbiota transplantation" and "inflammatory bowel disease." Eligible studies included randomized controlled trials (RCTs), cohort studies, systematic reviews, and meta-analyses involving adult patients with UC or CD. Due to clinical and methodological heterogeneity, a structured narrative synthesis was performed in accordance with Synthesis Without Meta-analysis (SWiM) guidelines. Nine studies comprising 1,847 participants met the inclusion criteria, including five RCTs, two systematic reviews, and two meta-analyses. In patients with UC, clinical remission rates ranged from 32% to 40%, with response rates between 44% and 52%. In CD, remission rates ranged from 24% to 31%, although evidence remained limited and heterogeneous. Multi-donor stool preparations and repeated FMT administrations were associated with improved clinical outcomes compared with single-donor protocols or single-dose protocols. Adverse events occurred in approximately 12-15% of patients and were predominantly mild gastrointestinal symptoms, while serious adverse events were rare (<2%). Current evidence suggests that FMT may induce clinical remission in a subset of patients with UC, while evidence in CD remains less consistent. Larger randomized trials with standardized protocols and long-term follow-up are needed to determine optimal donor selection, dosing strategies, and long-term safety.},
}

@article {pmid42093897,
year = {2026},
author = {Zhang, H and Du, Z and Lu, P and Jiang, A and Guo, Y and Liu, Y and Song, Z and Dai, B and Zhang, W},
title = {Intratumoral Microorganisms in Tumors: Current Understanding and Emerging Therapeutic Strategies.},
journal = {MedComm},
volume = {7},
number = {},
pages = {e70754},
pmid = {42093897},
issn = {2688-2663},
abstract = {Recent advances in high-throughput sequencing, spatial omics, and integrative multiomics analyses have established reproducibly detectable microbial communities within tumor tissues, leading to the conceptualization of tumors as complex ecosystems encompassing an "intratumoral microbiota." These microorganisms have increasingly been recognized as contributing to tumorigenesis, progression, and therapeutic response through interactions with the immune system, immunometabolic reprogramming of tissues, chronic inflammation, and genomic instability. Nevertheless, current evidence remains piecemeal and descriptive, with limited systematic consolidation of microbial composition, functional mechanisms, and translation to clinical application, particularly across tumor types and microenvironmental contexts. This review summarizes microbial diversity, tumor-type-specific associations, and multilayered mechanisms including immune modulation, metabolic reprogramming, and signaling rewiring, and discusses emerging applications such as biomarker discovery, prognostic stratification, and microbiome-targeted therapeutics. Special focus is placed on tumor microenvironment, microbiota-derived metabolites, and determinants of immunotherapy responsiveness. Overall, this review underscores the intratumoral microbiota as a dynamic and context-dependent regulatory layer in cancer biology and offers an integrated framework to realize microbiome-informed precision oncology, along with avenues for enhanced patient stratification and personalized therapeutic approaches.},
}

@article {pmid42093997,
year = {2026},
author = {Kuang, J and Zhang, M and Bian, X and Wang, X and Li, X and Wu, Q and Li, J},
title = {Diagnostic and metabolic insights into secondary lactose intolerance in infants via fecal lactose quantification and gut microbiome profiling.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1711945},
pmid = {42093997},
issn = {1664-3224},
mesh = {Humans ; *Lactose Intolerance/diagnosis/metabolism/microbiology ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; *Lactose/analysis/metabolism ; Infant ; Male ; Female ; Fatty Acids, Volatile/metabolism ; Dysbiosis ; },
abstract = {BACKGROUND: Secondary Lactose intolerance (SLI) is common among infants in China, primarily resulting from secondary lactase deficiency due to mucosal damage. Current diagnostic methods are limited by poor sensitivity and specificity.

OBJECTIVE: To investigate gut microbial composition and metabolic dysfunction in infants with SLI and to explore the potential utility of residual fecal lactose as a non-invasive indicator related to SLI.

RESULTS: SLI infants exhibited significantly higher residual fecal lactose and lactate levels accompanied by reduced fecal short-chain fatty acid (SCFA) availability, consistent with incomplete lactose digestion and altered microbial fermentation. Microbiota profiling revealed marked depletion of Bacteroidetes and certain Firmicutes (e.g. Ruminococcaceae, Erysipelotrichaceae, Peptostreptococcaceae, Megasphaera), along with reduced glycolysis pathways. In vitro fermentation assays demonstrated a consistent reduction in total acid, acetate, and propionate production across multiple media, while lactate and gas production were significantly elevated in SLI samples under lactose, FOS, GOS, and starch-enriched conditions. Butyrate synthesis was partially preserved under protein-rich or minimal carbon media, indicating selective resilience of butyrogenic pathways. Microbial β-diversity analysis confirmed structural dysbiosis, with increased abundance of gas-associated taxa, including Clostridium.

CONCLUSION: Residual fecal lactose, when interpreted alongside microbial and metabolic profiles, may serve as a non-invasive indicator associated with secondary lactose intolerance in infants. These findings delineate microbiota-metabolism features consistent with SLI pathophysiology and provide a conceptual framework for future validation studies and the development of nutritional or probiotic interventions.},
}

Humans
*Lactose Intolerance/diagnosis/metabolism/microbiology
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome
*Lactose/analysis/metabolism
Infant
Male
Female
Fatty Acids, Volatile/metabolism
Dysbiosis

@article {pmid42094015,
year = {2026},
author = {Öz, M and Üstüner, E and Çifci, S},
title = {Medicinal and Aromatic Plant Oils in Aquafeeds: Mechanistic Perspectives on Growth Promotion, Immunomodulation, and Stress Resilience.},
journal = {Aquaculture nutrition},
volume = {2026},
number = {},
pages = {8992384},
pmid = {42094015},
issn = {1365-2095},
abstract = {The aquaculture industry is increasingly transitioning toward sustainable aquafeeds, driven by the economic and environmental necessity to replace marine-derived fishmeal and fish oil with plant- and insect-based alternatives. This nutritional shift introduces physiological challenges, accelerating the search for natural, sustainable functional additives. The primary goal of this review is to comprehensively evaluate the application of medicinal and aromatic plant oils (MAPOs) in aquafeeds, providing mechanistic perspectives on their roles in growth promotion, immunomodulation, and stress resilience. We synthesize current literature to link MAPO chemical composition, particularly phenolic monoterpenes and phenylpropenes, with biological responses, advanced delivery systems, and metabolic pathways. Key findings demonstrate that MAPOs can effectively stimulate appetite, modulate the gut microbiome, and enhance antioxidant defenses via the Nrf2-Keap1 pathway, thereby improving disease resistance. However, a critical limitation in the current literature is the high variability and inconsistent outcomes reported across different aquatic species and developmental stages. These discrepancies are largely attributed to strong chemotypic variability of essential oils, unstandardized extraction protocols, and dose-dependent responses that can sometimes yield neutral or suppressive effects. To successfully transition MAPOs from experimental trials to reliable commercial applications, future research must prioritize standardized dose-response evaluations, address species-specific variability, and utilize advanced formulation technologies such as nanoemulsions.},
}

@article {pmid42094080,
year = {2026},
author = {Park, EM and Makowski, L and Cook, KL},
title = {Editorial: The microbiome in cancer therapy response.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1815455},
pmid = {42094080},
issn = {2813-4338},
}

@article {pmid42094244,
year = {2026},
author = {Hasib, A and Ogada, S and Maina, S and Kuria, S and Peng, MS and Yu, J and Ommeh, SC},
title = {Fecal Microbiota Profiling in Indigenous Backyard and Commercial Chickens Reveals Distinct Taxonomic Signatures.},
journal = {Veterinary medicine international},
volume = {2026},
number = {},
pages = {3146713},
pmid = {42094244},
issn = {2090-8113},
abstract = {Farm management conditions and feeding practices in free-range (backyard), semi-intensive, or intensive production systems significantly influence the poultry gut microbiome, thereby impacting their productive performance and overall health. Here, fecal samples from asymptomatic indigenous backyard chickens raised in a free-range production system, characterized by little to no biosecurity measures in place, and from commercial chickens raised in an intensive production system with enhanced biosecurity measures were subjected to 16S rRNA sequencing analysis. Taxonomic assignment identified 19 bacterial phyla, 137 families, and 238 genera. The most prevalent phyla in indigenous backyard and commercial chickens were Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Spirochaetes. Similarities were detected between bacterial families and genera in both indigenous backyard and commercial chickens; however, the bacterial family Bacillaceae and genus Anoxybacillus were only observed in commercial chickens. Statistical tests performed to evaluate the alpha-diversity and beta-diversity metrics showed no significant difference in the fecal bacterial microbiota of indigenous backyard and commercial chickens, as indicated by the Wilcoxon rank-sum (p = 0.94) and PERMANOVA tests (p = 0.26). This study highlights bacteria that may affect the growth, development, and health of indigenous and commercial poultry raised under various production systems, thereby providing vital insights for the development of effective poultry farm management practices.},
}

@article {pmid42094309,
year = {2026},
author = {Amevor, FK and Uyanga, VA and Velleman, SG and Scanes, CG},
title = {Editorial: Integrated approaches to understanding and improving poultry health, immunity, and productivity: unraveling the role of metabolism.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1844387},
pmid = {42094309},
issn = {1664-042X},
}

@article {pmid42094360,
year = {2026},
author = {Yang, R and Severn, M and Aiken, E and Zhou, W and Voigt, A and Walker, G and Koh, A and Gong, M and Thapa, M and Li, S and Milstone, L and Oh, J},
title = {Species and strain diversity in Staphylococcus drive divergent host responses in human skin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.30.720712},
pmid = {42094360},
issn = {2692-8205},
abstract = {The skin microbiome regulates key skin processes, yet the functional diversity of a dominant genus, Staphylococcus, remains poorly resolved at the strain level for multiple species across its pathogenic and commensal continuum. It is likely that Staphylococcus' effects on skin are diverse at these finest taxonomic resolutions, but current skin models lack the physiological relevance and scalability needed to profile this diversity. Using an organotypic 3D human skin model (reconstructed human epidermis, RHE), we profiled skin responses to 187 Staphylococcus strains across seven dominant species. Canonically 'pathogenic' species (e.g., S. aureus) induced broad inflammatory responses, whereas prototypical 'commensal' species (e.g., S. hominis) elicited more nuanced effects on innate immune and skin barrier responses. Strikingly, S. epidermidis displayed pronounced strain-level heterogeneity, with subsets inducing either 'commensal' or 'pathogen'-like responses despite lacking canonical virulence factors, suggesting pleiotropic effects. Comparative genomics, dual-transcriptomics, untargeted metabolomics, and growth phenotyping revealed species- and strain-specific traits underlying these differential effects on RHE, including the presence of select cell surface proteins and differential arginine metabolism. Together, our study provides the first high-throughput, species- and strain-resolved analysis of skin-Staphylococcus interactions, offering mechanistic insights and a platform for microbiome-based strategies to modulate skin inflammation and diseases.},
}

@article {pmid42094415,
year = {2026},
author = {Wills, LJ and Wang-Heaton, H and Polichnowski, AJ and Thomas, KL and Jewett, BE and Jewett, S and Aldridge, G and Ordway, GA and Brown, RW and Chandley, MJ},
title = {PARP inhibition with 3-aminobenzimide attenuates behavioral, cardiovascular, and neuroinflammatory effects of chronic stress.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.721400},
pmid = {42094415},
issn = {2692-8205},
abstract = {BACKGROUND: Major depressive disorder (MDD) affects approximately 20% of the population, with over 30% of cases demonstrating treatment resistance. Postmortem analyses have revealed increased poly (ADP-ribose) polymerase 1 (PARP-1) expression in prefrontal cortical white matter of individuals with MDD, suggesting PARP-1 as a potential therapeutic target. Chronic stress, a major risk factor for depression, affects multiple physiological domains including behavior, cardiovascular function, neuroinflammation, and gut-brain axis signaling.

METHODS: We conducted a comprehensive multi-system investigation of PARP inhibition effects on stress-induced pathophysiology using the social defeat stress/chronic unpredictable stress (SDS+CUS) rodent model. In the primary study, male Sprague-Dawley rats (N=32) underwent 10 days of SDS+CUS while receiving daily treatment with the PARP inhibitor 3-aminobenzamide (3-AB; 40mg/kg), selective serotonin reuptake inhibitor fluoxetine (FLX; 10mg/kg), or saline (0.9% NaCl), with non-stressed controls included. Behavioral outcomes were assessed via sucrose preference and social interaction tests. Neurobiological analyses examined PARP-1 expression, microglial morphology, and proinflammatory cytokine levels (IL-1β, TNF-α, IL-6) in relevant brain regions. In a parallel cardiovascular study, a separate cohort of stressed rats (N=8) received either saline or 3-AB treatment while hemodynamic parameters were monitored via telemetry before, during, and after stress exposure. Exploratory gut microbiome analyses were also conducted (see Supplemental Materials).

RESULTS: Saline-treated stressed rats demonstrated significantly elevated anhedonia and social avoidance compared to all other groups, while 3-AB treatment prevented these behavioral deficits. Cardiovascular monitoring revealed that stressed saline-treated rats developed significant elevations in systolic and mean blood pressure with decreased heart rate compared to baseline, whereas 3-AB treatment prevented these hemodynamic changes. Neurobiological analyses showed that FLX-treated stressed rats unexpectedly exhibited elevated PARP-1 expression in prefrontal cortical gray matter. Microglial morphological analysis revealed significantly more prolate (activated) microglia in the saline-treated stressed rats compared to all other treatment groups. Saline-treated stressed rats exhibited significantly increased hippocampal proinflammatory cytokines, with 3-AB treatment specifically normalizing TNF-α levels.

CONCLUSION: PARP inhibition with 3-AB provides multi-system protection against chronic stress effects, preventing behavioral deficits, cardiovascular dysfunction, and neuroinflammation. These findings establish PARP-1 as a key mediator in the systemic pathophysiology of chronic stress and highlight PARP inhibition as a promising therapeutic approach for stress-related disorders with treatment-resistant features.},
}

@article {pmid42094498,
year = {2026},
author = {Singh, J and Grant, TD and Gulick, AM},
title = {Structure of a Stand-Alone Homodimeric NRPS Condensation Domain Reveals Occlusion of the Canonical Carrier-Protein Interface.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.24.720670},
pmid = {42094498},
issn = {2692-8205},
support = {R01 GM133998/GM/NIGMS NIH HHS/United States ; R35 GM136235/GM/NIGMS NIH HHS/United States ; R35 GM158053/GM/NIGMS NIH HHS/United States ; },
abstract = {Fatty acid amides (FAAs) produced by gut-resident bacteria act as potent modulators of host G protein-coupled receptor signaling, yet the enzymatic mechanisms underlying their biosynthesis remain poorly understood. In many bacteria from the gut microbiome, including Coprococcus eutactus , FAA production is mediated by a nonribosomal peptide synthetase-like pathway that includes OaaC, a free-standing condensation domain that catalyzes amide bond formation between acyl carrier protein (ACP) tethered fatty acids and small-molecule amine acceptors. Here, we combine structural, biophysical, biochemical, and evolutionary analyses to interrogate the molecular basis of OaaC function. Solution scattering and X-ray crystallography reveal that OaaC adopts an atypical homodimeric architecture that occludes the canonical ACP-binding surface and donor access pathways. Mass photometry demonstrates that this homodimer is stable in the absence of substrates and is insensitive to free fatty acids, free amines, and apo-ACP. In contrast, holo or acyl-loaded OaaACP selectively destabilizes the homodimer forming the OaaC-OaaACP complex population. LC-MS reconstitution assays confirm that OaaC catalyzes fatty acid amide formation in vitro and can utilize acyl donors spanning multiple chain lengths and saturation states. Phylogenetic and sequence analyses place FAA-associated condensation domains in a distinct clade most closely related to starter condensation domains and reveal a conserved noncanonical active site motif that differentiates them from PCP-dependent NRPS condensation domains. Together, these findings support a model in which OaaC activity is regulated through substrate-dependent modulation of oligomeric state, providing a model framework for understanding FAA biosynthesis in gut microbes and expanding the known functional diversity of NRPS condensation domains.},
}

@article {pmid42094537,
year = {2026},
author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J},
title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.29.721577},
pmid = {42094537},
issn = {2692-8205},
abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.},
}

@article {pmid42094709,
year = {2026},
author = {Mallick, S and Pavloudi, C and Chakkalakkal, GJ and Lažetić, V and Saw, J and Eleftherianos, I},
title = {A dataset on microbiome alterations in Drosophila melanogaster infected by entomopathogenic nematodes.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112794},
pmid = {42094709},
issn = {2352-3409},
abstract = {The fruit fly Drosophila melanogaster is an excellent model for dissecting the molecular processes that regulate host-microbe interactions and the role of the microbiome in host homeostasis. More recently, the fly has also been used as a model for understanding entomopathogenic nematode infection and host response against these parasites. To gain insights into the effect of entomopathogenic nematode infection on the insect microbiome, D. melanogaster larvae were exposed to Heterorhabditis bacteriophora containing their symbiotic bacteria Photorhabdus luminescens (symbiotic worms) and nematodes lacking their bacterial symbionts (axenic worms). Microbiome changes were examined through 16S rRNA sequencing. Data were collected at 24- and 48-hours following infection of D. melanogaster larvae with either type of nematode. The complete set of raw sequencing data generated in this study has been deposited in the European Nucleotide Archive under accession number PRJEB85826.},
}

@article {pmid42094772,
year = {2026},
author = {Luo, H and Shen, Z and Jian, Y and Wang, M and Luo, S and Wang, J and Nan, L and Tang, L and Rehman, MU and Carbonero, F},
title = {Editorial: Unravelling the wildlife gut microbiome: the crucial role of gut microbiomes in wildlife conservation strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1838495},
pmid = {42094772},
issn = {1664-302X},
}

@article {pmid42094775,
year = {2026},
author = {Nguyen, D and Ovadia, O and Masasa, M and Tarnecki, A and Brennan, NP and Rhody, NR and Main, KL and Guttman, L},
title = {Microbial dynamics along nutrient flow and removal in an integrated multitrophic aquaculture system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781931},
pmid = {42094775},
issn = {1664-302X},
abstract = {Microbial community assembly in marine integrated multi-trophic aquaculture (IMTA) systems remains poorly understood, particularly across interconnected extractive compartments spanning spatial and temporal scales. Two-step biofilters that incorporate seaweeds and multi-species biofilms (periphyton) are widely used to remove excess nitrogen and phosphorus from aquaculture effluents while simultaneously generating protein-rich, edible biomass. Variations in nutrient composition along these biofilters suggest that microbial diversity and functionality may be differentially shaped within the system. To address this knowledge gap, in this study, using the 16S rRNA gene amplicon sequencing technique, we examined the assembly and potential functions of aquatic microbial communities along the treatment of marine effluent by Ulva fasciata and periphyton, where species selection may occur spatially through microbial colonization of the different plant substrates or through changes in water-nutrient content. At the same time, we assessed temporal dynamics by the weekly changes over 5 weeks. Community structure and functionality demonstrated that environmental heterogeneity primarily determined dissimilarity among microbial communities across the biofilter's compartments. Microbial beta diversity of periphyton, Ulva thallus, and rearing water was distinct over time. This confirmed the important role of environmental selection despite hydraulic homogeneity caused by the high dispersal rate of running water within the interconnected biofilters. The periphyton microbial community harbored the highest alpha diversity, followed by the water microbiome and Ulva-associated microbiota. In terms of functional potential, nitrogen and sulfur metabolism were generally higher in periphyton than in the water and Ulva assemblies. While nitrate reduction by periphyton is associated with the high prevalence of genes involved in denitrification, the Ulva-microbes interaction benefits the alga through bacterial dissimilatory nitrate reduction to ammonia. Overall, these findings provide novel insights into the spatial and temporal dynamics of microbiomes in integrated culture systems, contribute to optimal IMTA designs and microbial management in holistic mariculture.},
}

@article {pmid42095016,
year = {2026},
author = {Li, R and Zhang, S and Liu, Q and Wang, B and Mi, S and Wang, C and Chen, X and He, K and Lv, Y and Gao, X and Fan, Y and Tang, J and Hua, D and Wang, X},
title = {Effects of cotton straw and apple pomace mixed ensilage on growth performance, slaughter performance, meat quality, rumen microbiota and metabolome of Xinjiang Brown cattle.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1796588},
pmid = {42095016},
issn = {2297-1769},
abstract = {This study aimed to investigate the effects of replacing traditional corn silage with cotton straw and apple pomace mixed ensilage feed on the growth performance, slaughter performance, meat quality, rumen microbiota and metabolome of Xinjiang Brown Cattle. Twenty 22-month-old Xinjiang Brown Cattle with similar body conditions were randomly divided into a control group (Con, corn silage) and an experimental group (Tre, cotton straw and apple pomace mixed ensilage). The experiment lasted for 180 days, during which growth performance was evaluated. At the end of the experiment, 6 cattle were randomly selected from each group for slaughter to determine slaughter performance and meat quality. Meanwhile, rumen fluid samples were collected to analyze the rumen microbial community structure using 16S rRNA gene sequencing, and rumen fluid metabolites were analyzed with untargeted metabolomics (LC-MS) technology. The results showed that there were no significant differences in growth performance (average daily gain and final weight) between the two groups. However, compared to the Con group, the carcass weight, dressing percentage and drip loss of the Tre group were significantly decreased (p < 0.05). Rumen fermentation results indicated that the rumen pH value of the Tre group was significantly increased (p < 0.05), while the acetic acid content was significantly decreased (p < 0.05). Microbiome analysis showed that the α-diversity (Shannon and Chao1 indices) of rumen microbiota in the Tre group was significantly higher, and there was a significant difference in β-diversity (p < 0.05); the relative abundance of fiber-degrading bacteria such as Fibrobacter in the Tre group was significantly increased. LC-MS analysis revealed that the contents of beneficial metabolites such as N-Acetyl-L-methionine and Resveratrol were increased in the Tre group. In conclusion, cotton straw and apple pomace mixed ensilage feed can be used as an effective substitute for corn silage, modulating the rumen microbial community structure and altering the metabolite profile, thereby improving meat juiciness. This study provides theoretical support for the resourceful and high-value utilization of agricultural by-products such as cotton straw and fruit pomace in Xinjiang.},
}

@article {pmid42095017,
year = {2026},
author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X},
title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1768985},
pmid = {42095017},
issn = {2297-1769},
abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.},
}

@article {pmid42095188,
year = {2026},
author = {Li, J and Yang, Y and Wang, Y and Liu, J and Huang, X and Li, Z and Li, J},
title = {Society and the Microbiome: A Biopsychosocial Window Into Comprehensive Well-Being: A Review.},
journal = {Health science reports},
volume = {9},
number = {5},
pages = {e72162},
pmid = {42095188},
issn = {2398-8835},
abstract = {BACKGROUND AND OBJECTIVES: In addition to biological factors, human social behavior, societal structures, and environmental contexts significantly influence the human microbiome. This review examines how socially relevant factors relate to the microbiome to clarify underlying mechanisms and health impacts, aiming to inform effective preventive and therapeutic strategies.

METHODS: We synthesized relevant literature from PubMed using a biopsychosocial framework, integrating structural socio-political and contextual factors to elucidate interactions between social behavior and the microbiota.

RESULTS AND CONCLUSIONS: Social behavior shapes the microbiome through complex biological, psychological, and socio‑cultural pathways, with health consequences involving immune, mental, and metabolic functions. Future research should clarify the fundamental drivers of this relationship, identify individual differences, and employ longitudinal designs to measure sustained effects.},
}

@article {pmid42095223,
year = {2026},
author = {Cheng, Y and Zhang, L and Zhang, M and Yu, J},
title = {Advances in research on the effects of bile acids and their receptors on intestinal function.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1821418},
pmid = {42095223},
issn = {2296-861X},
abstract = {Bile acids (BAs), once regarded primarily as detergents facilitating lipid digestion, are now recognized as pivotal signaling molecules that orchestrate intestinal and systemic physiology through a diverse network of nuclear and membrane receptors, with distinct receptor classes mediating complementary transcriptional and rapid signaling responses, including Farnesoid X Receptor (FXR), Takeda G protein-coupled Receptor 5 (TGR5), Pregnane X Receptor (PXR), Peroxisome Proliferator-Activated Receptor α (PPARα), Vitamin D Receptor (VDR), and Mas-related G protein-coupled Receptor member X4 (MRGPRX4). This review synthesizes recent advances in understanding the molecular architecture of BA signaling, emphasizing receptor structural diversity, spatiotemporal expression patterns along the gastrointestinal tract, ligand specificity shaped by BA chemical modifications, and the emerging roles of microbiota-derived bile acid derivatives and selected non-canonical host targets in intestinal immune and metabolic regulation. Central to this signaling axis is the gut microbiome, which enzymatically reprograms the BAs pool through deconjugation, dehydroxylation, oxidation, and epimerization, as well as emerging reconjugation/amidation pathways, thereby generating classical secondary BAs as well as structurally novel metabolites that modulate host receptor activity and immune-cell programs. In turn, BAs shape microbial composition, establishing a dynamic bidirectional feedback loop critical for maintaining intestinal homeostasis. In addition to classical receptor signaling, selected microbiota-derived BAs metabolites can also influence immune-associated transcriptional regulators, thereby expanding the scope of BAs signaling in mucosal immune homeostasis. Beyond metabolism, BAs-receptor interactions integratively regulate gut barrier integrity via tight junction reinforcement, modulate immune responses through anti-inflammatory pathways and tolerogenic cell induction, and influence gut motility and neuroendocrine signaling. Dysregulation of BAs receptor and metabolite-mediated signaling axes is increasingly implicated in the pathogenesis of inflammatory bowel disease, bile acid malabsorption, diarrhea-predominant irritable bowel syndrome, colorectal cancer-via DNA damage and Wnt/β-catenin pathway activation-and systemic conditions such as obesity, non-alcoholic fatty liver disease, and sepsis-related intestinal injury. Emerging therapeutic strategies aim to restore BAs signaling balance through next-generation receptor modulators, tissue-targeted delivery systems, microbiome-directed interventions, rational use of sequestrants, and synergistic combination therapies, thereby supporting the development of more precise and mechanism-based interventions. Future progress will hinge on interdisciplinary approaches integrating metabolomics, gnotobiotic models, and clinical translation to harness the full therapeutic potential of the BAs signaling network in gastrointestinal and metabolic health.},
}

@article {pmid42095655,
year = {2026},
author = {Weis, AM and Matthews, OJ and Bell, R and Pershing, NL and Dankwardt, A and Fleming, BA and Gigic, B and Schneider, M and Hardikar, S and Toriola, AT and Shibata, D and Li, CI and Byrd, DA and Stephens, WZ and Ulrich, CM and Mulvey, MA and Round, JL},
title = {Isolation of a highly virulent colibactin-positive tumor-promoting strain of Escherichia coli from the gut microbiota of an adult.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0021926},
doi = {10.1128/msphere.00219-26},
pmid = {42095655},
issn = {2379-5042},
abstract = {Recent studies have pointed to critical roles for microbes in both exacerbation of and protection from the development of colon cancer. While much has been learned, the field remains understudied, with functional studies available for only a handful of bacteria. To identify novel microbes associated with colorectal cancer (CRC) development, we employed a preclinical chemical carcinogenesis CRC mouse model using germ-free mice that were colonized with human microbiotas. During the course of these studies, we identified a microbiota that exacerbated CRC, from which we isolated an Escherichia coli strain that had disseminated to the mouse kidneys. This strain, which we designated as AW001, was genetically similar to the reference adherent-invasive E. coli (AIEC) strain NC101 and encoded the DNA-damaging toxin colibactin. In relevant animal models, AW001 worsened both colitis and sepsis, making it a colitogenic AIEC-like strain with the capacity to cause invasive systemic infections similar to extraintestinal pathogenic E. coli (ExPEC). This strain will be a relevant tool to study human-associated intestinal E. coli strains capable of causing disease in mice.IMPORTANCEColorectal cancer (CRC) is a significant burden on human health. A growing body of work has pointed to critical roles for microbes in the exacerbation of and protection from the development of CRC. Specific Escherichia coli strains can produce colibactin, a genotoxin that has been implicated in exacerbating CRC. In this study, we tested human microbiotas in a mouse model of CRC and isolated a colibactin-positive Escherichia coli strain that led to tumorigenesis, disseminated from the gut to the mouse kidneys, caused death, and worsened both colitis and sepsis in murine models. Identification of this strain enhances our collective knowledge and adds an important tool for future studies on the role of microbes and CRC tumorigenesis.},
}

@article {pmid42096014,
year = {2026},
author = {Ng, WS and Ng, NC and Wong, RS and Goh, BH},
title = {Fermented Durian Tempoyak as a Source of Probiotics for Colorectal Cancer Prevention through Gut Microbiome Modulation.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42096014},
issn = {1534-312X},
mesh = {Humans ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/prevention & control/microbiology ; *Gastrointestinal Microbiome ; *Fermented Foods/microbiology ; Dysbiosis/complications ; },
abstract = {PURPOSE OF REVIEW: Colorectal cancer (CRC) remains a major global and Malaysian public health concern, with increasing recognition of gut dysbiosis as a contributor to colorectal tumorigenesis. This review examines fermented durian tempoyak as a culturally relevant, probiotic-rich traditional food with potential application in CRC prevention through gut microbiome modulation.

RECENT FINDINGS: Dysbiosis may promote CRC through disruption of gut barrier integrity, chronic mucosal inflammation, immune dysregulation, reactive oxygen species (ROS)-mediated DNA damage, and altered microbial metabolism leading to carcinogenic metabolites such as secondary bile acids and hydrogen sulphide. Tempoyak commonly contains lactic acid bacteria, particularly Lactiplantibacillus plantarum, as well as Limosilactobacillus fermentum and Levilactobacillus brevis. Preclinical evidence suggests that related LAB strains can attenuate NF-κB, MAPK, STAT3, IL-17, and COX-2-associated inflammatory pathways, reduce immune-cell infiltration and oxidative stress, restore mucus and tight junction proteins, modulate bile acid metabolism, and reduce tumor burden in CRC or colitis-associated CRC models. Current evidence supports the mechanistic plausibility of tempoyak-associated LABs as microbiome-based agents for CRC chemoprevention. However, direct evidence using tempoyak-derived strains remains limited, and translation is constrained by strain-specific effects, microbial variability, sensory acceptability, safety and standardisation issues, and uncertain LAB viability after cooking. Future studies should prioritise strain characterisation, starter culture standardisation, probiotic stabilisation strategies, CRC-specific preclinical models, and well-designed human trials in high-risk populations.},
}

Humans
*Probiotics/therapeutic use
*Colorectal Neoplasms/prevention & control/microbiology
*Gastrointestinal Microbiome
*Fermented Foods/microbiology
Dysbiosis/complications

@article {pmid42096024,
year = {2026},
author = {Hu, X and Chen, J and Zhou, Y and Ji, X and Shen, S and Qian, J and Li, T and Xu, F and Zhou, Y and Zhou, D and Zhang, X},
title = {n-3 Polyunsaturated Fatty Acids Improve DSS-Induced Acute Colitis in Mice via Intestinal Barrier Fortification and Gut Microbiome Modulation.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42096024},
issn = {1573-2568},
support = {82404257//the National Natural Science Foundation of China/ ; 82273621//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The increasing global burden of ulcerative colitis (UC) is showing a high incidence in developed countries and a swift rise in developing countries. n-3 polyunsaturated fatty acids (PUFAs), particularly eicosatetraenoic acid (EPA) and docosahexaenoic acid (DHA), have demonstrated anti-inflammatory effects. However, their exact mechanisms in intestinal barrier repair for UC remain incompletely elucidated.

METHODS: Acute UC was induced using 2% dextran sulfate sodium (DSS) and the therapeutic effects of mesalazine, EPA, DHA, and EPA + DHA were evaluated. The mucus barrier was assessed histologically. RT-qPCR and Western blot were used to quantify the expression of Mucin2, mechanical barrier proteins (Claudin-1/Occludin), and key signaling pathways (PI3K/Akt, TNF-α/NF-κB, GPR120/PKA/CREB). Gut microbiome composition was analyzed via 16S rRNA sequencing.

RESULTS: EPA + DHA intervention demonstrated optimal efficacy in alleviating colitis, through establishing an anti-inflammatory colonic lipid microenvironment by elevating the EPA/AA and DHA/AA ratios. Inhibiting PI3K/Akt/NHE3, downregulating TNF-α/NF-κB/DRA, activating GPR120/PKA/CREB/AQP) improved the mucosal barrier and restored tight junction to enhance the mechanical barrier. Furthermore, EPA + DHA significantly increased the abundance of beneficial microbiome like Lachnospiraceae and Ruminococcaceae.

CONCLUSION: EPA + DHA effectively alleviates acute UC in mice by fortifying the colonic mucus-mechanical dual barrier and regulating gut microbiome homeostasis, providing a novel potential strategy for UC adjunctive treatment.},
}

@article {pmid42096120,
year = {2026},
author = {Wu, R and Yao, G},
title = {Research advancement on the correlation between gut microbiota and chronic kidney disease.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42096120},
issn = {1572-9699},
support = {010086//the Beijing Major Epidemic Prevention and Control Key Specialty Intensive Care Medicine Construction Project under Grant/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Renal Insufficiency, Chronic/microbiology/therapy ; Dysbiosis/microbiology ; Probiotics ; Animals ; },
abstract = {Chronic kidney disease (CKD) represents a significant global health challenge, with its progression and complications associated with dysbiosis of the gut microbiota. Patients with CKD demonstrate stage-dependent alterations in the composition of gut microbiota and a reduction in diversity, which is characterized by a decline in beneficial bacteria (e.g., Bifidobacterium, Lactobacillus) and an increase in pathogenic species. This dysbiosis disrupts the gut-kidney axis, resulting in a depletion of protective metabolites such as short-chain fatty acids (SCFAs) and secondary bile acids, while facilitating the accumulation of toxic metabolites including trimethylamine N-oxide (TMAO), indoxyl sulfate (IS), and p-cresyl sulfate (pCS). These toxins contribute to the progression of CKD and cardiovascular complications through mechanisms that involve oxidative stress, inflammation (e.g., NF-ĸB/NLRP3 activation), fibrosis (e.g., TGF-β/Smad signaling), and endothelial dysfunction. Therapeutic strategies aimed at modulating the gut microbiota encompass dietary interventions (such as increasing fiber and plant-based protein), microecological agents (including probiotics and prebiotics), fecal microbiota transplantation (FMT), and adsorbents (e.g., targeting uremic toxins). Although these approaches show promise in delaying CKD progression and alleviating complications, they necessitate further validation through large-scale clinical trials to confirm their efficacy, safety, and the development of personalized protocols. Investigating the gut-kidney axis may provide novel biomarkers and therapeutic opportunities for enhancing CKD outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Renal Insufficiency, Chronic/microbiology/therapy
Dysbiosis/microbiology
Probiotics
Animals

@article {pmid42096418,
year = {2026},
author = {Santini, AT and Cerqueira, AES and Moran, NA and Resende, HC and Santana, WC and de Paula, SO and da Silva, CC},
title = {Gut microbiota of Brazilian Melipona stingless bees: Dominant members and their localization in different gut regions.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0326546},
pmid = {42096418},
issn = {1932-6203},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Brazil ; Symbiosis ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that play crucial role in nutrition, pathogen defense and host fitness. While the core microbiota of honeybees and bumblebees is well characterized, the composition, spatial organization, and evolutionary dynamics of the microbiota of stingless bees remain poorly understood. This gap is particularly evident in the diverse genus Melipona, where Snodgrassella and Gilliamella, ubiquitous symbionts of honeybees and bumblebees, appear rare or absent, indicating a shift in microbiota composition in these stingless bees. Here, we address this gap by characterizing the microbiota of multiple Melipona species using 16S rRNA amplicon sequencing of newly collected and previously published data from field-collected samples. We also mapped the spatial localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides through targeted dissection. The Melipona microbiota is dominated by members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus, and Bombella, with striking regional structure. Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae are most abundant in the ventriculus. The ileum lacks Snodgrassella and Gilliamella but contains a putative new symbiont closely related to Floricoccus, as well as strains of Bifidobacterium, Lactobacillaceae (including Apilactobacillus), and Bombella. The rectum is dominated by Bifidobacterium and Lactobacillus. These findings reveal a distinct microbiota architecture in Melipona that differs from other corniculate bees yet retains compartment-specific specialization, suggesting an alternative symbiotic strategy that may reflect unique dietary ecology and evolutionary history. Understanding these patterns advances our knowledge of host-microbe symbiosis and provides a baseline for microbiome conservation in declining stingless bee populations.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Brazil
Symbiosis
*Bacteria/genetics/classification/isolation & purification
Phylogeny

@article {pmid42096491,
year = {2026},
author = {Ma, Z and Shi, H and Bai, X and Wang, Z and Cao, J and Dong, Y and Chen, Y},
title = {Host metabolism shapes the intestinal microbiota: a top-down paradigm of environmental selection pressure.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2667735},
doi = {10.1080/19490976.2026.2667735},
pmid = {42096491},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Dysbiosis/microbiology/metabolism ; Energy Metabolism ; *Host Microbial Interactions ; Intestinal Mucosa/metabolism/microbiology ; Bacteria/metabolism/genetics/classification ; Homeostasis ; },
abstract = {Intestinal homeostasis is not a stochastic microbial assembly but a deterministic outcome orchestrated by host-mediated metabolic gating. Traditional research has prioritized the microbiota's impact on host physiology. However, the consistent expansion of facultative anaerobes, such as Enterobacteriaceae, observed in pathological states like intestinal inflammation, suggests that dysbiosis is fundamentally a consequence of impaired host regulation. Here, we propose a "top-down" paradigm of host metabolic regulation, framing the host as an "ecological engineer" that actively shapes the microbiome through metabolism. We detail three critical metabolic filters: (1) the maintenance of epithelial hypoxia via mitochondrial β-oxidation to suppress aerobic respiration; (2) the implementation of "nutritional immunity" to restrict glucose and inflammation-derived electron acceptors (nitrate and tetrathionate); and (3) the energy-dependent synthesis of the gel-forming mucin 2 (MUC2) mucus layer and antimicrobial peptides (AMPs). We argue that the breakdown of these filters leads to "niche opening," which acts as the fundamental driver of dysbiosis. Finally, we discuss therapeutic strategies aimed at restoring host bioenergetics-including Peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists, melatonin, and ketogenic diets-to rebuild the host's ecological filtration capacity and fundamentally correct dysbiosis.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals
Dysbiosis/microbiology/metabolism
Energy Metabolism
*Host Microbial Interactions
Intestinal Mucosa/metabolism/microbiology
Bacteria/metabolism/genetics/classification
Homeostasis

@article {pmid42096550,
year = {2026},
author = {Xie, M and Xu, C and Xiang, N and Liao, T and Liu, X and Liu, Z and Feng, X and He, Q and Liang, Z and Wang, W and Dai, Y and Yan, L and Pogoreutz, C and Barra, L and Au, SWN and Jiang, L and Voolstra, CR and Luo, H},
title = {Trait-based signatures associated with persistence and thermal benefit in a genomically decayed coral probiotic.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag106},
pmid = {42096550},
issn = {1751-7370},
abstract = {A key bottleneck in microbiome engineering is ensuring long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of population MC10, identified by such signatures, showed persistent coral colonization in a companion study. Whether this persistence translates into measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both controls. To understand the mechanistic basis, we characterized the functional profile of MC10-B4 using integrated multi-omics. The MC10 genome is enriched in host-interaction genes, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, confirmed phenotypically by iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated "motile-to-sessile" proteomic reprogramming, downregulating flagellar motor components whereas upregulating flagellin and biofilm regulators. This response was distinct from sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4's functional profile, particularly its oxidative stress sensitivity, contrasts with traits favored in conventional probiotic screens. Our results provide mechanistic insight into traits associated with long-term host association and thermal benefit, validating an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities for rational probiotic design.},
}

@article {pmid42096749,
year = {2026},
author = {Kafkoutsou, AL and Stewart, M and Bakali, U and Beaver, CC and O'Connor, G and Kobetz, EN and Caban-Martinez, AJ and Deo, SK and Daunert, S and Schaefer Solle, N},
title = {Vaginal polycyclic aromatic hydrocarbons (PAHs), HPV infection, and vaginal microbiome in firefighters: A cross-sectional study.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142072},
doi = {10.1016/j.jhazmat.2026.142072},
pmid = {42096749},
issn = {1873-3336},
abstract = {Female firefighters are routinely exposed to combustion-derived toxicants, yet the reproductive health implications of this exposure are largely unknown. We investigated whether polycyclic aromatic hydrocarbons (PAHs) are detectable in the vaginal tract of female firefighters and whether these contaminants are linked to high-risk human papillomavirus (HPV) infection and vaginal microbiome alterations. In this cross-sectional study 49 female firefighters and 51 community controls self-collected vaginal swabs for analysis of 16 EPA-priority PAHs, high-risk HPV, and microbial composition. All 16 PAHs were detectable and median total PAHs were 3-fold higher in firefighters than controls (p < .0001). PAH burden increased with firefighting tenure showing a strong positive correlation between high- and low-molecular-weight congeners (r = 0.85). High-risk HPV was detected in 12.2% of firefighters versus 3.9% of controls and was associated with higher PAH levels (p = 0.02). Firefighters exhibited a microbiome shift characterized by increased relative abundance of Gardnerella (r = 0.32 with total PAHs) and reduced Lactobacillus dominance. Detection of vaginal PAHs along with their associations with HPV and dysbiosis, suggests a previously unrecognized pathway by which occupational exposures may elevate cervical cancer risk. Targeted exposure reduction policies and vigilant gynecologic screening should be considered for this underserved workforce.},
}

@article {pmid42096978,
year = {2026},
author = {Crespo-García, C and Taaffe, DR and Peddle-McIntyre, CJ and Jeffery, E and Campbell, JP and Thomas, R and Galvao, DA and Newton, RU},
title = {Precision nutrition in breast cancer: Towards patient- and tumour-informed dietary strategies.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106670},
doi = {10.1016/j.clnu.2026.106670},
pmid = {42096978},
issn = {1532-1983},
abstract = {Dietary strategies are increasingly recognized as important modulators of breast cancer outcomes, acting through effects on metabolic regulation, weight management, hormone signalling, immune function, and the gut microbiome. However, breast cancer heterogeneity and inter-individual variability mean that generic dietary guidelines may not fully capture patient needs. Precision nutrition offers the opportunity to align dietary interventions with tumour subtype, treatment context, and host biology, potentially enhancing therapeutic response and survivorship in patients diagnosed with breast cancer. In this narrative review, we summarize evidence on dietary patterns and prognosis, and explore how targeted interventions, including fasting regimens, ketogenic diets, and caloric restriction, may be informed by and targeted to host factors such as obesity, metabolic dysfunction, genetics and epigenetics, and microbiome composition, as well as tumour and treatment characteristics. We also discuss the emerging role of digital tools and multi-omics approaches to support personalization. While clinical translation is at an early stage, refining dietary recommendations through precision approaches may open new opportunities to improve prognosis and long-term care in breast cancer.},
}

@article {pmid42097107,
year = {2026},
author = {Panyakhamlerd, K and Rungruxsirivorn, T and Panichaya, P and Nimitpanya, P and Payungporn, S and Ariyasriwatana, C and Suwan, A and Visedthorn, S and Ruengket, P and Tanprasertkul, C},
title = {The effect of hormone therapy on vaginal microbiota in women with genitourinary syndrome of menopause: A double-blind, randomized, placebo-controlled trial.},
journal = {Maturitas},
volume = {209},
number = {},
pages = {108963},
doi = {10.1016/j.maturitas.2026.108963},
pmid = {42097107},
issn = {1873-4111},
abstract = {This double-blind, randomized, placebo-controlled trial investigated the effects of oral combined menopausal hormone therapy (MHT) on vaginal microbiota and clinical outcomes in postmenopausal women with genitourinary syndrome of menopause (GSM). Thirty-four healthy postmenopausal women aged 40-60 years with moderate to severe GSM were randomized to receive either oral estradiol 1 mg/dydrogesterone 5 mg (Femoston conti®) or placebo daily for 12 weeks. Vaginal microbiota was assessed at baseline and week 12 using 16S rDNA gene sequencing. Clinical outcomes, including the most bothersome symptom (MBS), vaginal atrophy score (VAS), vaginal pH, vaginal health index (VHI) and vaginal maturation value (VMV), were evaluated at baseline, week 6, and week 12. The MHT group demonstrated significant more improvement in all clinical measures compared with placebo: MBS (p = 0.008), VAS (p < 0.001), vaginal pH (p = 0.001), VHI (p < 0.001) and VMV (p < 0.001). However, no significant differences were observed in microbial composition or diversity between groups after treatment. These findings suggest that while systemic hormone therapy provides meaningful symptom relief and improves vaginal tissue health, these clinical benefits can occur without concurrent, statistically significant changes in the vaginal microbiota. This supports the clinical value of early systemic MHT in managing GSM, even in the absence of microbiome restoration.},
}

@article {pmid42097142,
year = {2026},
author = {El Mouali, Y and Tawk, C and Huang, KD and Sivapornnukul, P and Mengoni, C and Segata, N and Strowig, T},
title = {Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.006},
pmid = {42097142},
issn = {1934-6069},
abstract = {In the human gut, oxygen levels decrease with increasing distance from the epithelium, creating a gradient that dictates the spatial distribution of commensal bacteria based on varying oxygen tolerance. However, dietary and lifestyle changes can disrupt this ecosystem. Segatella copri, a prevalent ancestral commensal, typically displays greater oxygen sensitivity than Bacteroides species. Here, we find that the transcriptional regulator PerR controls a genetic network underlying S. copri's oxygen response that is critical for gut colonization. Notably, a subset of S. copri strains have acquired an additional oxygen response regulator, OxyR, likely through horizontal gene transfer from other Bacteroidales, conferring enhanced oxygen tolerance. Interestingly, OxyR-positive strains are more prevalent in industrialized countries yet absent in contemporary humans with traditional lifestyles and in ancient human samples. These findings point to recent evolutionary pressures on Segatella, potentially driven by lifestyle changes, which may impact the spatial distribution of the human gut microbiome.},
}

@article {pmid42097143,
year = {2026},
author = {Antunes Fernandes, K and Sanders, F and Cafiero, TR and Huang, C and Reyes, J and Biswas, A and Lim, AI},
title = {Maternal helminths rewire the microbiota to promote offspring antiviral immunity.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.009},
pmid = {42097143},
issn = {1934-6069},
abstract = {Maternal environmental exposures can alter microbiome composition and lead to changes in offspring immunity. Industrialization has led to significant shifts in the microbiome, but whether these have transgenerational impacts remains unclear. Here, we discovered that maternal helminths, an evolutionarily conserved mammalian partner lost in industrialized societies, confer broad and lasting protection against respiratory viruses in offspring. This heterologous antiviral immunity is mediated by helminth-induced changes in the maternal microbiota. The tryptophan metabolite indole-3-propionic acid (IPA), derived from helminth-altered microbiota, induces lung epithelial IFN-I responses and is sufficient to protect offspring from respiratory syncytial virus (RSV) and influenza A virus infections. Analysis of chronically helminth-infected human populations reveals gut microbiota enriched for tryptophan metabolic capacity. Additionally, IPA treatment is sufficient to enhance antiviral IFN-I signaling in human bronchial epithelial cells. Collectively, this work uncovers the importance of maternal helminth-driven trans-kingdom crosstalk across generations and highlights microbial metabolites as actionable strategies to strengthen antiviral defense.},
}

@article {pmid42097354,
year = {2026},
author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S},
title = {Integrative Machine Learning Models to Unravel Gut Microbial Dysbiosis and Functional Disruption in Polycystic Ovary Syndrome.},
journal = {F&S science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.xfss.2026.04.005},
pmid = {42097354},
issn = {2666-335X},
abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared to healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.

DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PolyCystic Ovary Syndrome (PCOS) MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.

RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of pro-inflammatory taxa such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals including Roseburia hominis and Prevotella copri. These compositional shifts indicate a pro-inflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome based machine learning models achieved a diagnostic accuracy of 84.25% (AUC 0.93), underscoring their predictive potential.

CONCLUSION: The gut microbiome in PCOS is characterized by a pro-inflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.},
}

@article {pmid42097383,
year = {2026},
author = {Yang, Z and Liang, Z and Cao, L and Li, S and Gao, L and Tian, D and Qiu, Z and Chen, J},
title = {Altitude-Dependent Variations in Environmental Conditions and Human Activities Regulate Microbial Community Assembly and Carbon Metabolism Patterns in Headwater Rivers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124656},
doi = {10.1016/j.envres.2026.124656},
pmid = {42097383},
issn = {1096-0953},
abstract = {Microorganisms are core drivers of biogeochemical processes in headwater stream ecosystems, yet the response mechanisms of their community composition and carbon metabolic traits to altitudinal gradients and local environmental conditions remain poorly resolved. Elucidating these altitude-dependent patterns is critical for understanding microbiome-mediated ecosystem functioning in vulnerable headwater freshwater habitats. Here, we investigated microbial community structure and carbon substrate utilization in three headwater streams with >1000 m altitudinal span, combining 16S rRNA gene amplicon sequencing, Biolog EcoPlate metabolic phenotyping, and multivariate statistics to characterize microbial taxonomic and functional diversity and their key environmental drivers. Proteobacteria (45.7% average relative abundance) and Bacteroidota (13.6%) dominated all samples, collectively accounting for >60% of the total community. A 1000 m altitude was identified as the ecological threshold, with significant divergences in microbial diversity, community assembly, and carbon utilization patterns across this boundary. Stochastic processes dominated community assembly in steep-gradient streams (68% relative contribution), while deterministic homogeneous selection prevailed in topographically gentle streams (67% contribution); increasing human activity shifted the dominant assembly process from homogeneous selection (67%) to heterogeneous dispersal (52%). Microbial carbon utilization efficiency showed three distinct altitudinal patterns (decreasing, hump-shaped, U-shaped). Variation partitioning analysis revealed that altitude, hydrochemistry, and water physical parameters independently explained 21%, 17%, and 9% of community variation, respectively. Proteobacteria acts as the key phylum governing carbon utilization. This study confirms that altitude is a pivotal driver of headwater microbial diversity and metabolic function, and microbes can adapt to environmental changes by adjusting carbon substrate utilization strategies. Our findings provide new insights into the links between microbial functional traits, ecosystem stability, and nutrient cycling in headwater streams.},
}

@article {pmid42097542,
year = {2026},
author = {Habibyan, YB and Sharkey, KA and Nasser, Y},
title = {PROTEASES AND ABDOMINAL PAIN - OLD DOG, NEW (MICROBIAL) TRICKS.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101803},
doi = {10.1016/j.jcmgh.2026.101803},
pmid = {42097542},
issn = {2352-345X},
}

@article {pmid42097543,
year = {2026},
author = {Peisl, S and Melum, E},
title = {From Kimchi to PSC: Leuconostoc citreum LB-P8 as a microbiome-based therapeutic approach.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101800},
doi = {10.1016/j.jcmgh.2026.101800},
pmid = {42097543},
issn = {2352-345X},
}

@article {pmid42097977,
year = {2026},
author = {Krifors, A and Larsson, T and Wångdahl, A and Stensvold, CR},
title = {Time to rethink Blastocystis in faecal microbiota transplantation.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.04.005},
pmid = {42097977},
issn = {1471-5007},
abstract = {Blastocystis commonly colonises the human gut, but its presence has traditionally led to the exclusion of faecal microbiota transplantation donors. Emerging evidence links it to greater microbial diversity and favourable metabolic profiles, while no harm is seen in immunocompetent recipients. Routine screening may be unnecessary, except for subtype-specific testing in immunocompromised patients.},
}

@article {pmid42098022,
year = {2026},
author = {Baba, Y},
title = {[Esophageal Cancer and Gut Microbiome].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {53},
number = {3},
pages = {158-161},
pmid = {42098022},
issn = {0385-0684},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Esophageal Neoplasms/microbiology/therapy ; },
abstract = {The gut microbiota has recently garnered considerable attention across the medical field, as its involvement has been reported in a broad spectrum of conditions including cancer, obesity, inflammatory bowel disease, and even neuropsychiatric disorders. The human body is composed of approximately 30 trillion human cells and an almost equal number of bacterial cells, forming a highly integrated symbiotic relationship. While the human genome encodes only about 20,000 genes, the gut microbiota harbors several million to tens of millions of genes, offering an overwhelmingly greater genetic repertoire. The composition of the microbiota is influenced by diet, lifestyle, medications, and aging, thereby shaping unique individual - specific patterns. Regional and temporal variations are also recognized, and functional redundancy among different bacterial taxa, known as"functional mimicry,"further underscores its flexibility. Thus, the gut microbiota should be regarded as a dynamic and modifiable ecosystem rather than a fixed entity, making it a promising target for disease prevention and therapeutic intervention. In the context of esophageal cancer, emerging evidence indicates that alterations in the microbiota may affect carcinogenesis, disease progression, and therapeutic responses. These insights highlight the potential of the microbiota as both a biomarker and a therapeutic target, and suggest that integrating microbiome research into clinical oncology could open new avenues for improving patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Esophageal Neoplasms/microbiology/therapy