@article {pmid42299637,
year = {2026},
author = {Wen, X and Fu, Y and Xiang, L and Harindintwali, JD and Wang, Y and Gao, Z and He, C and Jiang, J and Jiang, X and Naidu, R and Dercon, G and Rillig, MC and Wang, F},
title = {Microbial-Plant Synergy Underpins the Mitigation of Atrazine Phytotoxicity in Soybean by a Multifunctional Bacterial Seed Coating.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c16332},
pmid = {42299637},
issn = {1520-5118},
abstract = {Residual herbicides from intensive maize cultivation, particularly atrazine, constrain the soybean establishment in rotation or intercropping systems. To address this, we developed a multifunctional seed coating incorporating a synergistic microbial consortium containing the atrazine-degrading Paenarthrobacter sp. AT5 and the plant growth-promoting Arthrobacter sp. A6. Beyond the consortium's intrinsic traits, the multifunctional seed coating activated systemic resistance in soybeans by upregulating jasmonic acid, salicylic acid, and isoflavonoid biosynthesis. Elevated isoflavonoids selectively reshaped the soybean microbiome, enriching bacterial taxa with potential capacities for atrazine degradation and growth promotion. This plant-microbe feedback loop redirected atrazine metabolic pathways toward accelerated degradation and enhanced conversion to the less phytotoxic hydroxyatrazine. Collectively, the multifunctional seed coating mitigated phytotoxic symptoms and promoted soybean growth by coupling efficient microbial detoxification with reinforced plant defense. Our results uncover a microbiome-mediated phytoprotection mechanism and demonstrate a scalable strategy to mitigate legacy herbicide effects, thereby improving crop establishment and sustainable agricultural productivity.},
}

@article {pmid42299829,
year = {2026},
author = {Giovagnorio, F and Del Fabro, G and Zanus-Fortes, A and Negri, C and Callegari, A and Zanusso, C and Basso, B and Grazioli, S and Del Pup, M and Zanier, A and Castaldo, V and Reffo, I and Venturini, S},
title = {Eravacycline in sepsis complicated by Clostridioides difficile infection: a brief case series.},
journal = {Journal of chemotherapy (Florence, Italy)},
volume = {},
number = {},
pages = {1-5},
doi = {10.1080/1120009X.2026.2684333},
pmid = {42299829},
issn = {1973-9478},
abstract = {Clostridioides difficile infection complicating severe bacterial infections presents a therapeutic challenge, when antimicrobial discontinuation is unfeasible. Eravacycline, a synthetic fluorocycline with broad-spectrum activity against Gram-positive, Gram-negative and anaerobic bacteria, including C. difficile, carries a relatively low risk of inducing C. difficile. Although approved for complicated intra-abdominal infections, emerging evidence indicates its potential for other severe infections. We report three cases of C. difficile infection during systemic antibacterial therapy for severe infections complicated by sepsis. In all cases, antibiotics could not be discontinued due to uncontrolled infection. Switching to intravenous eravacycline, alongside C. difficile-directed therapy, allowed clinical improvement of the underlying infection and resolution of diarrhea, with no eravacycline-related adverse events. Two patients survived to discharge without recurrence at 90-day follow-up, whereas one patient died from unrelated complications. This limited experience indicates that eravacycline might be a microbiome-sparing stewardship option in selected severe infections complicated by C. difficile infection.},
}

@article {pmid42299860,
year = {2026},
author = {Barandouzi, ZA and Eng, T and Khanna, N and Shelton, J and Scott, I and Patel, P and Remick, J and Jin, R and Meador, R and Bruner, DW},
title = {Gut Microbiome Associations With Depressive Symptoms in Women With Gynecologic Cancer: A Longitudinal Study.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {10998004261461549},
doi = {10.1177/10998004261461549},
pmid = {42299860},
issn = {1552-4175},
abstract = {About one-quarter of women diagnosed with gynecologic cancer experience depressive symptoms. While the precise mechanism remains unclear, little is known about the association between gut microbiota and depressive symptoms in gynecologic cancer. Thus, this study aimed to evaluate the associations between gut microbiota and depressive symptoms in women with gynecologic cancer over cancer treatment. Thirty-seven women with cervical or endometrial cancer were followed at pre-treatment (T0), 6-8 weeks (T1), and 6 months post-radiation (T2). Depressive symptoms were assessed using the Patient Health Questionnaire-9 (PHQ-9). Rectal swabs were collected at each visit and sequenced for the V4 region of the 16S rRNA gene. MaAsLin2 models evaluated cross-sectional associations between gut microbial taxa and depressive symptoms at each time point, whereas GEE models assessed longitudinal associations over the course of cancer treatment. The patients had an average age of 60 years, and 43% were Black. At baseline (T0), 24% of patients exhibited depressive symptoms, which decreased to 21% at T1 and further to 13% at T2. GEE models showed that lower α-diversity (Shannon index, p = 0.05), dissimilar β-diversity (Bray-Curtis distance, p = 0.02), and reduced abundance of the genus Ruminococcus (p = 0.02) were predictive factors associated with depressive symptoms throughout cancer treatment. Higher depressive symptoms were longitudinally associated with lower gut microbial Shannon diversity, dissimilar microbial community composition, and lower abundance of the genus Ruminococcus. Larger longitudinal studies using shotgun metagenomic sequencing are needed to validate these findings and further elucidate the microbial mechanisms underlying depressive symptoms in women with gynecologic cancers.},
}

@article {pmid42300105,
year = {2026},
author = {Wilson, SMG and Oliver, A and Alkan, Z and Patil, BS and Kable, ME and Lemay, DG},
title = {Association between dietary polyphenol intake and polyphenol-utilizing bacteria in healthy adults.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00158k},
pmid = {42300105},
issn = {2042-650X},
abstract = {Dietary polyphenols are bioactive compounds with a bidirectional impact on the gut microbiome; they shape the microbial community and are transformed through bacterial metabolism. However, there are limited studies pairing metagenomic and dietary data to investigate the relationship between polyphenol intake and the taxonomic and functional profiles of the human gut microbiome. We examined if dietary polyphenol intake associates with microbial composition and polyphenol utilization capacity. Healthy adults participated in a cross-sectional study balanced for age, sex, and BMI. Polyphenol intake was previously estimated by mapping multiple 24 h dietary recalls to the Food Database (FooDB). We coupled intake with microbial taxonomic and functional profiles from shotgun-sequenced fecal metagenomes (n = 313). Microbial reads were mapped to dbPUP, a database with 60 experimentally characterized, gut-associated polyphenol utilization proteins (PUPs). We assessed the relationship of polyphenol intake on microbial diversity, abundance of microbes with PUP genes, PUP gene counts, and select lipopolysaccharide (LPS) producers, accounting for age, sex, BMI, fiber intake, and diet quality. Specific polyphenols associated with an increased abundance of nine PUP-containing genera. We found 117 associations between polyphenol intake and microbial PUP genes, with 85 associations involving hydrolysis PUPs. Diversity in polyphenol intake was positively associated with diversity in PUP genes but not with microbial diversity. Lastly, we detected a positive relationship between intake of olive-related polyphenol classes and abundance of order Bacteroidales, a producer of immunoinhibitory LPS. Dietary polyphenol intake may influence the gut microbiome's capacity for polyphenol utilization, particularly its hydrolytic activity, without impacting taxonomic diversity or composition.},
}

@article {pmid42300458,
year = {2026},
author = {Sun, M and Wang, X and Zhang, Q and Wang, Z and Luo, J and Xu, J and Li, X},
title = {Xylitol ameliorates ASD-like behavior in Chd8[+/-] mice via modulations of the gut microbiome, neurotransmitters, and dendritic spine morphology.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01006g},
pmid = {42300458},
issn = {2042-650X},
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition with complex etiology involving gut-brain axis interactions. It remains elusive how prebiotics modulate this axis to alleviate ASD symptoms. This study aimed to investigate whether xylitol, a potential prebiotic, improves behavioral and neural deficits in Chd8[+/-] mice, a genetic model of ASD, and to explore the associated roles of the gut microbiome, neurotransmitters and synaptic morphology in these effects. We found that Chd8[+/-] mice exhibited disrupted gut microbiota and imbalanced levels of key neuromodulators including indole-3-lactic acid (ILA), asparagine (Asn) and glycine (Gly), as well as reduced dendritic spine density and maturity in the mPFC and hippocampal CA1 regions and diminished c-Fos activation in response to social stimuli. Xylitol supplementation significantly ameliorated social deficits, restored microbial composition and neurotransmitter metabolite profiles, and rescued synaptic maturation and neuronal activity in these mice. These findings suggest that xylitol may act via the gut-brain axis to reverse ASD-like phenotypes, although direct causal evidence remains to be established. Nonetheless, this work supports the potential of xylitol as a dietary intervention for ASD.},
}

@article {pmid42300531,
year = {2026},
author = {Basit, A and Mueed, A and Shahzad, R and Rong, W and Shahrokh, K and Shehzad, A and Khan, S and Shutian, T},
title = {Dietary chlorogenic acid improves lipid metabolism through modulation of the gut-liver microbiota axis in hyperlipidemic mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00434b},
pmid = {42300531},
issn = {2042-650X},
abstract = {In this study, the protective mechanisms of chlorogenic acid (CGA) supplementation against high-fat diet-induced hyperlipidaemia and glucose dysregulation were investigated using an integrated multi-omics approach in C57BL/6J mice, encompassing serum biochemistry, targeted hepatic gene expression, gut microbiome profiling, and untargeted metabolomics of gut and liver tissues, complemented by molecular docking analysis. CGA supplementation significantly reduced serum total cholesterol, triglycerides, and low-density lipoprotein cholesterol, attenuated hepatic lipid accumulation, and improved glucose handling through downregulation of lipid metabolism-related genes (LOX, CPTP, FABP4, and LPCAT3) and concurrent activation of IRS1 signaling and modulation of CD36-mediated lipid uptake. At the microbial level, CGA markedly reshaped gut microbial composition by enriching Lactobacillus, Ligilactobacillus, and Bacteroides, while restoring key gut metabolites involved in lipid and glucose regulation, including L-glutathione, chenodeoxycholic acid glycine conjugate, N-acetylaspartic acid, and N-acetylcysteine. Liver metabolomic profiling further revealed elevated levels of lithocholic acid, L-proline, and 4-methylcatechol, metabolites associated with enhanced energy metabolism and ferroptosis resistance. Integrative correlation analysis identified a coordinated Lactobacillus-4-methylcatechol-glycerophospholipid metabolism axis as a central mechanistic signature underlying CGA-mediated metabolic improvement. Collectively, these findings demonstrate that CGA exerts pronounced anti-hyperlipidaemic and glucose-regulatory effects by simultaneously restoring gut microbial balance, remodelling host metabolite networks, and activating IRS1/CD36 signalling pathways, supporting its potential as a promising dietary intervention for the prevention and management of metabolic disorders.},
}

@article {pmid42300638,
year = {2026},
author = {Wang, G and Zhang, Y and Wang, F and Xiao, W and Zhou, W and Chen, X and Gu, Q and Li, P},
title = {Latilactobacillus sakei ZFM232 alleviates age-related lipid metabolism disorders and enhances antioxidant defense in Caenorhabditis elegans.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01144f},
pmid = {42300638},
issn = {2042-650X},
abstract = {Lactic acid bacteria (LAB) are widely recognized as beneficial microorganisms within the human microbiome; however, the mechanisms underlying their health-promoting effects remain largely elusive. Here, we show that Latilactobacillus sakei ZFM232 (LS232) exhibits tolerance to acidic conditions and moderate salt stress, along with relatively stable antioxidant capacity in vitro. Using Caenorhabditis elegans as an in vivo model, we found that long-term intake of LS232 significantly improved nematode survival under oxidative, osmotic, and heavy-metal stress conditions, with increases of 40%, 36.5%, and 11.9%, respectively, compared to the control group. LS232 feeding also reduced age-related lipid droplet accumulation and triglyceride levels, indicating improved lipid metabolic status during aging. Concurrently, LS232 enhanced glutathione S-transferase 4 (GST-4) activity, promoted superoxide clearance, and improved redox balance in vivo. Moreover, LS232 feeding was associated with increased nhr-49 expression, enhanced nuclear enrichment of NHR-49, and upregulation of lipid metabolism-related genes, including fat-5, fat-6, fat-7, and acs-2. In the nhr-49 mutant background, the beneficial effects of LS232 on lipid accumulation and redox balance were significantly attenuated, further supporting the involvement of an NHR-49-associated regulatory program in mediating these responses. Overall, these results suggest that LS232 has potential applications in alleviating aging-related lipid metabolism disorders and oxidative damage.},
}

@article {pmid42300758,
year = {2026},
author = {Kelliher, JM and Horak, R and Prime, KJ and Rodriguez, FE and Johnson, LYD and Roux, S and Lynch, W and Miller, SN and Bonito, G and Eloe-Fadrosh, EA},
title = {Microbiome Science Certificate Program for workforce development and multi-omics expertise.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0001226},
doi = {10.1128/jmbe.00012-26},
pmid = {42300758},
issn = {1935-7877},
abstract = {Microbiome research is a dynamic, rapidly growing, and interdisciplinary field that generates valuable insights across the human health, agricultural, and environmental sectors. Despite this growth, gaps remain in educational content and professional development opportunities specifically tailored for microbiome science rather than traditional microbiology. The National Microbiome Data Collaborative (NMDC) has developed a Microbiome Science Certificate Program aimed at undergraduates but available to any learner or researcher interested in this field. The curriculum includes 12 modules to further technical knowledge, as well as practical and professional skills. The modules each include prepared slide decks, recorded lectures, resource documents, expert interviews, reading assignments, knowledge assessments, and an overall glossary. The modular content can be readily applied within the classroom as a stand-alone semester-long course or as supplementary to existing curricula. An asynchronous, online, certificate-granting implementation of the content is available through the American Society for Microbiology. We have outlined future laboratory, workforce development, and data science "mini-modules" that can be further developed with the help of educators. Improvements will be made to the program content based on feedback from learners and educators. This program aims to promote practical skills to empower the next generation of microbiome researchers.},
}

@article {pmid42300775,
year = {2026},
author = {Hawkes, CG and Carroll, BO and Moylan, AD and Stiker, MEJ and Wang, T and Serrano, MG and Ridlon, JM and Miller, DP},
title = {Genomic and phenotypic insights into the novel species Selenomonas lamontii type strain ATCC 33150, currently described as Selenomonas sputigena.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0034126},
doi = {10.1128/spectrum.00341-26},
pmid = {42300775},
issn = {2165-0497},
abstract = {Selenomonas sputigena is an anaerobic, gram-negative bacterium found in the human mouth and upper respiratory tract. This organism is emerging as an important contributor to human health and disease. In the oral cavity, S. sputigena contributes to periodontitis and is associated with early childhood caries. Much of our current understanding of the genus Selenomonas and its relation to human health derives from studies of a single species, S. sputigena, and is further limited to the type strain, ATCC 35185. As S. sputigena is emerging as a significant contributor to human health, we sought to characterize the S. sputigena ATCC 33150 strain. Genomic analyses revealed that ATCC 33150, previously described as S. sputigena, is a novel Selenomonas sp., and we propose the name Selenomonas lamontii. Phenotypic comparison to S. sputigena reveals that S. lamontii grows more slowly and to a lower density in vitro. S. lamontii is more motile than S. sputigena and does not form surface-attached biofilms. Re-analysis of existing metagenomic data revealed the consistent presence of ATCC 33150 across all samples, with significantly elevated relative abundance in periodontitis-associated saliva compared to healthy donor controls. Collectively, we have identified ATCC 33150 as a new Selenomonas sp. and conducted one of the first direct comparative studies of traits relevant to colonization and persistence among Selenomonas spp.IMPORTANCERecognizing that strain ATCC 33150, historically described as Selenomonas sputigena, is a previously undescribed species has important implications for microbial systematics, physiology, and pathogenesis. Accurate taxonomic assignment underpins all downstream biological interpretation (e.g., comparative genomics, microbiome composition studies, virulence studies, and metabolic modeling). The identification of a novel species, therefore, refines the phylogenetic framework of the genus Selenomonas, enables more precise genotype-phenotype correlations, and may uncover previously unrecognized adaptations relevant to oral biofilm ecology and host interactions. Beyond taxonomy, this discovery strengthens the foundation and rigor of future mechanistic studies and provides context for discrepancies in previous studies involving this strain and ATCC 35185.},
}

@article {pmid42300841,
year = {2026},
author = {Dovhalyuk, V and Globisch, D},
title = {Impact of preparation methods and storage conditions for optimization of the fecal metabolome storage stability.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6an00237d},
pmid = {42300841},
issn = {1364-5528},
abstract = {Untargeted fecal metabolomics has gained a higher scientific interest in the past decade, due to the increased importance of the gut microbiome metabolism. It is highly sensitive to preanalytical variations. However, the impact of sample collection, storage, and preparation on the metabolome composition remains insufficiently studied. In this study, we have systematically evaluated the effects of two sample preparation protocols: 5% DMSO/water solvation, followed by solvent substitution to methanol, referred to as the double-liquid extraction (DLE) protocol in this study, and methanol homogenization with FastPrep lysing matrices. Additionally, we examined long-term storage at -80 °C in a freezer, including fresh and freeze-dried samples, with and without methanol, at various stages of sample preparation. Global feature coverage and sensitivity analyses revealed that efficient mechanical homogenization is critical for maximizing metabolite recovery, particularly for intracellular and microbially derived compounds (enterolactone, allolithocholic acid). However, complete depletion of water and extraction in pure methanol resulted in a reduced feature coverage and lower signal intensities, particularly for polar metabolites such as proline and tyrosine. In the case of a freeze-drying step, reintroduction of water during sample preparation substantially improved extraction efficiency, underscoring the importance of maintaining controlled hydration of the fecal matrix to improve the solubility of the metabolite mixture.},
}

@article {pmid42301089,
year = {2026},
author = {Wang, H and Liang, Y and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y},
title = {Dietary High Fiber and N-Carbamylglutamate Enhance Sow Reproductive Performance via Modulating Lactobacilli, Lipid Metabolites, and the PI3K-Akt Signaling Pathway.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {12},
pages = {e72059},
doi = {10.1096/fj.202601343R},
pmid = {42301089},
issn = {1530-6860},
support = {2025M780240//China Postdoctoral Science Foundation/ ; 2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; },
mesh = {Animals ; *Glutamates/pharmacology/administration & dosage ; Female ; *Lactobacillus/drug effects/metabolism ; Signal Transduction/drug effects ; Swine ; *Proto-Oncogene Proteins c-akt/metabolism ; *Reproduction/drug effects ; *Dietary Fiber/pharmacology/administration & dosage ; *Phosphatidylinositol 3-Kinases/metabolism ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; },
abstract = {The aim of this study was to investigate the combined effects of a high-fiber diet supplemented with N-carbamylglutamate (NCG) (H + N) on the gut microbiota, metabolites, and transcriptome in Landrace × Yorkshire sows using a multi-omics approach. Sows were allocated to four groups in a 2 × 2 design: Low-fiber or high-fiber diets, each with or without 0.05% NCG supplementation. The H + N treatment significantly increased litter weight at weaning. Metagenomic analysis revealed H + N significantly altered gut microbiota composition and function, particularly enriching Lactobacillus at multiple taxonomic levels from order to species (including Lactobacillus sp. 910 589 175). Plasma metabolomics identified two key lipid mediators, L-α-glycerylphosphorylcholine and taurocholic acid, whose abundances were significantly elevated by H + N and positively correlated with the enriched Lactobacillus. Transcriptomic profiling showed activation of the PI3K-Akt signaling pathway in response to H + N, which was associated with observed improvement in litter weight at weaning. Collectively, the multi-omics study uncovered a novel synergistic axis wherein H + N modulated the gut microbiome (specifically Lactobacillus enrichment), which in turn shaped the lipid metabolome to activate the PI3K-Akt pathway, ultimately enhancing sow reproductive efficiency.},
}

Animals
*Glutamates/pharmacology/administration & dosage
Female
*Lactobacillus/drug effects/metabolism
Signal Transduction/drug effects
Swine
*Proto-Oncogene Proteins c-akt/metabolism
*Reproduction/drug effects
*Dietary Fiber/pharmacology/administration & dosage
*Phosphatidylinositol 3-Kinases/metabolism
*Lipid Metabolism/drug effects
Gastrointestinal Microbiome/drug effects
Animal Feed/analysis

@article {pmid42301310,
year = {2026},
author = {Cosoveanu, A and González-Carracedo, MA and Sopena Lasala, J and Pérez Pérez, JA and Cabrera, R},
title = {Shaping Fungal Communities in Cenchrus setaceus: Host Condition and Habitat Filtering.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02805-3},
pmid = {42301310},
issn = {1432-184X},
abstract = {We investigated the leaf-associated fungal communities of Cenchrus setaceus across a host condition gradient (high- vs. low-condition plants) and environmental zones (coast vs. hill; trade-wind exposure) on Tenerife (TF) and La Palma (LP). We hypothesized that community assembly reflects both host-driven deterministic filtering and abiotic promotion of richness in favourable environments via two mechanisms: (i) high-condition plants promote stable, guild-structured communities; (ii) humid, topographically buffered zones enhance fungal richness, especially for endophytes and saprotrophs. Nanopore sequencing and functional guild annotation revealed island- and zone-specific fungal assemblages. In TF, low-condition plants were associated with genera linked to stressed or exposed conditions whereas high-condition plants, especially in humid northern hills, supported more recurrent yeast-like and niche-associated taxa. In LP, high-condition plants in eastern hill zones were associated with distinct taxa, while drier western coastal low-condition plants were enriched in stress-related fungi. Fungal genera richness (Hill0) was consistently higher in low-condition plants (TF: 146 vs. 95; LP: 94 vs. 76; p < 0.05), while Shannon diversity diverged: greater in high-condition plants on LP (3.29 vs. 2.98), but lower on TF (3.10 vs. 3.28; p < 0.05). Community structure was shaped primarily by host condition in TF (PERMANOVA R[2] = 8.6%, p < 0.05), and by zone in LP (R[2] = 15.0%, p < 0.05). On TF, low-condition plants hosted significantly higher richness of saprotrophic, endophytic and plant-pathogenic genera (all p ≤ 0.001), whereas in LP zone × condition effects shaped guild richness patterns, with saprotroph richness increasing 2.66-fold in high condition plants from eastern hills relative to the eastern coast. Overall, high-condition plants supported less diverse but compositionally more stable fungal communities, while favourable environments enhanced guild richness independently of host condition.},
}

@article {pmid42301325,
year = {2026},
author = {van Wesemael, AJ and de Kroon, RR and Frerichs, NM and van Weissenbruch, MM and van Kaam, AH and de Boer, NK and Struys, EA and Niemarkt, HJ and de Meij, TG and , },
title = {Longitudinal fecal amino acid profiles in extremely preterm infants: early-life determinants and associations with late-onset sepsis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {4},
pages = {},
pmid = {42301325},
issn = {1573-3890},
mesh = {Humans ; *Amino Acids/metabolism/analysis ; *Feces/chemistry ; Female ; Infant, Newborn ; Male ; *Infant, Extremely Premature/metabolism ; *Sepsis/metabolism/microbiology ; Longitudinal Studies ; Metabolomics ; Tandem Mass Spectrometry ; Gestational Age ; },
abstract = {INTRODUCTION: Fecal microbiome and metabolome alterations precede late-onset sepsis (LOS) in preterm infants, but clinical determinants of fecal amino acid (AA) composition and association with LOS development remain poorly understood.

OBJECTIVES: This study assessed the early-life determinants of fecal AA composition and AA profiles prior to clinical LOS onset to improve pathophysiological understanding.

METHODS: Infants (< 28 weeks' gestation) with non-staphylococcal LOS were included in a discovery (n = 12) and validation cohort (n = 8), each matched 1:1 to non-LOS controls (n = 20), based on gestational and postnatal age. Using targeted liquid chromatography-tandem mass-spectrometry, this study identified early-life determinants of fecal AAs, analyzing fecal samples collected at week 1 to 4 in controls. Additionally, AA profiles prior to LOS onset were assessed to improve pathophysiological understanding, analyzing samples at t0 and t-3 days from LOS-affected infants and controls.

RESULTS: The most common LOS pathogens were Escherichia coli (n = 8), Serratia species (n = 4), and Streptococcus agalactiae (n = 3). Postnatal age, full-enteral feeding status, probiotic administration, and delivery mode significantly influenced fecal AAs. In the discovery cohort, threonine and glutamine were significantly decreased in affected infants (median [Q1-Q3], threonine: 43.8 [29.3-66.3] vs. 64.5 [48.1-107.3] μmol/L, p = 0.02; glutamine: 19.0 [9.0-38.3] vs. 34.1 [27.0-69.8], p = 0.01), while the validation cohort solely showed a non-significant decrease of threonine. When combining both cohorts, threonine achieved an area under the curve of 0.65 (95%-CI: 0.53-0.76).

CONCLUSIONS: These findings suggest several clinical characteristics influence fecal AAs, and altered threonine metabolism may contribute to LOS pathophysiology, warranting evaluation of related metabolites and multi-marker approaches in future studies.},
}

Humans
*Amino Acids/metabolism/analysis
*Feces/chemistry
Female
Infant, Newborn
Male
*Infant, Extremely Premature/metabolism
*Sepsis/metabolism/microbiology
Longitudinal Studies
Metabolomics
Tandem Mass Spectrometry
Gestational Age

@article {pmid42301501,
year = {2026},
author = {Öz, M and Üstüner, E},
title = {Omics technologies in aquafeed: unlocking the black box towards systems biology.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42301501},
issn = {1438-7948},
mesh = {Animals ; *Systems Biology/methods ; *Aquaculture/methods ; Multiomics ; Metabolomics ; *Fishes/genetics/metabolism/growth & development ; Animal Feed ; Proteomics/methods ; Nutrigenomics ; },
abstract = {The aquaculture industry is undergoing a critical transition from marine-based to plant-based and novel protein sources. However, the physiological impacts of these dietary shifts remain largely obscured when evaluated solely by traditional performance metrics such as Feed Conversion Ratio (FCR) and Specific Growth Rate (SGR). This 'Black Box' approach fails to detect sub-clinical metabolic disorders, gut dysbiosis, and molecular stress responses until phenotypic losses occur. This review provides a comprehensive synthesis of how omics technologies - nutrigenomics, proteomics, metabolomics, and metagenomics - are elucidating the molecular mechanisms underlying fish nutrition. We examine the capacity of transcriptomics to identify early markers of soybean meal-induced enteritis and the role of proteomics in assessing muscle quality beyond mere gene expression. Furthermore, we highlight the integration of these layers into a 'Systems Biology' approach, utilizing multi-omics and bioinformatics to unravel the complex diet-microbiota-host axis. Finally, the review discusses the transition towards 'Precision Aquafeed.' It identifies the current challenges in cost, data standardization, and bioinformatics that must be overcome to implement these high-throughput tools in commercial feed formulation.},
}

Animals
*Systems Biology/methods
*Aquaculture/methods
Multiomics
Metabolomics
*Fishes/genetics/metabolism/growth & development
Animal Feed
Proteomics/methods
Nutrigenomics

@article {pmid42301752,
year = {2026},
author = {Deutsch, E and Levy, A and Zitvogel, L},
title = {Redefining radiotherapy: the gut as an active target in Immuno-Oncology.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-26-1177},
pmid = {42301752},
issn = {1557-3265},
abstract = {Low-dose intestinal irradiation challenges the long-standing view of the gut as a radiation-sensitive organ to avoid. Clinical and mechanistic data suggest that targeted exposure of the small intestine within a 1 to 3 Gy window can remodel the microbiome and enhance systemic antitumor immunity.},
}

@article {pmid42301898,
year = {2026},
author = {Gargouri, M and Bates, PD and Declerck, S},
title = {Modulation of microbial communication by lipid exudates.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag156},
pmid = {42301898},
issn = {1751-7370},
abstract = {Root exudates comprise a diverse mixture of non-polar and amphiphilic compounds that are only partially recovered by aqueous extraction methods, yet can rival polar metabolites as carbon sources for microorganisms. Because many quorum-sensing (QS) signals are fatty-acyl derivatives, lipid-rich microhabitats at the root-soil interface are likely to influence signal partitioning, persistence, and local QS thresholds. We propose a lipid-mediated framework in which plant-derived lipids modulate QS through four nodes: receptor mimicry/antagonism, quorum quenching, membrane/microenvironment regulation, and lipid-dependent resource gating. These mechanisms operate across two lipid-rich interfaces - the rhizosphere and the arbuscular mycorrhizal fungi (AM fungi) hyphosphere - where host lipid fluxes may restructure microbial community composition. Combined with QS-sensitive changes in root exudation, this spatially structured lipid circuit could generate feedbacks influencing microbiome composition and function, with potential implications for microbiome engineering.},
}

@article {pmid42302279,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Rachid, D},
title = {From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
pmid = {42302279},
issn = {1477-4054},
support = {//University Mohammed VI Polytechnic (UM6P), Morocco/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Biomarkers ; *Colorectal Neoplasms/microbiology/genetics ; Machine Learning ; *Precision Medicine ; Causality ; Mendelian Randomization Analysis ; Metagenomics ; },
abstract = {Human gut microbiome research has generated many disease associations, yet few translate into clinical applications. A central obstacle is not a lack of data, but the limited integration of causal reasoning, as most studies report correlations without establishing directionality, confounding control, or mechanistic evidence. We propose a unified causal inference framework that integrates directed acyclic graphs, Mendelian randomization, double machine learning, mediation analysis, and tests of causal reversibility into a single decision-aware workflow. Unlike prior applications of these tools in isolation, our framework explicitly separates assumption mapping, causal identification, effect estimation, and mechanistic interpretation, introducing "assumption guardrails" that constrain interpretation at each stage and prevent overinterpretation of observational findings. Using a colorectal cancer case study with public metagenomic data, we demonstrate how the framework operates under real-world constraints, transforming observational associations into testable, mechanism-based hypotheses. The contribution is architectural in that it organizes existing tools into a disciplined, integrated pipeline that clarifies the strength of evidence at each stage. This operational blueprint provides a reproducible path from correlation to causation in microbiome research and toward precision interventions.},
}

Humans
*Gastrointestinal Microbiome
*Biomarkers
*Colorectal Neoplasms/microbiology/genetics
Machine Learning
*Precision Medicine
Causality
Mendelian Randomization Analysis
Metagenomics

@article {pmid42302341,
year = {2026},
author = {Sha, Y and Yan, Z and Dong, J and Bai, J and Tang, Y and Chen, G and Li, X and Gao, Y and Gao, X and Yuan, H and Zhang, J and Zhu, P},
title = {Disruption of macrophyte-induced algal defence by a cyanobacterial competitor through metabolic shifts and microbiome dysbiosis.},
journal = {Ecotoxicology and environmental safety},
volume = {321},
number = {},
pages = {120384},
doi = {10.1016/j.ecoenv.2026.120384},
pmid = {42302341},
issn = {1090-2414},
abstract = {Eutrophication and global warming are intensifying cyanobacterial blooms, complicating macrophyte-based restoration. Submerged macrophytes can suppress cyanobacteria and induce defensive aggregation in green algae, but the effects of toxic cyanobacterial metabolites on macrophyte-alga signaling remain unclear. Here, we used a dialysis-bag co-culture system to test how toxic Microcystis aeruginosa affects interactions between Ceratophyllum demersum and Chlorella vulgaris. We quantified C. vulgaris growth, photosynthetic pigments, oxidative responses, apoptosis, and cell aggregation, and profiled C. demersum metabolites and epiphytic bacterial communities. In the absence of M. aeruginosa, C. demersum inhibited C. vulgaris growth and induced strong cell aggregation, accompanied by elevated reactive oxygen species, peroxidase activity, malondialdehyde accumulation, and clustered apoptotic signals. Metabolomic and microbial analyses indicated enhanced flavonoid and organic acid metabolism and coordinated shifts in epiphytic bacteria, suggesting a plant-microbe feedback that strengthened allelopathic and aggregation-inducing effects. In contrast, diffusible secretions from M. aeruginosa altered the C. demersum metabolic profile toward terpenoid-dominated responses, reshaped the epiphytic microbiome, and weakened metabolite-bacteria correlations. These changes reduced the capacity of C. demersum to induce aggregation in C. vulgaris and modified oxidative and apoptotic responses. The findings suggest that toxic cyanobacteria can interfere with macrophyte-mediated interspecific signaling by reprogramming host metabolism and destabilizing plant-associated microbial networks. Cyanobacterial secondary metabolites and lysis products should therefore be considered when assessing macrophyte-based interactions.},
}

@article {pmid42302500,
year = {2026},
author = {Habib, YH and Gwaily, NA and Ali, MY and Fawzy, MA and Zakaria, MA and Ali, MA},
title = {Repurposing anti-inflammatory therapeutics fordisorders of the microbiome-gut-brain axis.},
journal = {Journal of neuroimmunology},
volume = {419},
number = {},
pages = {579000},
doi = {10.1016/j.jneuroim.2026.579000},
pmid = {42302500},
issn = {1872-8421},
abstract = {The microbiome-gut-brain axis (MGBA) redefines the field of anti-inflammatory therapeutics by shifting from targeting isolated immune pathways in an organ to a bidirectional, integral network, composed of gut microbiota, the peripheral immune system, barrier tissues, and neural circuits. Such reframing is predominantly pertinent for certain CNS and systemic diseases, including Alzheimer's disease and ischemic stroke. These diseases have been resistant to conventional anti-inflammatory agents that either poorly pass the blood-brain barrier or do not inhibit the upstream inflammatory drivers. Increasing evidence demonstrates that microbial communities and their metabolites modulate systemic and central immune tone, and affect barrier integrity, hence brain inflammation frequently presents with a measurable fingerprint in the gut and vice versa. Targeted microbiome therapies, metabolite replacement, and biomarker-guided patient stratification all emerge as promising new strategies when acknowledging the gut is a modifiable source. Mechanistically, the crosstalk between neuro-immune-microbial trails creates concrete therapeutic entry points. These include: (1) altering microbial enzymes that produce pro-inflammatory metabolites, (2) delivering beneficial metabolites to support homeostatic glial states, and (3) modulating afferent neural pathways like vagus nerve stimulation, which triggers the cholinergic anti-inflammatory pathway (CAP). The future of MGBA-targeted therapeutics will mostly repurpose current anti-inflammatory agents and neuromodulatory strategies into combinatorial ones that pair source control (gut-restricted drugs) with targeted central modulation (microglial modulators such as minocycline) and neural orchestration (vagus nerve stimulation, VNS). These repurposing strategies are increasingly guided by baseline inflammatory and microbiome biomarkers and may help in establishing new therapeutic paradigms for these intersecting disorders of the gut, immune system, and brain in appropriately defined patient subgroups.},
}

@article {pmid42302624,
year = {2026},
author = {Malematja, E and Mafuna, T and Sebola, NA and Kolobe, SD and Mabelebele, M},
title = {Effects of replacing commercial zinc bacitracin with insect meal (Macrotermes subhylanus) on caeca bacteria composition, haematology, and growth performance in commercial broiler chicks at the starter phase.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107218},
doi = {10.1016/j.psj.2026.107218},
pmid = {42302624},
issn = {1525-3171},
abstract = {The effects of Macrotermes subhylanus meal as a substitute for zinc bacitracin on the composition of caecal bacteria, haematology, and performance parameters were evaluated in broiler chicks during the starter phase. Three isoproteic and isoenergetic diets, NC (negative control; basal diet only), PC (positive control; basal diet with 0.05 g of zinc bacitracin per kg DM) and InsecM (basal diet with 100 g of insect meal per kg DM), were used in this study. A total of 150 one-day-old broiler chicks were randomly assigned to each of the 3 treatments, with 10 chicks per replicate and 5 replicates per treatment in a completely randomised design. Data on bacterial composition, apparent nutrient digestibility, blood profiles, and growth parameters were measured on day 14 and analysed using DADA2 and SAS software for statistical purposes. The results revealed that Firmicutes was the predominant (P < 0.05) phylum, proportionate to Actinobacteriota, Bacteroidota, Cyanobacteria, Proteobacteria, Verrucomicrobiota, and Vertebrata in chicks fed an InsecM diet compared to those on NC and PC diets. Furthermore, the NC diet reduced (P < 0.05) apparent dry matter (83.2%) and crude protein, while crude fibre digestibility (75.62%) was significantly lower in the InsecM diet. The apparent crude protein (CP) digestibility on the InsecM diet was significantly improved (86.24%) when compared to the NC and PC diets. Plasma enzyme alanine aminotransferase was also significantly reduced by an InsecM diet (0.87 U/L). However, uric acid (0.27 mmol/l) was elevated (P < 0.05) in chicks fed an InsecM diet. Body weight gain (483.28 g/bird) and the feed conversion ratio (1.12) were improved in chicks fed the InsecM diet. It is concluded that broiler chicks on a diet containing 100 g of M. subhylanus meal per kg DM and those on a diet with 0.05 g zinc bacitracin improved caecal bacterial composition, CP digestibility, and growth performance, without causing negative effects on the birds' metabolic pathways and health status. Nonetheless, further studies are encouraged to confirm these findings.},
}

@article {pmid42302635,
year = {2026},
author = {Naseem, MT and Zaman, W},
title = {Toxicology and biodistribution of plant-derived extracellular vesicles for drug delivery: Quality control, safety mechanisms, and translational testing priorities.},
journal = {Toxicology letters},
volume = {422},
number = {},
pages = {111944},
doi = {10.1016/j.toxlet.2026.111944},
pmid = {42302635},
issn = {1879-3169},
abstract = {Plant-derived extracellular vesicles and plant-derived exosome-like nanoparticles are increasingly investigated as natural nanocarriers for drug delivery and as bioactive materials with intrinsic therapeutic potential. However, their translational development is limited by unresolved questions surrounding safety, biodistribution, product identity, and batch consistency. In this review, we synthesize current knowledge on the toxicology and biodistribution of plant-derived extracellular vesicle products, with emphasis on route-dependent exposure, barrier interactions, immune recognition, hemocompatibility, microbiome effects, and off-target organ accumulation. We argue that an edible plant origin should not be considered a surrogate for safety, particularly when products are administered at high doses, repeatedly, or through non-oral routes. We further identify quality control as a central determinant of both efficacy and safety, because plant source, growth conditions, harvest timing, isolation workflow, storage, and co-isolated contaminants can substantially alter vesicle composition and biological activity. To address these challenges, we propose a translational framework that integrates chemistry, manufacturing, and control principles with route-specific nonclinical toxicology testing and mechanism-linked potency assays. The framework highlights minimum expectations for identity, purity, potency, stability, and contaminant testing, including microbial burden, endotoxin-like activity, pesticide residues, and heavy metals. We also outline research priorities needed for regulatory-grade development, including harmonized nomenclature, reference materials, orthogonal characterization strategies, and mechanistic studies that distinguish vesicle-intrinsic effects from cargo- or impurity-driven toxicity. Collectively, this review positions toxicology and product quality as the key organizing principles for the safe and reproducible development of plant-derived extracellular vesicles in drug delivery.},
}

@article {pmid42302785,
year = {2026},
author = {Zhou, Q and Lu, Y and Wang, L and Zhou, W and Oba, H and Zhou, Y and Shen, M and Qu, X and De Souza, C and Rayner, A and Chen, Y and Cheng, TY and Ling, Z and Li, L and Liu, C and Voigt, AY and Xiong, R and Oh, J and Spakowicz, D and Dravillas, C and Tian, AW and Nicolls, MR and Huynh, AT and Chen, X and Hu, J and He, M and He, F and Snyder, MP and Yang, J and Zhou, X},
title = {Power and sample-size estimation in human microbiome research.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {101174},
doi = {10.1016/j.medj.2026.101174},
pmid = {42302785},
issn = {2666-6340},
abstract = {Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.},
}

@article {pmid42302870,
year = {2026},
author = {Zhao, J and Wang, J and Li, S and Lu, Q and Zhang, P and Qi, Y and Xu, X and Fan, J and Chen, C and Zhang, W},
title = {Chlorella pyrenoidosa reduces fecal heavy metal concentrations and antibiotic resistance gene abundance in lambs by modulating the gastrointestinal microbiota.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135186},
doi = {10.1016/j.biortech.2026.135186},
pmid = {42302870},
issn = {1873-2976},
abstract = {Using feed additives and their residues leads to the accumulation of heavy metals and antibiotics in the feces of fattening sheep, thereby posing a threat to the surrounding soil and ecological cycle. Chlorella, a novel feed raw material or additive widely applied in aquaculture, has the potential to mitigate such ecological risks. In this study, we investigated the potential of Chlorella pyrenoidosa as a dietary supplement for fattening lambs to mitigate multi-pollutant emissions from manure via gastrointestinal microbiome modulation. The results demonstrated that dietary supplementation with 3% Chlorella pyrenoidosa (W3) markedly reduced fecal concentrations of several heavy metals (Fe, Cu, Zn, Cr, As, Pb) and total phosphorus, while shifting phosphorus speciation toward more stable forms. Metagenomic analysis revealed that W3 reshaped the metabolic functional profile of the gastrointestinal microbiota and drove the succession of key microbial taxa, particularly promoting the proliferation of Clostridium and other genera in feces. Furthermore, Chlorella pyrenoidosa reduced the abundance of high-risk antibiotic resistance genes (ARGs, e.g., macB). It simplified the ARG-metal resistance gene co-occurrence network and was associated with an attenuated potential for vertical transmission of resistance genes along the digestive tract. Structural equation modeling further confirmed that pollutant reduction was closely associated with the functional remodeling of the microbiome. Thus, this study suggests that Chlorella pyrenoidosa may mitigate the environmental risks associated with heavy metals, bioavailable phosphorus, and ARGs in manure by regulating the gastrointestinal microbial ecosystem. This provides a novel strategy and theoretical basis for reducing source pollution in animal husbandry.},
}

@article {pmid42302978,
year = {2026},
author = {Wang, Y and Yan, N and Liu, H and Liu, K and Li, Z and Wang, J and Ma, X and Wang, J and Zhang, J and Li, J and Wang, L},
title = {The association between inhaled tire-wear particle exposure and cognitive dysfunction in rats.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128596},
doi = {10.1016/j.envpol.2026.128596},
pmid = {42302978},
issn = {1873-6424},
abstract = {Tire wear particles (TWPs), an emerging environmental contaminant, have poorly understood impacts on cognitive function and underlying mechanisms. Herein, environmental samples from main traffic arteries were analyzed to determine TWPs concentrations, based on which Sprague-Dawley rats were allocated into control, low-TWPs, and high-TWPs exposure groups. An exposure model of TWPs was established in Sprague-Dawley rats by continuous nose and mouth inhalation of TWPs for 14 and 28 days. The experimental results demonstrated that TWPs induced multiple adverse effects in rats, primarily manifested as impaired learning and memory behavior, dysbiosis of the gut microbiota, and pathological damage accompanied by impairments in the lung, brain and hippocampal tissues. Malondialdehyde (MDA) levels were significantly elevated in both the Low and High concentration exposure groups. Gut microbiota shifts included reduced beneficial bacteria (e.g., norank_f_Ruminococcaceae, Eubacterium, Bacillus) and increased harmful bacteria (e.g., Turicibacter). Metabolomics analysis revealed altered metabolite levels and pathways linked to neurodegeneration and oxidative stress. Collectively, inhaled TWPs may alter gut microbiota and metabolome, potentially contributing to cognitive deficits.},
}

@article {pmid42302983,
year = {2026},
author = {Chen, C and Zhang, Y and Jin, Y and Zhou, J and Jiang, X and Chen, S and Zhang, R and Li, H and Gui, Z},
title = {Exogenous microbial agents interact with housefly larvae to reshape the microbiome and accelerate cellulose degradation in silkworm (Bombyx mori) excrement.},
journal = {Journal of insect physiology},
volume = {},
number = {},
pages = {105017},
doi = {10.1016/j.jinsphys.2026.105017},
pmid = {42302983},
issn = {1879-1611},
abstract = {Silkworm (Bombyx mori) excrement accumulates in large quantities and causes severe environmental pollution, with highly crystalline cellulose limiting efficient resource utilization. The development of effective cellulose-degrading bacterial technologies is crucial for advancing biotechnological applications. This study investigated the effects of exogenous microbial agents and housefly larvae composting on cellulose biodegradation in silkworm excrement. After six days, the cellulose content decreased by 52.6%, 58.2%, and 64.0% in the treatment groups, respectively, which was significantly greater than the 39.41% reduction in the control group without exogenous agents. The combination of exogenous microbial agents and housefly larvae reshaped the bacterial community, increasing the relative abundance of cellulose-degrading taxa. Specifically, Firmicutes and Actinobacteria were enriched, and the abundances of Bacillus, Pseudomonas, and Cellulosimicrobium increased. Functional predictions via PICRUSt indicated that carbohydrate metabolism was predicted to dominate bacterial activity, while Tax4Fun analysis suggested that exogenous agents were associated with increased predicted abundances of endo-β-1,4-glucanase and exo-β-1,4-glucanase genes in excrement, which may relate to accelerated cellulose degradation. This study suggests that the combination of exogenous microbial agents and housefly larvae could promote cellulose-degrading bacterial populations and the genetic potential for cellulase activity, representing a possible strategy for silkworm excrement bioconversion.},
}

@article {pmid42303128,
year = {2026},
author = {Ortiz-Morales, G and Vera-Duarte, GR and Moya-Villamar, JA and Barcelo-Canton, RH and Navas, A and Ramirez-Miranda, A and Graue-Hernandez, EO},
title = {Predisposing Factors of Infectious Keratitis in Chronic Cicatrizing Conjunctivitis.},
journal = {The ocular surface},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtos.2026.06.010},
pmid = {42303128},
issn = {1937-5913},
abstract = {PURPOSE: To review the multifactorial predisposing factors to infectious keratitis (IK) in patients with chronic cicatrizing conjunctivitis (CCC), and to highlight diagnostic challenges and preventive strategies in this high-risk population.

METHODS: Literature review.

RESULTS: IK in CCC arises from an interplay of mechanical-anatomical, immunological, and microbiological factors. Key contributors include lid malposition, persistent epithelial defects, tear film instability, use of contact lenses or keratoprostheses, altered microbiome, and long-term immunosuppressive therapy. Staphylococcus aureus, coagulase-negative staphylococci, Corynebacterium spp., Herpesviridae, and Candida spp. are the most common causal organisms. Infections are often polymicrobial and drug-resistant, and may present atypically due to corneal hypoesthesia, tear-film instability, aqueous tear deficiency, and scarring. Diagnosis is frequently delayed, increasing the risk of corneal melting and perforation. Preventive strategies include eyelid reconstruction, cautious use of ocular devices, prophylactic antibiotics, periodical microbiological testing, and early recognition of subtle clinical signs.

CONCLUSION: Patients with CCC face a heightened risk of IK due to profound ocular surface disruption. Understanding the specific predisposing factors and implementing tailored preventive and therapeutic approaches are essential to minimizing vision-threatening complications in this vulnerable population.},
}

@article {pmid42303620,
year = {2026},
author = {Maxime, A and André, B and Tigran, P and Tiphaine, LR and Maude, LG},
title = {The gastric ecosystem: assessing resident microbiome vs. transient microorganisms in obesity and following bariatric interventions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01058-9},
pmid = {42303620},
issn = {2055-5008},
abstract = {Long considered a sterile environment due to its acidity, the stomach is increasingly recognized as a low-biomass but structured microbial ecosystem. Advances in culture-independent sequencing reveal a diverse gastric microbiome shaped by acid secretion, mucosal physiology, diet, medication use, and Helicobacter pylori colonization, although distinguishing metabolically active residents from transient oropharyngeal or dietary microorganisms remains a significant challenge. In healthy individuals, gastric mucosal communities primarily consist of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Fusobacteriota, with genera such as Streptococcus, Prevotella, Rothia, and Veillonella consistently detected. Obesity is associated with altered gastric physiology, including higher pH, delayed emptying, and increased bile reflux, alongside distinct microbial signatures. Helicobacter pylori remains a dominant ecological factor modifying acidity, inflammation, and niche structure, while proton-pump inhibitors significantly "oralize" the gastric microbiome. Although animal models suggest that bariatric surgery can remodel the gastric microbiome, no human study has yet characterized gastric microbial changes following sleeve gastrectomy, gastric bypass, or endoscopic bariatric therapies, leaving the translational relevance of preclinical findings uncertain. Given the central role of the stomach in nutrient sensing and metabolic hormone secretion, its microbial ecosystem warrants dedicated investigation.},
}

@article {pmid42303658,
year = {2026},
author = {Chen, W and Zhao, Q and Li, J and Ainiwaer, Z and Zhang, C and Palihati, A and Fu, W and Wu, H and Huang, X},
title = {Fecal and colonic microbiota differ in composition, function, diagnostic utility and correlation with inflammatory cytokines in ulcerative colitis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-56144-x},
pmid = {42303658},
issn = {2045-2322},
support = {2025D01D28//the Key Project of Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Fecal samples have been frequently used to investigate ulcerative colitis (UC)-related gut microbiota study due to their easy availability. However, whether fecal microbiota accurately represents the mucosal microbiome of UC patients remains controversial. This study aims to analyze the gut microbiota in feces and colonic tissue, and to demonstrate from different perspectives whether the gut microbiota in feces can fully characterize the gut microbiota in colonic tissue. We employed 16S rRNA sequencing and standardized microbiome analysis for fecal and colon tissue samples from 12 UC patients and 16 non-IBD controls (NIC). And we also integrates ELISA, functional analysis, and machine learning techniques to discuss the similarities and differences among differentially identified UC-related microorganisms screened from two sample types. As results, colonic tissue exhibited greater microbial diversity than feces. And some taxa were only detected in colonic tissue. In UC, α-diversity was higher in colonic tissue but lower in feces compared to NIC. Only two microbial genera (Ligilactobacillus and Intestinimonas) showed consistent differential abundance across both sample types. At the functional pathway level, both fecal and colonic microbiota were primarily associated with metabolic pathways; however, colonic microbiota were additionally linked to immune-related pathways, such as the NOD-like receptor signaling pathway. IL-1β, IL-17 and IL-22 were significantly overexpressed in UC. Most fecal differential microbes were negatively correlated with those three cytokines. Regarding the two shared differentially expressed genera, abundance of Ligilactobacillus in tissues was more strongly correlated with the expression of inflammatory cytokines. The correlation between the abundance of Intestinimonas and the expression levels of inflammatory cytokines showed opposite trends in tissues and feces. The combined SHAP and random forest algorithms shown that the UC classification model based on tissue markers was more stable and exhibited weaker overfitting than the model based on fecal markers. In general, fecal microbiota profiles did not adequately represent the microbial landscape of colonic tissue in patients with UC. For studies investigating disease mechanisms, colonic tissue was the more appropriate sample type. However, due to its accessibility, fecal samples remained a promising source for microbial biomarker discovery and the development of diagnostic models.},
}

@article {pmid42303682,
year = {2026},
author = {Song, Q and Gao, Y and Sun, Y and Zeng, X and Liang, Q and Wang, M and Feng, Y and Wang, Q},
title = {Effect of organic material addition combined with tillage systems on organic carbon components and microbial communities in corn-fields of North East China.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-56399-4},
pmid = {42303682},
issn = {2045-2322},
support = {2023YFD1501600//National Key R&D Program of China/ ; YQ2022C031//Natural Science Foundation of Heilongjiang Province/ ; CX23JQ01//Heilongjiang Provincial Agricultural Science and Technology Innovation Leap Project Agricultural Science and Technology Basic Innovation Outstanding Young Scientist Program/ ; LBH-Q21178//Hei-longjiang Postdoctoral Scientific Research Developmental Fund/ ; },
abstract = {Organic material return (OMAR) and tillage systems are crucial agricultural management practices that govern soil microbial properties and organic carbon (OC) content, thereby fundamentally determining soil fertility. However, the precise mechanisms by which these practices mediate microbial activity to enhance distinct OC fractions remain poorly understood. Through a field experiment, we systematically evaluated changes in OC components and soil microbial properties under four treatments (CT, CTS, NTS, and BC). Results indicated that, compared to the CT treatment, BC significantly increased the concentrations of total organic carbon (TOC), light fraction organic carbon (LFOC), and particulate organic carbon (POC) by 181.9%, 1649.4%, and 2778.6%, respectively. Conversely, NTS and CTS increased the content of labile organic carbon (LOC) by 225.6% and 206.6%, and dissolved organic carbon (DOC) by 9.7% and 21.9%. Furthermore, OMAR significantly altered microbial α-diversity and community structure, driving a proportional increase that favored copiotrophic bacteria, such as Bacteroidetes (26.0%-209.4%), Firmicutes (90.5%-268.4%), and Actinobacteria (2.2%-52.1%), while concomitantly depleting oligotrophic K-strategists, including Alphaproteobacteria (24.9%-39.4%) and Acidobacteria (2.9%-34.2%). Random forest modeling revealed that NTS drove LOC accumulation (explaining 32.95% of the variance) primarily by stimulating Actinobacteria, Ruminococcaceae_UCG-013, Romboutsia, Parasutterella, and Candidatus_Pelagibacter. In contrast, BC maximized TOC (73.51%), LFOC (77.77%), and POC (74.02%) accumulation by significantly boosting the abundances of Bacteroidetes, Leptospirillum, Filimonas, Dyadobacter, and Anaerolinea. This investigation elucidates the mechanistic linkages between microbial taxonomic shifts and specific OC fraction dynamics under varying OMAR and tillage regimes, providing critical insights for optimizing carbon sequestration and sustaining long-term soil fertility in agricultural ecosystems.},
}

@article {pmid42303895,
year = {2026},
author = {Cornelio-Martínez, S and Frade-Pérez, MD and González-Dávalos, ML and Varela-Echavarría, A and Mora-Izaguirre, O},
title = {Diet-Dependent Variations in the Gut Microbiota and Metabolic Pathways of the land slug Deroceras laeve.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02811-5},
pmid = {42303895},
issn = {1432-184X},
support = {IN204526//PAPIIT-UNAM/ ; IN203924//PAPIIT-UNAM/ ; CBF2023-2024-834//SECIHTI/ ; CF-2023-I-1881//SECIHTI/ ; },
abstract = {The slug Deroceras laeve has emerged as a valuable model for biological research, but limited knowledge exists of the microbiota that inhabit the digestive tract of this species. This study assessed the bacterial microbiota of the stomach and intestine of D. laeve fed either a diet formulated for rodents (RD) or a diet of fresh vegetables (VD). Pseudomonadota was the most abundant phylum in both digestive compartments, although it decreased in abundance with the VD diet. The genus Rahnella was the most abundant in both regions with a decrease caused by the VD diet and a concomitant increase in richness. Predicted metabolic pathways indicated that fatty acid biosynthesis predominated in the stomach of slugs fed the RD, whereas pyruvate fermentation and amino acid biosynthesis were enriched in VD animals. In the intestine, aerobic respiration, pyruvate fermentation, fatty acid and amino acid biosynthesis were identified as conserved pathways. Predictive functional profiling revealed that signaling and cellular processes, genetic information processing, and metabolism were predominant functions across all groups. These results reveal a more diverse microbiome in slugs fed VD, paralleling the findings in other animals and providing a good grounding for the study of ecological adaptations of this species to its environment.},
}

@article {pmid42304055,
year = {2026},
author = {Kantirakoon, S and Klinhom, S and Kunasol, C and Huayhongthong, C and Sukuprakarn, P and Korawat, W and Kaemthubtim, S and Purintarabal, T and Simmasien, W and Pakpien, S and Thongnamchaima, B and Arkajak, J and Arkajak, R and Chattipakorn, N and Chattipakorn, SC and Thitaram, C},
title = {Characterization of gut microbiota in wild Asian elephants (Elephas maximus) from five forests across Thailand.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57801-x},
pmid = {42304055},
issn = {2045-2322},
support = {2565-081//the CMU Presidential Scholarship and Chiang Mai University/ ; N42A670594//Research Chair Grant from the National Research Council of Thailand/ ; N42A660301//Distinguished Research Professor Grant from the National Research Council of Thailand/ ; RSA6280095//Thailand Research Fund/ ; },
abstract = {The gut microbiota plays a critical role in mammalian health, yet remains poorly understood in wild Asian elephants (Elephas maximus). This study characterized the gut microbiome of wild elephants using 16S rRNA sequencing of fecal samples collected from five natural habitats in Thailand: Doi Pha Mueang Wildlife Sanctuary (DPM), Khao Ang Rue Nai Wildlife Sanctuary (KARN), Khao Yai National Park (KY), Phuluang Wildlife Sanctuary (PL), and Sublangka Wildlife Sanctuary (SLK), representing distinct geographic regions. Across all sites, Thai wild elephants shared a core gut microbiota dominated by fiber-degrading bacteria. Firmicutes was the most abundant phylum, followed by Bacteroidota, Actinobacteriota, and Proteobacteria. At the family level, Lachnospiraceae predominated, followed by Oscillospiraceae, Anaerovoracaceae, and Christensenellaceae. Environmental variable, including geographic coordinates and minimum elevation, significantly influenced microbial community composition and explained patterns of beta diversity, indicating distinct gut microbiota profiles among elephant populations from different forest regions. These findings establish baseline gut microbiome data for wild Asian elephants and provide a foundation for future ecological and conservation-focused microbiome studies.},
}

@article {pmid42304226,
year = {2026},
author = {Yan, Y and Liang, S and Li, S and Xie, S and Wang, X and Zhang, H},
title = {Gut dysbiosis modulates hyperoxia-induced bronchopulmonary dysplasia by promoting EMT through activating TLR4/NF-κB pathway.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {},
number = {},
pages = {},
doi = {10.1186/s10020-026-01529-x},
pmid = {42304226},
issn = {1528-3658},
support = {2024BS022//Research foundation of Guangzhou Women and Children's Medical Center for Clinical Doctor/ ; 011302064//Guangzhou Postdoctoral Science Foundation/ ; 20261A031030//Guangzhou Health and Wellness Science and Technology Youth Talent Cultivation Project/ ; },
abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) is a major cause of morbidity and mortality in premature infants. Although gut microbial dysbiosis is implicated in BPD pathogenesis, the underlying mechanisms are poorly defined. This study aims to elucidate the specific pathway through which gut dysbiosis drives BPD pathology and to identify potential therapeutic targets.

METHODS: The experimental BPD model was established by hyperoxia (FiO2 85%) in neonatal mice from postnatal days 1 to 14. Pulmonary alveolarization and inflammation were analyzed at postnatal day 15. The modulatory role of gut microbiota was assessed using antibiotic-induced dysbiosis and fecal microbiota transplantation (FMT) from normoxic mice. Gut microbiome analysis was performed using 16S rRNA gene sequencing. The specific signaling pathway was investigated using a pharmacological inhibitor of TLR4. Furthermore, the molecular mechanisms were investigated through western blotting, real-time quantitative PCR, ELISA, and immunofluorescence.

RESULTS: Hyperoxia exposure induced impaired alveolarization, disrupted gut barrier integrity, and gut dysbiosis. These pathological changes were accompanied by elevated pulmonary inflammation, potent activation of the TLR4/NF-κB pathway, and upregulation of epithelial-mesenchymal transition (EMT) associated markers. These changes were exacerbated by early postnatal antibiotic administration, whereas FMT from normoxic mice rescued these phenotypes, restored gut barrier function, suppressed TLR4/NF-κB signaling, and reversed EMT progression. Notably, pharmacological inhibition of TLR4 mirrored the protective effects of FMT, effectively attenuating hyperoxia-induced lung injury and EMT.

CONCLUSIONS: Our findings establish a mechanistic link for the gut-lung axis in BPD, demonstrating that gut dysbiosis is a critical modulator of lung development impairment and pathological EMT via activation of the TLR4/NF-κB pathway.},
}

@article {pmid42304343,
year = {2026},
author = {Cimerman, M and Papić, B and Nemec Svete, A and Avberšek, J and Kušar, D and Petek, S and Bajc, M and Pohar, K and Ihan, A and Domanjko Petrič, A},
title = {Exploratory analysis of gut microbiota and its association with peripheral blood immune cell populations in canine myxomatous mitral valve disease.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05629-y},
pmid = {42304343},
issn = {1746-6148},
support = {Young Researcher Core Funding//The Slovenian Research and Innovation Agency/ ; P4-0092//The Slovenian Research and Innovation Agency/ ; P4-0053//The Slovenian Research and Innovation Agency/ ; P4-0092//The Slovenian Research and Innovation Agency/ ; P4-0053//The Slovenian Research and Innovation Agency/ ; },
abstract = {BACKGROUND: There is increasing evidence that gut microbiota is associated with cardiovascular health. In this exploratory study, the 16 S rRNA amplicon sequencing was employed to investigate the composition and differential abundances of bacterial gut microbiota of dogs at different stages of myxomatous mitral valve disease (MMVD): dogs with congestive heart failure (CHF, n = 38), dogs in the preclinical stage of the disease (non-CHF, n = 23) and healthy controls with no apparent heart disease (n = 17). Flow cytometry was performed to quantify T lymphocytes and their subtypes, as well as monocytes, natural killer (NK) cells and B lymphocytes. Concentrations of selected chemokines, N-terminal pro-B-type natriuretic peptide (NT-proBNP) and C-reactive protein (CRP) were also measured. Correlation analysis was performed between immunological parameters and bacterial taxa of the gut microbiota.

RESULTS: Alpha diversity did not differ significantly between the study groups; however, several differentially abundant taxa were identified. Escherichia/Shigella was overabundant in the CHF group and showed a positive correlation with activated T lymphocyte levels, whereas Megamonas was overabundant in the control group and was negatively correlated with monocytes and NT-proBNP levels. Lachnospiraceae was overabundant in the non-CHF group.

CONCLUSIONS: These findings suggest that dogs with varying severity of heart disease differ in gut microbiota composition. The observed associations between microbiota profiles, immunological parameters and disease status indicate potential microbiome-immune interactions in disease progression.},
}

@article {pmid42304393,
year = {2026},
author = {Wilson, TM and Allen, B and Harris, JK and Kuhn, KA and Deane, KD and Humphries, SM and Lee, JS and Solomon, JJ and Demoruelle, MK},
title = {Sputum lautropia is decreased in rheumatoid arthritis-associated pulmonary fibrosis.},
journal = {Arthritis research & therapy},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13075-026-03845-3},
pmid = {42304393},
issn = {1478-6362},
support = {Scientist Development Award//Rheumatology Research Foundation/ ; T32 AR07534/AR/NIAMS NIH HHS/United States ; P30 AR079369/AR/NIAMS NIH HHS/United States ; P30 AR079369/AR/NIAMS NIH HHS/United States ; R01 AR076450/AR/NIAMS NIH HHS/United States ; K23 HL138131/HL/NHLBI NIH HHS/United States ; },
abstract = {OBJECTIVE: To investigate whether lung microbial composition differs between individuals with rheumatoid arthritis and pulmonary fibrosis (RA-PF) compared to those without fibrosis (RA-no-PF).

METHODS: We enrolled 54 RA patients (22 RA-PF, 32 RA-no-PF) from rheumatology and pulmonary clinics. PF was defined by high-resolution computed tomography (HRCT) findings. Induced sputum was analyzed using 16 S rRNA sequencing to identify the relative abundance of sputum bacteria. Taxonomic differences between groups were evaluated using three independent analytic approaches: Mann-Whitney U, DESeq2, and EdgeR, with false discovery rate correction. Logistic regression examined associations between Lautropia abundance and clinical variables.

RESULTS: Individuals with RA-PF were older, more often male, and had a higher history of smoking than those with RA-no-PF. Alpha diversity was lower in RA-PF, while beta diversity did not differ between groups. Across the three analytic methods, Lautropia consistently showed decreased abundance in RA-PF compared to RA-no-PF. In multivariable models adjusting for age, sex, and smoking, RA-PF remained independently associated with undetectable levels of Lautropia (OR = 0.14, p = 0.023). Within RA-PF, when Lautropia was undetectable, there was no difference in pulmonary physiology but did show a trend towards more lung fibrosis.

CONCLUSION: Sputum Lautropia is significantly reduced in RA-PF, and its absence may correlate with more severe fibrosis. These findings support a potential role for the lung microbiome in the pathogenesis of pulmonary fibrosis and raise the possibility that commensal taxa such as Lautropia modulate fibrotic pathways. Longitudinal and mechanistic studies are needed to determine whether Lautropia depletion precedes fibrosis and whether microbial-directed approaches represent new therapeutic avenues in RA.},
}

@article {pmid42304441,
year = {2026},
author = {Jafarlou, M and Jafarlou, V and Nouri, S and Alizadeh, N and Tabrizi, ZA and Iravani, M and Ghorbaninezhad, F and Shakiba, D and Baradaran, B},
title = {Immunotherapy resistance in colorectal cancer: therapeutic strategies and biomarker-guided approaches.},
journal = {Cancer cell international},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12935-026-04385-1},
pmid = {42304441},
issn = {1475-2867},
abstract = {Overcoming immunotherapy resistance remains a major challenge in colorectal cancer (CRC), particularly because most tumors are microsatellite stable/proficient mismatch repair (MSS/pMMR) and respond poorly to immune checkpoint inhibitors (ICIs). In contrast, deficient mismatch repair/high microsatellite instability (dMMR/MSI-H) tumors show greater sensitivity to PD-1/PD-L1 and CTLA-4 blockade due to high tumor mutational burden, neoantigen generation, and immune-inflamed tumor microenvironments. However, both primary and acquired resistance continue to limit durable clinical benefit. Resistance arises from tumor-intrinsic mechanisms, including impaired antigen presentation, MHC-I downregulation, oncogenic signaling, and chromatin remodeling defects, as well as tumor-extrinsic mechanisms such as immune suppression, stromal exclusion, inhibitory cytokines, metabolic stress, and gut microbiome dysbiosis. This review distinguishes itself by linking specific resistance barriers to therapeutic strategies rather than discussing immunotherapy approaches in isolation. We summarize emerging strategies, including rational ICI combinations, targeted therapies, adoptive cell therapies, CAR-T cells, BiTEs, cancer vaccines, oncolytic viruses, microbiome-modulating approaches, and cytokine/adjuvant-based therapies. We also highlight clinically relevant biomarkers, including MSI/MMR status, tumor mutational burden, immune contexture, Immunoscore, circulating tumor DNA, microbiome profiles, and spatial or AI-assisted multi-marker models. This review summarizes emerging strategies to enhance therapeutic efficacy in CRC and maps each modality to the tumor-intrinsic or tumor-extrinsic resistance barriers it is most likely to overcome.},
}

@article {pmid42304541,
year = {2026},
author = {Dutta, R and Obayomi, O and Yosef, AF and Ghazaryan, L and Chalifa-Caspi, V and Lapidot, M and Gillor, O},
title = {A cooperative cobalamide biosynthesis guild in the endosphere of the edible aquatic plant Wolffia globosa Mankai.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00917-4},
pmid = {42304541},
issn = {2524-6372},
support = {16-38-0038//Ministry of Agriculture and Rural Development/ ; },
abstract = {BACKGROUND: Cobalamin (vitamin B12) is synthesized only by certain bacteria and archaea and is rarely found in plant-derived foods because plants neither synthesize nor require this cofactor. The edible duckweed Wolffia globosa Mankai is unusual in containing bioavailable cobalamin, suggesting a microbial origin. However, how cobalamin biosynthetic capacity is organized within angiosperm-associated microbiomes remains largely unresolved. Here, we investigated bacterial community structure and cobamide biosynthetic potential across the cultivation medium, plant surface, and internal tissues of Mankai to determine how cobalamin production is maintained in this aquatic plant microbiome.

RESULTS: Bacterial communities differed significantly among compartments, with the endosphere forming a low-diversity, host-filtered microbiome enriched in specialized taxa. Genome-resolved metagenomics showed that only a minority of endophytic bacteria encoded near-complete cobamide biosynthesis pathways consistent with de novo synthesis. In contrast, many co-occurring taxa lacked multiple biosynthetic steps but were enriched in genes associated with cobamide precursor salvage and remodeling. Network analysis identified putative producer taxa as highly connected hubs linked to salvager populations, consistent with metabolite cross-feeding. Comparative genomic analysis demonstrated reduced cobamide biosynthetic gene complements in endophytic genomes relative to closely related free-living strains, supporting adaptive pathway reduction in the host-associated niche.

CONCLUSIONS: Cobalamin production in the Mankai endosphere appears to arise from a metabolically interdependent bacterial consortium rather than from single autonomous producers. These findings identify cooperative micronutrient biosynthesis as an organizing principle in plant-associated microbiomes and position Mankai as a tractable model for studying cobamide-mediated microbial cooperation in aquatic crops. Understanding these interactions may support microbiome-informed strategies to stabilize micronutrient production and functional resilience in controlled aquatic plant cultivation systems.},
}

@article {pmid42304659,
year = {2026},
author = {Daniels, NC and Wilson, EA and Serbanescu, MA},
title = {The leaky gut and microbiome in critical illness: emerging insights into microbial "translocation".},
journal = {Current opinion in critical care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCC.0000000000001399},
pmid = {42304659},
issn = {1531-7072},
abstract = {PURPOSE OF REVIEW: Microbial translocation has long been viewed as a nonspecific consequence of gut barrier failure in critical illness, with downstream effects attributed primarily to the host immune response. This review examines emerging evidence that the gut microbiome plays a more active and specific role in this process than previously appreciated.

RECENT FINDINGS: Dysbiosis during critical illness directly contributes to barrier dysfunction through depletion of metabolites that sustain epithelial integrity. Culture-independent approaches have revealed that gut-derived organisms are a major reservoir for secondary infection, with translocation governed by microbial virulence, community dynamics, and immune cell-mediated transport rather than barrier permeability alone. In parallel, organism-specific microbial components - including structurally diverse forms of lipopolysaccharide and bacterial DNA detected across multiple blood fractions - enter the circulation and differentially modulate host immune responses. Recent studies link circulating microbial DNA composition to distinct inflammatory phenotypes in sepsis and acute respiratory distress syndrome, suggesting these signals contribute to clinical heterogeneity.

SUMMARY: These findings support a revised framework in which translocation reflects the composition of the dysbiotic gut, not barrier integrity alone. Integrating microbial data with host phenotyping may enable more precise risk stratification and microbiome-informed therapeutic strategies in critical illness.},
}

@article {pmid42304699,
year = {2026},
author = {Feng, YC and Liu, XX and Yu, H and Liu, R and Pang, TS and Wang, HN and Peng, ZW},
title = {Fecal Microbiota Transplantation From Patients With Social Anxiety Disorder Is Associated With General Anxiety-Like Behavior and Gut Microbiota Alterations in Mice.},
journal = {Brain and behavior},
volume = {16},
number = {6},
pages = {e71561},
pmid = {42304699},
issn = {2162-3279},
support = {82171512//National Natural Science Foundation of China/ ; XJZT25QN50//Xijing Hospital/ ; LHJJ24YF06//Xijing Hospital/ ; //Boost plan of Xijing Hospital/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; *Gastrointestinal Microbiome/physiology ; Mice ; Male ; Humans ; *Anxiety/microbiology ; *Phobia, Social/microbiology/therapy ; *Behavior, Animal/physiology ; Female ; Mice, Inbred C57BL ; Adult ; *Dysbiosis/microbiology ; Tryptophan/blood ; },
abstract = {PURPOSE: Growing evidence implicates gut microbiota dysbiosis in social anxiety disorder (SAD), yet direct causal evidence remains limited. This study investigated whether fecal microbiota transplantation (FMT) from individuals with SAD was associated with general anxiety-like behaviors and accompanying gut microbial and predicted metabolic alterations in mice.

METHODS: Fecal samples were collected from five patients diagnosed with SAD and five matched healthy controls and transplanted into antibiotic-treated mice. Anxiety-like behaviors were evaluated using the open-field test (OFT) and elevated-plus maze test (EPMT). Gut microbiota composition was assessed by 16S rRNA gene sequencing, microbial functional potential was inferred using PICRUSt2, and plasma tryptophan-pathway metabolites were quantified.

RESULTS: Mice receiving SAD microbiota (SAD group) showed general anxiety-like behaviors, characterized by more time spent in the periphery of the OFT and fewer entries and less time in the open arms of the EPMT compared to mice receiving healthy control microbiota (control group). Although α-diversity did not differ significantly, β-diversity was distinct between groups. The SAD group showed enrichment of Bacteroidota/Bacteroidales-related bacteria (e.g., Muribaculum), whereas the control group had higher abundance of butyrate producers (e.g., Butyricimonas). Functional prediction indicated lower predicted abundance of selected DNA-repair and biosynthetic pathways in the SAD group. Plasma tryptophan levels were nominally lower in the SAD group.

CONCLUSIONS: These findings suggest that specific gut microbiota alterations and predicted functional pathway changes in individuals with SAD may be associated with anxiety-related behavioral phenotypes, supporting the gut microbiome as a potential contributing factor to the pathophysiology of SAD.},
}

Animals
*Fecal Microbiota Transplantation/adverse effects
*Gastrointestinal Microbiome/physiology
Mice
Male
Humans
*Anxiety/microbiology
*Phobia, Social/microbiology/therapy
*Behavior, Animal/physiology
Female
Mice, Inbred C57BL
Adult
*Dysbiosis/microbiology
Tryptophan/blood

@article {pmid42294656,
year = {2026},
author = {Dumandan, NG and Kagaoan, ACT and Arreola, SLB and Arguelles, EDLR},
title = {Draft genome sequence of Priestia flexa BCA501, a tannin-degrading bacterium isolated from the gut of silver therapon (Leiopotherapon plumbeus).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0052426},
doi = {10.1128/mra.00524-26},
pmid = {42294656},
issn = {2576-098X},
abstract = {The draft genome sequence of Priestia flexa BCA501, isolated from the gut of silver therapon (Leiopotherapon plumbeus), is reported. Genome analysis revealed genes associated with tannin degradation, including a putative tannase, indicating its potential application in bioprocessing tannin-rich substrates.},
}

@article {pmid42294659,
year = {2026},
author = {Rosin, A and Kissner, MS and Lemoine, L and Neuhaus, K},
title = {Draft genomes of 10 skin bacteria isolated from human forearm.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0043726},
doi = {10.1128/mra.00437-26},
pmid = {42294659},
issn = {2576-098X},
abstract = {The human skin microbiome plays a crucial role in skin homeostasis. In this study, we present the draft genomes of 10 bacterial strains isolated from the volar forearms of five healthy donors.},
}

@article {pmid42294667,
year = {2026},
author = {Aponte Rolón, B and Kristy, B and Shade, A and Stopnisek, N and Lebeis, SL and Howe, A and Benucci, GMN},
title = {BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0025126},
doi = {10.1128/mra.00251-26},
pmid = {42294667},
issn = {2576-098X},
abstract = {Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.},
}

@article {pmid42294689,
year = {2026},
author = {Thomsen, AMR and Alvarenga, DO and Rousk, K},
title = {Nitrogen deposition homogenizes moss-microbiomes and associated nitrogen fixation but with host-specific responses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0082826},
doi = {10.1128/aem.00828-26},
pmid = {42294689},
issn = {1098-5336},
abstract = {UNLABELLED: Moss microbiomes contribute significantly to terrestrial nitrogen (N) cycling through N fixation, especially in nutrient-poor environments. Yet, the relative roles of environment (abiotic factors) and host species (biotic factors) in shaping these microbiomes remain understudied even though this could reveal how host-specific moss-associated microbiomes are. To assess whether moss-associated microbiomes are shaped predominantly by the moss host or by the environment, we compared three common moss species (Hylocomium splendens, Pleurozium schreberi, and Sphagnum sp.) from ecosystems that differ in atmospheric N deposition rates: a temperate forest with >15 kg N ha[-1] yr[-1] and a boreal forest with 2 kg N ha[-1] yr[-1] of deposition. We further tested if moss-associated microbiomes and N fixation rates become more similar between the boreal and temperate mosses upon N additions to the boreal mosses. Nitrogen fixation, measured as acetylene reduction, was overall higher in the boreal mosses than in the temperate mosses. Microbial community composition, assessed with 16S rRNA gene sequencing, showed that both environment and host species influence the moss microbiome, but that the environment exerts the stronger influence. Nitrogen additions significantly reduced N fixation rates and changed the composition of moss microbiomes substantially, causing the microbiomes of two of the three investigated mosses to become more similar to each other. Our findings show that the environment (i.e., forest type with different N deposition rates) exerts a strong influence on the moss microbiome and that N deposition favors certain moss-associated microorganisms but lowers N input via moss-associated N fixation considerably.

IMPORTANCE: Mosses host diverse microbiomes that contribute to terrestrial N cycling through processes such as nitrogen (N) fixation. Thus, these microbial communities play important roles in nutrient-poor environments where mosses often dominate. Here, N fixation is a key source of N input, making it important to understand what drives microbiome composition and associated N fixation activity. We ascertained the roles of the environment and moss-host species in shaping the moss-microbiomes and associated N fixation rates in two forest types with varying N deposition rates. We showed that forest type shapes moss-associated microbiomes and N fixation activity, while aligning N availability also aligned N fixation activity and changed the moss microbiomes with implications for the ecosystem functions they provide.},
}

@article {pmid42294712,
year = {2026},
author = {Taillefer, B and Dairy, Y and Brault, A and Briand, M and Charpin, P and Armengaud, J and Sarniguet, A},
title = {Specific and broad-spectrum antibacterial effectors of type VI secretion system drive competition of Stenotrophomonas rhizophila against bacteria from seed microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0353225},
doi = {10.1128/spectrum.03532-25},
pmid = {42294712},
issn = {2165-0497},
abstract = {The type VI secretion system (T6SS) is a bacterial weapon that injects deadly effectors (T6Es) directly into a target competitor encountered in a microbial community. Stenotrophomonas rhizophila CFBP13503 (Sr), a seed-borne bacterium, uses its T6SS to target a wide range of other bacterial species, impacting seed microbiota assembly, and controlling phytopathogen transmission from seed to seedling. How the large T6E repertoire and other features contribute to S. rhizophila's impact was investigated. Using transcriptional and translational reporters combined with fluorescence microscopy and proteomic approaches, we confirmed the expression and production of nine effectors secreted by a highly dynamic T6SS. This resulted in killing target cells through four major cell death phenotypes, with different frequencies depending on the target species. The systematic deletion of single effectors revealed a general synergy in killing a wide range and diverse seed-borne bacteria, but also a target-specific killing. Comparative genomics suggests that Sr-T6Es are commonly shared in the Stenotrophomonas genus diversity but are also highly plastic and acquired from diverse bacterial families. Inversely, T6SS-resistance markers, such as capsule and orthologous immunities, are weakly distributed in seed microbiota, and do not explain resistance to Sr-T6SS. Importantly, two amidases explained the major T6SS antibacterial activity, and only the Rhs-fused effector targeted a Gram-positive bacterium. Our work depicts the generalist or specific role of each effector in the S. rhizophila T6SS activity targeting either aggressive, closely related, broad, or Gram-positive bacteria from seed microbiota.IMPORTANCEThe type VI secretion system (T6SS) is largely distributed among seed-borne bacteria. However, it remains important to understand how this interbacterial competition weapon could provide a competitive advantage for some strains and influence microbiome assembly during seed-to-seedling transmission. The Stenotrophomonas rhizophila CFBP 13503 strain, a seed-associated bacterium, cumulated several T6SS features like a constitutive and highly dynamic T6SS associated with 12 putative antibacterial T6Es that shape microbiota assembly through broad and strain-specific targeting within seed microbiota. Hence, genomic analysis suggests that S. rhizophila T6E repertoire is adaptive thanks to genetic gain and loss or through gene regulation. In the context of microbiome engineering, the relevance of this study is to highlight the need to associate broad-effective and competitive S. rhizophila strains, as well as T6SS-resistant strains, in bacterial synthetic communities as seed inoculum against phytopathogens.},
}

@article {pmid42294719,
year = {2026},
author = {Regan, MR and McDevitt, CJ and Robinson, LR and Issifou, S and Wadsworth, CB},
title = {Put your money where your mouth is: surveillance of antibiotic resistance within the commensal Neisseria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0072526},
doi = {10.1128/spectrum.00725-26},
pmid = {42294719},
issn = {2165-0497},
abstract = {Commensal Neisseria species are major reservoirs of adaptive genetic variation, including antimicrobial resistance, for their pathogenic relatives, yet they remain poorly characterized. This gap limits our ability to anticipate resistance mechanisms that may ultimately emerge in Neisseria gonorrhoeae and Neisseria meningitidis. Here, we analyzed 166 novel commensal Neisseria isolates collected from 31 study participants and measured minimum inhibitory concentrations (MICs) for seven antimicrobials: azithromycin, cefixime, ceftriaxone, ciprofloxacin, doxycycline, penicillin, and gentamicin. Resistance, defined using the Clinical and Laboratory Standards Institute guidelines, was highly prevalent for azithromycin (76%) and doxycycline (52%), while no resistance to gentamicin was observed. High-level doxycycline resistance was always associated with the inheritance of tetM. Reduced susceptibility to azithromycin was linked to an MtrD K823E substitution, and reduced susceptibility to ciprofloxacin was associated with GyrA T91I (Neisseria subflava) or S91V (Neisseria mucosa). Across all antimicrobials, MICs varied widely, indicating the presence of additional modulating mutations. Finally, the genetic determinants underlying low-level doxycycline resistance and reduced penicillin susceptibility remain unresolved. Overall, here, we continue to build on the foundation of surveillance efforts in the commensal Neisseria and continue to flesh out what is known and unknown about this early warning system-or canary in the coal mine-for emerging resistance and clinically consequential evolution in pathogenic Neisseria.IMPORTANCECommensal Neisseria species constitute a vast and dynamic reservoir of genetic diversity that can be exchanged with pathogenic relatives, Neisseria gonorrhoeae and Neisseria meningitidis. However, these commensals remain substantially undercharacterized, limiting our ability to anticipate the evolutionary trajectories of antimicrobial resistance in clinically important species. By systematically analyzing commensal isolates and defining phenotypic resistance patterns alongside their genetic determinants, this study, and others like it, function as an early warning system for the emergence and spread of antimicrobial resistance. The high prevalence of azithromycin and doxycycline resistance, identification of specific mutations associated with reduced susceptibility, and evidence of additional unexplained contributors to minimum inhibitory concentration variation highlight both known and cryptic pathways of adaptation. These findings underscore the necessity of integrating commensal surveillance into resistance monitoring frameworks, improving our capacity to forecast clinically consequential evolution and to inform stewardship, diagnostics, and therapeutic development before resistance becomes entrenched in pathogenic Neisseria.},
}

@article {pmid42294877,
year = {2026},
author = {Nardini, L and Zakhia, R and Czarnecki, J and Brito-Fravallo, E and Geneve, C and Mavridis, K and Fricaux, T and Vontas, J and Riehle, M and Vernick, K and Le Goff, G and Mitri, C},
title = {Anopheles resistance to deltamethrin can be caused by the increased abundance of an enteric Aeromonas taxon.},
journal = {mBio},
volume = {},
number = {},
pages = {e0023626},
doi = {10.1128/mbio.00236-26},
pmid = {42294877},
issn = {2150-7511},
abstract = {The enteric bacteriome of Anopheles mosquito vectors has been linked with vectorial competence; however, its influence on insecticide resistance is poorly understood. We found that antibiotic treatment-administered either through sugar feeding (penicillin/streptomycin and gentamicin) or via a blood meal (amoxicillin)-which depleted the bacterial microbiome in susceptible Anopheles strains, led to greater than 50% insecticide deltamethrin tolerance compared to untreated mosquitoes. Simultaneous inhibition of cytochrome P450 activity reverted the antibiotic-induced tolerance phenotype, indicating that the antibiotic-induced deltamethrin tolerance is P450-dependent. We found that the antibiotic treatment, while suppressing most enteric bacterial taxa, allowed proliferation of a particular antibiotic-tolerant Aeromonas taxon, most closely related to Aeromonas hydrophila. Increasing the abundance of this taxon in mosquitoes not treated with antibiotics phenocopied the tolerance phenotype, converting deltamethrin-susceptible Anopheles mosquitoes to deltamethrin-tolerant mosquitoes. Collectively, these results highlight a mechanistic interplay in Anopheles mosquitoes between antibiotic-induced enteric dysbiosis and cytochrome P450-mediated detoxification that promotes insecticide tolerance. This effect could influence mosquito vectorial capacity, especially in Africa, where antibiotic self-medication is highly prevalent.IMPORTANCEOur findings highlight an unexpected link between antibiotic use and the effectiveness of mosquito control strategies. It shows that disrupting the natural gut bacteria of malaria-carrying mosquitoes can make them significantly more tolerant to insecticides commonly used in public health programs. This occurs because antibiotic treatment alters the microbial balance, allowing certain antibiotic-resistant bacteria to thrive and enhance the mosquito's internal detoxification systems. As a result, mosquitoes that would normally be killed can survive exposure. These findings are important because they suggest that widespread antibiotic use-especially in regions heavily affected by malaria-could unintentionally reduce the impact of insecticide-based interventions such as bed nets and indoor spraying. This adds a new layer of complexity to vector control efforts and highlights the need to consider microbial and environmental factors alongside traditional approaches. Understanding this interaction could help improve strategies to combat insecticide resistance and better control mosquito-borne diseases.},
}

@article {pmid42294883,
year = {2026},
author = {Dai, T and Zhou, J and Ran, S and Sun, H and Wei, H and Peng, J and Zhou, Y},
title = {Astragalus polysaccharides ameliorate perinatal metabolic syndrome in sows via enhancing butyrate-producing bacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0302925},
doi = {10.1128/spectrum.03029-25},
pmid = {42294883},
issn = {2165-0497},
abstract = {UNLABELLED: Astragalus polysaccharide (APS), a bioactive phytomacromolecule from Astragalus membranaceus, exhibits anti-inflammatory, antioxidant, and immunomodulatory activities. Given mammals' lack of endogenous glycosidases for APS catabolism, this study hypothesizes its bioactivity stems from gut microbial interactions, investigating APS-mediated microbiome remodeling and therapeutic effects on perinatal metabolic syndrome (PeriMS) in sows. In vitro fermentation showed that APS significantly increased short-chain fatty acid (SCFA) production, with acetate (44.51 mmol/L), propionate (17.37 mmol/L), and butyrate (22.04 mmol/L) levels notably elevated and enriched canonical butyrate-producing taxa (g_norank_f_Muribaculaceae, g_Monoglobus, g_unclassified_f_Lachnospiraceae, P < 0.05). In vivo, gestational APS supplementation (from day 90) improved piglet weaning weight, reduced maternal backfat loss during lactation, shortened post-weaning estrus interval, elevated intestinal butyrate, alleviated systemic inflammation/oxidative stress, and mitigated PeriMS. Mechanistic analysis associated PeriMS improvement with butyrate-producing bacteria, with butyrate playing a key role in gut health enhancement. These findings establish APS as a prebiotic, highlighting the gut microbiota-SCFA axis as a therapeutic target for PeriMS. This study provides targeted mechanistic evidence that the gut microbiota-SCFA axis mediates PeriMS improvement by APS. Mechanistic analysis linked PeriMS improvement to butyrate-producing bacteria, with butyrate playing a key role in gut health enhancement, which was verified by a sodium butyrate rescue experiment. These findings establish APS as a prebiotic, highlighting the gut microbiota-SCFA axis as a therapeutic target for PeriMS. This work provides novel evidence for microbiota-SCFA axis involvement in sow perinatal metabolic health, offering translational strategies to improve livestock metabolic health through APS supplementation.

IMPORTANCE: In intensive pig farming, 40% of multiparous sows develop perinatal metabolic syndrome (PeriMS) around farrowing, causing $150-$200 annual loss per sow due to inflammation (e.g., higher IL-6), oxidative stress, and extended weaning-to-estrus intervals (2.1 days). Gut dysfunction-marked by fewer butyrate-producing bacteria and increased endotoxin-triggers barrier damage and inflammation. Supplementing with Astragalus polysaccharides (APS, 10 g/day) enhances beneficial bacteria like Muribaculaceae and butyrogenic Bacteroides, raising butyrate in vitro. In sows, APS lowers endotoxemia and gut inflammation (calprotectin), correlating with reduced postpartum IL-6 and reactive oxygen species. It also improves productivity: less backfat loss and heavier weaned piglets. By targeting gut-barrier crosstalk, APS breaks the inflammation-metabolism cycle, providing a sustainable alternative to antibiotics to enhance peripartum sow health and profitability.},
}

@article {pmid42294884,
year = {2026},
author = {Tao, E and Wang, L and Yuan, T},
title = {The gut microbiome in preterm infants: development, dysbiosis, and disease implications.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0008826},
doi = {10.1128/cmr.00088-26},
pmid = {42294884},
issn = {1098-6618},
abstract = {SUMMARYPreterm infants face a unique trajectory of gut microbiome assembly, shaped by the convergence of physiological immaturity, necessary clinical interventions, and the neonatal intensive care unit environment. This dysbiotic ecosystem-characterized by low diversity, depletion of beneficial commensals such as Bifidobacterium, and expansion of pathobionts, including Enterobacteriaceae-is increasingly recognized as a central mediator of neonatal morbidity. This review synthesizes current evidence on preterm microbiome development, its role in necrotizing enterocolitis through mechanisms involving Toll-like receptor 4 signaling, bile acid dysmetabolism, and immune dysregulation, and its systemic impact via gut-organ axes linking the intestine to the brain, lung, eye, and systemic circulation. We critically evaluate microbiome-targeted interventions across the translational spectrum, from foundational practices such as human milk feeding and antibiotic stewardship to active modulation with probiotics and prebiotics, and emerging precision strategies, including postbiotics, phage therapy, and fecal microbiota transplantation. Methodological advances in multi-omics, machine learning, and digital twin modeling are paving the way for personalized, predictive microbiome-mediated care. We also address the hidden burden of antimicrobial resistance in the preterm gut and the challenges of translating mechanistic insights into clinical practice. Looking forward, embracing the complexity of the preterm microbiome as a dynamic, multi-kingdom ecosystem is essential for developing holistic interventions that improve both short-term survival and long-term neurodevelopmental, respiratory, and metabolic outcomes.},
}

@article {pmid42294912,
year = {2026},
author = {Zhang, T and Qian, Q and Zhen, Q and Zhang, J and Sun, Y and Zhang, J and Guo, L and Liu, X and Zou, D and Zhou, B and Liu, C and Chi, S and Shang, G and Cui, B and Zhang, Y and Cui, Y and Zhang, Y and Han, S},
title = {Prevotella bivia promotes cervical cancer progression and modulates macrophage polarization, while Lactobacillus iners suppresses these processes: evidence from multiomics analysis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0037426},
doi = {10.1128/mbio.00374-26},
pmid = {42294912},
issn = {2150-7511},
abstract = {The incidence and mortality rates of cervical cancer are high among women. Growing evidence suggests the key roles of the intratumor microbiome in various solid tumors. However, the intratumoral microbiome in patients with cervical cancer has not been well characterized. In this study, 16S rRNA sequencing was performed on 76 tissues to reveal the features of the intratumoral microbiome, and the highly differentially abundant bacteria Lactobacillus iners/Prevotella bivia were selected for functional verification. Flow cytometry, transwell migration, and invasion experiments, among others, were performed in vitro; subcutaneous tumor formation and lung metastasis experiments were performed in vivo. Additionally, macrophages were cocultured with the L. iners/P. bivia supernatant to evaluate how the intratumoral microbiome affects their polarization, and tumor cell and macrophage transcriptome sequencing was subsequently performed to explore the potential molecular mechanisms involved. Metabolomic analysis of tissues and bacterial supernatants was performed to search for potential carcinogens and cancer suppressors. We determined that the abundance of microbes was greater in cervical cancer tissues than in normal cervical and paracancerous tissues. The relative abundance of Prevotella was correlated with deep stromal invasion, tumor size, clinical stage, and poor survival prognosis in cervical cancer patients. L. iners inhibited the proliferation and promoted the apoptosis of tumor cells, whereas P. bivia significantly promoted cervical cancer cell migration and invasion. Mechanistically, the modulation of phosphorylated PI3K/AKT/mTOR signaling may be involved in the observed effects. P. bivia promoted M2 macrophage polarization by activating phosphorylated STAT3 and NF-κB, but the role of L. iners remains unknown. The amino acid metabolism, carbohydrate metabolism, and lipid metabolism pathways were enriched in differentially abundant metabolites such as glycine, which may be a key molecule. This study provides evidence that the intratumoral microbiome, represented by L. iners/P. bivia, affects tumor biology and macrophage polarization in patients with cervical cancer.IMPORTANCEThe microbiome in cervical cancer tissues significantly differed from that in normal cervical tissues and showed significant correlations with clinicopathological features and survival prognosis. The tumor microbiome affects the biological behavior of cervical tumor cells and the polarization of macrophages through metabolite production, thus playing an important role in the occurrence and development of cervical cancer.},
}

@article {pmid42294914,
year = {2026},
author = {Miller, MGA and Bergmann, GE and Alcalá Briseño, RI and Lan, Y-H and Søndreli, KL and Busby, PE and LeBoldus, JM},
title = {The interaction between Septoria stem canker and the mycobiome of Populus trichocarpa stems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0005526},
doi = {10.1128/msystems.00055-26},
pmid = {42294914},
issn = {2379-5077},
abstract = {UNLABELLED: Sphaerulina musiva, a fungal pathogen causing leaf spot and canker disease of poplar trees (Populus spp.), was recently introduced to the Pacific Northwest, where it threatens commercially valuable plantations and native riparian ecosystems. Vascular tissue was collected from the stems of 410 symptomatic and asymptomatic trees in an S. musiva-infested Populus trichocarpa plantation. Resident fungal endophyte communities were characterized with ITS amplicon sequencing. Canker expression and S. musiva presence corresponded with reduced fungal diversity across multiple indices. Fungal endophyte communities of symptomatic tissues were frequently dominated by S. musiva and thus compositionally distinct from those of asymptomatic tissues. Asymptomatic-tissue communities from healthy and diseased stems did not differ in composition or diversity, indicating disease-associated low-diversity mycobiome states are local to the cankered site. The relative abundance of S. musiva was positively correlated with stem cankering. S. musiva was negatively correlated with key non-pathogenic fungal endophytes, which were themselves strongly inter-correlated. Our results illustrate S. musiva's ability to exploit the vascular microhabitat of susceptible Populus trichocarpa stems and dominate resident fungal assemblies at the site of infection.

IMPORTANCE: Plant-associated microbial communities can both mediate and be modified by pathogen infection. Thus, understanding disease outcomes of complex plant pathosystems requires characterization of pathogen-phytobiome interactions. Efforts to characterize these interactions have yielded microecological insights with applied relevance for disease management in herbaceous leaf- and root-associated pathosystems. However, pathogen-phytobiome interactions in the vascular tissues of hardwood stems remain largely unexplored. Our findings illuminate the ecological organization of the Populus trichocarpa stem mycobiome under S. musiva disease pressure and advance understanding of microfungal community dynamics in the Septoria stem canker pathosystem. Additionally, we identify potentially interactive fungal taxa that may disproportionately shape mycobiome structure and disease dynamics in Populus trichocarpa stems.},
}

@article {pmid42294916,
year = {2026},
author = {Mulakala, BK and Salinas, ML and Davidson, LA and Romero, S and Read, QD and Fox, R and LeRoith, T and Cai, JJ and Chapkin, RS and Donovan, SM and Yeruva, L},
title = {Bifidobacteria infantis and human milk oligosaccharides have independent and synergistic effects on immune response and amino acid metabolism in germ-free mouse models.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0039226},
doi = {10.1128/msystems.00392-26},
pmid = {42294916},
issn = {2379-5077},
abstract = {UNLABELLED: Early-life microbial colonization is essential for gut and immune development. Human milk oligosaccharides (HMOs) support the growth of Bifidobacterium infantis (BI). Here, we studied the individual and combined effects of BI and HMOs on the immune and colon transcriptomes and on serum and cecal metabolome. Germ-free mice were randomly assigned to four groups (10-14/group: HMO, BI, BI + HMO, and control [no HMO or BI]). HMO and BI + HMO groups received 5 mg/day each of 2'-fucosyllactose, lacto-N-tetraose, and 3'-sialyllactose for 14 days. BI and BI + HMO received BI ATCC 15,697 (1 × 10[9] CFU/day) on days 1, 4, and 9. Mono-colonization with BI increased monocytes, macrophages, B cells, CD4[+] T cells, and Treg cells in mesenteric lymph nodes (MLN) relative to controls. In the spleen, BI alone increased B cells, dendritic cells, Th17 cells, and ILC3 cells, and enriched serum amino acid metabolism pathways. Additionally, BI influenced colonocyte gene expression and modulated serum metabolites that regulate circadian rhythms. BI + HMO increased MLN Th17 cells and spleen monocytes compared with HMO alone. Collectively, the results of this study highlight the complex interplay among host-microbe-diet interactions and emphasize the importance of considering these interactions when designing strategies to modulate infant health during early life.

IMPORTANCE: Early life immune and gut microbiome development are shaped by human milk (HM). One of the most important drivers of these processes is the human milk oligosaccharides (HMOs). Bifidobacterium infantis (BI) possesses a unique enzymatic system that enables efficient HMO uptake and intracellular metabolism, providing a competitive advantage over other microbial species in the breastfed infant gut. To date, the potential direct and synergistic effects of BI and HMO have not been fully explored. The knowledge generated herein identified the independent and synergistic effects of HMOs and BI on gut immune response, serum and cecal metabolites, and colonic gene expression.},
}

@article {pmid42294946,
year = {2026},
author = {Thonghem, A and Chattipakorn, N and Chattipakorn, SC},
title = {Potential Roles of Gut Microbiome and Metabolomes in Interstitial Lung Disease: Evidence across Preclinical and Clinical Research.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag138},
pmid = {42294946},
issn = {1365-2672},
abstract = {Interstitial lung disease (ILD) is a heterogeneous condition that affects the lung parenchyma with varying degrees of inflammation and/or fibrosis. Several studies have suggested a potential link between the gut microbiome and the pathophysiology of lung diseases, including ILD. Accumulating evidence supports bidirectional gut-lung axis interactions potentially mediated by the microbiota. Alterations in the gut microbiome have been associated with the onset and severity of interstitial lung disease. This review aims to summarize findings from in vivo and clinical studies that have investigated the associations between the gut microbiome and ILD. Changes in the gut microbiome have been consistently found in various ILD subtypes, including idiopathic pulmonary fibrosis, radiation pneumonitis, silicosis, coal worker's pneumoconiosis, and connective tissue disease-related ILD. Preclinical studies demonstrate that gut dysbiosis is associated with altered immune responses, increased pro-inflammatory cytokines, and enhanced fibrotic pathways, with mechanistic evidence suggesting the involvement of specific microbial metabolites (short-chain fatty acids, bile acids, and immune mediators. Interventional studies in animal models suggest that fecal microbiota transplantation may attenuate pulmonary inflammation and fibrosis; however, clinical evidence remains limited. This review synthesizes findings across study types, highlights proposed mechanistic pathways, discusses contradictory results, and identifies critical knowledge gaps requiring future investigation to establish causality and inform potential therapeutic development.},
}

@article {pmid42295073,
year = {2026},
author = {Sobocińska, W and Kubicka, G and Kołodyński, Ł},
title = {Positive effects of probiotics in people living with HIV: a narrative review.},
journal = {Folia medica Cracoviensia},
volume = {66},
number = {1},
pages = {133-144},
pmid = {42295073},
issn = {2957-0557},
mesh = {Humans ; *Probiotics/therapeutic use ; *HIV Infections/drug therapy ; *Dysbiosis ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {Despite effective antiretroviral therapy (ART), no clear guidelines exist on microbiome-targetednadjuncts for people living with HIV (PLWH). Human immunodeficiency virus (HIV-1) infection damages the gastrointestinal tract by altering the mucosal surface and prompting dysbiosis. Gut microbial imbalance, characterized by the predominance of opportunistic bacteria, leads to increased microbial translocation, which, in turn, results in chronic inflammation, digestive tract symptoms, and reduced quality of life. PLWH have substantial dysbiosis compared to healthy controls. In addition, gastrointestinal complications occur as a side effect of ART treatment. Gut-associated lymphoid tissue (GALT) harbors the majority of CD4+ lymphocytes, and this population is significantly depleted during HIV-1 infection. Antiretroviral therapy does not facilitate CD4+ lymphocyte restoration in GALT tissue. Even if the general CD4+ lymphocyte count increases, the GALT CD4+ count, despite therapy, remains stable and low due to unknown causes. Research assessing probiotics in PLWH on ART has yielded mixed results. Some studies report that probiotics may increase CD4+ T cell counts, improve gut barrier integrity, and reduce the incidence of diarrhea in HIV-positive patients. These benefits may be linked to specific probiotic strains that possibly enhance immune function by promoting regulatory T cell populations, thus decreasing microbial translocation. On the other hand, multiple studies did not show any consistent or significant benefits from probiotic supplementation for PLWH. This article assesses critical clinical trials and systematic reviews on this topic, based on limited existing research data. More data from large clinical trials on this topic is needed to assess whether this is or is not a justified new clinical approach for HIV-1-positive patients.},
}

Humans
*Probiotics/therapeutic use
*HIV Infections/drug therapy
*Dysbiosis
*Gastrointestinal Microbiome/drug effects

@article {pmid42295075,
year = {2026},
author = {Szwarkowska, M and Sobieszek, KA and Bartus, K and Sadowski, J},
title = {Current evidence of gut microbiota dysbiosis and its role in atrial fibrillation and cardiovascular diseases.},
journal = {Folia medica Cracoviensia},
volume = {66},
number = {1},
pages = {155-171},
pmid = {42295075},
issn = {2957-0557},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/complications/microbiology/physiopathology ; *Atrial Fibrillation/microbiology/physiopathology ; *Cardiovascular Diseases/microbiology/physiopathology ; Oxidative Stress ; },
abstract = {The human gut microbiota has emerged recently as an important regulator of cardiovascular physiology through its effects on metabolism, immune signaling, and systemic inflammation. Increasing evidence suggests that alterations in intestinal microbial composition (dysbiosis) may contribute to the development and progression of atrial fibrillation (AF). This review summarizes current evidence on gut microbiota alterations, microbiota-derived metabolites, and their mechanistic links to atrial fibrillation pathogenesis and potential therapeutic strategies. Patients with AF demonstrate reduced microbial diversity and characteristic shifts in bacterial taxa, including depletion of short-chain fatty acid-producing bacteria and enrichment of potentially pro-inflammatory microorganisms. Gut microbiota-derived metabolites appear to play a key role in mediating these effects. Trimethylamine N-oxide (TMAO), lipopolysaccharide (LPS), and phenylacetylglutamine (PAGln) promote oxidative stress, endothelial dysfunction, and activation of inflammatory pathways such as NF-κB and the NLRP3 inflammasome, leading to atrial fibrosis, electrical remodeling, and increased arrhythmogenic susceptibility. In contrast, short-chain fatty acids exert anti-inflammatory and cardioprotective effects that may stabilize cardiac electrophysiology. Importantly, the relationship between gut microbiota and atrial fibrillation appears to be bidirectional, as cardiovascular disease itself may influence intestinal barrier integrity and microbial composition. Understanding the gut-heart axis may open new perspectives for risk stratification and therapeutic strategies, including dietary interventions and microbiome-targeted therapies. Further clinical studies are required to determine whether modulation of the gut microbiota can effectively prevent or modify the course of atrial fibrillation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/complications/microbiology/physiopathology
*Atrial Fibrillation/microbiology/physiopathology
*Cardiovascular Diseases/microbiology/physiopathology
Oxidative Stress

@article {pmid42295167,
year = {2026},
author = {Jonouchi, D and Shenoy, S and Saintlouis, R and Singh, A and Kashyap, D and Bhargavi, C and Mansoor, R and Mansoor, E and Honnavar, P},
title = {Vaginal microbiome composition in pregnant and non-pregnant women: community structure, population variation, clinical impact, and metagenomics approaches.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0054225},
doi = {10.1128/iai.00542-25},
pmid = {42295167},
issn = {1098-5522},
abstract = {The vaginal microbiome plays a critical role in reproductive health and undergoes characteristic remodeling during pregnancy that influences maternal and neonatal outcomes. Although the non-pregnant vaginal microbiome shows substantial inter-individual variability, pregnancy is associated with reduced microbial diversity and increased dominance by Lactobacillus species, creating a protective environment for fetal development. Disruption of this balance, termed vaginal dysbiosis, has been linked to adverse obstetric and neonatal outcomes. This narrative review synthesizes current evidence on pregnancy-associated vaginal microbiome dynamics, with emphasis on community state types (CSTs), gestational changes, population-specific variation, and clinical implications. We review studies that use 16S rRNA sequencing, next-generation sequencing, and shotgun metagenomics to characterize microbial composition across pregnancy and the postpartum period. Lactobacillus-dominated communities, particularly those dominated by Lactobacillus crispatus, are consistently associated with microbiome stability and favorable pregnancy outcomes, whereas high-diversity anaerobic communities (CST IV) are linked to bacterial vaginosis, preterm birth, miscarriage, gestational diabetes mellitus, and infection-related complications. The vaginal microbiome composition varies significantly across racial, ethnic, and geographic populations. African-descended populations more often show L. iners-dominant or diverse anaerobic profiles, whereas European populations more commonly show L. crispatus dominance. Future longitudinal and mechanistic studies across diverse populations are needed to establish causality and evaluate microbiome-based interventions to improve maternal and neonatal health.},
}

@article {pmid42295179,
year = {2026},
author = {Guitart-Matas, J and Ramayo-Caldas, Y and González-Rodríguez, O and Giler-Baquerizo, N and Migura-Garcia, L and Ballester, M},
title = {Implementation of a high-throughput microfluidic platform for antimicrobial resistance surveillance in swine production systems.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
pmid = {42295179},
issn = {2057-5858},
mesh = {Animals ; Swine/microbiology ; Metagenomics/methods ; Feces/microbiology ; *Microfluidics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Shotgun Sequencing ; },
abstract = {Antimicrobial resistance poses a serious threat to public health worldwide and demands interventions with a One Health perspective. A key challenge is determining the collection of antimicrobial resistance genes of a specific environment, also known as the resistome. Surveillance and monitoring of the resistome are essential for tracking the emergence and dissemination of resistance mechanisms. In this study, we took advantage of shotgun metagenomics and metatranscriptomics sequencing data of piglets treated with different post-weaning diarrhoea treatments to generate an antimicrobial resistance gene catalogue of the pig gut microbiome during pre-weaning and post-weaning stages. The selected catalogue, comprising a total of 102 genes and representing the majority of antibiotic classes, has been implemented in the microfluidic Biomark[™] X9 System and validated using total DNA and RNA extracted from piglets' faecal samples. Additionally, this platform has been verified by demonstrating a strong and statistically significant correlation with resistome quantification data from both metagenomic and metatranscriptomic sequencing. Overall, the microfluidic qPCR platform implemented here demonstrated enhanced detection of low-abundance targets, successfully identifying genes and transcripts that remained below the stochastic detection threshold of shotgun sequencing. This approach enables high-throughput monitoring and surveillance of antimicrobial resistance, providing a critical tool to support the reduction of antimicrobial use in farms.},
}

Animals
Swine/microbiology
Metagenomics/methods
Feces/microbiology
*Microfluidics/methods
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
High-Throughput Nucleotide Sequencing/methods
Gastrointestinal Microbiome/genetics
*Bacteria/genetics/drug effects
Shotgun Sequencing

@article {pmid42295208,
year = {2026},
author = {Chaudhary, A and Lin, X and Vitaterna, MH and Auch, B and Liachko, I and Green, SJ},
title = {Metagenome-assembled genome sequence of an uncultured Roseburia sp. generated from mouse fecal DNA from the International Space Station.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0104725},
doi = {10.1128/mra.01047-25},
pmid = {42295208},
issn = {2576-098X},
abstract = {The effects of spaceflight stressors, such as microgravity, cosmic radiation, and confinement, on the host physiology and gut microbiome remain unclear. Here, we report the metagenome-assembled genome (MAG) sequence of an uncultured Roseburia sp. strain that showed a significant gravity dose response in the gut microbiome of mice during spaceflight.},
}

@article {pmid42295257,
year = {2026},
author = {Ang, MY and Kamaludin, NH and Latif, MT and Jiang, J-J and Wan Ahmad, WAN and Mohd Mokhtar, N and Feisal, NAS},
title = {16S rRNA gene sequencing baseline for the atmospheric microbiome of traffic-impacted urban centers in the Klang Valley, Malaysia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0047726},
doi = {10.1128/mra.00477-26},
pmid = {42295257},
issn = {2576-098X},
abstract = {We report the 16S rRNA gene (V3-V4) amplicon dataset of microbial communities from outdoor air filters at three traffic-exposed locations in the Klang Valley, Malaysia. This baseline characterization of the tropical atmospheric microbiome contributes to understanding airborne microbial diversity in Southeast Asian urban environments.},
}

@article {pmid42295377,
year = {2026},
author = {Thalib, HI and Khan, S and Sideeque, S and Sheriff, TZ and Muzammil, A and Hassan, FE},
title = {Emerging therapeutic strategies in multiple sclerosis: a focus on innovative and targeted approaches.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42295377},
issn = {1432-1912},
abstract = {Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system marked by damage to myelin and nerve cells. Current treatments help control inflammation but have limited success in progressive stages and repairing nerve damage. This review aims to summarize new therapies for MS that target both inflammation and neurodegeneration beyond traditional immunosuppressive drugs. We conducted a thorough literature search to summarize key findings from original studies, including clinical trials investigating novel MS treatments such as Bruton's tyrosine kinase (BTK) inhibitors, CAR T-cell therapy, vaccines targeting Epstein-Barr virus (EBV) and specific antigens, drugs promoting remyelination, monoclonal antibodies, stem cell therapy, sphingosine-1-phosphate receptor modulators, cytokine blockers, gut microbiome interventions, and nanotechnology-based drug delivery. Emerging therapeutic strategies in MS increasingly target mechanisms beyond conventional immunosuppression, including B-cell and microglial modulation, immune tolerance induction, remyelination, cytokine signaling, microbiome regulation, and enhanced central nervous system drug delivery. BTK inhibitors and S1P receptor modulators demonstrated anti-inflammatory activity in clinical trials, although some agents failed to show superiority over established therapies. Cell-based therapies, including CAR T-cell therapy and stem cell transplantation, showed early promise in refractory disease but remain limited by safety concerns and insufficient long-term data. Remyelination-promoting agents and EBV-targeted immunotherapies demonstrated encouraging preliminary findings; however, many approaches remain in preclinical or early-phase clinical stages. Nanotechnology-based delivery systems and microbiome-directed therapies represent emerging areas with potential translational relevance. Emerging therapies in MS reflect a growing shift toward mechanism-based and potentially personalized therapeutic strategies. Although several approaches demonstrate promising preclinical and early clinical results, many remain investigational, and further large-scale studies are required to establish long-term efficacy, safety, and clinical applicability.},
}

@article {pmid42295492,
year = {2026},
author = {Zeng, D and Wang, L and Gong, Y and Zhou, W and Wang, W and Wang, S and Xu, G and Chen, A},
title = {Arbuscular mycorrhizal symbiosis suppresses tomato bacterial wilt by coordinating plant systemic resistance with microbiome antagonism.},
journal = {Mycorrhiza},
volume = {36},
number = {3},
pages = {},
pmid = {42295492},
issn = {1432-1890},
support = {32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; 32472831//the National Natural Science Foundation of China/ ; },
mesh = {*Solanum lycopersicum/microbiology ; *Mycorrhizae/physiology ; *Plant Diseases/microbiology/prevention & control ; *Ralstonia solanacearum/physiology ; *Symbiosis ; *Microbiota ; Rhizosphere ; Plant Systemic Acquired Resistance ; Soil Microbiology ; Disease Resistance ; },
abstract = {Tomato bacterial wilt, caused by Ralstonia solanacearum, is a globally devastating soil-borne disease that poses a serious threat to the sustainable development of tomato production. Arbuscular mycorrhizal fungi (AMF) are well-recognized beneficial soil microorganisms that significantly promote plant growth, enhance nutrient uptake, and improve resistance to various biotic and abiotic stresses. However, a comprehensive understanding of the potential of AMF to suppress tomato bacterial wilt is still lacking. In this study, we demonstrate that AMF inoculation remarkably reduces the disease index of bacterial wilt in tomato plants, upregulates the expression of pathogenesis-related (PR) genes, and enhances antioxidant enzyme activities, collectively strengthening systemic disease resistance. High-throughput 16 S rRNA gene sequencing revealed that AMF colonization drives substantial reassembly of the rhizosphere microbiome. Notably, AMF colonization promoted the recruitment of beneficial bacterial genera, including Bacillus and Brevibacillus, while significantly suppressing the abundance of Ralstonia. Furthermore, we isolated two Brevibacillus strains, designated AQC211 and AQC296, from the mycorrhizosphere of healthy tomato plants, both exhibited antagonistic activity against R. solanacearum in vitro. Pot experiments confirmed that inoculation with the AQC211 strain significantly reduced the incidence and severity of bacterial wilt. These findings indicate that AMF can not only directly prime plant systemic resistance but also indirectly enhance protection against bacterial wilt by shaping a disease-suppressive rhizosphere microbiome.},
}

*Solanum lycopersicum/microbiology
*Mycorrhizae/physiology
*Plant Diseases/microbiology/prevention & control
*Ralstonia solanacearum/physiology
*Symbiosis
*Microbiota
Rhizosphere
Plant Systemic Acquired Resistance
Soil Microbiology
Disease Resistance

@article {pmid42295521,
year = {2026},
author = {Ferdous, J and Islam, SMR and Chakma, K and Hasan, MM and Tanni, AA and Ahmed, R and Sikder, U and Biswas, S and Siddiki, AZ and Crandall, KA and Rahnavard, A and Hussain, MH and Sharifuzzaman, SM and Chowdhury, MSN and Mannan, A},
title = {Antimicrobial resistance and gut microbiome profiles in wild and cultured shrimp (Penaeus monodon) from the coast of the northern Bay of Bengal, Bangladesh.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42295521},
issn = {1573-2959},
mesh = {Animals ; *Penaeidae/microbiology ; Aquaculture ; Bangladesh ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Bays ; Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; },
abstract = {The coastal waters of Bangladesh support rich aquatic biodiversity, including the commercially important shrimp Penaeus monodon. However, antimicrobial resistance (AMR) poses a growing threat to aquaculture, ecosystem stability, and human health. In this study, we investigated bacterial AMR profiles and characterized the gut microbiomes of wild (Natural) and cultured P. monodon from the northern Bay of Bengal, Bangladesh. Culture-based and biochemical methods were used to identify bacterial pathogens of shrimp shells, and antimicrobial susceptibility was assessed using the disc diffusion method. Shotgun metagenomic sequencing was used to characterize gut microbial diversity and identify antibiotic resistance genes (ARGs). All Klebsiella isolates were resistant to ampicillin (100%) and showed high resistance to azithromycin (83%) and nitrofurantoin (73%). Pseudomonas isolates were 93.10% resistant to ampicillin, whereas Vibrio isolates had notable resistance to azithromycin (71.05%) and colistin (63.16%). Metagenomic analysis revealed comparable alpha diversity between wild and cultured shrimp, with Vibrio being predominant in both groups and V. parahaemolyticus as the most abundant species. Cultured shrimp harbored greater microbial diversity, including additional genera such as Shewanella, Lactococcus, and Enterobacter. A total of 30 ARGs were detected, primarily associated with β-lactams and tetracycline resistance. Cultured shrimp exhibited a broader ARG spectrum, reflecting potential anthropogenic impacts on aquaculture practices. These findings suggest that cultured shrimp environments can serve as reservoirs of resistant bacteria and ARGs. Therefore, improved antimicrobial stewardship and regular monitoring are essential to curb the spread of AMRs in marine ecosystems.},
}

Animals
*Penaeidae/microbiology
Aquaculture
Bangladesh
*Gastrointestinal Microbiome
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Bays
Bacteria/drug effects/genetics
Anti-Bacterial Agents/pharmacology
Environmental Monitoring

@article {pmid42295642,
year = {2026},
author = {Wu, M and Jin, J and He, Q},
title = {Low-protein brown rice in CKD: dietary substitution or microbiome signal?.},
journal = {Clinical and experimental nephrology},
volume = {},
number = {},
pages = {},
pmid = {42295642},
issn = {1437-7799},
}

@article {pmid42295754,
year = {2026},
author = {Catani, G and Juez, LD and O Connor, JM and Spinelli, A and Perea, J},
title = {Emerging trends in early-onset gastrointestinal cancers - a comparative review with late-onset cancers.},
journal = {Expert review of anticancer therapy},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/14737140.2026.2690189},
pmid = {42295754},
issn = {1744-8328},
abstract = {INTRODUCTION: Early-onset gastrointestinal (GI) cancers, defined as those diagnosed before the age of 50, are increasing worldwide, whereas the incidence of late-onset GI cancers has stabilized or declined. These trends highlight the need to better understand age-related differences in disease biology and risk factors.

METHODS: This narrative review compares early- and late-onset GI malignancies. We discuss differences in epidemiology, molecular and genetic features, clinical presentation, and management strategies. Relevant literature was identified through a non-systematic search of PubMed and additional sources, and selected according to scientific relevance and quality. Publications from 2000 to March 2026 were reviewed, with inclusion of selected landmark historical studies when appropriate.

RESULTS: Early-onset tumors are more frequently diagnosed at advanced stages and may reflect the impact of early-life environmental exposures, metabolic dysregulation, and microbiome alterations. Although they share several molecular features with late-onset disease, younger patients often present distinct clinical and survivorship needs, including genetic counseling and fertility preservation. Current treatment strategies remain largely similar across age groups due to limited age-specific evidence.

CONCLUSION: Early-onset GI cancers should be understood within an age-specific biological and environmental framework. Improved understanding of these tumors may support better prevention, earlier diagnosis, and more personalized management strategies.},
}

@article {pmid42295802,
year = {2026},
author = {Zhang, S and Jiang, Q and Ma, J and Zou, J and Wang, F and Lv, F and Huang, Y and Wang, Y and Xu, Z},
title = {A Single-Cell Transcriptomic Atlas of the Ovine Rumen Microbiome Characterizes Lineage-Specific Metabolic Shifts Associated with Host Heat Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76152},
doi = {10.1002/advs.76152},
pmid = {42295802},
issn = {2198-3844},
support = {8257030475//National Natural Science Foundation of China/ ; 2025M770277//China Postdoctoral Science Foundation/ ; 2025YFF0512800//National Key R&D Program of China/ ; 2024C03005//Pioneer R&D Programs of Zhejiang/ ; 2024SSYS0022//Key R&D Program of Zhejiang/ ; nycytxgxcxtd-2021-09//Guangxi Innovation Team Construction Project of National Modern Agricultural Industry Technology System/ ; AB2506910008//Science and Technology Major Project of Guangxi/ ; },
abstract = {The adaptation of complex, host-associated microbiomes to environmental perturbations is a critical determinant of ecosystem stability and resilience to climate change, as exemplified in ruminants. While single-microbe RNA sequencing advances community interrogation, complex microbial cell walls severely constrain unbiased single-cell transcriptomic profiling in the rumen. In this study, we developed an optimized 25 min time-resolved enzymatic lysis strategy using smRandom-seq to map the sheep rumen microbiome at single-cell resolution. By profiling 60 748 cells across 21 samples, we captured previously intractable lineages, resolving the transcriptional states of 213 genera and 662 species, achieving a physiologically relevant 0.303% recovery of methanogenic archaea. Unsupervised clustering partitioned the ecosystem into seven cross-species functional clusters, uncovering a spatial coupling between microbial lifestyle and metabolic specialization. Applying this framework to a model of host thermal adaptation demonstrated that host resilience was associated with rapid transcriptional activation of key energy-metabolism clusters. Notably, a lineage-specific metabolic shift toward a glycolytic phenotype in Anaerovibrio lipolyticus contributes to a compensatory "nutritional sparing" effect associated with host resilience. This dataset provides a foundational resource for rumen microbial ecology and establishes a technical framework for dissecting phenotypic plasticity within complex microbiomes.},
}

@article {pmid42296178,
year = {2026},
author = {Xu, C and Snelson, M and Marques, FZ},
title = {Cardiovascular-kidney-metabolic syndrome through the lens of gut‑derived uremic toxins.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2685906},
pmid = {42296178},
issn = {1949-0984},
mesh = {Humans ; *Uremic Toxins/metabolism ; *Metabolic Syndrome/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Cardio-Renal Syndrome/metabolism/microbiology ; *Cardiovascular Diseases/metabolism ; },
abstract = {Cardiovascular-Kidney-Metabolic (CKM) syndrome represents a complex, interconnected cluster of cardiovascular disease, chronic kidney disease, and metabolic disorders such as obesity and type 2 diabetes. These conditions share overlapping metabolic, inflammatory, and vascular pathways, with the gut microbiome increasingly recognised as a key contributor and common underlying risk factor. Uremic toxins, traditionally considered waste products of host and microbial metabolism, are now recognised as active mediators of tissue damage across the CKM spectrum, particularly in the context of impaired renal function. Their production and accumulation are amplified by disrupted intestinal barrier integrity, chronic inflammation, and reduced renal clearance, collectively driving systemic toxicity throughout the CKM continuum. This review explores the origins and impact of gut-derived uremic toxins, including trimethylamine-N-oxide (TMAO), indoxyl sulfate (IS), p-cresol sulfate (PCS) and its associated metabolites, p-cresol and p-cresol glucuronide (PCG), phenylacetylglutamine (PAGln), and imidazole propionate (ImP) within the context of CKM syndrome. These toxins originate from an imbalanced gut microbiome, often shaped by poor diets, such as low-fibre and high-meat intake. We discuss their production by the microbiome and their roles from cardiovascular, renal, and metabolic perspectives and highlight emerging microbiome-targeted strategies to mitigate their pathogenic effects.},
}

Humans
*Uremic Toxins/metabolism
*Metabolic Syndrome/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
Animals
*Cardio-Renal Syndrome/metabolism/microbiology
*Cardiovascular Diseases/metabolism

@article {pmid42296270,
year = {2026},
author = {Singh, R and Kaur, J and Upadhyay, B},
title = {Environmental diabetogens: biochemical links between microplastic exposure, endocrine disruption, and glucose metabolic dysfunction.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42296270},
issn = {2191-0286},
abstract = {The increase in the incidence of type 2 diabetes mellitus (T2DM) worldwide cannot be attributed solely to genetic and lifestyle factors, underscoring the growing role of environmental metabolic disruptors. Microplastics are increasingly being identified as potential environmental diabetogens, owing to the high risk of human exposure and the potential of microplastics to act as EDC carriers. This review aims to integrate the biochemical and molecular evidence for the association between microplastic exposure and the development of impaired glucose metabolism via endocrine, inflammatory, and metabolic signaling pathways. These microplastics and additives, such as bisphenols, phthalates, and POPs, interact with nuclear hormone receptors, including the estrogen receptor, peroxisome proliferator-activated receptor, and aryl hydrocarbon receptor, resulting in aberrant transcriptional control of genes involved in the regulation of metabolism. Microplastics exposure may cause oxidative stress-mediated activation of stress kinases, inhibition of insulin receptor substrate-1, suppression of PI3K-Akt signaling, GLUT4 translocation, and mitochondrial dysfunction, which together result in systemic insulin resistance. In addition, β-cell damage, systemic inflammation, and changes in the gut microbiome interfere with the regulation of glucose metabolism in the liver, muscle, and adipose tissues.},
}

@article {pmid42296370,
year = {2026},
author = {Villarreal, ES and Marinho, Y and Loya, O and Aboagye, SY and Costa, G and Oliveira, F and Gupta, M and Oliveira, KC and Silva, CLM and Sun, J and Erzurum, SC and Lutz, SE and Williams, DL and Oliveira, RFK and de Jesus Perez, V and Oliveira, SD},
title = {Endothelial c-IAP2 loss amplifies P2X7 receptor-driven inflammation and worsens schistosomiasis-associated pulmonary hypertension.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {25},
pages = {e2513158123},
doi = {10.1073/pnas.2513158123},
pmid = {42296370},
issn = {1091-6490},
support = {HL159037/GF/NIH HHS/United States ; 2R25 GM121212-06/GF/NIH HHS/United States ; AI177493/GF/NIH HHS/United States ; },
mesh = {Animals ; *Receptors, Purinergic P2X7/metabolism/genetics ; *Hypertension, Pulmonary/metabolism/etiology/parasitology/pathology ; Mice ; Apoptosis ; *Inhibitor of Apoptosis Proteins/metabolism/genetics ; Endothelial Cells/metabolism/pathology ; *Inflammation/metabolism/pathology ; Lung/metabolism/pathology ; Disease Models, Animal ; Female ; Male ; Mice, Knockout ; },
abstract = {Schistosomiasis-associated pulmonary hypertension (Sch-PH) is the most common form of group I PH worldwide. Recently, data revealed that the preclinical Sch-PH animal model exhibited gut and lung microbiome dysbiosis, associated with significant lung endothelial cell (EC) dysfunction and microvascular apoptosis. However, the role of pro-/antiapoptosis sensors, such as the inhibitor of apoptosis protein 2 (c-IAP2) and the purinergic receptor P2X7 (P2X7R), remained unclear. Using Cdh5cre-ER[T2];cIAP1[-/-];cIAP2[fl/fl] animal model, this study investigated the contribution of endothelial c-IAP2 in this process, revealing pulmonary P2X7R overexpression as a putative target in the onset of Sch-PH. Pharmacologically, inhibition of P2X7R function confirmed its role in promoting lung EC death and disease progression. Moreover, data suggest that microbiome-associated metabolic alterations in Sch-PH seem linked to microvascular EC apoptosis driven by ATP/P2X7R overactivation and suppressed c-IAP2 expression. Indeed, genetic ablation of endothelial c-IAP2 expression was sufficient to induce PH-like features in mice, with echocardiography indicating a higher pulmonary acceleration time (PAT), PAT/pulmonary ejection time, and right ventricular free wall thickness (RVFWTH) after IP/IV-Egg challenge compared to controls, an effect linked to the female prevalence of the disease. These findings suggest a significant contribution of lung EC-P2X7R activation and c-IAP2 suppression to sex-linked Sch-PH pathology, highlighting them as promising therapeutic targets for this life-threatening illness.},
}

Animals
*Receptors, Purinergic P2X7/metabolism/genetics
*Hypertension, Pulmonary/metabolism/etiology/parasitology/pathology
Mice
Apoptosis
*Inhibitor of Apoptosis Proteins/metabolism/genetics
Endothelial Cells/metabolism/pathology
*Inflammation/metabolism/pathology
Lung/metabolism/pathology
Disease Models, Animal
Female
Male
Mice, Knockout

@article {pmid42296782,
year = {2026},
author = {Nasimi, F and Ashtari, S and Moafi, S and Baneshi, F and Feizollah, R and Samadi, A},
title = {Macrophage plasticity as a therapeutic target in inflammatory bowel disease: Immunomodulatory and regenerative strategies.},
journal = {International immunopharmacology},
volume = {185},
number = {},
pages = {116991},
doi = {10.1016/j.intimp.2026.116991},
pmid = {42296782},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD), which mainly includes Crohn's disease and ulcerative colitis, is a chronic inflammatory disorder of the gastrointestinal tract characterized by recurrent episodes of intestinal inflammation. The development of IBD is influenced by multiple factors, including genetic predisposition, intestinal dysbiosis, epithelial barrier impairment, and abnormal immune activation. Among innate immune cells, macrophages are key regulators of intestinal immune homeostasis and are involved in inflammatory responses, tissue remodeling, and mucosal repair. Their ability to adopt different functional states in response to local environmental signals has made them an important focus of current therapeutic research in IBD. Traditionally, macrophages have been classified into pro-inflammatory M1 and anti-inflammatory M2 phenotypes. However, recent findings from single-cell transcriptomic and spatial analyses suggest that intestinal macrophages represent a far more diverse and dynamic population than this simplified classification implies. Multiple macrophage subsets with inflammatory, regulatory, reparative, and fibrosis-associated functions coexist within the intestinal microenvironment and contribute differently to disease progression and tissue healing. These observations highlight the importance of developing more selective and targeted macrophage-based therapeutic approaches. In this review, we discuss the current understanding of macrophage plasticity and its role in the pathogenesis of IBD. Particular attention is given to newer macrophage-targeted therapeutic strategies, including adoptive macrophage transfer, engineered macrophages, receptor-targeted therapies, nanoparticle-based delivery systems, microbiome modulation, microbial metabolite regulation, gene-editing approaches, organoid technologies, and biomaterial-assisted platforms. We also examine the contribution of macrophages to epithelial regeneration, mucosal healing, fibrosis, and intestinal tissue remodeling. In addition, we address several major challenges that currently limit the clinical translation of macrophage-targeted therapies. A better understanding of macrophage biology, together with continued advances in immunology, regenerative medicine, microbiome research, and biomaterials science, may support the development of more precise and personalized therapeutic strategies for patients with IBD.},
}

@article {pmid42297106,
year = {2026},
author = {Khoiwal, K and Kalita, D and Gupta, S and Gaurav, A and Manisha, P and Yerkade, V and Mathuria, YP and Chaturvedi, J},
title = {Diversity of Cervicovaginal Microbiome among HPV-Positive versus HPV-Negative Women of Sub-Himalayan region of India.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101176},
doi = {10.1016/j.ijmmb.2026.101176},
pmid = {42297106},
issn = {1998-3646},
abstract = {PURPOSE: Recent studies from Western countries suggest an association between cervicovaginal microbiome (CVM) and HPV persistence. This study aims to identify CVM diversity within HPV-negative/positive women and to establish an association between HPV infection and CVM in Indian women.

METHODS: This was a pilot, hospital-based, prospective study conducted at a tertiary care center in India over 6 months. Seventy-two participants underwent HPV genotyping, yielding 20 HPV-positive samples. Of these, 16 samples with good-quality DNA, along with 16 matched HPV-negative samples, were identified for CVM analysis.

RESULTS: Sequencing of bacterial 16S ribosomal RNA region and bioinformatic analysis were performed in 32 samples. Baseline characteristics were similar for HPV-positive and HPV-negative women. Out of 16 HPV-positive women, 9 had HPV-16 genotype, one had HPV-16&18, and 6 had other genotypes. Seven patients had cervical cancer on histopathology, 7 had NILM, 1-ASCUS, and 1-ASC-H on cytology. HPV-negative women's CVM had a larger abundance of lactobacillus species than HPV-positive women (43.24% vs 2.44%). Whereas CVM among HPV-positive women was characterized by a greater abundance of anaerobes, such as Prevotella (12.46% vs. 4.59%), Atopobium (6.66% vs. 1.98%), Anaerococcus (5.27% vs. 0.57%), and Porphyromonas (2.98% vs. 0.67%), compared with HPV-negative women.

CONCLUSION: The current study from the Sub-Himalayan region of India characterizes the diversity of CVM in HPV-positive and HPV-negative women. This makes a significant geographical contribution to vaginal microbiome research worldwide.},
}

@article {pmid42297164,
year = {2026},
author = {Ye, X and Balasubramanian, B and Li, S and Mai, X and Liu, Y and Liao, F and Liu, W},
title = {Seaweed polysaccharides as multifunctional biotherapeutics in modulating gut microbiome, metabolic disorders and beyond: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153057},
doi = {10.1016/j.ijbiomac.2026.153057},
pmid = {42297164},
issn = {1879-0003},
abstract = {Seaweed-derived polysaccharides-fucoidan, laminarin, alginates, ulvan, and carrageenan-are often described as promising prebiotics with potential to influence the gut-liver-brain axis. Resistant to upper gastrointestinal digestion, they reach the colon where gut microbiota ferment them into metabolites, chiefly short-chain fatty acids (SCFAs). These metabolites in turn modulate intestinal barrier integrity, immune and metabolic homeostasis, and inter-organ signaling. However, a critical caveat is that each polysaccharide type exhibits substantial structural variability in molecular weight, degree and position of sulfation, monosaccharide composition, and linkage pattern, depending on species, harvest time, and extraction method. This variability fundamentally alters fermentation kinetics and SCFA profiles, yet most studies treat these polysaccharides as uniform entities. This review critically synthesizes current in vitro and in vivo evidence and emphasizes that the therapeutic significance of seaweed polysaccharides lies in their microbiota-mediated, multi-organ actions rather than in isolated biological effects. In addition, we analyzed the main challenges for food and health applications, including variability in polysaccharide sources and extraction methods, limited bioavailability, pollution risk, and the lack of coordinated global regulations. Addressing these gaps is essential for translating promising biological activities into safe, standardized functional components and for developing these polysaccharides into functional ingredients that can modulate the gut-liver-brain axis.},
}

@article {pmid42297324,
year = {2026},
author = {Qian, P and Ren, P and Zhang, M and Dai, K and Gao, C and Qu, C and Kong, C and Huang, Q and Wu, Y and Cai, P},
title = {The dissemination of a broad-host-range ARG-carrying plasmid to putative pathogens across agricultural soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128594},
doi = {10.1016/j.envpol.2026.128594},
pmid = {42297324},
issn = {1873-6424},
abstract = {The spread of antibiotic resistance genes (ARGs) in agricultural soils poses a major global health challenge, yet the magnitude and directionality of ARG dissemination within complex soil microbial communities remain poorly characterized. Here, we systematically quantified and tracked the dissemination of a broad-host-range ARG-carrying plasmid across 52 agricultural soils. Plasmid transfer and transconjugant communities were characterized using quantitative PCR, fluorescence-activated cell sorting, and 16S rRNA gene sequencing. Our results demonstrate that substantial ARG transfer occurred in soil microbial communities, with the abundance of disseminated plasmids approximately 30 times higher than those retained by residual donor cells. Multivariate analyses indicated that the donor survival rate was most strongly associated with variation in ARG dissemination, while soil fertility and heavy metals were negatively associated with dissemination. ARG acquisition occurred preferentially in phylogenetically related lineages, with dispersal limitation and homogeneous selection shaping the assembly of the transconjugant community. Notably, approximately 77% of disseminated ARGs were acquired by putative pathogenic taxa, despite their low relative abundance in the original soils. Partial least squares path modeling further suggested that donor survival may serve as a key mediator through which edaphic and microbial factors influence ARG transfer to putative pathogens. Collectively, our findings indicate that plasmid-borne ARGs are preferentially acquired by putative pathogens, and the extent of this acquisition is strongly associated with donor viability.},
}

@article {pmid42297533,
year = {2026},
author = {Bhardwaz, S and Schunkert, H and Sager, HB},
title = {Exercise as medicine: Improving cardiovascular health through physical activity.},
journal = {Atherosclerosis},
volume = {417},
number = {},
pages = {120721},
doi = {10.1016/j.atherosclerosis.2026.120721},
pmid = {42297533},
issn = {1879-1484},
mesh = {Humans ; *Cardiovascular Diseases/prevention & control/physiopathology/blood ; *Exercise/physiology ; Animals ; *Cardiovascular System/physiopathology/metabolism ; Heart Disease Risk Factors ; Oxidative Stress ; *Exercise Therapy ; *Risk Reduction Behavior ; Vascular Health ; *Healthy Lifestyle ; },
abstract = {Cardiovascular diseases remain the leading cause of global mortality, and growing evidence shows that regular exercise is one of the most effective non-pharmacological strategies to prevent and modify their progression. Exercise exerts its benefits on the cardiovascular system in multiple ways. It improves lipid metabolism by lowering LDL-cholesterol, reducing triglycerides, and increasing HDL-cholesterol, which provides a protective function by slowing atherosclerotic plaque development. Exercise also reduces chronic inflammation by lowering circulating inflammatory markers and shifting immune cells toward anti-inflammatory profiles. In addition, regular physical activity enhances autonomic balance, increases heart rate variability, and supports healthier blood pressure regulation. Mitochondrial function and antioxidant capacity improve with exercise, helping to reduce oxidative stress and support overall cardiac health. Exercise further influences vascular and metabolic health through epigenetic mechanisms, myokine release, and favorable changes in the gut microbiome. These molecular and systemic adaptations translate into meaningful clinical benefits, including improved recovery after myocardial infarction, better heart failure management, and a reduced risk of ischemic and hemorrhagic stroke. Overall, regular physical activity is a powerful and accessible tool for reducing cardiovascular disease risk and promoting long-term health.},
}

Humans
*Cardiovascular Diseases/prevention & control/physiopathology/blood
*Exercise/physiology
Animals
*Cardiovascular System/physiopathology/metabolism
Heart Disease Risk Factors
Oxidative Stress
*Exercise Therapy
*Risk Reduction Behavior
Vascular Health
*Healthy Lifestyle

@article {pmid42297781,
year = {2026},
author = {Pan, L and Tan, H and Yue, T and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Shi, Y and Chang, S and Guo, C and Zheng, X and Weng, J},
title = {Multi-omics reveals microbiota, metabolite, and immunological heterogeneity of age-related endotypes in type 1 diabetes.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {42297781},
issn = {2059-3635},
support = {2025T028AH//China Postdoctoral Science Foundation/ ; 8247087//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 1/immunology/microbiology/genetics ; Multiomics ; Child ; *Metabolome/immunology/genetics ; Female ; Male ; *Microbiota/immunology/genetics ; Lipidomics ; Child, Preschool ; Gene Expression Profiling ; },
abstract = {Type 1 diabetes (T1D) exhibits age-related heterogeneity in clinical progression and immune pathology, yet the underlying molecular mechanisms remain poorly understood. Here, we integrate microbiome, metabolome, lipidome, and transcriptome profiling from 108 newly diagnosed pediatric patients with T1D, along with 56 healthy controls, to investigate age-related endotypes. Patients were stratified into early-onset (E-T1D, <7 years), intermediate-onset (I-T1D, 7-12 years), and late-onset (L-T1D, ≥13 years) groups. Multi-omics analyses revealed distinct molecular signatures among T1D subgroups. The most enriched microbial signatures were the genus Acetatifactor in E-T1D, the phylum Firmicutes A in I-T1D, and the family Bacteroidaceae in L-T1D (Linear Discriminant Analysis scores = 3.49, 5.56, and 5.78, respectively). For metabolites, pipecolic acid increased most in E-T1D, testosterone in I-T1D, while N-acetylhomocitrulline was most enriched in L-T1D. Lipidomic profiling revealed subgroup-specific alterations, with increased levels of LPA(16:1) in E-T1D, TG(16:0/18:2/18:3) in I-T1D, and TG(18:0/18:1/18:1) in L-T1D. The proportion of peripheral B cells to total lymphocytes was the highest in E-T1D (median = 11.64%) and associated with upregulated immune-related pathways, lowest in L-T1D (median = 5.99%) and linked to metabolic processes, while I-T1D (median = 8.47%) exhibited intermediate features of both groups. Integration of multi-omics interaction networks and experimental validation revealed that the microbial species Dialister invisus may promote peripheral B cell proliferation via docosapentaenoic acid, potentially contributing to early-onset T1D. Together, these findings provide a molecular framework for understanding age-related T1D endotypes and suggest potential targets for precision intervention. Workflow and key findings of the study.A multi-omics integration strategy was applied to newly diagnosed pediatric type 1 diabetes (T1D) patients stratified by age at diagnosis: early-onset (E-T1D), intermediate-onset (I-T1D), and late-onset (L-T1D), to delineate age-related T1D endotypes. Comprehensive profiling included gut microbiome, serum metabolome, lipidome, and peripheral immune transcriptome analyses. An integrated multi-omics interaction network revealed 665 direct microbiota-gene connections and 2,608 microbiota-metabolite/lipid-gene triadic interactions, highlighting a D. invisus-docosapentaenoic acid (DPA)-STMN1 axis mediating B-cell activation in early-onset T1D.},
}

Humans
*Diabetes Mellitus, Type 1/immunology/microbiology/genetics
Multiomics
Child
*Metabolome/immunology/genetics
Female
Male
*Microbiota/immunology/genetics
Lipidomics
Child, Preschool
Gene Expression Profiling

@article {pmid42297802,
year = {2026},
author = {Ghosh, S and Sundararajan, P and Gelena Kelbessa, B and Ghadamgahi, F and Whisson, SC and Dubey, M and Chawade, A and Vetukuri, RR},
title = {Phyllosphere microbiome responses to spray-induced gene silencing targeting Phytophthora infestans in potato.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42297802},
issn = {2055-5008},
support = {0074727//Novo Nordisk Fonden/ ; 2019-01316//Svenska Forskningsrådet Formas/ ; CTS 20:464//Carl Tryggers Stiftelse/ ; },
mesh = {*Solanum tuberosum/microbiology ; *Phytophthora infestans/genetics/drug effects ; *Gene Silencing ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention & control ; RNA, Double-Stranded/genetics ; RNA Interference ; Plant Leaves/microbiology ; Bacteria/classification/genetics ; },
abstract = {Recent years have seen a growing interest in the use of RNA interference to control filamentous pathogens, creating a new niche in plant disease management. Strategies like spray-induced gene silencing (SIGS) offer effective and environmentally friendly alternatives to chemical disease control but remain underexplored. Given the profound influence of microbiomes on plant health and crop productivity, knowledge of how spraying double-stranded RNAs (dsRNAs) can impact plant microbial communities is needed to facilitate the transition of SIGS from the laboratory to practical large-scale use. We have therefore investigated changes in the bacterial and fungal communities of the phyllosphere in the economically important potato plant after spraying with dsRNA targeting the phytopathogen Phytophthora infestans. Spraying with dsRNA alone had little effect on the relative abundance of the dominant species found in the native potato phyllosphere. However, there were small time-dependent changes in the composition of the bacterial communities, and much larger changes in bacterial community metrics were observed after P. infestans inoculation. We also observed maintenance of potentially beneficial bacterial genera in dsRNA-treated plants in addition to composition changes linked to the plant's natural defense response upon P. infestans infection. Together, these observations support the view that dsRNA spraying enables safe and targeted pathogen control in potato.},
}

*Solanum tuberosum/microbiology
*Phytophthora infestans/genetics/drug effects
*Gene Silencing
*Microbiota/drug effects
*Plant Diseases/microbiology/prevention & control
RNA, Double-Stranded/genetics
RNA Interference
Plant Leaves/microbiology
Bacteria/classification/genetics

@article {pmid42297837,
year = {2026},
author = {Potratz, P and Häder, A and Kursawe, L and Kikhney, J and Gaßler, N and Lauf, T and Radosa, L and Sandhaus, T and von Samson, P and Chen, X and Wang, L and Brakhage, AA and Moter, A and Panagiotou, G and Doenst, T and Deinhardt-Emmer, S and Löffler, B},
title = {The human lung microbiome progressively diminishes in the distal alveolar regions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01047-y},
pmid = {42297837},
issn = {2055-5008},
support = {13N15745//Bundesministerium für Bildung und Forschung/ ; SFB 1278/2 "PolyTarget" B02//DFG/ ; SFB 1278/2 "PolyTarget" D02//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Extensive investigations with sequencing methods demonstrate a large and diverse microbiome even in profound areas of the lung. However, there is still substantial lack of cultivation-based evidence and of the viability of the resident microorganisms. We collected human tissue specimens obtained from various regions during lung transplantations and from operations in distal alveolar areas. We characterized the samples by histology and applied sequencing, culture and imaging methods. Sequencing data detected the following trends in the composition of the microbiome: (i) From proximal to distal samples we observed a bacterial shift from Staphylococci, Streptococci and Corynebacteria towards preferentially anaerobically growing bacteria; (ii) we found large variations between individual patients regarding the detected bacterial genera. Culture and imaging methods revealed almost no viable microorganism in the distal alveolar regions in these patients. Bacterial signals detected by sequencing in the lung are likely due to very low numbers of bacteria and/or their remnants.},
}

@article {pmid42297997,
year = {2026},
author = {Dixon, M and Afkairin, A and Manter, D and Godfrey, J and Hamm, A and Munoz, N and Bloodsworth, K and Balasubramanian, VK and Buchanan, C and Ippolito, JA and Burnet, M and Vivanco, J},
title = {The root exudates of wild tomato compared to a modern variety maintain elevated soluble soil phosphorous by interacting with rhizosphere microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57400-w},
pmid = {42297997},
issn = {2045-2322},
abstract = {Wild plants are periodically exposed to nutrient flushes, whereas modern cultivars are acclimated to regular nutrition from fertilizers. Phosphorus (P) fertilizers, however, convert into unavailable forms in soil. Here, we assessed plant growth, rhizosphere microbiome, and root exudation of a wild and modern tomato to determine how a wild crop relative responds to a flush of P fertilization. We found that the modern tomato relatively lacked P-mineralizers and grew quickly, depleting soil P. Conversely, wild tomato continued growth and promoted an array of beneficial soil bacteria, resulting in higher bioavailable soil P across development. This microbial strategy was driven by its root exudates, which were subsequently found to be enriched in trehalose and glycerol compounds. In vitro testing showed that these compounds promoted microbial P solubilization. Finally, we grew modern tomato in P-fertilized soils following a previous planting of either wild or modern tomato. Modern tomato grown in wild tomato-conditioned soils increased biomass compared to those grown in modern tomato-conditioned soils. The change may be associated with residual soil P as the wild-induced microbial community changes diminished. The root exudate driven strategy of wild tomato helps maintain soluble soil P and may be utilized in agriculture to prevent fertilizer loss.},
}

@article {pmid42298353,
year = {2026},
author = {Strokach, A and Zakharevich, N and Aginova, V and Grigoryevskaya, Z and Petukhova, I and Bagirova, N and Romanov, M and Dyachkova, M and Morozov, M and Veselovsky, V and Kanaeva, V and Kalinin, D and Larin, A and Shitikov, E and Klimina, K},
title = {Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681788},
pmid = {42298353},
issn = {1949-0984},
mesh = {Humans ; *Immunotherapy ; *Melanoma/therapy/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome ; Female ; Cohort Studies ; *Bacteria/classification/genetics/isolation & purification ; Male ; Russia ; Metagenomics ; Metagenome ; *Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Aged ; Treatment Outcome ; Adult ; },
abstract = {Melanoma is an aggressive malignancy with a significant risk of mortality. In recent years, treatment strategies have undergone a paradigm shift with the advent of immunotherapy, particularly immune checkpoint inhibitors (ICIs). Despite notable clinical success, a substantial proportion of patients fail to respond or eventually develop resistance to ICIs. Emerging evidence highlights the gut microbiota as a critical modulator of host immune responses and is one of the potential determinants of immunotherapy efficacy. We performed a cross-cohort analysis of gut microbiome profiles from melanoma patients treated with ICIs. The study integrated the first Russian cohort (62 patients) with six previously published international datasets, comprising a total of 490 patients across seven cohorts. In all cases, metagenomic sequencing was performed using various Illumina platforms, and raw sequencing data were processed using a unified bioinformatic pipeline. Analysis revealed 527 metagenome-assembled genomes (MAGs) significantly associated with treatment outcome: 239 with response and 288 with non-response. Notably, the species Faecalibacterium sp900539945, Phocaeicola vulgatus, Bifidobacterium adolescentis, Faecalibacterium taiwanense, and Gemmiger qucibialis were consistently associated with response, while Enterobacter ludwigii was linked to non-response. Analysis of the Russian cohort revealed both conserved and population-specific microbial signatures, highlighting the coexistence of globally shared and region-dependent microbiome features. Our results also show that species-level annotations may obscure opposing response associations within the same taxa, highlighting the need for MAGs or strain profiling. Together, this study demonstrates that cross-cohort analysis enables the identification of robust and reproducible bacterial markers of immunotherapy response, providing a foundation for microbiome-based prediction and modulation strategies in melanoma.},
}

Humans
*Immunotherapy
*Melanoma/therapy/microbiology/immunology/drug therapy
*Gastrointestinal Microbiome
Female
Cohort Studies
*Bacteria/classification/genetics/isolation & purification
Male
Russia
Metagenomics
Metagenome
*Immune Checkpoint Inhibitors/therapeutic use
Middle Aged
Aged
Treatment Outcome
Adult

@article {pmid42298377,
year = {2026},
author = {Elsaghir, A and Wadan, AS and Witte, T},
title = {The potential role of the gut microbiota in the development of autoantibodies associated with Spondyloarthritis: a narrative review.},
journal = {BMC immunology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12865-026-00855-3},
pmid = {42298377},
issn = {1471-2172},
abstract = {Spondyloarthritis (SpA) is a set of immune-inflammatory conditions characterized by musculoskeletal and extra-articular manifestations. Increasing evidence indicates that alterations in the gut microbiota (dysbiosis) may influence both mucosal and systemic immune responses, potentially contributing to the loss of tolerance and the development of autoantibodies in SpA.This narrative review examines the current evidence linking gut dysbiosis to autoantibody development in SpA, with particular focus on ankylosing spondylitis (AS) and psoriatic arthritis (PsA).We summarized key mechanistic pathways, including Th17 axis activation, molecular mimicry, increased intestinal permeability ("leaky gut"), and altered microbial metabolite signaling. We discussed the potential relevance of these mechanisms to SpA-associated autoantibodies such as anti-CD74, anti-HSP65, and anti-Kaiso. Where direct evidence in SpA is limited, findings from other autoimmune diseases are considered as mechanistic analogies rather than definitive parallels.We further review microbiome-targeted therapeutic strategies, including probiotics, prebiotics, and bacterially based therapies, and highlight differences between preclinical findings and available clinical data. Although biologically plausible mechanisms, direct causal evidence linking gut dysbiosis to autoantibody production in SpA remains limited, and clear methodological heterogeneity persists across microbiome studies.Overall, while modulation of the gut-immune axis represents a promising research direction in SpA, further mechanistic and longitudinal human studies are required before microbiota-targeted interventions can be considered applicable for autoantibody modulation.},
}

@article {pmid42298382,
year = {2026},
author = {Raj, K and Sharma, P and Riyaz, M and Shouche, YS and Multani, K and Sharma, M and Dhaliwal, M},
title = {Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05248-5},
pmid = {42298382},
issn = {1471-2180},
support = {S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; },
abstract = {BACKGROUND: The human gut microbiome consists of a complex and diverse community of commensal microorganisms and has been under extensive research consideration in the past few decades. Although several recent studies have targeted the determination of bacterial composition of the ecosystem, the knowledge about the mycobiome, virome, and functional attributes of the same remains scarce. The aim of the present study was to investigate the functional and resistome profile of the gut microbiome in the Pangwala tribal community of India using a combined Whole Metagenome Shotgun (WMS) sequencing and bioinformatics approach.

RESULTS: The findings revealed a remarkable diversity of microorganisms inhabiting the gut of both groups, with similar level of diversity among the dominant genera like Prevotella, Bifidobacterium and Succinivibrionaceae. The mycobiome was dominated by the subkingdom Dikarya (74%), while Fungi incertae sedis accounted for 23% of the total fungal species in both groups. The virome analysis showed the dominance of the Caudoviricetes class, with bacteriophages being the most dominant. Moreover, functional analysis identified the prominent metabolic pathways and the key gene families involved in the pathways, highlighting Prevotella copri as the major contributor. Additionally, the study identified the resistome and showed that there were more than 100 potential antibiotic-resistant genes (ARGs) and high levels of resistance to vancomycin in both groups.

CONCLUSION: This study presents a comprehensive overview of the gut microbiome in the Pangi population, detailing both in its taxonomic structure and functional traits. The results show that, despite the high degree of diversity in the gut microbiome, there seems to be evident functional redundancy, which underlines a core stable microbiome. The resistome profile offers complete exploratory picture of the resistome and establishes a valuable baseline for future studies. Furthermore, we anticipate that these findings will add valuable insights to understand the Antimicrobial resistance (AMR) stewardship in the light of one health aspect.},
}

@article {pmid42298567,
year = {2026},
author = {Zhu, L and He, J and Xu, X and Lu, S and Yu, Y and Wong, WH and Bischoff, FZ and Zhang, X},
title = {Uterine microbiome signatures associated with endometriosis.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02659-8},
pmid = {42298567},
issn = {1741-7007},
abstract = {BACKGROUND: Endometriosis is a chronic inflammatory disorder affecting ~ 10% of reproductive-age women, often causing pelvic pain and infertility. Despite its prevalence, diagnosis remains delayed due to non-specific symptoms and lack of reliable non-invasive biomarkers. Emerging evidence implicates the microbiome in disease pathogenesis.

RESULTS: We analyzed uterine microbiomes from 266 tissue samples collected during either the proliferative or secretory phase, using 16S rRNA gene sequencing. Genus-level analysis revealed variable Lactobacillus abundance among all individuals. Prevotella showed borderline enrichment in proliferative-phase patients. Sub-genus analyses identified a small number of differentially abundant taxa, though none remained significant after FDR correction. To capture subtle microbial shifts, we developed a feature set combining weakly differential taxa, algorithmically selected taxa via machine learning, and a functional dysbiosis score. A supervised classifier trained on proliferative-phase data achieved moderate predictive performance (AUC = 0.70), while secretory-phase models performed more poorly (AUC = 0.58).

CONCLUSIONS: The uterine microbiome shows phase-dependent differences in its potential to inform endometriosis status. Although no robust individual microbial biomarkers were identified, machine learning models incorporating subtle community features from the proliferative phase yielded modest diagnostic potential. These results highlight the importance of menstrual cycle-aware sampling and support further development of microbiome-informed diagnostic tools for endometriosis.},
}

@article {pmid42298579,
year = {2026},
author = {Boroomand, F and Karimi, MA and Karimzadeh-Soureshjani, E and Kiani-Shamsabadi, D and Farhang, F and Mardani, H and Jafari, A},
title = {The nutrigenomic-epigenetic axis in cancer: from dietary bioactives to precision oncology.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01147-8},
pmid = {42298579},
issn = {1743-7075},
abstract = {Cancer development and progression are increasingly understood to arise from dynamic interactions between genetic alterations and environmentally driven epigenetic regulation, with dietary exposures representing one of the most biologically influential and modifiable factors. Given the expanding evidence linking nutrition to epigenomic remodeling, a comprehensive synthesis of how specific dietary components influence cancer-relevant epigenetic mechanisms is needed to clarify their preventive and therapeutic relevance. This review brings together mechanistic, epidemiologic, and translational findings to delineate the effects of bioactive dietary constituents, including polyphenols, isoflavones, carotenoids, folate, zinc, vitamin D, sulfur-containing phytochemicals, and microbiome-derived short-chain fatty acids, on DNA methylation, histone modifications, chromatin accessibility, and non-coding RNA regulation. Across these domains, consistent patterns emerge: compounds such as epigallocatechin-3-gallate, resveratrol, quercetin, genistein, and sulforaphane have been shown in preclinical studies to inhibit DNA methyltransferases, modulate histone acetylation and methylation, reprogram microRNA networks, and promote tumor-suppressive transcriptional states; dietary patterns rich in cruciferous vegetables, green tea, grapes, whole grains, marine-derived polyunsaturated fatty acids, and fermentable fibers correlate with reduced cancer incidence; and pro-inflammatory diets high in red meat, processed foods, and added sugars are associated with oxidative stress, inflammation-associated DNA damage, and epigenetic dysregulation. Emerging evidence also highlights the roles of gut microbial metabolites such as butyrate, caloric restriction, and ketogenic regimens in shaping tumor immunometabolism through epigenetically active intermediates, while germline polymorphisms and tumor-intrinsic epigenetic heterogeneity contribute to inter-individual variability in dietary responsiveness. These insights position nutrition as a mechanistically coherent regulator of the cancer epigenome with implications for prevention, prognosis, and integrative oncology, underscoring the need for biomarker-guided dietary interventions and rigorously designed clinical studies to determine the therapeutic potential of personalized nutritional epigenetics.},
}

@article {pmid42298599,
year = {2026},
author = {Jallow, BJJ and Luciano, A and Liu, M and Ma, Y and Huo, Y and Tan, S and Huang, J and Cai, J and Meng, F},
title = {Comparative study on the diversity and abundance of bacterial composition in four non-biting synanthropic flies from The Gambia and China.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05620-7},
pmid = {42298599},
issn = {1746-6148},
support = {32370554 & 32460248//National Natural Science Foundation of China/ ; 2022JJ30693//Science Foundation of Hunan Province/ ; XYD2024C05//Research and Innovation Team Project, Xinjiang Medical University/ ; },
abstract = {BACKGROUND: Non-biting synanthropic flies from the order Diptera have long been implicated as mechanical vectors to several human and animal pathogens, yet their microbiome variations across different regions remain poorly understood. Here, we compared the abundance of gut microbial composition in four species (Chrysomya megacephala, Lucilia cuprina, Musca domestica, and Physiphora clausa of non-biting synanthropic flies from two countries (The Gambia and China), providing insights into the potential pathogenic bacterial taxa they harbor. This study was conducted in Kanifing Municipal Council, The Gambia, and Changsha city, China, with sampling occurring between August and November 2023. Illumina NovaSeq6000 sequencing was used to amplify the V3-V4 region of the 16S rDNA from the midgut of these flies, which were pooled (n = 20 per sample) into 21 samples comprising Chrysomya megacephala, Lucilia cuprina, Musca domestica (from both cities), and Physiphora clausa (from KMC). Alpha and beta diversity indices were used to compare bacterial composition in the midguts of these flies. All bioinformatics and statistical analyses were performed using the BMKCloud online platform (http://www.biocloud.net).

RESULTS: Taxonomic classification was annotated into 2 kingdoms, 44 phyla, and 2,379 species. Proteobacteria (41.14%) and Firmicutes (39.51%) dominated across all the samples. Significant geographic differences were observed. Shannon Alpha diversity analyses differed significantly between countries (P = 0.023), and Bray-Curtis-based PERMANOVA confirmed distinct bacterial compositions (R²=0.201, P = 0.001). Gambian flies harbored more Wohlfahrtiimonas chitiniclastica (13.79%), while Changsha samples contained higher Pseudomonas (3.99%). To the best of our knowledge, this is the first description of the gut microbiome of P. clausa, which was dominated by Corynebacterium (15.82%). These geographic and species-specific patterns highlight flies as reservoirs for regionally relevant pathogens.

CONCLUSION: This study highlights the geographic variability in gut microbiota of non-biting synanthropic flies as potential carriers of regionally relevant bacterial taxa and motivates further investigation into fly-borne pathogen transmission in both regions. This study also provides, to the best of our knowledge, the first description of the gut microbiome of P. clausa.},
}

@article {pmid42298631,
year = {2026},
author = {Yan, Q and Li, M and Wang, G and Zhang, A and Li, Y and Guo, R and Zhang, Y and Yang, W and Zhang, Y and Liu, X and Li, X and Zheng, N and Wang, L and Fan, S and Ma, R and Lu, T and Zhou, S and Guan, T and Xing, G and Li, S and Wang, L and Li, Y},
title = {Cross-kingdom microbial associations characterize responsiveness to fecal microbiota transplantation in patients with irritable bowel syndrome.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08269-w},
pmid = {42298631},
issn = {1479-5876},
abstract = {BACKGROUND: Precise outcome prediction for fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) remains a clinical challenge. The roles of the gut virome and its interplay with bacteria in FMT efficacy are particularly underexplored. This secondary analysis aimed to conduct an exploratory, hypothesis-generating investigation into these cross-kingdom dynamics.

METHODS: We conducted a secondary, integrative analysis of a published cohort, performing longitudinal, cross-kingdom metagenomic profiling on 83 samples from 22 IBS patients and healthy donors. We integrative approach combined microbial diversity, species-specific biomarker identification, bacterial-viral associated networks, and exploratory random forest modeling to identify microbial features associated with FMT outcomes.

RESULTS: IBS patients showed higher bacterial and viral alpha diversity than donors. Cross-kingdom profiling identified 223 bacterial and 724 viral biomarkers. Donor-enriched biomarkers were predominantly health-associated Bacteroidetes (e.g., B. ovatus, B. faecis), whereas pre-FMT-enriched biomarkers were largely Firmicutes (e.g., B. obeum) with potential pathobiont roles. The Effect and No effect groups displayed different microbial trajectories. Although both groups shifted toward a donor-like composition initially, only responders maintained a stable donor-like ecology throughout the 12-month follow-up, supported by more resilient bacterial-viral association networks. Exploratory random forest modeling highlighted microbial features, such as R. pickettii, with high relative importance for outcome discrimination. However, permutation testing (p = 0.548-0.616) confirmed that model performance on this small cohort did not exceed chance level, underscoring the risk of overfitting and the exploratory nature of these computational findings.

CONCLUSIONS: This integrative re-analysis provides preliminary evidence that cross-kingdom gut microbiome profiles are strongly associated with FMT outcomes in IBS. Successful outcomes appear linked to sustained donor-like remodeling and stable bacterial-viral networks. Our findings are primarily hypothesis-generating and offer a framework of candidate biomarkers for future validation in larger cohorts. This work underscores the necessity of external validation to develop robust, microbiome-based tools for personalized FMT therapy.},
}

@article {pmid42298669,
year = {2026},
author = {Chen, Y and Hu, S and Ji, Y and Gu, F and Zhang, C and Gao, K and Wen, X and Wang, L and Dong, X and Tak, J and Xiao, H and Xia, Y},
title = {Unraveling the effector mechanism of citrulline on sow lactation and offspring growth: an integrative multi-omics analysis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42298669},
issn = {1674-9782},
support = {CARS-35//China Agriculture Research System/ ; 32472928//the National Natural Science Foundation of China/ ; R2022PY-QY007//Special fund for scientific innovation strategy-construction of high-level Academy of Agriculture Science/ ; 2024A1515010743//the Natural Science Foundation of Guangdong Province/ ; 2026ZYTS0202//Modern Seed Industry Innovation Capability Enhancement Project of Guangdong Academy of Agricultural Sciences/ ; },
abstract = {BACKGROUND: Citrulline (Cit), an effective precursor of arginine (Arg), escapes hepatic catabolism to be almost completely absorbed into the systemic circulation, thereby being efficiently converted to Arg in the kidneys to enhance its systemic bioavailability. This study investigated the effects of dietary Cit supplementation on lactation performance in sows, as well as the underlying mechanisms related to intestinal health in their suckling piglets, using multi-omics analyses.

RESULTS: Dietary Arg and Cit supplementation significantly increased average daily feed intake of lactating sows. Milk fat content and plasma nitric oxide (NO) concentration increased significantly in the Arg group and the 40%Cit group (P < 0.05), while milk threonine content increased slightly (P = 0.084). Consequently, the average daily gain of suckling piglets over the 21-day lactation period was also significantly improved. Furthermore, maternal 40%Cit supplementation improved the intestinal health of offspring by enhancing jejunal morphology and upregulating the expression of the tight junction protein occludin (P < 0.05), indicating a strengthened intestinal barrier. Mechanistically, this was achieved by activating the mTOR/S6 pathway in the piglets' jejunum. Maternal 40%Cit supplementation upregulated the expression of proteins related to mitochondrial fusion and fission (MFN2 and MFF, P < 0.05), and the protein expression of OPA1 showed an increasing trend (P = 0.097), indicating the structural and functional status of mitochondria was improved. Maternal 40%Cit supplementation also modulated the gut microbiota of piglets, increasing the abundance of beneficial bacteria (Lachnoclostridium). Metabolomic analysis of sow milk identified 58 differential metabolites. Among these metabolites, palmitic acid levels were significantly increased and positively correlated with the abundance of Lachnoclostridium in the intestine (P < 0.05).

CONCLUSIONS: Dietary Cit supplementation enhanced sow lactation performance and improved intestinal barrier function in their offspring via activation of the jejunal mTOR/S6 pathway and improved mitochondrial structure and function in the piglet jejunum. These benefits were further supported by modulation of the gut microbiota and alterations in the milk fat and metabolome, ultimately promoting piglet growth.},
}

@article {pmid42298685,
year = {2026},
author = {Yanagawa, Y and Yoshida, N and Makiuchi, T and Kawashima, A and Uemura, H and Aoki, T and Mizushima, D and Gatanaga, H and Watanabe, K},
title = {Multi-omics profiling and bile-acid exposure assays implicate a gut microbiome-parasite axis linked to persistent Entamoeba histolytica carriage.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00845-1},
pmid = {42298685},
issn = {1757-4749},
support = {IN-JP-380-5724//Gilead Sciences/ ; JP26K10011//Japan Society for the Promotion of Science/ ; JP23fk0108680h0001//Japan Agency for Medical Research and Development/ ; },
abstract = {Asymptomatic Entamoeba histolytica (Eh) carriage is a major transmission reservoir, yet how the gut ecosystem-particularly microbiota-derived metabolites such as secondary bile acids-supports persistent colonization remains unclear. We investigated whether gut microbiome-metabolite features are associated with Eh carriage and could influence parasite phenotypes METHODS: We integrated shotgun metagenomics from a prospectively screened outpatient cohort (n=36) with functional in vitro assays. An ordinal stepwise model across detection states (Eh-, Eh_qPCR, Eh_Cyst) was used to identify candidate microbial features, followed by bile-acid exposure assays and transcriptomic profiling to evaluate impacts on parasite fitness and metronidazole susceptibility in vitro RESULTS: Microbiome profiling suggested taxon-specific shifts rather than wholesale dysbiosis. Community-level beta diversity showed no significant separation, whereas genus richness was higher in Eh_Cyst (unadjusted p=0.046). Multivariable modeling yielded concordant directional but non-significant trends (all q>0.9), highlighting Firmicutes genera including Coprococcus, Ruminococcus, and Catenibacterium as candidate taxa. We then evaluated deoxycholic acid (DCA), a microbiota-modified secondary bile acid. In vitro, 100 μM DCA extended Eh survival under nutrient-limited conditions and reduced metronidazole susceptibility after pretreatment. Transcriptomic profiling showed that DCA induced a distinct response, including an 8.34-fold induction of the ABC transporter P-glycoprotein-2 and upregulation of lipid remodeling and stress-response genes, supporting a bile acid-driven adaptive program consistent with intestinal persistence CONCLUSIONS: Our findings suggest that secondary bile acids, exemplified by DCA, can reprogram Eh gene expression and attenuate metronidazole susceptibility in vitro. In the context of cyst-associated microbiome signatures, this supports the plausibility of a microbiome-bile acid-parasite axis that may promote persistence in asymptomatic carriers and could influence treatment efficacy.},
}

@article {pmid42298736,
year = {2026},
author = {Amat, S and Holman, DB and Luecke, SM and Gzyl, KE and Anas, M and Stokka, G},
title = {The bovine ocular microbiome: a multi-approach study of composition and antimicrobial activity.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00587-0},
pmid = {42298736},
issn = {2524-4671},
support = {20-21-2022; 22-14-0231; 24-30-0265//North Dakota State Board of Agricultural Research and Education/ ; },
abstract = {BACKGROUND: Despite widespread use of antimicrobials and vaccines, the incidence of infectious bovine keratoconjunctivitis (IBK), or pinkeye, continues to increase in North American beef cow-calf operations. Recent research suggests that there is potential for the commensal ocular microbiome to help mitigate IBK. Therefore, this study characterized the ocular microbiome of cattle with and without IBK using culture-based methods and shotgun metagenomic sequencing and assessed the ability of commensal bacteria to inhibit Moraxella spp. in vitro. Ocular swabs (n = 143) were collected from IBK-affected (n = 102) and healthy cattle (n = 41) before antimicrobial treatment from North Dakota herds. Bacteria were cultured aerobically and anaerobically on five different media and the isolates were identified. A subset of swabs (37 IBK-affected; 12 healthy) underwent shotgun metagenomic sequencing. The genomes of 31 isolates, including Moraxella bovoculi, Moraxella bovis, and commensal bacteria, were also sequenced. Fifty-two commensal isolates were screened for inhibition of Moraxella spp. using an agar slab method, with five isolates further tested by qPCR for inhibition in the presence of the culturable ocular microbiome.

RESULTS: The 351 bacterial isolates taxonomically identified represented 61 genera from three phyla. The majority of isolates belonged to Bacillus (25.9%), Streptococcus (11.1%), Staphylococcus (10.1%), and Moraxella (9.4%) genera. Shotgun metagenomic analysis revealed significant differences in ocular microbial species composition between IBK-affected and healthy cattle (R² = 0.05; P = 0.015) based on Bray-Curtis dissimilarity. Dominant bacterial species included Cutibacterium acnes, Mannheimia pernigra, Mesomycoplasma bovoculi, Moraxella bovis, and Moraxella bovoculi. Eight bacterial species, including Bifidobacterium globosum and Bacillus licheniformis, were more abundant in healthy cattle, while Arthrobacter luteus was enriched in IBK cases. Thirty-seven high-quality metagenome-assembled genomes were also recovered, with 27% classified as Mesomycoplasma bovoculi. Moraxella spp. genomes exhibited strain-specific antimicrobial resistance and virulence gene diversity. Seventeen commensal isolates inhibited Moraxella, with Weizmannia coagulans, Lentilactobacillus buchneri, and Paenibacillus polymyxa showing strong activity. Selected isolates maintained inhibitory effects in co-culture with the ocular microbiome.

CONCLUSION: The ocular surface of beef cattle is inhabited by a diverse microbiome that includes several bacterial strains that have the potential to be used as therapeutics to inhibit IBK pathogens.},
}

@article {pmid42298760,
year = {2026},
author = {Worthington, C and Raitses-Gurevich, M and Innamorati, G and Hart, PA and Wilkie, TM and Tau, N and Brin, D and Yablecovitch, D and Laish, I and Keith, D and Giles, K and Permuth, JB and Simeone, DM and Zogopoulos, G and Brand, RE and Graff, JJ and Earl, J and , },
title = {Pancreatic Cancer Early Detection Biomarkers for High-Risk Individuals: Insights From the PRECEDE Consortium.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70592},
pmid = {42298760},
issn = {1097-0215},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers due to its asymptomatic progression, late-stage diagnosis, and treatment resistance. Efforts in early detection have centered on identifying imaging features and liquid biopsy biomarkers capable of detecting PDAC and its high-grade precursors before clinical symptoms arise in patients at elevated risk of PDAC development. Classical imaging-based surveillance strategies, aligned with current guidelines, form the foundation of screening high-risk individuals, while organ-specific fluid analyses-such as cyst fluid and pancreatic juice-offer promising complementary tools with enhanced specificity. Recent advances in radiomics, liquid biopsy, microbiome, and multi-omics profiling are expanding the frontier of early detection. Despite advances, significant challenges persist. Precursor lesions are difficult to non-invasively diagnose; are not radiologically or endosonographically visible, or cannot be definitively graded prior to resection. Though biomarkers show promise for early detection, they present unique challenges: early-stage neoplasias release low levels of many biomarkers and thresholds for these biomarkers that define malignant transformation-and thus guide surgical intervention-remain poorly established. Multi-institutional initiatives like the Pancreatic Cancer Early Detection consortium (PRECEDE) are critical to bridging discovery and clinical translation. Our international cohort study of high-risk individuals was designed to discover and validate diagnostic biomarkers according to the PROBE study design. Continued collaboration, technological integration, and patient-centered approaches are essential to transform early detection research into tangible survival benefits for those at risk of PDAC.},
}

@article {pmid42298774,
year = {2026},
author = {Chen, X and Ding, S and Tang, H and Yang, Q and Yuan, L and Zhang, A and Li, Y and Wang, Q and Yan, X and Wang, Z and Wang, M and Zheng, Z},
title = {Monochromatic light reprograms transcription, metabolism, and rhizosphere microbial communities in Salvia miltiorrhiza.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2686334},
pmid = {42298774},
issn = {1559-2324},
mesh = {*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics ; *Rhizosphere ; *Light ; *Microbiota/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; *Transcription, Genetic/radiation effects ; },
abstract = {Salvia miltiorrhiza is a valuable medicinal plant with diverse pharmacological applications and high market demand. Light quality is a critical environmental factor regulating plant growth, secondary metabolism, and interactions with rhizosphere microorganisms. However, the effects of short-term, pure monochromatic light exposure on S. miltiorrhiza remain largely unexplored. In this study, we employed integrated transcriptomic, metabolomic, and rhizosphere metagenomic analyzes to investigate the responses of S. miltiorrhiza under different monochromatic light conditions: ultraviolet (UV), blue (B), red (R), and far-red (FR), with white light (WL) as the control. GO enrichment analysis indicated that all monochromatic light treatments activated defense responses, while specific pathways related to light stimulus, wounding, and reactive oxygen species were uniquely enriched under B, R, and FR light. Metabolomic analysis showed a general decrease in metabolite abundance under monochromatic light compared to WL, with the R treatment inducing the highest number of significantly upregulated metabolites. Integrated KEGG pathway analysis of differential transcripts and metabolites highlighted the enrichment of secondary metabolic pathways, including diterpenoid, monoterpenoid, and phenylpropanoid biosynthesis. Notably, quantitative HPLC analysis confirmed that UV, R, and FR light significantly promoted the accumulation of dihydrotanshinone I and tanshinone IIA, while decreasing salvianolic acid A content. Metagenomic analysis revealed that monochromatic light, especially B light, reduced rhizosphere microbial alpha diversity and altered the abundance of specific bacterial families and species. Functional gene annotation also showed treatment-specific shifts in microbial metabolic potential and virulence factors. In conclusion, short-term monochromatic light culture, particularly R and FR, effectively modulates the transcriptome and metabolome of S. miltiorrhiza, enhancing the accumulation of key bioactive tanshinones, while simultaneously reshaping its rhizosphere microbial community. These findings offer a potential light-based strategy for improving the quality of S. miltiorrhiza.},
}

*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics
*Rhizosphere
*Light
*Microbiota/radiation effects
Gene Expression Regulation, Plant/radiation effects
*Transcription, Genetic/radiation effects

@article {pmid42291329,
year = {2026},
author = {Zeng, Y and Jiang, Y and Huang, Y and Yin, S and Yang, Z and Zhang, F},
title = {The dialogue between breast cancer and microorganisms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1738739},
pmid = {42291329},
issn = {2235-2988},
mesh = {Humans ; *Breast Neoplasms/microbiology/pathology/therapy ; Female ; Tumor Microenvironment ; *Microbiota ; Animals ; Dysbiosis ; Cell Transformation, Neoplastic ; Estrogens/metabolism ; },
abstract = {Breast cancer is a complex pathological process involving multiple factors and stages, characterized by pronounced molecular and phenotypic heterogeneity. Its global incidence and mortality rates have shown a continuous upward trend. With the advancement of microbiome research, microbial communities have been recognized as key determinants influencing host health and disease states. Increasing evidence suggests a close association between breast tissue-resident and systemic microbiota and the initiation and progression of breast cancer. Specifically, microorganisms may be associated with abnormal proliferation and malignant transformation of mammary epithelial cells through diverse mechanisms, including the modulation of estrogen metabolism, production of bioactive metabolites, induction of chronic inflammation, and remodeling of the tumor microenvironment. In addition, certain microbes may directly interact with host cells, potentially inducing DNA damage and contributing to the transition from normal to malignant phenotypes. This review systematically summarizes the origins and compositional characteristics of the breast microbiota, with a particular focus on current evidence regarding its roles in breast cancer initiation, progression, metastasis, therapeutic response, and prognosis. Currently, the majority of evidence originates from cross-sectional studies and in vitro/in vivo model, to better evaluate the current evidence, the limitations of different research designs and the levels of evidence are summarized in Table 1, aiming to provide new theoretical insights and research perspectives for microbiota-based strategies in breast cancer diagnosis and therapy.},
}

Humans
*Breast Neoplasms/microbiology/pathology/therapy
Female
Tumor Microenvironment
*Microbiota
Animals
Dysbiosis
Cell Transformation, Neoplastic
Estrogens/metabolism

@article {pmid42291330,
year = {2026},
author = {Arishi, RA and Cheema, AS and McEachran, JL and Gridneva, Z and Vlaskovsky, P and Norrish, I and Bilston-John, SH and Zhou, X and Lai, CT and Payne, MS and Geddes, DT and Stinson, LF},
title = {Concentrations of selected human milk components influence the infant oral microbiome to a greater degree than estimated intakes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1765736},
pmid = {42291330},
issn = {2235-2988},
mesh = {Humans ; *Milk, Human/chemistry ; Infant ; *Microbiota ; Female ; *Mouth/microbiology ; Breast Feeding ; Lactose/analysis ; RNA, Ribosomal, 16S/genetics ; Australia ; Male ; Micronutrients/analysis ; Adult ; },
abstract = {BACKGROUND: Human milk is characterised by its complex composition, consisting of nutrient and bioactive components that play a crucial role in infant health. Although the infant oral cavity is directly exposed to these components during breastfeeding, their effects on the developing oral microbiome remains underexplored. This study aimed to assess associations between the concentrations and daily estimated intakes of human milk components (including minerals, lactose, and antimicrobial proteins) and the oral microbiome of exclusively breastfed infants.

METHODS: We profiled infant oral samples collected at 3 months of age using full-length 16S rRNA gene sequencing, alongside paired analyses of human milk components from 45 mother-infant dyads in the Western Australian BLOSOM cohort. Concentrations of milk lactose, antimicrobial proteins (AMPs), and micronutrients (16 components in total) were measured, and their daily estimated intakes were calculated based on 24-hour milk intake.

RESULTS: The composition of the infant oral microbiome was significantly associated with a number of AMPs and micronutrients, with concentration exerting a far stronger effect than estimated intakes. Lactose, the major sugar in human milk, was not associated with any feature of the infant oral microbiome. Both concentrations and estimated intakes of lactoferrin (P = 0.032 and P = 0.005, respectively), as well as estimated intakes of sodium and iodine (P = 0.041 and 0.022, respectively) were negatively associated with infant oral Shannon diversity. While some associations were consistent when both estimated intakes and concentrations were analysed, some appeared only in one analysis, suggesting differing mechanisms of action.

CONCLUSION: These findings underscore the influence of human milk composition on the developing oral microbiome during early life, highlighting that local, concentration-driven mechanisms are the primary drivers of these effects.},
}

Humans
*Milk, Human/chemistry
Infant
*Microbiota
Female
*Mouth/microbiology
Breast Feeding
Lactose/analysis
RNA, Ribosomal, 16S/genetics
Australia
Male
Micronutrients/analysis
Adult

@article {pmid42291363,
year = {2026},
author = {Trachu, N and Sensorn, I and Khiewngam, K and Monnamo, N and Chantratita, W and Sirachainan, E and Reungwetwattana, T and Oranratnachai, S},
title = {Gut microbiome in advanced non-small cell lung cancer: effect of chemotherapy and impact on efficacy.},
journal = {Translational lung cancer research},
volume = {15},
number = {5},
pages = {127},
pmid = {42291363},
issn = {2218-6751},
abstract = {BACKGROUND: While evidence linking the gut microbiome (GM) to cancer immunotherapy is growing, data regarding its role in chemotherapy remains limited. This study aims to investigate the effect of chemotherapy on GM composition and its potential as a predictive biomarker for treatment outcomes in advanced non-small cell lung cancer (NSCLC).

METHODS: Advanced NSCLC patients treated with chemotherapy at Ramathibodi Hospital were prospectively enrolled. Clinical data and stool samples were collected at three time points: baseline, post-evaluation, and at progression of disease (PD). Fecal bacterial DNA was extracted, followed by PacBio Sequel II sequencing and comprehensive bioinformatic analysis. Clinical data were summarized using descriptive statistics. Progression-free survival (PFS) and overall survival (OS) were estimated by the Kaplan-Meier method, and predictive factors were identified using Cox-regression analysis.

RESULTS: This study analyzed 54 stool samples from 27 NSCLC patients treated with platinum-doublet chemotherapy. The median PFS and OS were 5.3 months [95% confidence interval (CI): 2.4-8.4] and 13.8 months (95% CI: 5.2-not reached), respectively. Post-chemotherapy changes (n=20 paired samples) showed a significant decrease in microbial richness, as evidenced by reduced abundance-based coverage estimator (ACE) (P=0.02) and Chao1 (P=0.03) alpha diversity indices. Taxonomically, the relative abundance of Enterobacter was significantly decreased post-chemotherapy (P=0.03). Regarding treatment response (n=26 evaluable patients; 13 PD, 13 clinical benefit), baseline alpha diversity was not predictive of outcome. However, the relative abundance of Akkermansia was notably higher in the clinical benefit group, approaching statistical significance (P=0.07).

CONCLUSIONS: Chemotherapy significantly reduced GM by decreasing species richness (as measured by the ACE and Chao1 index), while species diversity (as measured by the Shannon and Simpson index) remained unchanged. Therefore, confirming the definitive role of the GM as a predictive biomarker in chemotherapy-treated NSCLC patients necessitates further investigation in a larger, more robustly powered cohort.},
}

@article {pmid42291470,
year = {2026},
author = {Agzamova, SA and Babadjanova, FR},
title = {Gut Microbiome and Short-Chain Fatty Acid Alterations After Cardiopulmonary Bypass are Associated with Nutritional and Functional Impairment in Young Children with Congenital Heart Defects.},
journal = {Clinical and experimental gastroenterology},
volume = {19},
number = {},
pages = {600414},
pmid = {42291470},
issn = {1178-7023},
abstract = {BACKGROUND: Cardiac surgery with cardiopulmonary bypass (CPB) in young children is associated with systemic stress, gastrointestinal dysfunction, and impaired nutritional recovery. The role of gut microbiome disruption and short-chain fatty acid (SCFA) metabolism in these processes remains insufficiently studied.

OBJECTIVE: To evaluate changes in gut microbiome composition, SCFA profiles, and nutritional status in children aged 0-3 years after CPB, and to assess their association with postoperative feeding intolerance and impaired growth.

METHODS: This prospective observational study included 20 children undergoing cardiac surgery with CPB. Stool samples were collected preoperatively and during the early postoperative period. Microbiota composition was assessed using culture-based microbiological methods, and fecal SCFA concentrations were measured by gas chromatography. Clinical, anthropometric, and laboratory parameters were assessed, and their associations with CPB characteristics and microbiome alterations were analyzed.

RESULTS: The postoperative period was characterized by significant intestinal dysbiosis, including reduced abundance of beneficial bacteria (Bifidobacterium, Lactobacillus, Bacteroides) and decreased SCFA-producing taxa. Fecal butyrate and propionate levels were significantly reduced. These changes were associated with increased intestinal inflammation, feeding intolerance, impaired nutrient absorption, and insufficient weight gain. The severity of dysbiosis correlated with CPB duration.

CONCLUSION: CPB in early childhood is associated with disruption of gut microbiota and reduced SCFA production, which are linked to postoperative feeding intolerance and impaired nutritional recovery. Targeted monitoring and modulation of the gut microbiome may improve clinical outcomes in pediatric cardiac surgery patients.},
}

@article {pmid42291758,
year = {2026},
author = {Zhang, S and Shoaie, S and Carpenter, GH},
title = {Suprathreshold non-volatile flavour perception is associated with multiple species rather than any single species via bacterial metabolism.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2686537},
pmid = {42291758},
issn = {2000-2297},
abstract = {BACKGROUND: The microbiome is the characteristic microbial community inhabiting a well-defined habitat with distinct physicochemical properties. During eating, food is masticated and mixed with saliva to form a bolus; non-volatile flavour molecules are released into the saliva and delivered to receptors on the tongue. Throughout this process, the oral microbiome is in direct contact with non-volatile flavour molecules. In this cross-sectional study, we hypothesised that the oral microbiome interacts with non-volatile flavour molecules to modulate suprathreshold taste perception.

MATERIALS AND METHODS: Fifty-three participants were included, with suprathreshold sensory data, salivary microbiome data (including both taxonomic and functional profiles), and salivary metabolome data. Associations were explored using fixed-effects linear-regression models and unsupervised clustering.

RESULTS: Suprathreshold non-volatile flavour perception was associated with the salivary microbiome via multispecies interactions rather than single-species effects. Taurine (an amino acid and confirmed bacterial metabolite) and ethanolamine (a phospholipid-related metabolite and confirmed bacterial metabolite) showed the greatest number of associations with suprathreshold taste perception in this study (6 of 8 sensory solution each).

CONCLUSION: This study suggested that suprathreshold taste perception was associated with inferred microbial metabolic pathways via multispecies interactions. Because inferred microbial metabolic pathways are encoded by multiple bacteria, they may better capture multispecies contributions than species-level taxonomic profiles.},
}

@article {pmid42291953,
year = {2026},
author = {Finlayson, CR and Hansen, NM and Stewart, S and Smith, M},
title = {Aetiology and Management of Acute Septic Arthritis and Prosthetic Joint Infection Presentations to Orthopaedics: An Evaluation of Tertiary Centre Performance.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e108830},
pmid = {42291953},
issn = {2168-8184},
abstract = {Background Septic arthritis (SA) and prosthetic joint infection (PJI) are common emergency referrals to orthopaedics in the United Kingdom. These infections carry a significant risk of harm due to chondrolysis and arthropathy and are a potential source of sepsis, requiring prompt assessment, investigation, and treatment. A joint aspirate is routinely sent for microscopy, culture , and sensitivities to aid treatment. In suspected PJI, this must be taken under sterile conditions to reduce the risk of iatrogenic PJI. Empirical antibiotics should then commence per the British National Formulary (BNF) or local policy. Due to the risks of delayed or ineffective treatment, evaluating local practice may identify areas to optimise treatment delivery and efficacy. Aims This study will evaluate the incidence of SA and PJI within a tertiary orthopaedic centre over 12 months. The culprit organisms and sensitivities, delivery of timely and appropriate antibiotics, serum infection markers, length of stay (LOS), and mortality will be reviewed. Methods Admissions to the orthopaedic unit between November 2023 and October 2024 were screened using the ICD-10 codes for pyogenic arthritis, prosthesis infection, or infection following a procedure. Further review confirmed cases of SA or PJI, excluding unsuitable admissions. Each patient's electronic record was examined for demographics, serum infection markers, LOS, 30-day mortality, relevant imaging, time to aspirate relative to admission, culture results, and timing and type of antibiotics initiated. Antibiotics used were compared to sensitivities and BNF recommendations to determine efficacy. Results A total of 27 admissions with SA and 24 of PJI were seen, accounting for 51 (1.9%) of 2,670 total admissions, relative to a mean annual arthroplasty incidence of 1,204 across the health board. The median age of PJI patients was 72 years, significantly higher than the median SA patient age of 52 years (p<0.01). Median LOS was also higher in PJI patients at 13.5 days compared to nine days in SA (p=0.036). Most infections were hip and knee joints at nine (33.3%) cases in SA, and 11 (45.8%) total knee replacements in PJI cohorts. Staphylococcus aureus was the most prevalent organism in each group; however, 11 (40.7%) of the SA aspirate cultures were negative. The median aspiration time, relative to admission, was 5.6 and 10.2 hours in SA and PJI, respectively. The median time to initiate antibiotics was 7.1 and 17.9 hours in SA and PJI, respectively. The majority of admissions received appropriate antibiotics at 20 (74.1%) of SA and 17 (70.8%) of PJI patients. Culture results confirmed sensitivity to recommended antibiotics in 14 (51.8%) of SA and 18 (75%) of PJI cases. The most initiated antibiotic overall was flucloxacillin. There was no significant difference in infection markers. Conclusion This study finds that PJI patients were typically older, with a greater LOS and comorbidity. Large joint infections, such as hips and knees, were the commonest presentation. The majority of each cohort was appropriately treated per the BNF, with S. aureus being the commonest cause. Factors such as prehospital antibiotics may reduce the bacterial yield of aspirations. Both groups show prolonged time taken to aspirate and treat, in which quality improvement interventions may reduce. Other centres may benefit from similar evaluations of the infective microbiome and the speed and efficacy of septic joint treatment.},
}

@article {pmid42292075,
year = {2026},
author = {Beattie McAliley, R and Hooper, L and Hoss, K and Vigerust, DJ},
title = {Test, Treat, Repopulate™ method reduces red complex bacteria and stabilizes the oral microbiome.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1839034},
pmid = {42292075},
issn = {2673-4915},
abstract = {Despite advances in dental hygiene and clinical interventions, preventable conditions such as tooth decay and gum disease remain widespread public health concerns. Recent research implicates complex, polymicrobial interactions as central drivers of disease pathogenesis, which often limits the effectiveness of traditional therapeutic approaches. Here, researchers evaluate the effectiveness of the Test, Treat, Repopulate method, a multi-phase oral health protocol combining scaling and root planing, targeted antibiotic therapy, use of a pH-balanced, prebiotic containing toothpaste and rinse, and daily oral probiotic use on the health of the oral microbiome. Retrospective analysis of RT-qPCR salivary diagnostic data from 38 de-identified U.S. patients, collected before and after treatment during routine care, demonstrated significant and sustained reductions in key oral pathogens following the combined treatment approach. Seven bacterial species were significantly reduced post-treatment, including Treponema denticola, Tannerella forsythia, Prevotella intermedia, Campylobacter rectus, Fusobacterium nucleatum, Fusobacterium nucleatum subsp. animalis, and Streptococcus mutans. Additional pathogens, including Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, were also reduced. The protocol had minimal impact on the fungal species Candida albicans, highlighting an area for potential optimization. Additionally, four viral targets were assessed pre- and post-protocol, making this one of the first studies to evaluate a dental intervention's effects on oral viruses. Comparison of the cohort with 35,570 pre-treatment salivary diagnostic tests across the United States shows that baseline pathogen distributions reflect national patterns, supporting the generalizability of the protocol. A structured protocol for patients with elevated red complex bacteria is detailed, providing clinicians with a data-driven, reproducible framework for precision oral healthcare. These findings underscore the potential for microbiome-focused interventions to achieve measurable, lasting improvements in oral health across diverse populations.},
}

@article {pmid42292333,
year = {2026},
author = {Reynolds, A and Glenn, E and Lavoie, B and Ishaq, SL and Li, Y},
title = {Plant-derived bioactives, the gut-brain axis, and neurodegenerative diseases: mechanistic roles of diet-microbiota interactions.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1815972},
pmid = {42292333},
issn = {1662-4548},
abstract = {Diet is increasingly recognized as a potential upstream modulator of the gut-brain axis (GBA) through its effects on the microbiome, microbial metabolites, and host immune and endocrine responses. The GBA is a complex, bidirectional network connecting the gastrointestinal tract and central nervous system, with diet influencing microbial community structure and metabolic output. Plant-based diets, such as Mediterranean and MIND, have been associated with increased production of anti-inflammatory microbial metabolites and improved barrier function, while high calorie/low nutrient diets are often linked to increased immune activation and barrier dysfunction. However, while microbial metabolites, especially short-chain fatty acids, indoles, bile acids, and isothiocyanates, have been proposed as mediators of neuroprotective effects, their role in neurodegenerative diseases remains an area of active investigation, with evidence largely derived from preclinical and associative human studies. Cruciferous vegetables, especially broccoli sprouts, are an emerging focus of research for their bioactive compound sulforaphane, which activates Nrf2-centered cytoprotective pathways. Animal and early human studies suggest sulforaphane can improve cognitive and behavioral outcomes, though larger clinical trials are needed. Personalized, microbiota-targeted dietary interventions may offer scalable strategies for managing neuroinflammatory and neurodegenerative conditions, and we emphasize the need for integrated research across diet, microbiome, and brain health.},
}

@article {pmid42292359,
year = {2026},
author = {Zhang, Y and Qin, Y and Cheng, Z},
title = {Innate immune regulation of adaptive immunity: mechanisms, implications, and bias.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847470},
pmid = {42292359},
issn = {1664-3224},
mesh = {Humans ; *Immunity, Innate ; *Adaptive Immunity ; Animals ; Signal Transduction ; Hypersensitivity/immunology ; Trained Immunity ; Epigenesis, Genetic ; Immune Tolerance ; },
abstract = {Innate immunity is not merely an early defensive system but a key regulator of adaptive immune fate. Through pattern-recognition receptor signaling, antigen presentation, cytokine production, and metabolic-epigenetic reprogramming, innate immune responses shape the strength, duration, and direction of T- and B-cell immunity. This review summarizes how innate immune regulation of adaptive immunity contributes to immune dysregulation in infection, autoimmunity, and allergic disease. We focus on three major mechanisms: remodeling of antigen presentation and costimulation, reshaping of cytokine microenvironments that guide T helper cell polarization, and metabolic-epigenetic programming associated with trained immunity or immune tolerance. We further propose that disease outcomes can be interpreted through three regulatory dimensions of innate immune signaling: insufficient signal strength promotes defective pathogen control and weak adaptive priming; persistent or excessive activation sustains autoimmune inflammation and loss of tolerance; and type 2-biased epithelial-innate signaling drives allergic inflammation through the alarmin-ILC2-Th2-IgE axis. By integrating molecular signaling, innate immune cell crosstalk, metabolic regulation, and epigenetic remodeling, this review provides a concise framework for understanding how innate immune imbalance shapes adaptive immune dysfunction and highlights therapeutic opportunities targeting interferon pathways, inflammasomes, epithelial alarmins, metabolic programs, and microbiome-related immune regulation.},
}

Humans
*Immunity, Innate
*Adaptive Immunity
Animals
Signal Transduction
Hypersensitivity/immunology
Trained Immunity
Epigenesis, Genetic
Immune Tolerance

@article {pmid42292378,
year = {2026},
author = {Gargaro, M and Fallarino, F and Zelante, T},
title = {Editorial: Host-microbe immunometabolic chat: a new era of organismal communication.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1882702},
doi = {10.3389/fimmu.2026.1882702},
pmid = {42292378},
issn = {1664-3224},
}

@article {pmid42292405,
year = {2026},
author = {Xiao, J and Duan, L and Yang, J and Deng, Y and Pang, S and Wang, H and Yin, X and Wang, H and Qiu, Y and Li, X and Gong, Y and Li, H},
title = {The landscape of cellular immune alteration in systemic lupus erythematosus.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1755310},
pmid = {42292405},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/immunology/metabolism/therapy ; Animals ; *Immunity, Cellular ; Dysbiosis/immunology ; Gastrointestinal Microbiome/immunology ; Autoantibodies/immunology ; },
abstract = {Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by multi-organ inflammation and profound immune dysregulation. Aberrant interactions among adaptive and innate immune cells-including T cells, B cells, dendritic cells, macrophages, neutrophils, and natural killer cells-disrupt immune tolerance and perpetuate chronic inflammation. This review provides a comprehensive overview of the dysfunctional cellular immune landscape in SLE, focusing on the pathogenic crosstalk among immune cell subsets and its contribution to disease progression. We highlight the imbalance of T cell subsets (Th1, Th17, Tfh, Treg), B cell hyperactivation, and impaired regulatory cell function. Furthermore, we discuss how excessive NETosis, type I interferon signaling, and impaired apoptotic clearance amplify autoantibody production and immune complex-mediated injury. Emerging evidence positions gut microbiome dysbiosis as a critical environmental driver of immune dysregulation in SLE, characterized by depletion of beneficial butyrate-producing commensals and enrichment of pro-inflammatory taxa. This dysbiosis contributes to disease pathogenesis through gut barrier dysfunction, molecular mimicry, and short-chain fatty acid deficiency. Finally, we examine potential therapeutic strategies, including immune checkpoint modulation, metabolic interventions, and novel cellular therapies, aimed at restoring immune equilibrium in SLE.},
}

Humans
*Lupus Erythematosus, Systemic/immunology/metabolism/therapy
Animals
*Immunity, Cellular
Dysbiosis/immunology
Gastrointestinal Microbiome/immunology
Autoantibodies/immunology

@article {pmid42292406,
year = {2026},
author = {Sun, B and Wang, T},
title = {The microbiota-metabolite-immune axis in colorectal cancer: mechanistic insights and emerging clinical applications.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1768792},
pmid = {42292406},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/immunology/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Tumor Microenvironment/immunology ; Dysbiosis/immunology ; Signal Transduction ; },
abstract = {Colorectal cancer (CRC) results from a complex interplay of host genetics, environmental factors, and gut microbiota. Increasing evidence suggests that intestinal microorganisms significantly affect the initiation and progression of CRC through metabolic and immunological reprogramming. Dysbiosis, defined as an imbalance between beneficial and harmful microbial species, leads to chronic inflammation, genotoxic stress, and disruption of epithelial homeostasis. Microbial metabolites, such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives, function as signaling molecules that influence epithelial proliferation, apoptosis, and immune cell activity. These metabolites regulate essential oncogenic and inflammatory pathways, including Wnt/β-catenin, NF-κB, and STAT3, and alter the tumor microenvironment by affecting regulatory T cells (Tregs), Th17 cells, macrophages, and myeloid-derived suppressor cells. Specific bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, illustrate how particular microbes can promote tumorigenesis through metabolite-mediated signaling and immune modulation. This review summarizes recent advances in understanding how gut microbiota and their metabolites contribute to colorectal carcinogenesis by influencing inflammatory signaling, epithelial homeostasis, and tumor immune responses. These mechanistic insights highlight the microbiota-metabolite-immune axis as a crucial driver of CRC initiation and progression. The increasing recognition that microbial alterations occur alongside early neoplastic changes and affect tumor behavior emphasizes their translational potential. Although further validation in large, well-controlled clinical settings is necessary, microbiome- and metabolite-based markers could enhance current strategies for the early detection, risk assessment, and therapeutic guidance of CRC. Ultimately, deepening our understanding of the intricate interactions between intestinal microbes, host metabolism, and immune regulation will facilitate the development of microbiome-informed approaches for CRC monitoring and intervention in the future.},
}

Humans
*Colorectal Neoplasms/immunology/metabolism/microbiology/etiology
*Gastrointestinal Microbiome/immunology
Animals
Tumor Microenvironment/immunology
Dysbiosis/immunology
Signal Transduction

@article {pmid42292417,
year = {2026},
author = {Wang, Y and Dong, C and Xiao, Y},
title = {Polystyrene nanoplastics promotes inflammation and aging in young mice through the oral-gut microbiome axis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1806158},
pmid = {42292417},
issn = {1664-3224},
mesh = {Animals ; *Polystyrenes/toxicity/adverse effects ; *Aging/drug effects/immunology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Inflammation/chemically induced/metabolism ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; *Microplastics ; *Nanoparticles/toxicity ; *Mouth/microbiology ; Inflammation Mediators/metabolism ; Dysbiosis/chemically induced ; Cellular Senescence/drug effects ; },
abstract = {With the escalating global pollution of nanoplastics, their impacts on organismal health have become a focal concern. The oral-gut microbiota axis plays a pivotal role in host health regulation, yet how nanoplastics influence this axis and drive inflammation and aging in young organisms remain undefined. This study aimed to investigate whether polystyrene nanoplastics (PS-NPs) promote inflammation and aging in young mice by disrupting the oral-gut microbiota axis. Therefore, we established a free-feeding model with 1000 μg/L PS-NPs using 8-week-old C57BL/6 mice. We quantified tissue inflammatory cytokines and cellular senescence markers to assess PS-NPs-induced inflammatory and aging effects, while 16S rRNA sequencing was employed to characterize oral and gut microbiota structural changes. We found that PS-NPs exposure significantly increased the expression levels of cellular senescence markers p21[Cip1/Waf] and p16[Ink4a] in lung and liver. Meanwhile, PS-NPs promoted the release of inflammatory cytokines such as IL-1β, IL-6 and TNF-α, by modulating the p38 MAPK pathway. In addition, PS-NPs also decreased the expression levels of antioxidant genes. Furthermore, 16S rRNA sequencing analysis revealed that PS-NPs exposure caused dysbiosis in oral and intestinal microbiota, manifested as significant alterations in microbial diversity and community structure. Our work provided mechanistic insights into nanoplastic toxicity and theoretical basis for developing preventive strategies.},
}

Animals
*Polystyrenes/toxicity/adverse effects
*Aging/drug effects/immunology
*Gastrointestinal Microbiome/drug effects
Mice
*Inflammation/chemically induced/metabolism
Cytokines/metabolism
Mice, Inbred C57BL
Male
*Microplastics
*Nanoparticles/toxicity
*Mouth/microbiology
Inflammation Mediators/metabolism
Dysbiosis/chemically induced
Cellular Senescence/drug effects