@article {pmid41923033,
year = {2026},
author = {Guo, Z and Yu, X and Liu, Y and Hu, Q and Zhang, Z and Zhang, C and Li, J},
title = {A comparative analysis of oral microbial communities in hypertensive patients with and without chronic periodontitis.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41923033},
issn = {1472-6831},
support = {2025A03J4171//Science and Technology Projects in Guangzhou/ ; },
abstract = {BACKGROUND: Hypertension and chronic periodontitis are both highly prevalent diseases with a well-established association. Dysbiosis of the oral microbiota, a key factor in oral health, may contribute to the mechanisms underlying their comorbidity. This study aimed to characterize the oral microbiota in hypertensive patients with and without periodontitis and explore its potential role in this disease association.

METHODS: Saliva samples from hypertensive patients without periodontitis (T, n = 17), periodontitis patients without hypertension (P, n = 18), comorbid patients (TP, n = 16), and healthy controls (HC, n = 16) underwent 16S rRNA gene (V3-V4) sequencing. Microbiota composition, diversity, differential taxa, and predicted function were analyzed.

RESULTS: Alpha diversity (Chao1/Ace indices) was significantly higher in HC versus disease groups (P < 0.05), while beta diversity showed greater similarity among disease groups but marked divergence from HC (P < 0.05). At genus/species levels, disease groups exhibited characteristic dysbiosis: the abundance of health-associated taxa decreased, while classic periodontal pathogens were significantly enriched. Notably, Streptococcus sp. I-G5 was uniquely enriched in the T group. Functionally, disease groups exhibited enriched lipid metabolism, immune response, and oxidative stress pathways (P < 0.05), contrasting with HC group dominance in xenobiotic biodegradation and amino acid metabolism. Ten differentially abundant genera and eleven species distinguished disease states, highlighting microbiome dysbiosis and metabolic shifts in oral-systemic disease interactions.

CONCLUSION: The oral microbial community of hypertensive patients exhibited dysbiosis analogous to those observed in periodontitis, characterized by a reduced alpha diversity, an enrichment of periodontal pathogens, and activation of pro-inflammatory metabolic pathways. These findings suggest that oral microbial dysbiosis is a shared feature in hypertensive and periodontitis patients. The specific enrichment of Streptococcus sp. I-G5 in hypertension alone may indicate a potential microbial signature for this condition, contributing to a better understanding of the oral microbiome’s role in hypertension.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-08144-6.},
}

@article {pmid42122957,
year = {2026},
author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ},
title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
pmid = {42122957},
issn = {2077-0383},
abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.},
}

@article {pmid42123280,
year = {2026},
author = {Aljaraedah, T and Al-Thnaibat, S and Nawasreh, AA and Alraei, W and Al-Trad, E},
title = {A Scoping Review of Gut Dysbiosis and Malnutrition in Neurological Disorders: Implications, Indications, and Promising Therapeutic Approaches.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
pmid = {42123280},
issn = {2077-0383},
abstract = {Background/Objectives: Neurological diseases are increasing worldwide, but the biological processes underlying these diseases remain poorly understood, and existing treatments have been ineffective at arresting disease progression. Emerging data indicate that dysbiosis of the microbiota-gut-brain axis and malnutrition are comorbid factors in neurological dysfunction. Methods: An extended search strategy was developed using a multifaceted approach across various databases to identify eligible studies published between January 2010 and February 2026. Results: Results showed uniform relationships among neurological conditions, loss of microbial richness, loss of short-chain fatty acid-producing bacteria, neuroinflammation, and nutritional susceptibility. The review also identifies methodological trends in microbiome profiling and nutritional assessment and suggests an integrative framework of symptom-linked microbial imbalance, malnutrition, and inflammatory processes. Conclusions: Although dietary modulation and microbiome-targeted interventions appear promising, the evidence is mostly correlational. Longitudinal and interventional studies should be well-designed to elucidate causal mechanisms and to provide effective clinical strategies.},
}

@article {pmid42123326,
year = {2026},
author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS},
title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123326},
issn = {1422-0067},
mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; },
abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.},
}

Animals
Chickens/microbiology
*Manure/microbiology
*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Metagenome
Microbiota/genetics
Biodiversity

@article {pmid42123347,
year = {2026},
author = {López-Tenorio, II and Constantino-Jonapa, LA and Jaimez-Alvarado, S and Hernández-Quiroz, F and Jorge-Galarza, E and Escalona-Montaño, AR and Amedei, A and Soria-García, R and Berrios-Barcenas, EA and Aguirre-García, MM},
title = {Gut-Heart Axis: Microbiome Involvement in Wild-Type Transthyretin Amyloidosis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123347},
issn = {1422-0067},
support = {CBF2023-2024-734//CONAHCYT/ ; IN212422, IN219025//UNAM-DGAPA-PAPIIT/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Amyloid Neuropathies, Familial/microbiology/metabolism ; Male ; Female ; Middle Aged ; Aged ; Biomarkers/metabolism ; Dysbiosis/microbiology ; },
abstract = {Cardiac amyloidosis is a rare and progressive condition characterized by the extracellular deposition of amyloid fibrils in multiple organs. Wild-type transthyretin amyloidosis (ATTR-wt) is the most common type affecting subjects above 60 years old. Recent and growing evidence suggests a potential link between GM and cardiac amyloidosis. In this scenario, the aim of the present study is to characterize the gut microbiota (GM), related metabolites and inflammatory biomarkers in ATTR-wt patients. In the ATTR patients we identified Prevotella_9 as the core OTUs (Operational Taxonomic Unit) of this group, alongside Prevotella 7, Prevotellaceae_UCG-003 and Prevotellaceae_NK3B31. In addition, there were increased levels of long fatty acids, including tetradecanoic, hexadecanoic and octadecanoic acids, in the ATTR group. The data obtained suggest that ATTR patients have an altered gut microbiota that could be used as a potential biomarker in metabolic and cardiovascular diseases, as well as a potential predictor of adverse prognosis in ATTR patients. In addition, the intestinal dysbiosis in ATTR patients could be associated with low-grade endotoxemia promoting a pro-inflammatory state due to the translocation of bacterial components, such as LPS (lipopolysaccharide), into blood circulation.},
}

Humans
*Gastrointestinal Microbiome
*Amyloid Neuropathies, Familial/microbiology/metabolism
Male
Female
Middle Aged
Aged
Biomarkers/metabolism
Dysbiosis/microbiology

@article {pmid42123418,
year = {2026},
author = {Bhoi, TK and Mahanta, DK and Samal, I and Jangra, S},
title = {Plant Defense Activation by Endophytic Metarhizium anisopliae and Beauveria bassiana Fungi Against Subterranean Termites.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123418},
issn = {1422-0067},
mesh = {Animals ; *Metarhizium/pathogenicity/physiology ; *Isoptera/microbiology ; *Beauveria/pathogenicity/physiology ; *Endophytes/physiology ; },
abstract = {Subterranean termites, particularly Odontotermes obesus, cause severe damage to forest nurseries and plantations in arid and semi-arid ecosystems. This study demonstrates the dual functional role of endophytic entomopathogenic fungi, Metarhizium anisopliae and Beauveria bassiana, in termite suppression and induction of plant defense responses. Laboratory bioassays revealed significantly higher virulence of M. anisopliae, with a lower LT50 (lethal time required to cause 50% mortality) of 33.1 h compared to B. bassiana (46.7 h), a steeper probit slope (5.4 ± 0.3), and strong model fit (R[2] = 0.95), indicating rapid and synchronized mortality. Endophytic colonization varied across host species and application methods, with soil incorporation consistently outperforming foliar inoculation. Maximum colonization (82.5%) was recorded in Tecomella undulata and exceeded 80% in Azadirachta indica under M. anisopliae. Biochemical analyses revealed significant increases in protein (up to 3.5 mg g[-1]), phenols (3.7 mg g[-1]), and tannins (2.7 mg g[-1]). Activity of defense enzymes was significantly enhanced, with catalase reaching 263.5 U mL[-1], while Phenylalanine ammonia-lyase and Tyrosine ammonia-lyase exceeded 170 and 198 U mL[-1], respectively, indicating activation of antioxidant and phenylpropanoid pathways. Molecular docking analysis further revealed strong interactions between fungal metabolites and termite cellulase, with Bassianin (-8.4 kcal mol[-1]) and Tenellin (-8.1 kcal mol[-1]) showing the highest binding affinities. These findings highlight the combined biochemical and molecular mechanisms underlying fungal-mediated termite suppression and plant defense induction, and future research should prioritize transcriptomic validation, rhizosphere microbiome interactions, formulation optimization, and long-term multi-location field evaluation to support sustainable termite management strategies.},
}

Animals
*Metarhizium/pathogenicity/physiology
*Isoptera/microbiology
*Beauveria/pathogenicity/physiology
*Endophytes/physiology

@article {pmid42123449,
year = {2026},
author = {Toboła, M and Kuryłowicz, A},
title = {Impact of Gut Microbiota on Bone Metabolism-Present Concepts and Therapeutic Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123449},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Dysbiosis/metabolism/microbiology ; Probiotics/therapeutic use ; Calcium/metabolism ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {The gut microbiota plays a multifaceted role in calcium homeostasis and bone metabolism -acting through metabolic, immunological, and hormonal pathways that collectively constitute the gut-bone axis. The microbiota influences calcium bioavailability through several overlapping mechanisms that act in the intestine. Moreover, microbial fermentation products may directly impact the osteoblast-osteoclast interplay and, by modulating immune and endocrine functions, are crucial for bone metabolism. A healthy microbiota supports bone formation; however, intestinal dysbiosis may impair bone structure and function. This narrative review aims to present pathways linking the gut microbiota to bone metabolism, both in health and disease. First, we will discuss the influence of gut microbiota on calcium absorption. We will then outline the role that microbial metabolites, such as bile acids and short-chain fatty acids (SCFAs), play in regulating bone structure and function. In the following section, we will discuss the role of the microbiota in the immunological and hormonal modulation of bone metabolism. Finally, we will discuss how dysbiosis affects bone and how therapeutic interventions, such as probiotics, prebiotics, and postbiotics, may influence bone tissue quality.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bone and Bones/metabolism
Animals
Dysbiosis/metabolism/microbiology
Probiotics/therapeutic use
Calcium/metabolism
Fatty Acids, Volatile/metabolism
Prebiotics

@article {pmid42123477,
year = {2026},
author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M},
title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123477},
issn = {1422-0067},
mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; },
abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.},
}

Humans
*Mineral Waters/therapeutic use
Balneology/methods
Animals
Skin/drug effects

@article {pmid42123484,
year = {2026},
author = {Ahmad, A and Ahmed, MM and Akhtar, A and Liu, W and Yang, R and Sun, X and Wang, X and Bibi, S and Khan, MB and Chen, S},
title = {Unlocking Grass Stress Resistance: Fungal Endophyte-Mediated Pathogen Recognition and RNA Regulation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123484},
issn = {1422-0067},
support = {32260356//National Natural Science Foundation of China/ ; (Outstanding Youth Project, Grant No. 2025DB003)//Corps Science and Technology Program/ ; (TDZKPY202607)//Tarim University of Agricultural Reclamation/ ; },
mesh = {*Endophytes/physiology ; *Stress, Physiological ; *Poaceae/microbiology/genetics/physiology ; *Host-Pathogen Interactions ; Symbiosis ; *Fungi/physiology ; Gene Expression Regulation, Plant ; Disease Resistance ; Plant Diseases/microbiology/genetics ; },
abstract = {Fungal endophytes are symbiotic microorganisms that establish strong relationships inside plant tissues, providing potential advantages, especially in grasses, by enhancing tolerance to both abiotic and biotic stresses. This review investigates the molecular mechanisms through which fungal endophytes mediate stress tolerance, targeting host-pathogen interactions. By modulating pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs), and effector proteins, fungal endophytes may contribute to priming the plant's immune system, enhancing its resistance to pathogen invasion. Moreover, endophyte colonization regulates core processes such as osmotic regulation, reactive oxygen species (ROS) detoxification, and secondary metabolite biosynthesis that enable plants to tolerate environmental stresses like drought, heat, and salinity. The review highlights the impact of endophytes on immune priming, systemic acquired resistance (SAR), and the regulation of non-coding RNAs that regulate host gene networks associated with stress tolerance. Furthermore, the integration of advanced multi-omics techniques genomics, transcriptomics, proteomics, metabolomics, and fluxomics has revealed emerging insights into the genetic and metabolic pathways driving these symbiotic associations. However, grass-specific molecular datasets remain limited, and the consistency of endophyte-mediated tolerance across host species and environmental conditions is not yet fully resolved. Fungal endophytes increase grass stress resilience through coordinated pathogen recognition, RNA regulation, and metabolic reprogramming while AI-assisted multi-omics approaches are emerging as tools for identifying candidate regulatory networks, although empirical validation in grass-endophyte systems remains limited. Together, these advances highlight the potential for climate-smart and sustainable crop improvement. Future research integrating functional genomics, field validation, and biosafety assessment will be essential for translating endophyte-based strategies into reliable agricultural applications.},
}

*Endophytes/physiology
*Stress, Physiological
*Poaceae/microbiology/genetics/physiology
*Host-Pathogen Interactions
Symbiosis
*Fungi/physiology
Gene Expression Regulation, Plant
Disease Resistance
Plant Diseases/microbiology/genetics

@article {pmid42123517,
year = {2026},
author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ},
title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123517},
issn = {1422-0067},
support = {10180//United States Department of Agriculture/ ; },
mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration & dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration & dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; },
abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.},
}

Humans
*Saliva/microbiology/drug effects
Female
Male
*Vaccinium macrocarpon/chemistry
*Polyphenols/pharmacology/administration & dosage/chemistry
*Microbiota/drug effects
Adult
Propylthiouracil
*Plant Extracts/pharmacology/chemistry/administration & dosage
*Photinia/chemistry
Taste/drug effects
*Mouthwashes/pharmacology/chemistry
*Fruit and Vegetable Juices
Young Adult

@article {pmid42123520,
year = {2026},
author = {Yılmaz, A and Park, HJ and Ahn, EM and Bae, J},
title = {Dietary Polyphenols in Aging: A Systems-Level Perspective on Mitochondrial Quality Control and Microbiome Interactions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123520},
issn = {1422-0067},
support = {RS-2026-25477916//National Research Foundation of Korea/ ; 2026-rise-15-110//Daegu Haany University Regional Innovation System & Education/ ; },
mesh = {Humans ; *Polyphenols/pharmacology ; *Aging/drug effects/metabolism ; *Mitochondria/metabolism/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; Diet ; Signal Transduction/drug effects ; },
abstract = {Aging is a multifactorial biological process characterized by progressive functional decline and increased susceptibility to chronic diseases. Targeting the molecular mechanisms underlying aging has therefore emerged as an important strategy for promoting healthy aging. Natural polyphenols, widely present in fruits, vegetables, tea, and medical and aromatic plants, have attracted considerable attention due to their geroprotective properties. This review examines current evidence on the ability of major dietary polyphenols, including resveratrol, epigallocatechin gallate (EGCG), curcumin, and quercetin, to modulate the hallmarks of aging, with particular emphasis on mitochondrial quality control as a central regulatory mechanism. Evidence indicates that polyphenols regulate key signaling pathways involved in aging biology, including AMP-activated protein kinase (AMPK), sirtuins (SIRT), mechanistic target of rapamycin (mTOR), nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor-κB (NF-κB). Through coordinated modulation of these pathways, polyphenols influence mitochondrial biogenesis, mitophagy, redox homeostasis, cellular senescence, and chronic inflammation. In addition, interactions between dietary polyphenols and the gut microbiome generate bioactive metabolites, such as urolithin A, which further contribute to mitochondrial regulation. Overall, polyphenols represent promising modulators of aging-associated pathways and may support strategies aimed at improving healthspan and reducing age-related disease risk.},
}

Humans
*Polyphenols/pharmacology
*Aging/drug effects/metabolism
*Mitochondria/metabolism/drug effects
Animals
*Gastrointestinal Microbiome/drug effects
Diet
Signal Transduction/drug effects

@article {pmid42123539,
year = {2026},
author = {Miranda, J and Maestre, N and Devia, M and Zapata, R and Ochoa-Díaz, MM and Annicchiarico, W},
title = {Inflammation at the Maternal-Fetal Interface: Mechanisms Linking Maternal-Fetal Immunity to Preeclampsia and Fetal Growth Restriction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123539},
issn = {1422-0067},
mesh = {Humans ; Pregnancy ; Female ; *Fetal Growth Retardation/immunology/pathology/etiology ; *Pre-Eclampsia/immunology/pathology ; *Inflammation/immunology/pathology ; *Placenta/immunology ; *Maternal-Fetal Exchange/immunology ; Animals ; },
abstract = {Inflammation is a physiological and tightly regulated component of normal pregnancy, contributing to implantation, placental development, and the initiation of parturition. The placenta functions as an active immunological hub, coordinating innate and adaptive immune responses to maintain tolerance while protecting against infection. Preeclampsia and fetal growth restriction (FGR) are major causes of maternal and perinatal morbidity worldwide and represent central manifestations of placental disease. Increasing evidence indicates that these conditions share key pathophysiological mechanisms, including placental dysfunction and maladaptive maternal immune responses. When immune regulation at the maternal-fetal interface becomes disrupted, inflammatory pathways contribute to impaired placental development and vascular maladaptation. In this context, excessive immune activation-driven by inflammasome signaling, Th1/Th17 polarization, and altered natural killer and macrophage function-can compromise placental perfusion, promote antiangiogenic imbalance, and lead to systemic endothelial dysfunction. This review, therefore, focuses on how immune dysregulation contributes to placental dysfunction in preeclampsia and FGR, synthesizing current knowledge of the maternal-fetal immune interface and exploring therapeutic strategies that link pathogenic mechanisms to targeted interventions. A deeper understanding of placental immunology and inflammatory signaling is essential to develop precision therapies. Established therapies, including low-dose aspirin, low-molecular-weight heparin, and antenatal corticosteroids, aim to mitigate inflammation and optimize fetal outcomes, while adjunctive strategies target oxidative stress, nutritional deficits, and the maternal microbiome. Emerging approaches such as cytokine-targeted biologics, inflammasome inhibitors, and mesenchymal stem cell therapies show promise but require rigorous safety and efficacy evaluation. Future research should prioritize biomarker validation, pathway-specific interventions, and equitable implementation to reduce inflammation-driven pregnancy complications.},
}

Humans
Pregnancy
Female
*Fetal Growth Retardation/immunology/pathology/etiology
*Pre-Eclampsia/immunology/pathology
*Inflammation/immunology/pathology
*Placenta/immunology
*Maternal-Fetal Exchange/immunology
Animals

@article {pmid42123569,
year = {2026},
author = {Osredkar, J and Fabjan, T and Godnov, U and Jekovec-Vrhovšek, M and Osredkar, D and Finderle, P and Kumer, K and Zorec, M and Fanedl, L and Avguštin, G},
title = {Microbiome-Derived Short-Chain Fatty Acids and Tryptophan Metabolites in Children with Autism Spectrum Disorder: A Stool-Urine Multi-Omics Analysis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123569},
issn = {1422-0067},
support = {This research was funded by the scientific-research program grants P3-0124 and project J3-1756//The Slovenian Research and Innovation Agency/ ; },
mesh = {Humans ; *Tryptophan/metabolism/urine ; *Autism Spectrum Disorder/metabolism/microbiology/urine ; Male ; *Fatty Acids, Volatile/metabolism/urine ; Female ; *Feces/chemistry/microbiology ; Child ; *Gastrointestinal Microbiome ; Child, Preschool ; Metabolomics/methods ; Cross-Sectional Studies ; Case-Control Studies ; Metabolome ; Multiomics ; },
abstract = {Autism spectrum disorder (ASD) has been associated with alterations in the gut microbiota and its metabolites, particularly short-chain fatty acids (SCFAs) and microbiota-derived tryptophan catabolites, which may influence neurodevelopment through immune and epigenetic mechanisms. We investigated whether stool SCFAs and tryptophan-pathway metabolites differ between children with ASD and typically developing controls, and whether these metabolites associate with ASD severity and systemic biochemical signatures. In this cross-sectional study, we analyzed stool samples from 229 children (160 with ASD, 69 controls) with complete SCFA and tryptophan-metabolite data, while urine metabolomics data were available for a subset and were used for exploratory stool-urine integration analyses. Children with ASD and controls were similar in age, but the ASD group had a higher proportion of males. Absolute concentrations of individual SCFAs, total SCFAs, and derived indices were broadly comparable between groups; nominal differences in propionate/acetate ratio and caproate did not remain significant after false discovery rate correction. Similarly, stool tryptophan-pathway metabolites reported as ng/a.u. based on the NanoDrop-derived proxy (tryptophan, kynurenine, indole-3-acetic, indole-3-lactic, indole-3-propionic, indole-3-aldehyde, N-acetyl-tryptophan, serotonin, melatonin, tryptamine) and functional ratios (kynurenine/tryptophan, indole-derived/tryptophan, serotonin/tryptophan) showed no robust ASD-control differences; N-acetyl-tryptophan was nominally higher in ASD but did not survive multiple-testing correction. In the ASD subgroup with available Childhood Autism Rating Scale (CARS) data (n = 34), SCFA and tryptophan indices showed only weak, non-significant correlations with global ASD severity. In contrast, correlation analyses revealed two coherent metabolic modules, i.e., an SCFA block with very strong internal correlations among individual SCFAs and total SCFAs and a tryptophan block with strong correlations between metabolites and their normalized ratios, while cross-module correlations were modest. These results indicate that stool SCFA and microbiota-derived tryptophan profiles do not robustly distinguish ASD from controls in this cohort, but they form stable metabolic modules compatible with microbiome-epigenome frameworks.},
}

Humans
*Tryptophan/metabolism/urine
*Autism Spectrum Disorder/metabolism/microbiology/urine
Male
*Fatty Acids, Volatile/metabolism/urine
Female
*Feces/chemistry/microbiology
Child
*Gastrointestinal Microbiome
Child, Preschool
Metabolomics/methods
Cross-Sectional Studies
Case-Control Studies
Metabolome
Multiomics

@article {pmid42123593,
year = {2026},
author = {Sibarani, JN and Iqhrammullah, M and Hidayat, AA and Alfaray, RI and Nurkolis, F and Santini, A},
title = {Multi-Axis Reprogramming of Muscle-Metabolic Crosstalk by HiLo Platinum™ Restores Strength in Prediabetes via Mitochondrial Activation and Gut Microbiome Remodeling.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123593},
issn = {1422-0067},
mesh = {Animals ; Male ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Sprague-Dawley ; *Prediabetic State/metabolism/drug therapy ; *Muscle, Skeletal/metabolism/drug effects ; *Muscle Strength/drug effects ; *Mitochondria/metabolism/drug effects ; Biomarkers/metabolism ; Dietary Supplements ; Sarcopenia/metabolism ; Disease Models, Animal ; },
abstract = {Prediabetes is increasingly recognized as a risk factor for sarcopenia, driven by chronic low-grade inflammation, insulin resistance, and impaired anabolic signaling. Nutritional interventions containing whey protein, hydroxymethylbutyrate (HMB), glucosamine, and micronutrients may offer a multi-target strategy to counteract muscle deterioration. This study aimed to evaluate the efficacy of HiLo Platinum™ supplementation in attenuating muscle strength decline in a prediabetic rat model, with integrated analysis of metabolic biomarkers and gut microbiome profiles. A randomized preclinical trial was conducted using male Sprague Dawley rats assigned to four groups: normal diet (ND), prediabetic control induced by cholesterol- and fat-enriched diet with fructose (CFEDF), and two treatment groups receiving low-dose (0.63 g/kg BW) or high-dose (1.26 g/kg BW) HiLo Platinum™. The intervention lasted six weeks. Muscle strength was assessed via a four-limb grip strength test (reverse hang time and holding impulse). Biomarkers related to inflammation, mitochondrial function, and anabolic signaling (TNF-α, IL-10, PGC-1α, IGF-1, SIRT-1, AMPK, mTOR, and myostatin), lipid profile, and blood glucose were analyzed. Gut microbiome composition and diversity were evaluated using taxonomic profiling and multivariate analyses. HiLo Platinum™ supplementation significantly improved muscle strength, evidenced by increased reverse hang time and holding impulse (p < 0.001). Both doses reduced blood glucose and improved lipid profiles, including increased HDL and decreased LDL, triglycerides, and total cholesterol. Anti-inflammatory effects were observed with reduced TNF-α and elevated IL-10 levels. Mitochondrial and metabolic regulators (PGC-1α, SIRT-1, AMPK) and anabolic mediators (IGF-1) were significantly upregulated, while mTOR levels decreased. Gut microbiome analysis revealed increased genus richness (Chao1 index) and distinct microbial shifts associated with improved metabolic and inflammatory markers. HiLo Platinum™ effectively mitigates prediabetes-induced muscle strength decline through integrated modulation of inflammatory pathways, mitochondrial function, metabolic homeostasis, and gut microbiome composition. These findings support its potential as a nutritional therapeutic strategy for preventing sarcopenia in prediabetic conditions, although further studies are needed to evaluate long-term effects and implications on muscle hypertrophy.},
}

Animals
Male
*Gastrointestinal Microbiome/drug effects
Rats
Rats, Sprague-Dawley
*Prediabetic State/metabolism/drug therapy
*Muscle, Skeletal/metabolism/drug effects
*Muscle Strength/drug effects
*Mitochondria/metabolism/drug effects
Biomarkers/metabolism
Dietary Supplements
Sarcopenia/metabolism
Disease Models, Animal

@article {pmid42123679,
year = {2026},
author = {Chu, Y and Huang, KH and Tseng, CN},
title = {Targeting the Gut-Heart Axis in Diabetic Heart Failure: Microbiota and SGLT2is as Converging Therapeutic Frontiers.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123679},
issn = {1422-0067},
support = {From Chang Gung Memorial Hospital, Linkou Branch, Taiwan. (CMRPG3F1831, CMRPG3F1832, CMRPG3H0991, CMRPG3H0992, CMRPG3H1801, CMRPG3K0051, CMRPG3K0052, CMRPG3K0221, CMRPG3K0222,CMRPG3K1901,CMRPG3M0121) and from National Science and Technology Council, Taiwa//Linkou Chang Gung Memorial Hospital/ ; },
mesh = {Humans ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Heart Failure/drug therapy/metabolism/etiology/microbiology ; *Diabetes Mellitus, Type 2/drug therapy/complications/microbiology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; },
abstract = {Emerging evidence highlights the gut microbiota as a critical modulator in the pathogenesis of heart failure (HF), particularly among patients with type 2 diabetes mellitus (T2DM). Dysbiosis contributes to systemic inflammation, endothelial dysfunction, and adverse cardiac remodeling via microbial metabolites such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs). However, the therapeutic intersection between the gut microbiota and pharmacological interventions remains insufficiently integrated. Sodium-glucose cotransporter-2 inhibitors (SGLT2is), a cornerstone of T2DM management, confer cardioprotective effects that may involve microbiota-mediated pathways. This review provides a novel synthesis of how SGLT2is influence gut ecology, specifically through altered glucose excretion and osmotic shifts, to potentially restore SCFA-producing taxa. By delineating the structural transitions from gut physiology to SGLT2i-modulated cardiac outcomes, we emphasize the gut-heart axis as a pivotal therapeutic target. This focused framework offers new insights into the triadic interplay between microbiome stability and cardiometabolic health, moving beyond traditional glucose-centric paradigms.},
}

Humans
*Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
*Heart Failure/drug therapy/metabolism/etiology/microbiology
*Diabetes Mellitus, Type 2/drug therapy/complications/microbiology/metabolism
Animals
Fatty Acids, Volatile/metabolism

@article {pmid42123693,
year = {2026},
author = {Seifert, O and Assarsson, M and Manoharan, L and Söderman, J},
title = {Integrated Host Genetics and Skin Microbiome Profiling Suggest an HLA-C-Peptostreptococcus Axis in Psoriasis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123693},
issn = {1422-0067},
support = {FUTURUM-1012326, FUTURUM-996859, and FUTURUM-1006909//Futurum - Akademin för Hälsa och Vård/ ; N/A//Swedish Psoriasis Association/ ; },
mesh = {Humans ; *Psoriasis/genetics/microbiology/immunology ; *Skin/microbiology ; *Microbiota/genetics ; Polymorphism, Single Nucleotide ; Male ; *HLA-C Antigens/genetics ; Female ; Genetic Predisposition to Disease ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Genotype ; Case-Control Studies ; Skin Microbiome ; },
abstract = {Psoriasis is a chronic immune-mediated disease driven by genetic susceptibility and environmental factors, including microbial exposure. While HLA-C-linked variants represent the strongest genetic risk factors, their relationship with the cutaneous microbiome remains incompletely understood. This study aimed to investigate host-microbiome interactions in psoriasis through integrative multi-omics analysis. Skin microbiome profiling using 16S rRNA sequencing and targeted genotyping of psoriasis-associated single-nucleotide polymorphisms (SNPs) was performed in lesional and non-lesional skin from patients with plaque psoriasis and in healthy controls. Integrated analysis was conducted using supervised multivariate modeling (DIABLO) to identify coordinated genetic and microbial features associated with disease status. Combined genetic and microbial signatures differentiated lesional, non-lesional, and healthy skin. Variants within the HLA-C susceptibility region, including rs12191877, rs10484554, and rs4406273, showed contributions to group separation and demonstrated positive associations with Peptostreptococcus anaerobius. Associations involving ERAP1 variants linked antigen-processing pathways with inflammation-associated microbial taxa in lesional skin. Importantly, genotype-microbiome correlations were also detected in clinically non-lesional skin, where an increased psoriasis risk allele dosage co-varied with a higher relative abundance of P. anaerobius and Aerococcus urinae. In contrast, commensal-associated taxa were enriched in healthy controls and formed genotype-linked clusters only in non-lesional skin. These findings suggest that psoriasis is characterized by coordinated host genetic and microbial interaction patterns centered on antigen presentation pathways. The presence of a genotype-microbiome coupling in non-lesional skin may indicate that genetically determined immune configurations could shape microbial community structure prior to visible lesion development. Rather than reflecting uniform dysbiosis, psoriasis may represent a dynamic host-microbe ecosystem in which genetic susceptibility influences microbial persistence and inflammatory readiness.},
}

Humans
*Psoriasis/genetics/microbiology/immunology
*Skin/microbiology
*Microbiota/genetics
Polymorphism, Single Nucleotide
Male
*HLA-C Antigens/genetics
Female
Genetic Predisposition to Disease
Adult
Middle Aged
RNA, Ribosomal, 16S/genetics
Genotype
Case-Control Studies
Skin Microbiome

@article {pmid42123776,
year = {2026},
author = {Wang, M and Zhu, L and Liao, J and Bao, L and Li, H and Deng, Z and Li, J and Zheng, L and Zhang, B},
title = {Human Milk Oligosaccharide LNnT Attenuates Colonic Barrier Dysfunction and Associated Cognitive Impairment via Modulating Sphingolipid Metabolism and Gut Microbiota.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {9},
pages = {},
pmid = {42123776},
issn = {1420-3049},
support = {No.82560639//National Natural Science Foundation of China/ ; No.20252BAC250147//Key Project of Natural Science Foundation of Jiangxi Province/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; Humans ; *Sphingolipids/metabolism ; *Cognitive Dysfunction/metabolism/drug therapy ; *Milk, Human/chemistry ; *Oligosaccharides/pharmacology/chemistry ; *Colon/drug effects/metabolism/pathology ; Male ; Galactose ; Intestinal Mucosa/metabolism/drug effects ; Oxidative Stress/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; },
abstract = {This study focuses on Lacto-N-neotetraose (LNnT), a core component of human milk oligosaccharides. Although LNnT has been demonstrated to promote early intestinal development and maintain gut homeostasis, its protective mechanism against D-galactose-induced intestinal injury and associated cognitive impairment remains unclear. This investigation systematically examined the protective effects and underlying mechanisms of LNnT against D-gal-induced colonic damage and cognitive impairment in mice. The results demonstrated that LNnT not only significantly improved systemic physiological phenotypes and upregulated the expression of colonic tight junction proteins to repair the intestinal barrier, but also effectively enhanced learning and memory abilities in mice. Concurrently, LNnT reduced serum proinflammatory factor levels, elevated the anti-inflammatory factor IL-10, and alleviated oxidative stress. Furthermore, LNnT remodeled the gut microbiome structure by increasing microbial diversity, enhancing beneficial bacteria abundance, and promoting short-chain fatty acid production. Untargeted metabolomics analysis further revealed that LNnT corrected metabolic disturbances by regulating key sphingolipid molecules (ceramide, sphingosine, S1P) and the expression of related metabolic enzymes (ACER2, SphK2). In summary, this study suggests that LNnT mitigates intestinal injury and improves cognitive function, potentially through modulation of the gut microbiota-sphingolipid metabolism axis, although further causal validation is warranted. These findings provide a mechanistic foundation for future studies exploring its potential as a functional dietary ingredient.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
Humans
*Sphingolipids/metabolism
*Cognitive Dysfunction/metabolism/drug therapy
*Milk, Human/chemistry
*Oligosaccharides/pharmacology/chemistry
*Colon/drug effects/metabolism/pathology
Male
Galactose
Intestinal Mucosa/metabolism/drug effects
Oxidative Stress/drug effects
Disease Models, Animal
Mice, Inbred C57BL

@article {pmid42123920,
year = {2026},
author = {Hachmeriyan, A and Panayotova, G and Todorova, H},
title = {From Plate to Mind: Scientific Perspectives on Foods That May Influence Anxiety and Depression.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42123920},
issn = {2072-6643},
mesh = {Humans ; *Fatty Acids, Omega-3/administration & dosage ; *Depression/diet therapy ; *Anxiety/diet therapy ; Gastrointestinal Microbiome ; Micronutrients/administration & dosage ; Dietary Supplements ; *Diet ; Randomized Controlled Trials as Topic ; Brain ; Probiotics/administration & dosage ; Vitamins/administration & dosage ; },
abstract = {Background: Nutritional psychiatry increasingly links diet quality and specific bioactive nutrients to depression and anxiety outcomes. Mechanistic evidence implicates neuroimmune activation, inflammation, altered neurotransmitter synthesis, and microbiota-derived metabolites. Objective: The objective of this study is to synthesize evidence on omega-3 polyunsaturated fatty acids (n-3 PUFAs), the microbiota-gut-brain axis, and vitamins and minerals that influence neurotransmitter synthesis, inflammation, and brain function and to translate these findings into food-based strategies. Methods: This study consisted of a focused synthesis of randomized controlled trials (RCTs), meta-analyses, and systematic reviews indexed in PubMed, Scopus and Web of Science, selected for relevance to omega-3s, probiotics/prebiotics, dietary patterns, and micronutrients (folate/B-vitamins, vitamin D, magnesium, zinc, and vitamin C/copper pathways). Results: RCT and meta-analytic evidence suggest modest benefits of omega-3 supplementation for anxiety severity and depressive symptoms, with heterogeneity by dose, EPA: DHA composition, and baseline inflammatory status. The gut-brain axis literature supports bidirectional effects of stress and microbiota, and meta-analyses of probiotics/prebiotics show small improvements in depressive and anxiety symptoms, likely dependent on strain and host phenotype. Micronutrients serve as enzymatic cofactors for monoamine and GABA synthesis and modulate immune signaling; clinical effects are the most consistent when correcting insufficiency or in biomarker-defined subgroups. A whole-diet RCT demonstrates that structured dietary improvement can reduce depressive symptoms as adjunctive therapy. Conclusions: A food-first approach emphasizing Mediterranean-style dietary patterns, omega-3-rich seafood, a diverse array of fiber, and micronutrient density is the most defensible. Supplementation may be considered selectively, guided by clinical context and nutritional status.},
}

Humans
*Fatty Acids, Omega-3/administration & dosage
*Depression/diet therapy
*Anxiety/diet therapy
Gastrointestinal Microbiome
Micronutrients/administration & dosage
Dietary Supplements
*Diet
Randomized Controlled Trials as Topic
Brain
Probiotics/administration & dosage
Vitamins/administration & dosage

@article {pmid42123927,
year = {2026},
author = {Rodziewicz, A and Bryl, E},
title = {The Role of Microbiome and Diet on Disease Activity and Immune-Inflammatory Status in Rheumatoid Arthritis.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42123927},
issn = {2072-6643},
support = {01-10026/0010451/01/262/0/2026//Gdańsk Medical University/ ; },
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/diet therapy/prevention & control ; *Gastrointestinal Microbiome ; *Diet ; Probiotics/administration & dosage ; Diet, Mediterranean ; Dietary Supplements ; Inflammation ; Prebiotics ; },
abstract = {Rheumatoid arthritis (RA) is a chronic inflammatory disease of autoimmune background and unknown etiology. The importance of genetic factors in RA development is well-established. Environmental factors have also been extensively researched in relation to risk of RA and managing its symptoms. Smoking, physical activity, diet, and gut microbiota are considered to be the most essential modifiable factors in RA. Among dietary interventions, the most researched is Mediterranean diet, monounsaturated fatty acids, fish consumption, and fish oil (EPA, eicosapentaenoic acid and DHA, that is, docosahexaenoic acid). Others concerned gluten-free and vegan or vegetarian diet, salt intake, supplementation with vitamin D, antioxidants, prebiotics, and probiotics. Diet modifications can alter the gut environment, and the association between RA development or severity and the composition of gut bacteria has already been shown. This review focuses on effectiveness and usefulness of various dietary approaches and supplements in RA prevention and management, including the influence on disease activity and inflammatory status. The composition of gut microbiota and its changes in response to dietary factors are also considered. There is a great need for further research into mutual dependencies of diet, microbiome, and RA activity. The current state of knowledge provides promising evidence for future nutrition and microbial therapies.},
}

Humans
*Arthritis, Rheumatoid/immunology/microbiology/diet therapy/prevention & control
*Gastrointestinal Microbiome
*Diet
Probiotics/administration & dosage
Diet, Mediterranean
Dietary Supplements
Inflammation
Prebiotics

@article {pmid42123931,
year = {2026},
author = {Maragno, P and Amoroso, C and Conforti, S and Michelon, M and Honcharyuk, I and Ciafardini, C and Noviello, D and Strati, F and Caprioli, F and Facciotti, F and Vecchi, M},
title = {The Assessment of Multidimensional Clinical, Biological and Patient-Reported Outcomes to Evaluate the Efficacy of Add-On Lactobacillus rhamnosus GG Supplementation in Mild Ulcerative Colitis: A Randomized Pilot Trial.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42123931},
issn = {2072-6643},
mesh = {Humans ; *Colitis, Ulcerative/therapy/drug therapy/microbiology ; Pilot Projects ; Female ; Male ; *Lacticaseibacillus rhamnosus ; Adult ; Double-Blind Method ; Middle Aged ; Mesalamine/therapeutic use/administration & dosage ; *Probiotics/administration & dosage/therapeutic use ; *Dietary Supplements ; Patient Reported Outcome Measures ; Quality of Life ; Gastrointestinal Microbiome/drug effects ; Treatment Outcome ; *Cholecalciferol/administration & dosage/therapeutic use ; Leukocyte L1 Antigen Complex/analysis ; Feces/chemistry/microbiology ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; },
abstract = {Background: Ulcerative colitis (UC) is a multifactorial disease characterized by aberrant mucosal immune activation in response to intestinal dysbiosis. Contemporary management strategies aim to target inflammation and microbiome alterations while reducing relapse risk. A multidimensional assessment integrating clinical, inflammatory, immune, and microbial endpoints may better capture therapeutic effects beyond symptom control. Aims: To evaluate whether supplementation with Lactobacillus rhamnosus GG co-formulated with vitamin D3 (Dicoflor IBD Immuno) as an adjunct to optimized mesalamine (5-ASA) is associated with coordinated changes across clinical and biological domains in mild-to-moderate UC, using a multidimensional assessment framework. Methods: This single-center, randomized, double-blind, placebo-controlled pilot trial was conducted at Fondazione Ca' Granda IRCCS Policlinico di Milano between May 2022 and May 2024. Thirty-six patients with mild-to-moderate UC receiving optimized 5-ASA were randomized to LGG+VitD3 (ALD3) or placebo (AP) for 4 weeks. Clinical activity, health-related quality of life (HRQoL), fecal calprotectin, peripheral immune cell subsets, and gut microbiota composition were assessed at baseline and week 4. Results: Both 5-ASA-LGG+VitD3 (ALD3)- and 5-ASA-placebo (AP)-treated patients showed significant improvement in clinical activity and HRQoL, without between-group differences. A higher proportion of clinical responders was observed in the ALD3 group, although this was not statistically significant. LGG+VitD3-supplemented patients showed reduced fecal calprotectin levels and increased frequencies of IL-22-producing CD4[+] T cells. Microbiome analysis revealed enrichment of short-chain fatty acid-producing taxa, including Coprococcus and Fusicatenibacter, in ALD3-treated patients. Conclusions: In patients with mild UC receiving optimized 5-ASA, LGG+VitD3 supplementation does not improve short-term clinical outcomes beyond placebo but is associated with favorable modulation of inflammatory, immune, and microbial parameters, supporting the relevance of multidimensional biological endpoints in adjunctive UC management.},
}

Humans
*Colitis, Ulcerative/therapy/drug therapy/microbiology
Pilot Projects
Female
Male
*Lacticaseibacillus rhamnosus
Adult
Double-Blind Method
Middle Aged
Mesalamine/therapeutic use/administration & dosage
*Probiotics/administration & dosage/therapeutic use
*Dietary Supplements
Patient Reported Outcome Measures
Quality of Life
Gastrointestinal Microbiome/drug effects
Treatment Outcome
*Cholecalciferol/administration & dosage/therapeutic use
Leukocyte L1 Antigen Complex/analysis
Feces/chemistry/microbiology
Anti-Inflammatory Agents, Non-Steroidal/therapeutic use

@article {pmid42123938,
year = {2026},
author = {Chiang, CK and Lai, CL and Chiu, MH and Huang, CJ},
title = {The Gut-Lung Axis in Allergic Asthma: A Narrative Review of Microbial Dysbiosis, Immune Regulation, and Nutritional Modulation.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42123938},
issn = {2072-6643},
support = {CGH-MR-B-11316//Cathay General Hospital/ ; },
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Asthma/immunology/microbiology ; *Lung/immunology/microbiology ; Animals ; Diet ; },
abstract = {Allergic asthma is a prevalent chronic inflammatory disease of the airways whose pathogenesis has traditionally been attributed to localized immune dysfunction within the lung. However, accumulating evidence from microbiome research supports a broader system-level perspective in which cross-organ interactions contribute to disease susceptibility and progression. In particular, the gut-lung axis has emerged as a key regulatory pathway linking intestinal microbial ecology, immune development, and respiratory health. This review synthesizes current epidemiological, mechanistic, and experimental evidence supporting the role of gut microbiota dysbiosis in allergic asthma. We examine how early-life environmental and nutritional exposures and gut microbiota establishment during critical developmental windows shape long-term immune tolerance and asthma susceptibility. We then summarize characteristic features of asthma-associated gut dysbiosis and discuss how microbial-derived metabolites, including short-chain fatty acids, tryptophan metabolites, pro-allergic lipid mediators such as 12,13-dihydroxy-9Z-octadecenoic acid, and bacterial-derived histamine, modulate distal airway immune responses through epigenetic, receptor-mediated, and immune trafficking mechanisms. Particular emphasis is placed on the role of diet as a key upstream regulator of gut microbiota composition and metabolic function. Finally, we evaluate experimental and translational studies targeting the gut-lung axis, including dietary modulation, microbiome-targeted interventions such as fecal microbiota transplantation, and emerging postbiotic approaches. Collectively, current evidence indicates that gut microbial composition and metabolic function are critical determinants of respiratory immune homeostasis. Targeting the gut-lung axis through nutrition- and microbiome-based strategies offers a promising avenue for the prevention and precision treatment of allergic asthma.},
}

Humans
*Dysbiosis/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Asthma/immunology/microbiology
*Lung/immunology/microbiology
Animals
Diet

@article {pmid42123967,
year = {2026},
author = {Blady, K and Pomianowski, B and Smółka, L and Strugała, M and Kursa, K and Stanek, A},
title = {The Therapeutic Potential of Polyphenols in Modulating Barrier Lipids, Microbiome Interactions, and Inflammatory Pathways in Atopic Dermatitis.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42123967},
issn = {2072-6643},
mesh = {Humans ; *Polyphenols/pharmacology/therapeutic use ; *Dermatitis, Atopic/drug therapy/microbiology/metabolism ; Filaggrin Proteins ; Animals ; Gastrointestinal Microbiome/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Inflammation/drug therapy ; *Lipid Metabolism/drug effects ; Epidermis/drug effects/metabolism ; Signal Transduction/drug effects ; *Microbiota/drug effects ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease with a complex pathogenesis involving epidermal barrier dysfunction, microbiome dysbiosis, and immune dysregulation. Despite significant advances in therapy, including biologics and targeted treatments, their use may be limited by adverse effects, highlighting the need for safe adjunctive strategies. Polyphenols are naturally occurring bioactive compounds that are abundant in plant-based foods and are known for their anti-inflammatory, antioxidant, and immunomodulatory properties, making them promising candidates for supportive AD management. This review integrates current evidence on the effects of polyphenols on epidermal barrier lipids, microbiome interactions, and key inflammatory pathways, including NF-κB and JAK/STAT signaling. Additionally, the role of polyphenols in modulating dendritic cell and neutrophil activity, and reducing reactive oxygen species (ROS) production and neutrophil extracellular trap (NET) formation, as well as their potential involvement in mitophagy regulation, is discussed. Polyphenols support epidermal barrier integrity by modulating the expression of key structural proteins, including filaggrin, involucrin, and loricrin, leading to a reduction in transepidermal water loss (TEWL). Furthermore, they interact bidirectionally with the gut microbiome, acting as metabolic substrates for beneficial bacteria and promoting the growth of short-chain fatty acid (SCFA)-producing species such as Lactobacillus, Bifidobacterium, and Akkermansia, while simultaneously inhibiting pathogenic strains. These findings highlight the role of polyphenols in maintaining microbiome homeostasis and supporting epidermal barrier integrity. The review encompasses findings from clinical studies, animal models, and mechanistic investigations, while also addressing limitations related to polyphenol bioavailability. Overall, polyphenols may represent a valuable adjunctive approach in AD management; however, further well-designed clinical and mechanistic studies are required to confirm their therapeutic potential.},
}

Humans
*Polyphenols/pharmacology/therapeutic use
*Dermatitis, Atopic/drug therapy/microbiology/metabolism
Filaggrin Proteins
Animals
Gastrointestinal Microbiome/drug effects
*Anti-Inflammatory Agents/pharmacology
Inflammation/drug therapy
*Lipid Metabolism/drug effects
Epidermis/drug effects/metabolism
Signal Transduction/drug effects
*Microbiota/drug effects

@article {pmid42124000,
year = {2026},
author = {Schubert, MG and Dentand, A and Karczewski, M and Morsy, Y and Beuschlein, F and Scharl, M and Krayenbuehl, PA},
title = {Dose-Dependent Alterations of the Human Gut Microbiome During Oral Iron Supplementation: A Randomized Study in Iron-Deficient Non-Anaemic Women.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124000},
issn = {2072-6643},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; Adult ; *Dietary Supplements ; *Iron/administration & dosage/adverse effects ; Administration, Oral ; Dose-Response Relationship, Drug ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Iron Deficiencies ; },
abstract = {Background/Objectives: Oral iron supplementation is widely used to treat iron deficiency but frequently causes gastro-intestinal side effects that limit treatment adherence. Unabsorbed luminal iron has been proposed to influence intestinal microbial communities, yet the effects of different oral iron doses on the human gut microbiome remain insufficiently characterized. Methods: In this randomized open-label study, 30 healthy premenopausal women with iron deficiency without anaemia received either low-dose oral iron supplementation (6 mg twice daily) administered under fasting conditions or standard-dose iron supplementation (100 mg once daily) taken with a meal for four weeks. Stool samples were collected before and after treatment and analyzed using 16S rRNA sequencing to evaluate microbiome composition. Results: Baseline characteristics, including age, body mass index, hemoglobin concentration and serum ferritin, were comparable between groups. After four weeks of treatment, distinct alterations in gut microbiome composition were observed between the low-dose and standard-dose groups. The genera Colidextribacter and GCA-900066575 decreased in the low-dose group but increased in the standard-dose group, whereas Oscillospira showed the opposite pattern. Gastrointestinal adverse events were reported by 87% of participants receiving standard-dose iron supplementation compared with 7% receiving low-dose iron supplementation (p < 0.0001). Conclusions: Oral iron supplementation induces dose-dependent changes in the intestinal microbiome and higher doses are associated with substantially increased gastrointestinal intolerance. These findings suggest that lower iron doses may reduce microbiome disruption and improve treatment tolerability.},
}

Humans
Female
*Gastrointestinal Microbiome/drug effects
Adult
*Dietary Supplements
*Iron/administration & dosage/adverse effects
Administration, Oral
Dose-Response Relationship, Drug
Feces/microbiology
Young Adult
RNA, Ribosomal, 16S/genetics
Iron Deficiencies

@article {pmid42124002,
year = {2026},
author = {Caserta, S and Martino, EA and Skafi, M and Vigna, E and Bruzzese, A and Amodio, N and Fiorillo, M and Lucia, E and D'Arrigo, G and Olivito, V and Labanca, C and Mendicino, F and Alvaro, ME and Tripepi, G and Morabito, F and Gentile, M},
title = {The Gut Microbiota in Hematologic Malignancies: Mechanisms, Clinical Associations, and Translational Opportunities.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124002},
issn = {2072-6643},
mesh = {Humans ; *Hematologic Neoplasms/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Animals ; Translational Research, Biomedical ; Dysbiosis ; },
abstract = {Hematologic malignancies arise and progress within a systemic ecosystem in which the gut microbiota is an increasingly recognized, partially modifiable component. Across acute leukemias, chronic lymphocytic leukemia, plasma cell disorders, lymphomas, and clonal myeloid neoplasms, human studies consistently report reduced microbial diversity, depletion of barrier-supportive, short-chain fatty acid-producing commensals, and enrichment of Gram-negative, pro-inflammatory, or hospital-adapted taxa. These alterations are associated with pre-leukemic clonal expansion, adverse genetic and immunological features, progression from precursor conditions, and inferior outcomes after chemotherapy, immunochemotherapy, chimeric antigen receptor T-cell therapy, and allogeneic hematopoietic stem cell transplantation. Mechanistic work in animal models and ex vivo systems demonstrates that microbiota-derived signals and metabolites-including Th17/IL-17-skewing consortia and the lipopolysaccharide intermediate ADP heptose sensed by the cytosolic receptor ALPK1-can actively modulate hematopoietic stem and progenitor cell fitness, inflammatory circuits, and malignant cell survival, supporting a causal role in disease biology. At the same time, major knowledge gaps remain because most human cohorts are small, single-center, and cross-sectional, frequently rely on 16S rRNA profiling, and are vulnerable to dietary, geographic, and treatment-related confounding. Within this context, three translational domains appear particularly promising: pharmaco-microbiomics, microbiome-informed risk stratification, and rational microbiota-targeted interventions, particularly diet-based strategies and antimicrobial stewardship. Here, we provide an integrated, disease-spanning synthesis of these data, emphasizing clonal hematopoiesis and myeloid neoplasms as emerging examples of microbiota-marrow crosstalk and outlining practical priorities for embedding microbiome science into future hematologic trials. Routine microbiome profiling or empiric microbiota-directed therapies cannot yet be recommended in everyday hematology practice, but integrating microbiome science into prospective therapeutic and transplant trials offers a realistic path to improved disease modeling, biomarker development, and rational adjunctive strategies to enhance outcomes for patients with hematologic malignancies.},
}

Humans
*Hematologic Neoplasms/microbiology/therapy
*Gastrointestinal Microbiome/physiology
Animals
Translational Research, Biomedical
Dysbiosis

@article {pmid42124012,
year = {2026},
author = {Zeng, Y and Ahmed, M and Zhang, H},
title = {Beyond Antioxidants: The Microbial Metabolic Landscape of Anthocyanins and Their Downstream Health Implications.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124012},
issn = {2072-6643},
support = {20243BCC31009//Key Project of Jiangxi Provincial Key Research and Development Program/ ; 32560560//National Natural Science Foundation of China/ ; },
mesh = {*Anthocyanins/metabolism/pharmacokinetics ; *Gastrointestinal Microbiome/physiology ; Humans ; *Antioxidants/metabolism ; Biological Availability ; Hydroxybenzoates/metabolism ; Animals ; Signal Transduction ; },
abstract = {BACKGROUND/OBJECTIVES: Anthocyanins are dietary pigments associated with reduced risk of chronic diseases, yet their low systemic bioavailability challenges the traditional direct antioxidant hypothesis. This review aims to reconceptualize anthocyanin bioactivity by proposing the gut microbiome as a key mediator that biotransforms these compounds into bioactive metabolites responsible for systemic health effects.

METHODS: This review synthesizes evidence on the microbial metabolism of anthocyanins and includes a structured appraisal of the literature using an evidence evaluation framework analogous to GRADE, focusing on their transit to the colon, enzymatic biotransformation by gut microbiota, and resulting production of phenolic metabolites such as protocatechuic acid (PCA). It also examines the role of specific bacterial taxa (e.g., Bifidobacterium and Lactobacillus) in enhancing bioavailability and explores the downstream cellular pathways modulated by these metabolites.

RESULTS: Gut microbiota convert anthocyanins into smaller phenolic metabolites such as PCA, syringic acid, gallic acid, and other respective metabolites, which achieve plasma concentrations up to 100-fold higher than parent compounds and can cross the blood-brain barrier. These metabolites exert systemic effects by modulating key signaling pathways (NF-κB and Nrf2) and restoring redox homeostasis. Additionally, beneficial gut bacteria enhance anthocyanin bioavailability and support the production of short-chain fatty acids (SCFAs).

CONCLUSIONS: Systemic health benefits of anthocyanins are largely mediated by gut microbiota through the generation of bioactive metabolites. This microbiota-driven process redefines the mechanistic understanding of anthocyanin action and highlights the microbiome as a critical determinant of their efficacy in preventing cardiometabolic and neurodegenerative diseases.},
}

*Anthocyanins/metabolism/pharmacokinetics
*Gastrointestinal Microbiome/physiology
Humans
*Antioxidants/metabolism
Biological Availability
Hydroxybenzoates/metabolism
Animals
Signal Transduction

@article {pmid42124014,
year = {2026},
author = {Uțu, D and Nodiți-Cuc, AR and Kiș, AM and Popovici, RA and Pitic, DE and Trusculescu, LM and Marian, D and Nan, AG and Matin, AS and Cîmpian, DM and Bodo, CR and Enache, A and Olariu, I},
title = {Diet-Microbiome-Brain Axis and Mental Health: Biological Mechanisms and Nutritional Implications.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124014},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mental Health ; *Brain/physiology ; Animals ; *Diet ; *Mental Disorders/prevention & control ; Probiotics ; Prebiotics/administration & dosage ; Dysbiosis ; },
abstract = {BACKGROUND/OBJECTIVES: Diet is a primary and modifiable determinant of gut microbiota composition, diversity, and metabolic activity, thereby shaping microbial-derived metabolites, immune and inflammatory signalling, neuroendocrine regulation, and neural communication with the central nervous system. Western dietary patterns, characterised by high intake of ultra-processed foods, saturated fats, and low dietary fibre, are consistently associated with gut dysbiosis, impaired intestinal barrier function, chronic low-grade inflammation, and increased risk of depression, anxiety, cognitive impairment, and neurodegenerative disorders.

METHODS: This narrative review synthesises evidence from human observational studies, randomised controlled trials, animal models, and mechanistic investigations examining interactions among diet, gut microbiota, and mental health or neurobiological outcomes. Literature searches were conducted in PubMed, Scopus, and Web of Science for articles published up to December 2025.

RESULTS: The study highlights the therapeutic potential and limitations of dietary interventions, prebiotics, probiotics, and psychobiotics, and critically evaluates them. Also facilitates an improved understanding of diet-microbiome-brain interactions, which may help the development of personalised, nutrition-based strategies integrated into mental health prevention and clinical care.

CONCLUSIONS: These findings support diet-based, microbiome-informed strategies as scalable adjuncts in mental health prevention and care.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mental Health
*Brain/physiology
Animals
*Diet
*Mental Disorders/prevention & control
Probiotics
Prebiotics/administration & dosage
Dysbiosis

@article {pmid42124034,
year = {2026},
author = {Kłosek, S and Szymczak-Paluch, M and Bernaś, A and Gawlak-Socka, S},
title = {Does Probiotic Intake Enhance the Efficacy of Oral Fungal Infection Treatment?.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124034},
issn = {2072-6643},
support = {503/2-148-07/503-21-001//Medical University of Lodz/ ; },
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Candidiasis, Oral/microbiology/therapy/drug therapy ; Antifungal Agents/therapeutic use ; Mouth/microbiology ; Microbiota ; },
abstract = {Oral candidiasis (OC) is the most frequent fungal infection among users of dental prosthetic devices, immunocompromised patients, and those who underwent chemotherapy treatment and had a complication of long-term antibiotic therapy. About 150 species of Candida fungi have been described, whereas over 80% of oral fungal infections are attributed to the opportunistic pathogen Candida albicans. Pain, dryness of oral mucosa, pathological lesions, and intermittent mucosal bleeding are the main symptoms that worsen the daily functioning of the abovementioned fungal-infected patients. A promising adjunctive strategy may involve the use of probiotic bacteria to attenuate fungal colonization in the oral cavity in order to reduce the need for conventional treatment, which carries a risk of antifungal drug resistance-a significant problem worldwide. Probiotic formulations mostly incorporate commensal bacteria that naturally inhabit oral ecosystems such as Lactobacillus spp., Bifidobacterium spp., Bacillus spp., and others. Probiotic organisms may contribute to the restoration of oral microbiome homeostasis through numerous mechanisms, such as competitive control of Candida species numbers, better adhesion to oral mucosa and production of bioactive compounds and antimicrobial metabolites. Despite many studies, the current evidence base remains heterogeneous. Well-designed studies across diverse populations are required to determine whether probiotic-based interventions can be an effective and clinically useful alternative or adjunct to standard antifungal therapy of OC.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Candidiasis, Oral/microbiology/therapy/drug therapy
Antifungal Agents/therapeutic use
Mouth/microbiology
Microbiota

@article {pmid42124041,
year = {2026},
author = {Son, JY and Do, Y and Seo, J and Choi, J},
title = {Gut-Derived Metabolic Imbalance in Autism Spectrum Disorder: Toward the Concept of a Metabolic Subtype.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124041},
issn = {2072-6643},
support = {Ky-lin Foundation in 2024//Daegu Haany University/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Fatty Acids, Volatile/metabolism ; Dysbiosis/metabolism ; *Gastrointestinal Tract/metabolism ; Animals ; },
abstract = {Autism spectrum disorder (ASD) is highly heterogeneous in symptom onset and severity, comorbidities, and treatment responsiveness, challenging the notion of a single pathogenic mechanism. Increasing evidence indicates that some individuals with ASD exhibit prominent peripheral physiological alterations, including gastrointestinal (GI) dysfunction, gut microbial dysbiosis, immune imbalance, oxidative stress, and mitochondrial/energy metabolic vulnerability. In this context, gut-derived metabolites-particularly short-chain fatty acids (SCFAs)-have emerged as plausible modulators of the neurodevelopmental milieu through the expanded gut-immune-metabolic-brain axis. This review synthesizes: (i) SCFAs' biogenesis and physiological roles, (ii) context- and developmental stage-dependent effects, (iii) the clinical heterogeneity of reported microbiome and SCFA alterations in ASD, and (iv) propionate as a frequently discussed candidate signal and the interpretive boundaries of preclinical evidence. Human studies show substantial inter-study variability in SCFA alterations (increases, decreases, or no differences), influenced by factors such as sample type (stool vs. blood), GI symptoms, diet, medication exposure, and analytical variability. Accordingly, SCFAs should not be treated as universal ASD biomarkers but rather as context-dependent metabolic signals relevant under specific clinical and biological conditions. Building on this premise, we propose the conceptual framework of "metabolic ASD" representing a metabolically informed dimension of biological variability in which peripheral metabolic-immune perturbations may contribute to neurodevelopmental vulnerability. To avoid premature causal claims, we outline design requirements for future research, including stratified study designs, longitudinal cohorts, and integrative multi-layer analyses. Ultimately, metabolic ASD should be positioned as a testable precision medicine research framework rather than a universal etiological model.},
}

Humans
*Autism Spectrum Disorder/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
*Fatty Acids, Volatile/metabolism
Dysbiosis/metabolism
*Gastrointestinal Tract/metabolism
Animals

@article {pmid42124048,
year = {2026},
author = {Thakur, D and Harmer, MJ},
title = {Circulating Short-Chain Fatty Acid Levels in Chronic Kidney Disease: A Systematic Review and Meta-Analysis.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124048},
issn = {2072-6643},
mesh = {Humans ; *Fatty Acids, Volatile/blood ; *Renal Insufficiency, Chronic/blood ; Child ; Adult ; Butyrates/blood ; Female ; Male ; Propionates/blood ; },
abstract = {BACKGROUND: Chronic kidney disease (CKD) is characterised by a disrupted gut-kidney axis, wherein intestinal dysbiosis is associated with the accumulation of uraemic toxins and the potential depletion of beneficial short-chain fatty acids (SCFAs). Whilst acetate, propionate, and butyrate are known to modulate systemic inflammation and blood pressure, their precise circulating concentrations across different CKD stages and age groups remain poorly defined. This systematic review and meta-analysis aimed to quantify blood SCFA concentrations in CKD patients compared to healthy controls.

METHODS: We conducted a systematic search of Medline, EMBASE, and the Cochrane Library for clinical studies reporting blood SCFA concentrations in humans with CKD. Methodological quality was assessed using the NIH tool. Standardised mean differences (SMDs) were calculated for the quantitative meta-analysis, with subgroup analyses performed for age, CKD stage, and treatment modality (dialysis vs. transplantation).

RESULTS: Twenty-one studies encompassing 9661 participants were included. Quantitative synthesis revealed a significant and consistent systemic depletion of circulating acetate and propionate in adult CKD patients compared to healthy controls (p < 0.05). This depletion followed a stage-dependent trajectory, worsening alongside declining glomerular filtration rates. Notably, a "butyrate paradox" was identified in paediatric cohorts; whilst adults showed progressive butyrate depletion, children with CKD often maintained or exhibited elevated levels, particularly in the context of hypertension. Furthermore, whilst haemodialysis patients exhibited the most profound SCFA deficiencies, kidney transplantation appeared to partially restore these metabolites toward healthy baseline levels.

CONCLUSIONS: CKD is associated with a profound systemic reduction in acetate and propionate, supporting the model of a compromised gut-kidney axis based on converging evidence. The divergent results for butyrate in paediatric versus adult populations suggest that SCFA metabolism is influenced by age-related factors or compensatory mechanisms. These findings highlight the potential for SCFA monitoring as a candidate or emerging markers for detecting early renal damage and stratifying risk.},
}

Humans
*Fatty Acids, Volatile/blood
*Renal Insufficiency, Chronic/blood
Child
Adult
Butyrates/blood
Female
Male
Propionates/blood

@article {pmid42124049,
year = {2026},
author = {Liu, H and Shi, CY and Fahey, JW},
title = {Sulforaphane in Cutaneous Disorders and Skin Injury: Mechanisms, Evidence, and Clinical Perspectives.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42124049},
issn = {2072-6643},
mesh = {Humans ; *Isothiocyanates/pharmacology/therapeutic use ; Sulfoxides ; *Skin Diseases/drug therapy/metabolism ; Animals ; *Skin/drug effects/metabolism/injuries ; Signal Transduction/drug effects ; Anti-Inflammatory Agents/pharmacology ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; },
abstract = {Cutaneous disorders such as atopic dermatitis, psoriasis, acne vulgaris, and rosacea, together with UV-induced skin injury and photoaging, are highly prevalent conditions that involve varying contributions from dysregulated immune responses, cutaneous inflammation, oxidative stress, barrier dysfunction, microbiome alteration, and exogenous injury. However, these conditions are biologically heterogeneous and should not be regarded as a single mechanistic class. Sulforaphane, a naturally occurring isothiocyanate found primarily in broccoli and other cruciferous vegetables, has attracted interest in dermatology because of its antioxidant, cytoprotective, and context-dependent anti-inflammatory properties. Sulforaphane exerts its biological effects by modulating key signaling pathways, particularly the Keap1/Nrf2 pathway and, in some settings, NF-κB-related signaling, thereby reducing oxidative stress and inflammation, regulating immune responses, enhancing skin barrier function, and potentially influencing the cutaneous microbiome. Preclinical studies and limited human data suggest that sulforaphane may reduce erythema, edema, and other markers of cutaneous damage in selected settings. This comprehensive review explores the role of sulforaphane across heterogeneous cutaneous conditions, with emphasis on molecular mechanisms, disease-specific differences, current evidence, and discusses key translational constraints including formulation, delivery, lack of standardized dosing, and the limitations of cell culture and animal models for predicting human efficacy. Overall, sulforaphane should presently be regarded as a promising but still early-stage translational candidate in dermatology. Robust human efficacy data remain lacking for chronic inflammatory dermatoses such as psoriasis, atopic dermatitis, acne, and rosacea, whereas the strongest current human evidence relates to UV-associated skin outcomes and photoprotection.},
}

Humans
*Isothiocyanates/pharmacology/therapeutic use
Sulfoxides
*Skin Diseases/drug therapy/metabolism
Animals
*Skin/drug effects/metabolism/injuries
Signal Transduction/drug effects
Anti-Inflammatory Agents/pharmacology
Oxidative Stress/drug effects
Antioxidants/pharmacology

@article {pmid42124376,
year = {2026},
author = {Moltrasio, C and Marzano, AV and Romagnuolo, M},
title = {The Multifaceted Role of Keratinocytes in Hidradenitis Suppurativa Pathogenesis.},
journal = {Experimental dermatology},
volume = {35},
number = {5},
pages = {e70269},
pmid = {42124376},
issn = {1600-0625},
support = {//Italian Ministry of Health (Ricerca Corrente) of Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan (Italy)./ ; },
mesh = {Humans ; *Hidradenitis Suppurativa/immunology/etiology/physiopathology ; *Keratinocytes/physiology ; Cytokines/metabolism ; Signal Transduction ; Inflammation ; Animals ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic autoinflammatory skin disorder of the pilosebaceous unit, with multiple factors contributing to its onset, activity and progression. Alongside a predisposing genetic background, hormonal and microbiome alterations, dysregulation of innate and adaptive immune response, as well as environmental/epigenetic factors contribute to its immunopathogenic landscape. In the past years, translational investigations identified several distinct inflammatory networks, not only in the chronic but also in the early stages of disease, making them potential therapeutic targets. Emerging evidence underlies the important role of keratinocytes in the pathogenesis and progression of HS, acting not only as targets of inflammatory signaling pathways but also as active producers of pro-inflammatory cytokines, chemokines and effector molecules that may influence disease onset and activity. Despite these insights, different aspects of their involvement remain underexplored, necessitating further targeted research. This review aims to highlight the experimental evidence supporting the crucial role of keratinocytes in the inflammatory response and overall pathophysiology of HS.},
}

Humans
*Hidradenitis Suppurativa/immunology/etiology/physiopathology
*Keratinocytes/physiology
Cytokines/metabolism
Signal Transduction
Inflammation
Animals

@article {pmid42124457,
year = {2026},
author = {Wang, C and Xu, Z and Ma, M and Fu, Z and Yao, K},
title = {Gallic Acid Protects Against DSS-Induced Colitis by Modulating Gut Microbiota and Suppressing the Activation of NF-κB/MAPK Signaling Pathway.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {9},
pages = {e70487},
doi = {10.1002/mnfr.70487},
pmid = {42124457},
issn = {1613-4133},
support = {LY22B070007//Natural Science Foundation of Zhejiang Province/ ; },
mesh = {Animals ; *Gallic Acid/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; *NF-kappa B/metabolism ; Mice, Inbred C57BL ; Caco-2 Cells ; Mice ; Dextran Sulfate/toxicity ; *MAP Kinase Signaling System/drug effects ; Male ; RAW 264.7 Cells ; *Colitis/chemically induced/prevention & control/drug therapy ; Cytokines/metabolism ; Colon/pathology/drug effects ; Coculture Techniques ; },
abstract = {To investigate the protective role and mechanisms of gallic acid (GA) against ulcerative colitis (UC), C57BL/6 mice were pretreated with GA (10 or 50 mg/kg) or saline for 21 days before colitis induction with 2.5% DSS for 7 days. An in vitro Caco-2/RAW 264.7 coculture model mimicking the intestinal epithelium was used. After 24-h GA pretreatment, inflammation was induced with LPS in Caco-2/RAW 264.7 coculture cell for 4 h. GA alleviated colitis symptoms, improving body weight, preventing colon shortening, reducing histopathological damage, and lowering pro-inflammatory cytokines (IL-6, IL-22, TNF-α, IL-17α). It enhanced intestinal barrier integrity by upregulating tight junction (TJ) proteins claudin-1 and occludin. Mechanistically, GA inhibited NF-κB and MAPK pathways by suppressing phosphorylation of p65, IκB, JNK, ERK, and P38 in colon tissue. GA also favorably modulated the gut microbiome, reducing pathobionts (e.g., Desulfovibrio) and enriching beneficial genera like Enterobacteria and Prevotella. In the cell coculture model, GA suppressed LPS-induced pro-inflammatory mediators, upregulated IL-10, and restored LPS-downregulated TJ protein expression. These findings indicate that GA alleviates DSS-induced UC by restoring intestinal homeostasis, exerting anti-inflammatory effects, and providing preventive benefits upon long-term use, supporting its potential as a prophylactic agent for UC.},
}

Animals
*Gallic Acid/pharmacology
*Gastrointestinal Microbiome/drug effects
Humans
*NF-kappa B/metabolism
Mice, Inbred C57BL
Caco-2 Cells
Mice
Dextran Sulfate/toxicity
*MAP Kinase Signaling System/drug effects
Male
RAW 264.7 Cells
*Colitis/chemically induced/prevention & control/drug therapy
Cytokines/metabolism
Colon/pathology/drug effects
Coculture Techniques

@article {pmid42124488,
year = {2026},
author = {Koynova-Tenchov, R},
title = {Molecular Dialogues in the Mitochondria-Microbiome Crosstalk: Metabolites, Signaling, and Immunity.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70164},
doi = {10.1002/cph4.70164},
pmid = {42124488},
issn = {2040-4603},
mesh = {Humans ; *Mitochondria/metabolism ; Animals ; Signal Transduction/physiology ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; },
abstract = {The bidirectional dialogue between mitochondria and the human microbiota-the mitochondria-microbiome axis-plays a pivotal role in regulating host metabolism, immune signaling, and overall physiological homeostasis. Growing evidence underscores the role of microbial metabolites-including short-chain fatty acids, secondary bile acids, and lipopolysaccharides-as direct modulators of mitochondrial bioenergetics, redox balance, and inflammatory cascades. Conversely, mitochondrial integrity governs the microbial landscape by regulating local oxygen tension, modulating immune-mediated selection, and secreting metabolic byproducts that shape commensal populations. Disruptions to this bidirectional crosstalk are linked to a diverse pathological spectrum. These include metabolic syndromes like obesity, type 2 diabetes, and NAFLD; neurodegenerative disorders such as Parkinson's and Alzheimer's; and systemic inflammatory conditions, notably inflammatory bowel disease and various autoimmune pathologies. Therapeutic interventions designed to modulate this axis-ranging from targeted probiotics, dietary interventions, and mitochondrial boosters-offer significant potential for reinstating physiological homeostasis. This review explores the molecular foundations of mitochondria-microbiome crosstalk, its role in disease pathogenesis, and the potential for microbiome-targeted therapies to restore mitochondrial health. Unraveling this complex dialogue may open new avenues for treating diseases rooted in metabolic and microbial dysbiosis. On the basis of a wide-ranging literature survey, the frontiers of the molecular dialogues involved in the mitochondria-microbiome communications are evaluated. By analyzing publication trends, we identify nascent perspectives and transformative concepts, mapping the mitochondria-microbiome axis research, aiming to bridge the gap between basic science and translational applications. This synthesis offers a fresh lens for treating diseases rooted in this intricate biological interplay.},
}

Humans
*Mitochondria/metabolism
Animals
Signal Transduction/physiology
*Microbiota/physiology
*Gastrointestinal Microbiome/physiology

@article {pmid42124590,
year = {2026},
author = {Schell, LD and Liow, YJ and Carmody, RN},
title = {Fasting and re-feeding independently alter mouse gut microbiota during intermittent fasting.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.25.707984},
pmid = {42124590},
issn = {2692-8205},
abstract = {Intermittent fasting (IF) elicits metabolic benefits that are partially driven by the gut microbiome. Studies have focused on endpoint IF-induced changes in the gut microbiome but have not explored whether the oscillating nature of IF elicits day-to-day microbiome changes that could independently affect health. To discriminate the long-term and short-term effects of IF on the gut microbiota, we fasted mice every other day (IF1:1) or every two days (IF1:2), measuring daily changes in body mass and composition, food intake, and gut microbiota composition. We show that short-term effects of fasting and re-feeding on gut microbiota composition outweigh longer-term effects of IF treatment, with composition responding differently to re-feeding and fasting. Re-feeding specifically promoted rapid expansion of Lactobacillus , a bacterial genus linked mechanistically to the metabolic benefits of IF. Our results highlight the plasticity of the gut microbiota, especially re-feeding effects, as a potential contributor to microbiome-mediated metabolic benefits of IF.},
}

@article {pmid42124632,
year = {2026},
author = {Adade, EE and Wang, R and Henneberry, CM and Lemus, AA and Stevick, RJ and Perez-Pascual, D and Audrain, B and Orsino, AJ and Farnsworth, DR and Ghigo, JM and Valm, AM},
title = {Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.26.708344},
pmid = {42124632},
issn = {2692-8205},
abstract = {The spatial organization of microbial communities is a critical determinant of host-microbe interactions, yet species-level mapping remains challenging due to high 16S rRNA sequence homology and spectral crosstalk in multiplexed fluorescence in situ hybridization (FISH). To address this challenge, we developed Cross-hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH, a pipeline that integrates strategic probe design with supervised machine learning. CIPHR-FISH transforms probe cross-hybridization and spectral overlap, traditionally viewed as experimental noise, into informative molecular signatures. Using a gnotobiotic zebrafish model colonized with a defined mix of 10 zebrafish bacterial strains, we trained a support vector machine (SVM) on empirical hybridization patterns from pure bacterial cultures. CIPHR-FISH achieved 99.2 % macro-averaged accuracy, significantly outperforming standard linear unmixing (62.5 %), and successfully discriminated strains with 99.7% sequence homology. Applying this tool to gnotobiotic zebrafish larvae revealed distinct biogeographies: the intestinal bulb hosted highly structured, multi-layered polymicrobial aggregates, while the skin exhibited sparse, uniformly dispersed individual bacterial cells. Notably, we observed significant inter-individual variation in spatial community structure that was obscured by traditional bulk 16S rRNA sequencing. CIPHR-FISH provides a robust, scalable framework for high-resolution spatial biology by converting the limitations of molecular labeling into a rich data source for taxonomic classification. This approach enables the quantification of micro-scale ecological and stochastic forces that shape the microbiome across hosts.},
}

@article {pmid42124675,
year = {2026},
author = {Badenoch, AJ and Pang, Z and Chung, CH and Robida, A and Badenoch, B and Natesan, R and Kakish, L and Li, J and Chandrasekaran, S},
title = {Modeling Microbiome Modulation of Tumor Metabolic Networks to Predict Synergistic Therapies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.25.707963},
pmid = {42124675},
issn = {2692-8205},
abstract = {Differences in microbiome composition profoundly influence drug response, yet methods to model the metabolic interplay between tumors, microbes, and therapeutics remain limited. We present a generalizable framework combining machine-learning and genome-scale metabolic modeling to prioritize combination therapies for colorectal cancer (CRC) in the presence of Fusobacterium nucleatum (Fn) and other pathogenic, probiotic, and commensal microbes. Trained on 6,514 drug combinations in microbe-free CRC cell lines, the model predicted synergistic combinations in both microbe-free and microbe-associated contexts and generalized to immunotherapy-associated conditions. Predictions were validated using an asymmetric co-culture system that mimics the colon's normoxic-anaerobic gradient, confirming synergistic combinations in HCT116 cells with Fn , including drugs not typically used in CRC therapy. Mechanistic analysis and targeted pharmacological perturbations revealed phospho-inositol metabolism and cysteine transport as key determinants of Fn -dependent drug synergy. Together, this work introduces a scalable, microbiome-aware framework to enable discovery of context-specific combination therapies.},
}

@article {pmid42124729,
year = {2026},
author = {Cho, B and Kostic, AD and Tierney, BT and Patel, CJ},
title = {The Oral Microbiome Is a Population-Scale Readout of the Exposome, Age, and Systemic Health.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.23.707541},
pmid = {42124729},
issn = {2692-8205},
abstract = {The oral microbiome interfaces humans and the environment and is implicated in diseases from caries to cardiovascular conditions. Yet, few studies systematically interrogate oral taxa associations with the host phenome and exposome in diverse populations. We developed a comprehensive oral microbiome atlas, deploying a Microbiome Association Study (MAS) evaluating relationships between host features including exposome, disease, and physiology and the microbiome in a 10,000-person representative US population. Evaluating demographics, 133 phenotypes, 473 exposures, and 20 disease outcomes across 1,349 taxa yielded >800k relationships and 45,757 FDR-significant associations. Age emerged as a major organizing axis, with genera following non-linear life-course patterns. Oral disease, smoking, and dietary sugar correlated with aciduric and anaerobic taxa, whereas oral health featured oxygen-tolerant Proteobacteria . The exposome and cardiovascular/respiratory disease linked to diverse taxa. These results establish the oral microbiome as a sensitive, population-scale indicator of the exposome, phenome, and systemic health.},
}

@article {pmid42125129,
year = {2026},
author = {Khantsi, M and Babalola, OO},
title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {},
pages = {e70157},
pmid = {42125129},
issn = {2575-6265},
abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.},
}

@article {pmid42125405,
year = {2026},
author = {Li, Q and Li, Z and Zeng, G and Zhang, M and Wang, F and Chen, P and Yan, S},
title = {Geographical and seasonal variations of soil microbiomes and metabolomes in the core production area of Jiang-flavor Baijiu: a multi-omics characterization.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1816391},
pmid = {42125405},
issn = {1664-302X},
abstract = {The unique flavor of Chinese Jiang-flavor Baijiu is hypothesized to be influenced by the regional environment. However, the specific contributions of soil microbiomes and metabolomes remain poorly characterized. This study systematically analyzed soil phenotypes, microbiomes, and metabolomes at five sampling sites near the Moutai production area across spring and autumn. Using high-throughput sequencing, untargeted metabolomics, and multi-omics integration, we explored the impacts of geographical location and seasonal changes. Results revealed significant differences in soil microbial biomass, dominant taxa, and differential metabolites among sites. Region-specific marker microorganisms and metabolic pathways were identified. Seasonal variations, particularly in Region A, strongly affected metabolite profiles. Multi-omics correlation analysis revealed that Ascomycota abundance was positively associated with flavor precursor metabolites including phenylpropanoids, organosulfur compounds, and nucleosides, which are known precursors of aromatic compounds found in Baijiu. This study characterizes the distinct ecological profiles of soils in the core production area, providing a foundational dataset for understanding the regional environmental context of Jiang-flavor Baijiu. These findings offer insights for protecting the regional ecological integrity associated with production areas.},
}

@article {pmid42125496,
year = {2026},
author = {Cho, MY and Eom, JH and Kim, JW and Kim, Y and Park, JA and Kim, HJ and Lee, JY and Han, HL and Ko, SJ and Her, SB and Ko, DY and Kim, HS and Baek, H},
title = {Oral microbiome profiles by periodontitis stage in a Korean population.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1809787},
pmid = {42125496},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Adult ; *Periodontitis/microbiology ; Republic of Korea/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; Pilot Projects ; *Mouth/microbiology ; DNA, Bacterial/genetics ; Dysbiosis/microbiology ; Biodiversity ; Aged ; },
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by oral microbial dysbiosis. Although the oral microbiome has been characterized in diverse populations, comprehensive profiling across periodontal disease stages defined by the 2018 AAP/EFP classification remains limited in Korean adults.

METHODS: In this pilot prospective cross-sectional study, oral microbiome profiles were characterized in 74 participants classified into three groups: healthy controls (n = 24), Stage I-II periodontitis (n = 12), and Stage III-IV periodontitis (n = 38). Mouthwash samples were collected and subjected to 16S rRNA gene sequencing of the V3-V4 hypervariable region. Alpha diversity, beta diversity (PERMANOVA with sequential covariate adjustment for age, sex, and smoking), differential abundance (MaAsLin2), and core microbiome analyses were performed.

RESULTS: Stage III-IV periodontitis was associated with significantly higher Shannon diversity, Simpson diversity, and Pielou's evenness compared to both healthy and Stage I-II groups, indicating increased evenness rather than species richness. Beta diversity analyses revealed significant community-level separation across groups after adjustment for demographic confounders (allp = 0.001). Differential abundance analysis identified 14 genera significantly associated with disease status. Twelve genera were enriched in Stage III-IV, including established periodontal pathogens Tannerella and Treponema, as well as emerging pathobionts Filifactor and Fretibacterium. Rothia and Kingella were enriched in periodontal health, consistent with their roles in nitrate reduction and maintenance of a health-compatible oral environment. Core microbiome analysis identified 40 universally present genera, with Anaeroglobus detected exclusively in Stage III-IV at 100% prevalence.

CONCLUSION: These findings support the polymicrobial synergy and dysbiosis model of periodontitis pathogenesis and provide a foundation for developing microbiome-based diagnostic tools for periodontal disease assessment in Korean populations.},
}

Humans
*Microbiota/genetics
Male
Female
Middle Aged
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Prospective Studies
Adult
*Periodontitis/microbiology
Republic of Korea/epidemiology
*Bacteria/classification/genetics/isolation & purification
Pilot Projects
*Mouth/microbiology
DNA, Bacterial/genetics
Dysbiosis/microbiology
Biodiversity
Aged

@article {pmid42125498,
year = {2026},
author = {Huang, Y and Tang, Y and Huang, Y and Wang, Y},
title = {Commentary: Gut and oral microbiome profiles in patients with obesity and ischemic heart disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1834415},
pmid = {42125498},
issn = {2235-2988},
}

@article {pmid42125597,
year = {2026},
author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK},
title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112791},
pmid = {42125597},
issn = {2352-3409},
abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.},
}

@article {pmid42125670,
year = {2026},
author = {Lim, JN and Oh, Y and Han, K and Mun, S and Lee, JY},
title = {Evaluation of digital colorimetric analysis as an objective indicator representing microbial diversity and biological succession of dental plaque.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2670840},
pmid = {42125670},
issn = {2000-2297},
abstract = {BACKGROUND: Visual assessment of dental plaque is limited by subjectivity and variability in imaging conditions.

OBJECTIVE: This study aimed to objectively quantify plaque maturation using CIE L*a*b*-based color difference (ΔE*) and evaluate its association with microbial community structure and pathogenicity.

DESIGN: Dental images were obtained from 30 participants after application of a plaque-disclosing agent. Plaque color was quantified as ΔE* relative to unstained tooth surfaces and classified into Low-ΔE* and High-ΔE* groups. Saliva and supragingival plaque samples from Low-ΔE* and High-ΔE* sites were collected, and full-length 16S rRNA gene sequencing was performed using the PacBio Sequel IIe platform.

RESULTS: Saliva showed significantly higher microbial diversity than plaque samples. The Low-ΔE* group was dominated by early colonizers, including Streptococcus sanguinis, whereas the High-ΔE* group showed enrichment of anaerobic and periodontal disease-associated taxa, including Prevotella, Treponema, Selenomonas, Campylobacter, and Porphyromonas endodontalis. The lightness value (L*) was negatively correlated with periodontal pathogens, including Treponema denticola and Tannerella forsythia. PICRUSt2 analysis indicated upregulation of inflammatory pathways, including NOD-like receptor signaling and apoptosis, in the High-ΔE* group.

CONCLUSIONS: ΔE*-based colorimetric analysis may serve as an objective indicator of dental plaque maturation and pathogenic potential, supporting personalized oral hygiene feedback.},
}

@article {pmid42125834,
year = {2026},
author = {de Souza, LHN and da Silva, GF and Dos Santos Ferreira, MCA and Mello, PL and Ferreira, LEN},
title = {Candida albicans, HIV And Immune System in a Holobiont Perspective.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {134},
number = {5},
pages = {e70224},
doi = {10.1111/apm.70224},
pmid = {42125834},
issn = {1600-0463},
mesh = {Humans ; *Candida albicans/immunology/physiology/pathogenicity ; *HIV-1/immunology/physiology ; *HIV Infections/immunology/microbiology/virology ; Host-Pathogen Interactions/immunology ; CD4-Positive T-Lymphocytes/virology/immunology ; },
abstract = {Holobiont describes all types of relationships between hosts and their associated microbial communities, which can also attenuate the virulence of pathogens by the host microbiome. The cross-kingdom interactions between HIV, Candida albicans, and the human immune system have presented intriguing biological aspects. The human immunodeficiency 1 (HIV-1) virus is responsible for causing the acquired immune deficiency syndrome (AIDS) by infecting CD4[+] cells. HIV-1 internalization also depends on binding to coreceptors in the cell membrane, such as CCR5 and CXCR4. The expression of these chemokine receptors, as well as their ligands, can be modulated by the presence of Candida albicans PAMPs. Thus, this review discusses the inflammatory response mechanism activated by the commensal fungi Candida albicans that can modify the rate of immune cell infection by HIV-1. Despite the possibility of this crosstalk modulation, future research must validate the clinical significance of this holobiont interaction.},
}

Humans
*Candida albicans/immunology/physiology/pathogenicity
*HIV-1/immunology/physiology
*HIV Infections/immunology/microbiology/virology
Host-Pathogen Interactions/immunology
CD4-Positive T-Lymphocytes/virology/immunology

@article {pmid42126047,
year = {2026},
author = {Asszonyi, J},
title = {Wheat Dwarf Virus as a Modulator of Multi-Stress Responses in Wheat.},
journal = {Physiologia plantarum},
volume = {178},
number = {3},
pages = {e70931},
pmid = {42126047},
issn = {1399-3054},
support = {IGA26-AF-IP-010//Mendelova Univerzita v Brně/ ; QL24010142//Mendelova Univerzita v Brně/ ; },
mesh = {*Triticum/virology/physiology ; *Plant Diseases/virology ; *Stress, Physiological ; *Geminiviridae/physiology ; Plant Growth Regulators/metabolism ; },
abstract = {Wheat dwarf virus (WDV) is an emerging constraint to cereal production whose epidemiological significance has intensified under climate change. Rising temperatures, extended vector activity, and the expansion of Psammotettix alienus into new regions have increased both the frequency and severity of WDV outbreaks. Beyond its direct effects on plant development, WDV acts as a powerful regulator of host physiology, functioning as a host signalling hub that reprograms hormonal signalling, alters source-sink relationships, disrupts redox homeostasis, and modulates responses to both abiotic and biotic stress. Recent molecular studies have revealed how viral proteins manipulate the cell cycle, transcriptional machinery, and RNA silencing pathways to optimise viral replication while attenuating defence responses. These processes intersect with core stress-response networks, particularly those governed by abscisic acid, gibberellins, cytokinins, and auxin, positioning WDV as a model system for investigating hormonal crosstalk under combined stress. Despite advances in genomics, transcriptomics, and vector biology, major knowledge gaps persist regarding WDV interactions with co-occurring fungal pathogens, its impact on the plant microbiome, and its role in shaping cereal resilience under drought, heat, or nutrient limitations. This review synthesises current understanding of WDV biology from the molecular to the ecological scale, highlights mechanisms underpinning stress integration, and outlines future research priorities essential for developing sustainable management strategies in a changing climate.},
}

*Triticum/virology/physiology
*Plant Diseases/virology
*Stress, Physiological
*Geminiviridae/physiology
Plant Growth Regulators/metabolism

@article {pmid42126821,
year = {2026},
author = {Prasad, A and Shuler, MS and Flanagan, R and Dayal, V and Lithander, FE},
title = {Dietary supplements for Parkinson's disease: State of the science.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261446386},
doi = {10.1177/1877718X261446386},
pmid = {42126821},
issn = {1877-718X},
abstract = {Parkinson's disease (PD) is the fastest growing neurological condition worldwide with its prevalence set to double by 2050. With no cure in sight, management has turned to lifestyle modification, in particular to diet and exercise. The disease-modifying potential of dietary approaches has been of recent interest, particularly given emerging links between diet and reductions in systemic inflammation, oxidative stress, and alterations in the gut microbiome composition, all of which may modulate neurodegeneration. This review summarises the current 'state of the science' of dietary supplements in modifying disease progression through a lens of the pathophysiological hallmarks of PD. Biomarkers and clinical outcomes that serve as proxy measurements for disease modification are examined, whilst looking ahead at which dietary supplements show the most promise and should be the focus of future research.},
}

@article {pmid42126887,
year = {2026},
author = {Guo, Y and Li, J and Nishio, S and Hattori, H and Nochi, T and Matsuda, T and Toda, M},
title = {Long-term antibiotic treatment attenuates the development of food allergy in a murine model.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbag069},
pmid = {42126887},
issn = {1347-6947},
abstract = {While short-term antibiotic exposure has been reported to exacerbate the development of allergies, the effects of long-term administration remain less understood. This study addressed the influences of prolonged antibiotic administration in a murine model of food allergy. Mice received a broad-spectrum antibiotic cocktail (ABX) for six weeks from pre-sensitization through allergen challenge. ABX reduced allergic reactions, serum IgE levels, and intestinal mast cell counts. Production of Th2 cytokine, but not of Th1 and Th17 cytokines, was lowered in allergen-stimulated splenocytes of ABX-treated allergic mice, whereas the levels of these cytokines in their intestines decreased. ABX did not significantly alter the levels of regulatory cytokine IL-10 in intestines and regulatory T cells in spleens. ABX reduced gut bacterial amount, though Lactobacillus, Lactococcus, and Streptococcus remained detectable. Collectively, the long-term ABX suppresses allergic reaction by modulating Th2-mediated events dominantly, providing insights into the complex role of antibiotics in allergy models.},
}

@article {pmid42127027,
year = {2026},
author = {Morikawa, Y and Kato, H and Umemura, T and Hirai, J and Shibata, Y and Hagihara, M and Asai, N and Mikamo, H and Iwamoto, T},
title = {Multicenter retrospective observational study on the clinical effectiveness of butyrate-producing Clostridium butyricum containing probiotics in patients with COVID-19.},
journal = {Virulence},
volume = {},
number = {},
pages = {2673650},
doi = {10.1080/21505594.2026.2673650},
pmid = {42127027},
issn = {2150-5608},
abstract = {Butyrate-producing bacteria, which are components of the gut microbiome, activate host defense mechanisms against several types of infections, including respiratory viral infections. However, the clinical effectiveness of butyrate-producing Clostridium butyricum (CB)-containing probiotics in patients with coronavirus disease 2019 (COVID-19) remains unclear. We investigated the in-hospital mortality, period of mechanical ventilation, and incidence of secondary bacterial pneumonia in patients with COVID-19 from 2020 to 2021. The patients were divided into the probiotic (27) and non-probiotic (256) groups. The two groups did not show a significant difference in the SOFA scores (probiotic vs. non-probiotic, 2.1 ± 2.3 vs. 2.1 ± 2.9). Additionally, all patients received antiviral agents to treat COVID-19; however, the two groups did not show significant difference in their distribution. However, patients receiving CB preparations showed the shorter periods of mechanical ventilation (1.1 ± 2.5 days vs. 3.9 ± 9.4 days). Although not statistically significant, they also showed lower incidence of secondary bacterial pneumonia (7.4% vs. 15.6%) and the lower in-hospital mortality (3.7% vs. 15.2%) compared to the non-probiotic group. This retrospective clinical study revealed that the administrations of CB preparations might attenuate clinical symptoms related to COVID-19 and improve mortality. However, further clinical and basic studies are required to validate our findings.},
}

@article {pmid42127284,
year = {2026},
author = {He, M and Zhao, N},
title = {A mixed effect similarity matrix regression model (SMRmix) for integrating multiple microbiome datasets at the community level.},
journal = {Biometrics},
volume = {82},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujag077},
pmid = {42127284},
issn = {1541-0420},
support = {R21AI154236/GF/NIH HHS/United States ; R01GM147162/GF/NIH HHS/United States ; U24OD023382/GF/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Computer Simulation ; Colorectal Neoplasms/microbiology ; Regression Analysis ; *Models, Statistical ; Dysbiosis/microbiology ; HIV Infections/microbiology ; Gastrointestinal Microbiome ; },
abstract = {Recent studies have highlighted the importance of the human microbiota in health and disease. However, in many areas of research, individual microbiome studies often provide inconsistent results due to limited sample sizes and the heterogeneity in study populations and experimental procedures. This inconsistency underscores the need for integrative analysis of multiple microbiome datasets. Despite the critical need, statistical methods that incorporate multiple microbiome datasets and account for study heterogeneity are not available in the literature. To address this, we propose a mixed effect similarity matrix regression (SMRmix) approach for identifying community-level microbiome shifts associated with outcomes. SMRmix has a close connection with the microbiome kernel association test, one of the most popular approaches for such a task, but it is only applicable when we have a single study. SMRmix enables researchers to consolidate findings from diverse microbiome studies. Through extensive simulations, we show that SMRmix maintains well-controlled Type I error rates and achieves higher power than competing methods. We further demonstrate its utility on two real-world datasets-17 HIV gut dysbiosis studies and 11 colorectal cancer studies-showing that SMRmix provides consistent results on community-level shifts in both applications.},
}

Humans
*Microbiota
Computer Simulation
Colorectal Neoplasms/microbiology
Regression Analysis
*Models, Statistical
Dysbiosis/microbiology
HIV Infections/microbiology
Gastrointestinal Microbiome

@article {pmid42127330,
year = {2026},
author = {Weinberg, J and Crandall, WJ and Jarrell, ZR and Lim, G and Liu, K and Lee, HY and Patel, S and Gacasan, CA and Go, YM and Jones, DP},
title = {Structural Diversity and Analytical Characterization of Acylhomocarnitines.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c01255},
pmid = {42127330},
issn = {1535-3907},
abstract = {Homocarnitine is a five-carbon analog of carnitine produced in mammals through hydroxylation of the microbiome-derived metabolite δ-valerobetaine. Here, we describe liquid chromatography-mass spectrometry methods for the measurement of fatty acyl-homocarnitines, a previously uncharacterized family of mammalian metabolites. These acyl-homocarnitines are homologs of acyl-carnitines, in which the fatty acid is extended by one carbon. We show that short-chain fatty acyl-CoAs are converted to corresponding acyl-homocarnitines by carnitine acetyltransferase and that these enzyme-generated standards exhibit retention times and ion dissociation patterns identical to acyl-homocarnitines produced by mammalian cells. In vitro [13]C3-homocarnitine isotope tracer studies showed that mammalian cells produce short-, medium-, and long-chain acyl-homocarnitines. Ion dissociation analyses established diagnostic product ions to distinguish acyl-homocarnitines from isomeric acyl-carnitines. Sample preparation and chromatographic methods are provided to separate and analyze isomers in extracts of mouse tissues. These findings expand knowledge of carnitine analogs and establish analytical strategies to differentiate acyl-homocarnitines from isomeric acyl-carnitines.},
}

@article {pmid42127415,
year = {2026},
author = {Ge, M and Maeda, T and Li, J and De Mares, MC and Kifaro, EG and Gidamo, GH and Shiroguchi, K and Moeller, AH and Zhang, Z and Jin, J},
title = {Standardized and batch effect-independent technologies enable global collaboration in microbiome research.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag122},
pmid = {42127415},
issn = {1751-7370},
}

@article {pmid42127418,
year = {2026},
author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC},
title = {Impact of Maternal, Infant, and Household Factors on Early-life Gut Microbiome Development in a Rural Setting.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag124},
pmid = {42127418},
issn = {1751-7370},
abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S rRNA gene sequencing, we characterized eukaryotic and bacterial gut microbiomes in an intensively sampled longitudinal cohort of ten infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing an unusually detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, as well as bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and mode of birth also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.},
}

@article {pmid42127598,
year = {2026},
author = {Wang, X and Duan, Y and Wang, H and Zhao, R and Wang, F and Tang, T and Wang, Q and You, J},
title = {Fritillaria hupehensis cultivated under the canopy of Magnolia officinalis demonstrated superior anti-inflammatory and expectorant effects.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158261},
doi = {10.1016/j.phymed.2026.158261},
pmid = {42127598},
issn = {1618-095X},
abstract = {BACKGROUND: Fritillaria hupehensis is a medicinal plant used for treating cough and inflammation. Its cultivation under the canopy of Magnolia officinalis (U-F. hupehensis) increases alkaloid content compared to traditionally field-grown cultivation (T-F. hupehensis).

PURPOSE: This study aims to evaluate the superior therapeutic efficacy of U-F. hupehensis against cough and inflammation and to elucidate the role of its rhizosphere bacterial community in enhancing the accumulatio of key bioactive compounds.

METHODS: The anti-inflammatory and expectorant efficacy of U-F. hupehensis was evaluated in animal models (ammonia-induced cough, phenol red excretion, and LPS-induced bronchitis). Network pharmacology and cellular experiments identified the key bioactive compounds. Soil physicochemical properties and 16S rRNA sequencing were used to analyze the rhizosphere bacterial community. The relationship between the rhizosphere microbiome and bioactive compound accumulation was analyzed using structural equation modeling.

RESULTS: U-F. hupehensis exhibited significantly stronger anti-inflammatory and expectorant effects than T-F. hupehensis. Hupehenine, peimine, and sipeimine were validated as the primary active components responsible for this enhanced efficacy. Understory cultivation increased rhizosphere microbial diversity. A specific keystone microbial module (Module 1) was identified and shown to directly mediate the accumulation of the bioactive compounds.

CONCLUSION: The superior anti-inflammatory and expectorant efficacy of understory-cultivated F. hupehensis is driven by a marked increase in the key bioactive alkaloids (hupehenine, peimine, and sipeimine). Our study identifies a specific rhizosphere microbial community as the pivotal mediator of this enhanced alkaloid accumulation. These results provide a pharmacologically relevant mechanism that explains the differential therapeutic potential of F. hupehensis from distinct cultivation sources.},
}

@article {pmid42127772,
year = {2026},
author = {Dejong, T and Bhatt, K and Rodrigues, A and Massenet, T and Lievens, S and Focant, JF and Stefanuto, PH},
title = {Comparative development of volatile-oriented multi-SPME and derivatisation-based GC×GC-TOFMS workflows for non-targeted faecal metabolomics.},
journal = {Talanta},
volume = {308},
number = {},
pages = {129954},
doi = {10.1016/j.talanta.2026.129954},
pmid = {42127772},
issn = {1873-3573},
abstract = {Gas chromatography-mass spectrometry (GC-MS) remains a key technique in metabolomics, yet most workflows rely on chemical derivatisation to enable the analysis of non-volatile metabolites. Although derivatisation broadens metabolite coverage, it increases sample preparation time and may introduce additional analytical variabilities. In contrast, solid-phase microextraction (SPME) enables rapid, solvent-free sampling of volatile and semi-volatile compounds, representing an attractive alternative for non-targeted studies. However, methodological developments integrating SPME with comprehensive two-dimensional gas chromatography (GC × GC-MS) remain limited. In this study, a simultaneous multi-SPME GC × GC-TOFMS workflow was developed for the non-targeted screening of faecal samples. Three identical fibres were used simultaneously to generate technical replicates from a single biological sample resulting strong performances in terms of relative standard deviation (10%). Dedicated fibre storage containers and optimised storage conditions were also developed to preserve analyte stability between sampling and injection. In parallel, commonly used GC × GC column configurations were evaluated. The optimised workflow was applied to stool reference materials generated within an interlaboratory metabolomics study coordinated by the National Institute of Standards and Technology (NIST), investigating the effects of diet (vegan vs. omnivore) and sample preservation (aqueous vs. lyophilised) to develop the more adequate stool reference material. SPME results were compared with derivatisation-based metabolomic and lipidomic workflows. Multivariate analysis revealed clear discrimination between diets and storage conditions, while data-fusion analysis highlighted the complementary nature of volatile, metabolomic, and lipidomic profiles. This work provides practical guidance for developing robust GC × GC-MS workflows for complex biological matrices, highlighting the need of multi-extraction approaches for comprehensive analytical coverage.},
}

@article {pmid42127813,
year = {2026},
author = {De Sordi, L},
title = {Making room for gut prophages in human health.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {766-769},
doi = {10.1016/j.chom.2026.03.018},
pmid = {42127813},
issn = {1934-6069},
mesh = {Humans ; *Prophages/physiology/genetics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/virology/genetics ; *Host Microbial Interactions ; *Gastrointestinal Tract/microbiology/virology ; },
abstract = {Prophages are pervasive in the human gut yet largely overlooked in microbiome research, despite substantial functional potential. Emerging evidence indicates that prophages regulate bacterial fitness, community structure, and microbe-host interactions. Here, I argue that integrating prophage biology is important to understand microbiota-driven functions in human health and disease.},
}

Humans
*Prophages/physiology/genetics
*Gastrointestinal Microbiome/physiology
*Bacteria/virology/genetics
*Host Microbial Interactions
*Gastrointestinal Tract/microbiology/virology

@article {pmid42127814,
year = {2026},
author = {Jin, Y and Zhao, J and Zuo, T},
title = {Potential impacts of antivirals on the virome.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {770-774},
doi = {10.1016/j.chom.2026.04.005},
pmid = {42127814},
issn = {1934-6069},
mesh = {*Antiviral Agents/pharmacology/therapeutic use ; *Virome/drug effects ; Humans ; Animals ; *Virus Diseases/drug therapy/virology ; *Microbiota/drug effects ; *Viruses/drug effects ; Gastrointestinal Microbiome/drug effects ; },
abstract = {The use of antivirals has transformed viral infection management and reduced mortality. However, the effect of antivirals on the commensal virome, a crucial player in microbiome homeostasis and mammalian health, is largely unclear. This Forum delves into this nascent area and discusses the potential impacts of antivirals on the virome.},
}

*Antiviral Agents/pharmacology/therapeutic use
*Virome/drug effects
Humans
Animals
*Virus Diseases/drug therapy/virology
*Microbiota/drug effects
*Viruses/drug effects
Gastrointestinal Microbiome/drug effects

@article {pmid42127816,
year = {2026},
author = {Che, Y and Kong, HH},
title = {The human skin virome: Ecological dynamics, aberrant profiles, and therapeutic opportunities.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {790-807},
doi = {10.1016/j.chom.2026.04.008},
pmid = {42127816},
issn = {1934-6069},
mesh = {Humans ; *Virome ; *Skin/virology/microbiology/immunology ; Microbiota ; Bacteriophages/physiology ; Bacteria/virology ; *Viruses/classification/genetics/isolation & purification ; Immunity, Innate ; Adaptive Immunity ; },
abstract = {Human skin harbors a complex microbial ecosystem in which viruses, including eukaryotic viruses, bacteriophages, and endogenous retroviruses, are integral yet comparatively understudied. Shaped by host physiology, genetics, and environmental exposures across the lifespan, the cutaneous virome interacts closely with resident bacteria, fungi, and immune cells. In this review, we synthesize current knowledge of virome composition, biogeography, and dynamics, with an emphasis on how bacteriophages influence bacterial ecology, gene flow, and antimicrobial resistance on the skin. We further discuss how human-tropic viruses engage innate and adaptive immunity to support homeostasis while also contributing to inflammatory, infectious, and neoplastic skin diseases. Finally, we highlight methodological advances and persisting technical challenges in virome detection and functional annotation, and we outline emerging translational opportunities, including bacteriophage-based therapeutics, microbiome-targeted interventions, and immunomodulatory strategies.},
}

Humans
*Virome
*Skin/virology/microbiology/immunology
Microbiota
Bacteriophages/physiology
Bacteria/virology
*Viruses/classification/genetics/isolation & purification
Immunity, Innate
Adaptive Immunity

@article {pmid42127821,
year = {2026},
author = {Li, XT and Feng, J},
title = {Diversity recruits resilience via metabolite signaling.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {820-822},
doi = {10.1016/j.chom.2026.03.022},
pmid = {42127821},
issn = {1934-6069},
mesh = {*Microbiota ; *Signal Transduction ; Rhizosphere ; *Glycine max/microbiology/physiology/metabolism ; Stress, Physiological ; Droughts ; Soil Microbiology ; Plant Roots/microbiology ; Biodiversity ; Adaptation, Physiological ; },
abstract = {The rhizosphere microbiome drives plant stress resilience. In this issue of Cell Host & Microbe, Chen et al. show that microbial diversity programs drought adaptation in soybeans by linking community complexity to host metabolism and microbiome assembly, with outcomes shaped by diversity-dependent metabolite signaling and selective recruitment of beneficial taxa.},
}

*Microbiota
*Signal Transduction
Rhizosphere
*Glycine max/microbiology/physiology/metabolism
Stress, Physiological
Droughts
Soil Microbiology
Plant Roots/microbiology
Biodiversity
Adaptation, Physiological

@article {pmid42127855,
year = {2026},
author = {Mei, Z and Zhou, H and Liu, K and Gao, C and Du, H and Sheng, Z and Gong, Y},
title = {Traditional Chinese medicine improves performance and intestinal health in laying hens under acute and chronic heat stress by modulating ileal metabolic functions.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {107056},
doi = {10.1016/j.psj.2026.107056},
pmid = {42127855},
issn = {1525-3171},
abstract = {Heat stress (HS) represents a significant challenge in poultry production, impairing thermoregulation, intestinal function, and productive performance. This study utilized acute (6 h) and chronic (14 d) HS models at 36°C in laying hens to characterize stage-dependent responses and evaluate the protective effects of a ten-ingredient traditional Chinese medicine (TCM) formulation. Both acute and chronic HS significantly increased rectal temperature and respiratory rate. Egg production declined by approximately 18% following acute HS and was further compromised under chronic exposure, along with reduced eggshell strength and weight. Dietary TCM supplementation (0.5%) alleviated physiological stress and partially restored laying performance, with more pronounced recovery observed under chronic HS. Serum analysis and histopathology indicated that TCM attenuated HS-induced impairment of ileal barrier function. Metabolomic profiling revealed stage-dependent responses: acute HS primarily disturbed redox balance, whereas chronic HS induced broader remodeling related to energy and nutrient utilization. TCM supplementation modulated metabolic functions to support immediate stress buffering under acute HS while stabilizing long-term energy support and intestinal capacity under chronic HS. Metagenomic analysis indicated that TCM selectively promoted microbial groups related to intestinal metabolism and nutrient utilization, aligning with metabolomic findings. Correlation analyses linked these TCM-associated microbial and metabolic signatures with improved thermoregulatory responses, oxidative status, and intestinal barrier indicators. Collectively, these results demonstrate that TCM supplementation enhances heat resilience in laying hens through stage-dependent modulation of the gut microbiota-metabolome axis, supporting its application as a nutritional strategy to maintain productivity under thermal challenge.},
}

@article {pmid41959837,
year = {2026},
author = {Irajizad, E and Fahrmann, JF and Katayama, H and Strati, P and Nair, R and Chihara, D and Ahmed, S and Iyer, SP and Locke, FL and Davila, M and Flowers, CR and Shpall, E and Jenq, R and Neelapu, SS and Hanash, S and Westin, J and Jain, MD and John, TM and Saini, NY},
title = {Pre-infusion plasma proteomics identifies an endothelial-immune priming signature predictive of severe cytokine release syndrome and neurotoxicity following CAR T-cell therapy in relapsed/refractory lymphoma.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.29.26349664},
pmid = {41959837},
abstract = {BACKGROUND: Severe cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) remain frequent, life-threatening complications of CD19 chimeric antigen receptor (CAR) T-cell therapy and constrain its safety, scalability, and outpatient adoption. Existing predictive models lack sufficient external validation for routine clinical use, and pre-infusion biomarkers that capture host susceptibility before infusion are urgently needed.

METHODS: We applied unbiased mass-spectrometry-based proteomics to pre-infusion biofluids from 98 prospectively-followed adults with relapsed/refractory (r/r) lymphoma at two academic centers (MD Anderson Cancer Center, n = 39, plasma; Moffitt Cancer Center, n = 59, serum). Logistic regression with backward feature selection on the MD Anderson cohort yielded panels for severe (Grade ≥ 2) CRS and ICANS that were locked and tested without refitting on the Moffitt cohort. Patients were stratified into low-, intermediate-, and high-risk tertiles. Ingenuity Pathway Analysis defined upstream regulators and canonical pathways. The 17 CRS-associated and 21 ICANS-associated consensus proteins were classified into mechanistic themes for biological interpretation.

RESULTS: A 5-marker CRS panel (SCRIB, MYL6, MTHFD1L, HSP90B1, MMP2) achieved AUCs of 0.85 (95% CI 0.72-0.98) and 0.76 (0.63-0.89) in the discovery and validation cohorts, respectively. An expanded 8-marker ICANS panel (the CRS panel plus SPOCK2, SLC3A2, CD84) achieved AUCs of 0.91 (0.81-1.00) and 0.67 (0.51-0.84). In the combined dataset, high-risk-tertile patients were 13.84-fold (95% CI 4.21-56.26) and 8.59-fold (2.87-29.09) more likely to develop Grade ≥ 2 CRS and ICANS, respectively. Pathway analysis converged on AKT-driven inflammation and endothelial activation. Functional clustering of the consensus proteins partitioned into mechanistically coherent themes consistent with a dual-anatomy model: severe CRS reflected peripheral macrophage priming and endothelial activation with surplus complement amplification (HSP90B1▴, CSF1▴, MMP2▴, HEG1▴, C3▴) and endotheliopathic coagulation (PROC▾, F7▾), whereas severe ICANS reflected cerebrovascular junction and basement-membrane stripping (CDH5▾, ITGB1▾, FN1▾, brain-enriched SPOCK2▾), hepatic synthetic suppression (TTR▾, APOA2▾, IGFBP3▾), compromised plasma antioxidant capacity (GPX3▾, PON1▾), and inflammasome dis-restraint via DPP9▾. PGLYRP2 and SCRIB depletion were shared by both signatures and identified a common upstream priming substrate.

CONCLUSIONS: Externally validated, pre-infusion proteomic panels predict severe CRS and ICANS following CAR T-cell therapy and define a coherent pre-infusion endothelial-immune priming axis (HSP90B1, MMP2, AKT) with mechanistically interpretable, druggable nodes. The dual-anatomy framework distinguishes peripheral CRS-biased from cerebrovascular ICANS-biased phenotypes downstream of a shared microbiome-host barrier priming substrate, providing a foundation for biomarker-guided risk stratification and cluster-matched prophylactic intervention to enhance the safety and outpatient feasibility of CAR T-cell therapy.},
}

@article {pmid42112445,
year = {2026},
author = {Furuya, R and Nishikawa, Y and Ota, Y and Prah, I and Mahazu, S and Kifushi, M and Yoshida, M and Suzuki, M and Hoshino, Y and Suzuki, T and Takeyama, H and Ablordey, A and Saito, R},
title = {Single-cell genomic profiling of antimicrobial resistance in Escherichia coli from the Densu River, Ghana.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797725},
pmid = {42112445},
issn = {1664-302X},
abstract = {INTRODUCTION: River water serves as a natural reservoir for antimicrobial resistance (AMR) factors. Although environmental AMR poses a global threat to public health as it spreads to local communities through the microbiome in aquatic environments, the actual situation remains unclear, especially in developing countries. In this study, we sought microbiome data, including AMR information, for multiple bacterial strains from river water samples using a single-cell genomics platform.

METHODS AND RESULTS: After antimicrobial selection of samples from the Densu River in Ghana, 16S rRNA amplicon sequencing revealed a high proportion of the genus Escherichia-Shigella with ampicillin and sulbactam selection. Single-cell genomic analysis revealed differences in AMR and virulence factor profiles among the same species of Escherichia coli, including the CTX-M-15 extended-spectrum β-lactamase-producing ones. Pan-genome analysis predicted 4,814 gene clusters, of which 2,264 were accessory, including 605 singletons. Phylogenetic tree analysis using the maximum likelihood method showed the heterogeneity of single-cell amplified genomes (SAGs), and cluster of orthologous gene analysis for each SAG confirmed the difference in the ratio of each functional group.

CONCLUSION: This study demonstrates the potential of single-cell genomics using the single-cell amplified genome in gel method to enhance environmental AMR surveillance with high resolution and accuracy. It also represents the first application of this approach to aquatic environments in Ghana, thereby contributing to the development of microbial ecology and genomic resources.},
}

@article {pmid42112609,
year = {2026},
author = {Cao, Y and Xu, H and Xu, C and Zu, M and Sun, J and Xiong, D and Ye, J and Han, K and Gao, Q and Shi, X and Li, L and Li, B and Shahbazi, MA and Cribbs, AP and Chai, J and Reis, RL and Kundu, SC and Liu, Y and Nie, G and Xiao, B},
title = {Zwitterionic Lipid Nanotherapeutics from Mulberry for Oral Treatment of Diabetic Colitis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c17183},
pmid = {42112609},
issn = {1936-086X},
abstract = {Diabetic colitis is a severe gastrointestinal complication of type 2 diabetes, which presents the key pathophysiological hallmarks of hyperglycemia, intestinal barrier disruption, immune dysregulation, and microbial metabolic imbalance, posing significant therapeutic challenges in clinical practice. Here, we leveraged artificial intelligence to identify the therapeutic potential of 1-deoxynojirimycin (DNJ) for addressing diabetic colitis. To improve its bioavailability and efficacy, we developed a mulberry-derived nanotherapeutic with surface functionalization of zwitterionic polymer (PpC) for DNJ encapsulation. Following oral administration, the resultant nanotherapeutics, PpC@DNJ-LNPs, efficiently traversed the gastrointestinal tract, enabling controlled DNJ release while inhibiting the α-glucosidase activity to regulate glucose homeostasis. Concurrently, they orchestrated colonic mucosa-microbiome interaction, promoting intestinal immune balance and microbiota remodeling. These synergistic effects collectively confer hypoglycemic, anti-inflammatory, antioxidant, and epithelial barrier-restoring effects, ultimately reshaping the glucose level and intestinal microecology. Our study demonstrates the translational potential of PpC@DNJ-LNPs as a safe and effective oral therapeutic platform for diabetic colitis.},
}

@article {pmid42112774,
year = {2026},
author = {Jourdain, L and Rossi, P and Charpagne, A and Chevalier, E and Praz, V and Marquis, J and Weber, J and Gu, W},
title = {A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70138},
pmid = {42112774},
issn = {1755-0998},
support = {200021_219222//Swiss National Science Fundation (SNF)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods/economics ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; DNA Primers/genetics ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA/methods ; },
abstract = {In-line barcoding offers a streamlined and scalable alternative to two-step PCR library preparation for 16S rRNA gene amplicon sequencing, enabling cost-effective, high-throughput profiling of microbial communities. Here, we tested 136 and 156 in-line barcoded primer pairs for bacterial and archaeal communities for their performance across environmental samples and a mock standard community. The primers were designed by combining widely used universal 16S rRNA gene primers with existing barcode sets from Illumina kits. The designed primer pairs produced efficient and consistent amplification with minimal dropout and no systematic taxonomic bias. Through clustering and performance-based filtering, we selected final sets of 96 pairs for both bacterial and archaeal communities that work efficiently and well together for direct further use. This in-line tagging strategy is easy to adopt with fewer processing steps and PCR-associated artefacts, allows straightforward sample tracking, and supports reliable large-scale microbiome studies. We also present a framework for evaluating barcode- or primer-induced biases. More broadly, the proposed in-line barcoding strategy can be adapted to any amplicon-sequencing application, as well as targeted sequencing, highlighting its relevance beyond 16S rRNA gene surveys. All validation datasets, open-source processing scripts, and barcode design resources are provided to promote reproducibility and community-wide adoption.},
}

*RNA, Ribosomal, 16S/genetics
*DNA Barcoding, Taxonomic/methods/economics
*Bacteria/genetics/classification
*Archaea/genetics/classification
DNA Primers/genetics
Cost-Benefit Analysis
High-Throughput Nucleotide Sequencing/methods
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA/methods

@article {pmid42112809,
year = {2026},
author = {Coates, LC and Storms, DH and Spearman, SS and Shahab-Ferdows, S and Christensen, SH and Lewis, JI and Mølgaard, C and Michaelsen, KF and Allen, LH and Lemay, DG and Kable, ME},
title = {Stool microbial composition is associated with recent and future diarrhea and fever events in breastfed Danish infants.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0013426},
doi = {10.1128/msystems.00134-26},
pmid = {42112809},
issn = {2379-5077},
abstract = {UNLABELLED: Gastroenteritis is an important cause of ailment among infants in high-income countries, including Denmark. There are many cases of diarrhea among Danish children for which no etiological agent is detected. This study investigated the associations between gastroenteritis-related morbidities (diarrhea, fever, and vomiting) and gut microbial community in well-nourished, breastfeeding Danish infants. Infant stool samples, morbidity questionnaires, and diet/breastfeeding questionnaires were collected at three time points during the first 8.5 months of life. The V4-V5 region of the 16S rRNA gene was amplified from stool DNA extracts, sequenced with Illumina MiSeq, and analyzed using QIIME2. PERMANOVA, linear mixed-effects modeling, and ANCOM-BC2 were used to identify associations between infant gut microbiome and gastroenteritis-related morbidities across all visits. Logistic regression and random forest models were employed to determine whether early gut microbial alpha diversity or abundance, respectively, could predict morbidity later in infancy. Alpha diversity was negatively associated with diarrhea. Granulicatella abundance was positively associated with diarrhea. From 3.5 to 6 months of age, Bacteroidales abundance was negatively associated with fever. Faith's phylogenetic diversity, Staphylococcales abundance, and Haemophilus abundance during 3.5 months of life were positively associated with future diarrhea during ages 3.5-8.5 months. Pielou's evenness and Actinobacteriota abundance within 3.5 months of life had negative and positive associations, respectively, with fever during ages 3.5-8.5 months. This study reveals diarrhea is associated with stool Granulicatella in well-nourished, breastfeeding Danish infants, as it is in children from low-income countries, and that the early gut microbiome may contribute to risks of diarrhea and fever morbidities later in infancy.CLINICAL TRIALSThis trial was registered at ClinicalTrials.gov as NCT03254329.

IMPORTANCE: Gastroenteritis continues to cause much morbidity among infants in high-income countries, and the relationship with the gut microbiome is not fully understood, especially for well-nourished and breastfeeding infants. In the study presented here, infant stool Staphylococcales abundance (comprised of Staphylococcus and Gemella) and Haemophilus abundance during the first few months of life were positively associated with later diarrhea in well-nourished and breastfeeding Danish infants. Meanwhile, the abundance of Granulicatella (a facultative anaerobe with pathogenic potential) was greater in stool from infants who had recent diarrhea, suggesting further research is needed to determine its possible role in diarrhea and recovery from diarrhea. Fever usually did not co-occur with diarrhea or vomiting. Early life Actinobacteriota abundance was positively associated with later fever. This phylum was represented here by both pathobionts (Actinomyces) and mutualists (bifidobacteria), which may have contributed to fever differently-pathobionts through infection and mutualists through promotion of effective immune response to infection.},
}

@article {pmid42112827,
year = {2026},
author = {Cao, TTT and Herckes, P and Straub, D and Sarkar, S and Garcia-Pichel, F},
title = {Growth and formaldehyde degradation of photoheterotrophic Methylobacterium within radiation fogs.},
journal = {mBio},
volume = {},
number = {},
pages = {e0046326},
doi = {10.1128/mbio.00463-26},
pmid = {42112827},
issn = {2150-7511},
abstract = {UNLABELLED: The atmosphere contains thousands to millions of bacterial cells per cubic meter. However, it remains unclear if microbes are at all active or growing in situ or whether they are merely being transported in an inactive state. Based on the analyses of 32 overland radiation fog events over a 2-year period, we show that fog waters, with bacterial concentrations similar to those in continental or marine bodies of water, contain microbiomes well differentiated in composition from those in the dry aerosol microbiomes that occur locally before, during, or after fog events. They are consistently and strongly enriched in photoheterotrophic Methylobacterium species, suggesting that fog populations may be metabolizing volatile C1 compounds in situ, although phototrophy seems much less important. Indeed, metabolically active bacteria in the fog, and representative isolates of the main field populations, can degrade formaldehyde at unprecedently high rates; most of this activity seems to play a detoxification role. The increase in bacterial aerobiome counts upon intervening fog events, the dependence of microbial concentration on ambient temperature, the increases in cell size and frequency of dividing cells in fog water with respect to cells in interstitial aerosols of fogs, in addition to their metabolic capacity, all suggest that the fog water microbiome is actually growing. Consequently, droplets of atmospheric water should be considered a potential aquatic microhabitat. Our results highlight the fog microbiome's role in atmospheric chemistry and have implications for fog harvesting as a source of fresh water for human use.

IMPORTANCE: While bacteria are common in the atmosphere, their activity in situ has remained unclear. Using stagnant radiation fogs as new study systems where sampling is optimal, the dynamics, composition, cellular characteristics, and metabolic rates of fog water microbiomes, dominated by Methylobacterium sp., show that they are a hub of active detoxification of atmospheric formaldehyde and likely growing in situ on the basis of heterotrophic or photoheterotrophic metabolism of volatile C1 compounds, with implications for atmospheric chemistry and fog harvesting as sources of freshwater.},
}

@article {pmid42112889,
year = {2026},
author = {Amechatte, G and Radouane, N and El Mouttaqi, A and Licastro, D and Hirich, A and Mohamed, H and Ahmed, B},
title = {Deterministic abiotic filtering and halophilic core microbiomes shape bacterial community assembly in coastal salt flats (sabkha) of southern Morocco.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0006126},
doi = {10.1128/aem.00061-26},
pmid = {42112889},
issn = {1098-5336},
abstract = {Coastal salt flats, locally known as sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistent alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root, and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical correspondence analysis identified electrical conductivity (EC), Na2O, K2O, and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria, and Marinococcus, with 66% of amplicon sequencing variants (ASVs) shared across compartments. Host identity played a secondary role as environmental filtering overshadowed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, including representatives of Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium, and Bacillus. These isolates exhibited robust growth on saline Marine Agar medium, indicating strong salt tolerance consistent with their occurrence in hypersaline environments. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shaped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions.IMPORTANCECoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.},
}

@article {pmid42112933,
year = {2026},
author = {Gee, M and Sharp, C},
title = {Bacterial weaponry and the ecological factors of competitive success.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250028},
pmid = {42112933},
issn = {1744-1358},
support = {N/A//University of Reading (UoR)/ ; },
abstract = {Bacteria have evolved complex protein systems known as bacterial weapons to inhibit or kill their competitors. These bacterial weapons are a remarkably diverse arsenal that influence the composition and function of important microbial communities such as the human microbiome. In turn, the spatial constraints, nutrient availability, environmental stressors, and the presence of competitors determine not only whether weapons are expressed, but which weapons provide the greatest advantage. While bacterial weaponry is widespread, the types, mechanisms, and abundance of these systems vary between, and even within, species. Recent research has highlighted the importance of bacterial weaponry in community invasion and pathogenicity. Their potency and narrow killing spectrum have also generated interest in exploiting bacterial weapons to engineer microbial communities or develop therapeutics that avoid the disruption of broad-spectrum antibiotics. Understanding how ecological context affects weapon efficacy could reveal new virulence mechanisms used by pathogens and inform the design of novel treatments and microbiome-based therapies. This review outlines three of the best-studied bacterial weapon systems (protein bacteriocins, the type VI secretion system, and contact-dependent inhibition), highlighting their roles in microbial ecology, pathogenicity and their potential as therapeutics.},
}

@article {pmid42113072,
year = {2026},
author = {Csikó, G and Palócz, O and Várhidi, Z and Sátorhelyi, P and Erdélyi, B and Jurkovich, V},
title = {Evaluation of the local tolerance and systemic safety of a novel intravaginal probiotic product in cows.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {42113072},
issn = {1573-7446},
mesh = {Animals ; *Probiotics/administration & dosage/adverse effects ; Female ; Cattle ; Administration, Intravaginal ; Vagina/microbiology/drug effects ; },
abstract = {Since its discovery, the microbiota has been increasingly recognised for its role in maintaining health and contributing to various disease conditions. In the reproductive tract, microbial populations can significantly influence endometrial health, internal homeostasis, and fertility. The preservation or restoration of a balanced microbiota through appropriate probiotic products may support reproductive health; in addition, candidate probiotics must be demonstrated to be safe for use. The aim of this study was to assess the local tolerance and systemic safety of a novel intravaginal probiotic product in cows. Twenty-four animals were enrolled and assigned to four groups: single-dose, three-, and five-fold dose of the test product, and a placebo group receiving excipients only. Physical examination and evaluation of the vaginal mucosa were conducted prior to each treatment, one day after and one and two weeks after the final probiotic administration. Blood and urine samples were collected before treatment and following treatment: one day after the last administration of intravaginal probiotic and again two weeks post-treatment. Blood haptoglobin, serum amyloid A, glucose, non-esterified fatty acids, and beta-hydroxybutyrate were measured to assess inflammatory and metabolic responses, and differences over time and between groups were statistically analysed. No dose-dependent systemic changes were observed; however, transient, time-related alterations were noted across all groups, including controls. The investigational probiotic product was well tolerated both locally and systemically, with tolerability comparable across all groups, including the placebo. These data establish a safety profile in healthy cows and support further investigation of this product in studies focusing on efficacy and microbiome modulation.},
}

Animals
*Probiotics/administration & dosage/adverse effects
Female
Cattle
Administration, Intravaginal
Vagina/microbiology/drug effects

@article {pmid42114033,
year = {2026},
author = {Pavitra, SP and Tan, KK and Tan, TK and Er, YX and Vinnie-Siow, WY and Ya'cob, Z and Low, VL and Lim, YAL},
title = {Microbial communities of the Southeast Asian black flies (Diptera: Simuliidae) based on multiple hypervariable regions of 16S rRNA.},
journal = {Journal of medical entomology},
volume = {63},
number = {3},
pages = {},
doi = {10.1093/jme/tjag051},
pmid = {42114033},
issn = {1938-2928},
support = {//Ministry of Higher Education, Malaysia/ ; MO002-2019//Higher Institution Centre of Excellence (HICoE)/ ; TIDREC-2023//Higher Institution Centre of Excellence (HICoE)/ ; },
mesh = {Animals ; RNA, Ribosomal, 16S/analysis/genetics ; *Simuliidae/microbiology ; Male ; Female ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; Malaysia ; High-Throughput Nucleotide Sequencing ; RNA, Bacterial/analysis ; },
abstract = {Black flies (Diptera: Simuliidae) are important vectors of disease-causing agents, but little is known about their microbiome in Southeast Asia, highlighting the need for further investigation. In Malaysia, Simulium cheongi, Simulium jeffreyi, and Simulium vanluni are among the most abundant black fly species and are of potential medical importance, making them suitable representatives for microbiome studies. In this study, their bacterial communities were characterized using next-generation sequencing (NGS) targeting seven hypervariable regions (V2, V3, V4, V6 to V7, V8, and V9) of the 16S rRNA gene to enable comprehensive community profiling. The alpha diversity of the bacterial community showed the highest values of Shannon and Simpson indices in S. jeffreyi and increased values of observed species and Chao1 indices in S. cheongi. Males showed greater microbial diversity than females in the alpha diversity analysis, with all alpha rarefaction plots reaching a plateau. Moreover, the beta diversity of the microbial communities measured by Bray-Curtis distance indices revealed three PCs coordinates with 63.75% of the total variance. However, no significant differences in alpha and beta diversity indexes were found among the three species. The bacterial composition included six phyla, 15 classes, 37 orders, 78 families, 143 genera, and 216 bacterial species, with the V3 region having the highest taxonomic identification. The V9 region had the least detection at all taxonomic levels, emphasizing the importance of selecting appropriate hypervariable regions to accurately assess the diversity of black fly bacterial communities.},
}

Animals
RNA, Ribosomal, 16S/analysis/genetics
*Simuliidae/microbiology
Male
Female
*Microbiota
*Bacteria/genetics/classification/isolation & purification
Malaysia
High-Throughput Nucleotide Sequencing
RNA, Bacterial/analysis

@article {pmid42114284,
year = {2026},
author = {Abd El-Hack, ME and Ashour, EA and Khafaga, AF and Khaleel, HK and Kamal, M and Taha, AE and Alfifi, AE and Al-Rasheed, M and Khan, MMH},
title = {Functional effects of rosmarinic acid on gut health and epigenetic regulation in antibiotic-free poultry diets.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {106943},
doi = {10.1016/j.psj.2026.106943},
pmid = {42114284},
issn = {1525-3171},
abstract = {Rosmarinic acid (RA), a bioactive polyphenol found in Salvia officinalis and other Lamiaceae herbs, has attracted attention for its functional feed application in animal nutrition. RA supplementation positively influences growth efficiency, liver antioxidant status, and serum biochemical indices in broilers. Its antimicrobial and immunomodulatory effects promote health and productivity. Studies suggest benefits for gut health and meat quality; however, epigenetic regulation of RA in poultry is considered a minor future perspective, being mostly based on mammalian studies. Hypothesized impacts of RA on chronic disease prevention and as a microbiome-engineering agent require further investigation. This review explores the regulatory effects of RA on DNA methylation, non-coding RNAs (ncRNAs), and histone modifications, which influence gut microbiome structure, nutrient absorption, and immune function in poultry. It emphasizes RA's potential as a functional food for gastrointestinal health, metabolic regulation, and chronic disease prevention, alongside its use in antibiotic-free poultry feed for microbiome engineering. The review also discusses RA's effects on lipid metabolism and oxidative stress, highlighting its role in maintaining intestinal barrier health. Nevertheless, certain limitations must be acknowledged, as successful nutritional interventions depend on understanding individual variability, including genetics, metabolism, age, and health status. Tailored methodologies, such as micronutrition and genomic nutrition, can improve diet quality, promote nutrient absorption, and enhance overall animal health. A tailored feeding regimen focuses on selecting nutrients with proven benefits for key health outcomes, such as omega-3 fatty acids, which scientific evidence shows promote brain and heart health while reducing inflammation.},
}

@article {pmid42114326,
year = {2026},
author = {Esen, S},
title = {An update on heat stress impacts on rumen microbiome composition, fermentation parameters, and mitigation approaches in ruminants.},
journal = {Journal of thermal biology},
volume = {139},
number = {},
pages = {104480},
doi = {10.1016/j.jtherbio.2026.104480},
pmid = {42114326},
issn = {0306-4565},
abstract = {Over the past decade, there has been an increasing amount of literature on heat stress (HS) effects on ruminant production systems, yet much uncertainty still exists about the relationship between HS and rumen microbial ecology across species. This narrative review synthesizes peer-reviewed evidence from 2020 to 2025, with the aim of providing a critical appraisal of HS effects on rumen microbiome composition and fermentation parameters in cattle, buffalo, sheep, and goats. A convergent pattern emerges from the available data: HS consistently reduces cellulolytic bacteria (Fibrobacter, Ruminococcus) while increasing lactate-producing and starch-fermenting taxa. Acetate proportions declined by 29-33% in buffalo and beef cattle, whereas total VFA in sheep increased during mild HS, reflecting species-dependent fermentation responses. A strong relationship between breed-level heat tolerance and rumen microbiome diversity has been reported in several recent studies, providing converging evidence that heat tolerance may be characterized as a holobiont phenotype. It has been demonstrated that HS extends beyond classical VFA changes to disrupt B-vitamin synthesis, amino acid metabolism, biogenic amine homeostasis, and bile acid biotransformation. Nutritional interventions, including probiotics, chromium, herbal supplements, and rumen-protected amino acids, have been shown to partially restore microbial balance, although responses vary with HS severity and host genotype. Notwithstanding these findings, the generalisability of much published research on this topic is limited by methodological heterogeneity across studies. Taken together, these findings highlight the need for standardized experimental protocols, multi-omics integration, and microbiome-targeted intervention strategies.},
}

@article {pmid42114574,
year = {2026},
author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J},
title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134795},
doi = {10.1016/j.biortech.2026.134795},
pmid = {42114574},
issn = {1873-2976},
abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.},
}

@article {pmid42114665,
year = {2026},
author = {Moerdijk, AS and van Genuchten, WJ and Duijnhouwer, AL and Snoeren, MMM and Hirsch, A and van den Berg, LEM and Boersma, E and Kauling, RM and van den Bosch, AE and Udink Ten Cate, FEA and Helbing, WA and Bartelds, B},
title = {Evaluation of high intensity interval training in patients with a right ventricle to pulmonary artery conduit in a randomized controlled trial - Rationale and design of the 'Right HIIT' study.},
journal = {American heart journal},
volume = {},
number = {},
pages = {107477},
doi = {10.1016/j.ahj.2026.107477},
pmid = {42114665},
issn = {1097-6744},
abstract = {BACKGROUND: Exercise training is a promising, relatively low cost strategy to optimize exercise capacity, primarily studied in patients with tetralogy of Fallot and Fontan physiology. However, rare and complex biventricular disorders are understudied. High intensity interval training (HIIT) is a time-efficient alternative to the more commonly studied aerobic training. Despite group level improvements in exercise capacity, individual variation suggests the existence of responders and non-responders to exercise training. We therefore designed a HIIT intervention trial for patients with complex outflow tract disorders aimed to test efficacy and identify predictors of response.

METHODS: The Right HIIT study is a multicenter, randomized controlled trial aiming to enroll 38 patients aged 12 to 45 years with a right ventricle to pulmonary artery conduit. Participants will be randomized to a 12-week home-based HIIT program (intervention) or standard of care (SoC) group. The primary endpoint is change in peak oxygen consumption from baseline to 12 weeks. Secondary endpoints include other cardiopulmonary exercise testing and imaging parameters, blood biomarkers, gut microbiome composition, quality of life and physical activity levels. After the randomized phase, the SoC group will receive the HIIT program, with repeated data collection after 12 weeks. Thus, pre-post HIIT data will be available in all patients, for the purpose of supportive analyses and identifying predictors of response.

CONCLUSION: The Right HIIT study will analyze whether a HIIT program improves exercise capacity in patients with a right ventricle to pulmonary artery conduit and which factors are associated with the ability to improve exercise capacity.},
}

@article {pmid42114750,
year = {2026},
author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E},
title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28157},
pmid = {42114750},
issn = {1525-3198},
abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.},
}

@article {pmid42114808,
year = {2026},
author = {Reynolds, GK and Dowling, MR and Valencia-Klug, J and Teh, BW and Anderson, MA and Vanguru, V and Harrison, SJ and Ho, PJ and Slavin, MA and Thursky, K},
title = {Infections in the first 30-days after CAR-T therapy in Patients Not Receiving Fluoroquinolone Prophylaxis.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.03.040},
pmid = {42114808},
issn = {2666-6367},
abstract = {BACKGROUND: Routine fluoroquinolone (FQ) prophylaxis may increase the risk of antimicrobial resistance, microbiome disruption, and Clostridioides difficile infection in patients receiving chimeric antigen receptor T-cell (CAR-T) therapy for haematological malignancy. In Australia, FQ prophylaxis is not routinely used. We evaluated the aetiology of early fever following CAR-T to better understand the incidence of infections, particularly bloodstream infections, in a cohort not receiving FQ prophylaxis.

METHODS: This bicentric Australian retrospective study included adults receiving standard-of-care CD19 CAR-T therapy for DLBCL (2019-2023). The primary outcome was the cause of sustained fever (≥38.0°C on ≥1 days) from infusion to day 30. Recurrent fever required ≥72 hours afebrile before a new fever. Infections were classified as microbiologically-confirmed, clinically-defined, or fever syndrome per consensus criteria.

RESULTS: 204 adults (median age 64 years, IQR:57-71) received tisagenlecleucel (50%) and axicabtagene (50%), after a median of 3 prior therapies (IQR:3-4). Sustained fever occurred in 131/204 patients (64%), comprising 161 episodes. Of these, 36 (21%, 28pts) were microbiologically-confirmed infections, 14 (9%, 14pts) were clinically-defined infections, and 110 (69%, 108pts) were fevers of unknown origin. Bacteremia occurred in 7/204 patients (3.4%; 9 events), with one fatal polymicrobial bacteremia. Other microbiologically-confirmed infections included C. difficile (7/36), URTI (13/36) and invasive fungal infection (5/36). Risk factors for early microbiologically-confirmed infection in univariate analysis included axicabtagene product (HR=2.5, p=0.019), grade ≥3 ICANS (HR=3.4, p=0.012), and prolonged neutropenia (ANC ≤ 0.5 × 10⁹/L for ≥14 days; HR=3.7, p=0.014).

CONCLUSION: Early bacteremia rates remain low without routine FQ prophylaxis. Initial sustained fevers are predominantly non-infectious. Our data do not support universal fluoroquinolone prophylaxis in CAR-T therapy.},
}

@article {pmid42115049,
year = {2026},
author = {Ha, S and Zhang, X and Li, L and Yu, J},
title = {MASLD and MASLD-associated HCC: emerging biomarkers and therapeutic avenues.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.04.048},
pmid = {42115049},
issn = {2095-9281},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading chronic liver disease on a global scale. With its increasing incidence and advances in research technologies, our understanding of the mechanisms, non-invasive diagnostic strategies and therapeutic approaches for MASLD and its more advanced forms, including metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC), has substantially expanded. This article reviews the pathophysiological mechanisms underlying MASLD and its transition to more severe forms, evolving from well-established mechanisms including insulin resistance, abnormalities in lipid metabolism and inflammation, to recently explored novel mechanisms, such as immune regulation, RNA modification and gut microbiome. Additionally, emerging biomarkers for diagnosis and prognosis, such as non-invasive serum markers and genetic variants are highlighted. This review evaluates contemporary therapeutic strategies, with particular emphasis on the recent FDA approval of resmetirom and semaglutide, alongside other pharmacological agents currently in phase 3 clinical trials. It also discusses innovative interventions aimed at improving the management of MASLD and MASLD-HCC, specifically in the context of gut modulation and enhancing the efficacy of immunotherapy. The necessity for strategies aimed at early detection and multifactorial treatment approaches is critical to address the rising burden of MASLD and its complications, with a call for further research into personalised medicine and innovative multidisciplinary therapeutic targets.},
}

@article {pmid42115134,
year = {2026},
author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Abdisalaam, I and Rijneveld, R and Klaassen, ES and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and Freyee, B and Platenkamp, K and van Poelgeest, ME and Rissmann, R and van Doorn, MBA and Niemeyer-van der Kolk, T},
title = {Lack of improvement after short-term topical antistaphylococcal endolysin SA.100 therapy in patients with mild-to-moderate atopic dermatitis: Results from a randomized, vehicle-controlled trial.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70608},
pmid = {42115134},
issn = {1365-2125},
support = {//Micreos Human Health B.V./ ; },
abstract = {Atopic dermatitis (AD) is a chronic immune-mediated inflammatory skin disease. An overgrowth of Staphylococcus aureus (S. aureus) and decreased microbial diversity is apparent in 70%-90% of AD patients. SA.100 is a recombinant endolysin targeting S. aureus that might be a novel treatment for patients with mild-to-moderate AD. To test safety, pharmacodynamics and efficacy of SA.100 a double-blind, randomized, vehicle-controlled trial in 53 subjects with mild-to-moderate AD was performed. Patients were randomized equally to topical SA.100 or vehicle with stratification for S. aureus positivity. SA.100 was safe and well tolerated. No reduction of S. aureus and no changes in microbiome features were seen after 2 weeks of treatment. Additionally, no statistically significant changes in clinical or patient-reported outcomes were observed compared to vehicle. In conclusion, topical SA.100 was safe and well tolerated in patients with mild-to-moderate AD, but our findings do not support short-term clinical use.},
}

@article {pmid42115189,
year = {2026},
author = {Wojciechowska, AW and Wojciechowski, JW and Zielinska, K and Soeding, J and Kosciolek, T and Kotulska, M},
title = {Aggregation in gut: on the link between neurodegeneration and bacterial functional amyloids.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01005-8},
pmid = {42115189},
issn = {2055-5008},
support = {2019/35/B/NZ2/03997//Narodowe Centrum Nauki/ ; 2023/05/Y/NZ2/00080//Narodowe Centrum Nauki/ ; 2019/35/B/NZ2/03997//Narodowe Centrum Nauki/ ; },
abstract = {Amyloids are insoluble protein aggregates with a cross-beta structure, which are traditionally associated with neurodegeneration. Similar structures, named functional amyloids, expressed mostly by microorganisms, play important physiological roles, e.g., bacterial biofilm stabilization. Using a bioinformatics approach, we identify gut microbiome functional amyloids and analyze their potential impact on human health via the gut-brain axis. The results point to taxonomically diverse sources of functional amyloids and their frequent presence in the extracellular space. The retrieved interactions between gut microbiome functional amyloids and human proteins indicate their potential to trigger inflammation, affect transport and signaling processes; pathways typically affected by host-microbiome interactions. We also find a greater relative abundance of bacterial functional amyloids in patients diagnosed with Parkinson's disease in two out of three analyzed datasets. Our results generate hypotheses on a tentative link between neurodegeneration and gut bacterial functional amyloids, which require further experimental validation.},
}

@article {pmid42115298,
year = {2026},
author = {Park, SH and Park, J and Kim, J and Choi, H and Kim, IG and Chung, EJ and Na, KJ},
title = {Analysis of unmapped RNA-seq data from cancer spatial transcriptome toward characterizing cancer microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52324-x},
pmid = {42115298},
issn = {2045-2322},
support = {RS-2024-00357094//National Research Foundation of Korea/ ; 2020R1C1C1007105//National Research Foundation of Korea/ ; 2620210050//Seoul National University Bundang Hospital/ ; },
abstract = {Spatial characterization of microbial-like signals in tumor tissues remains challenging, particularly in direct Visium data, where microbial reads are sparse and may not be fully retained in standard count matrices. Here, we present an extended unmapped-read analysis as a proof-of-concept workflow for summarizing microbial-like 16S rRNA signals in four direct Visium specimens from colorectal cancer (CRC), oral squamous cell carcinoma (OSCC), and head and neck squamous cell carcinoma (HNSC). The workflow uses a custom reference containing four selected 16S rRNA sequences and computes a per-spot mismatch ratio to quantify sequence-level dissimilarity relative to each reference. Compared with PathSeq, the workflow yielded different spatial signal patterns and mismatch summaries across the analyzed specimens. Among the four tested references, the CRC specimen showed lower mismatch ratios relative to the E. coli reference than the other analyzed specimens, an observation compatible with the intestinal context but not definitive evidence of species-level presence or evolutionary proximity. Given the small sample set, restricted reference panel, and lack of dedicated negative controls, these findings should be interpreted as hypothesis-generating. This study provides a complementary proof-of-concept framework for exploring microbial-like signals in direct Visium data.},
}

@article {pmid42115377,
year = {2026},
author = {Catani, G and O'Connor, JM and Spinelli, A and Perea, J},
title = {Early-onset colorectal cancer: a comprehensive review reframing hypotheses and defining research priorities.},
journal = {International journal of colorectal disease},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00384-026-05145-3},
pmid = {42115377},
issn = {1432-1262},
abstract = {PURPOSE: Early-onset colorectal cancer (EOCRC), defined as colorectal cancer diagnosed before the age of 50 years, is increasing worldwide and represents a growing clinical and public health challenge. Whether EOCRC constitutes a biologically distinct entity remains uncertain, and current diagnostic and therapeutic strategies are largely extrapolated from late-onset disease.

METHODS: This narrative review summarizes recent evidence on EOCRC biology, diagnosis, and management, focusing on molecular and genomic features, tumor microenvironment, exposome-related factors, diagnostic pathways, treatment paradigms, and emerging strategies for early detection. We critically examine the gap between biological insights and real-world clinical practice and outline priorities for future research.

RESULTS: EOCRC displays a heterogeneous molecular landscape that substantially overlaps with late-onset colorectal cancer. Although advances in multiomics profiling, liquid biopsy, and microbiome research have improved biological understanding, these findings have not yet translated into EOCRC-specific diagnostic or therapeutic approaches. Diagnosis remains delayed due to age-based screening paradigms and symptom misattribution, resulting in advanced-stage presentation. Younger patients frequently receive intensified treatment despite limited age-specific evidence and insufficient attention to long-term toxicity, fertility, and survivorship.

CONCLUSION: EOCRC underdiagnosis is likely multifactorial. While limitations in biological knowledge and diagnostic tools may play a role, the discrepancy between current paradigms and the age-specific risk profiles of younger patients likely represents an important contributing factor. Progress will require biology-informed, risk-adapted screening strategies and EOCRC-focused clinical research.},
}

@article {pmid42115408,
year = {2026},
author = {Cheng, B and Gong, L and Xu, H and Wang, Z and Huang, H and Guan, X and Wu, P},
title = {The microbiome across the prostate disease continuum: from health and BPH to prostatitis/CPPS and cancer.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {42115408},
issn = {1476-5594},
abstract = {Microbial contributions to prostate health and disease extend beyond the mere detection of organisms in urine or tissue. Rather than acting as stable colonisers, microbial influences on the prostate are better conceptualised as converging fluxes: systemically circulating gut-derived metabolites, immune education occurring in distal lymphoid compartments, and intermittent exposure to microbial products from the lower urinary tract. These inputs converge on a limited set of conserved mediator-receptor axes-including short-chain fatty acids, bile acids and indole derivatives-that calibrate epithelial barrier integrity, inflammatory thresholds, antigen-presentation capacity and myeloid cell fate. Crucially, the biological relevance of these axes is stage-dependent. In benign prostatic hyperplasia and chronic prostatitis/chronic pelvic pain syndrome, metabolite tone shapes inflammatory activation thresholds and barrier resilience. In localized prostate cancer, these same pathways intersect with antigen-processing machinery and immune exclusion. In castration-resistant disease, tumour-intrinsic metabolic plasticity and redox balance predominate, with microbial and host-derived metabolites assuming relevance when they modulate lipid remodelling and ferroptotic vulnerability. Interpretation is constrained by the intrinsically low biomass of urine and prostate tissue. Robust inference therefore requires quantitative anchoring, orthogonal validation and explicit separation of association from causality. Translational progress is most likely to emerge from calibrated measurement and stage-aware modulation rather than indiscriminate ecological manipulation. By integrating mechanistic, spatial and clinical evidence, this Review proposes a stage-aware framework for the gut-urinary-prostatic axis and delineates when microbial and metabolite signalling meaningfully conditions prostate disease biology-and when it does not.},
}

@article {pmid42115470,
year = {2026},
author = {Fragkou, PC and Moschopoulos, CD and Marová, D and Alahmad, B and Skevaki, C and , },
title = {Climate change-associated heat extremes and immune dysregulation: emerging links with autoimmunity, allergy, and infectious diseases.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {42115470},
issn = {1863-2300},
mesh = {Humans ; *Climate Change ; *Hypersensitivity/etiology/immunology/epidemiology/metabolism ; *Communicable Diseases/etiology/immunology/epidemiology ; Animals ; *Autoimmunity ; *Hot Temperature/adverse effects ; Disease Susceptibility ; *Autoimmune Diseases/etiology ; Environmental Exposure/adverse effects ; },
abstract = {Climate extremes are increasingly shaping both environmental and human health outcomes. Global warming has led to a rise in the frequency, duration, and intensity of extreme temperature events, with heatwaves emerging as one of the most hazardous weather-related threats. Beyond their well-recognized cardiovascular and respiratory effects, heat extremes are now understood to influence immune function. Growing evidence indicates that heat extremes along with air pollution, wildfires, humidity shifts, and ecosystem disruption can impair epithelial barrier integrity and disturb immune regulation. These stressors may promote chronic inflammation, alter adaptive immune responses, and compromise host defense mechanisms. Experimental and epidemiological data suggest that heat stress can reduce effective B-cell responses, modify antigen presentation, and increase inflammatory signaling, while combined exposures to heat and pollutants may further increase susceptibility to infectious, allergic, and autoimmune diseases. Although the physical drivers of climate change are well established, the biological pathways linking environmental stressors to immune dysregulation remain incompletely defined. This review synthesizes current evidence on the mechanisms by which extreme heat events influence immune tolerance and disease risk. We discuss implications for allergy, autoimmunity, and infectious diseases, highlight vulnerable populations, and outline key research priorities needed to inform clinical and public health adaptation.},
}

Humans
*Climate Change
*Hypersensitivity/etiology/immunology/epidemiology/metabolism
*Communicable Diseases/etiology/immunology/epidemiology
Animals
*Autoimmunity
*Hot Temperature/adverse effects
Disease Susceptibility
*Autoimmune Diseases/etiology
Environmental Exposure/adverse effects

@article {pmid42115547,
year = {2026},
author = {Chung, CS and Kherallah, K and Ashina, N and Beraja, GE and Budhiraja, A and Dienes, S and Goldberg, M and Xiong, G and Alhusayen, R and Goldberg, S and Gonzalez, T and Hsiao, JL and Lev-Tov, H and Sibbald, C and Piguet, V and Porter, M},
title = {Symposium on Hidradenitis Suppurativa Advances 2025 Proceedings.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42115547},
issn = {2193-8210},
}

@article {pmid42115794,
year = {2026},
author = {Chen, J and Chen, S and Sun, H and Wang, Y},
title = {Lower airway microbiome and metabolomic profiles of recurrent wheezing in infants: a case-control study.},
journal = {Allergologia et immunopathologia},
volume = {54},
number = {3},
pages = {49-80},
pmid = {42115794},
issn = {1578-1267},
mesh = {Humans ; Male ; Female ; Infant ; *Respiratory Sounds/etiology ; *Microbiota ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Metabolome ; Metabolomics ; Recurrence ; DNA, Bacterial/genetics ; Bacteria ; },
abstract = {OBJECTIVES: To characterize the microbiome shifts and subsequent metabolite alterations associated with recurrent wheezing (RW) in infants.

METHODS: A total of 33 subjects were enrolled in this study, including 18 infants diagnosed with RW, and 15 normal infants as controls. Bronchoalveolar lavage (BAL) fluid was collected from all the subjects. Bacterial DNA was then isolated and analyzed by 16S ribosomal RNA sequencing. In addition, the metabolomic profile of BAL fluid samples was analyzed with mass spectrometry using complementary chromatographic methods. Spearman's rank correlation analysis was conducted to explore associations between microbial taxa and metabolites.

RESULTS: The study had 21 (63.6%) boys and 12 (36.4%) girls. The mean age was 26.8 ± 4.9 months. Haemophilus (P = 0.003) and Porphyromonas (P = 0.007) genera showed significant difference between the two groups. The metabolites of "starch and sucrose metabolism pathway" and "pentose phosphate pathway" showed significant correlations with the two bacterial genera. For starch and sucrose metabolism pathway, glucose-6-phosphate showed significant positive correlations with Haemophilus (r = 0.44 and P = 0.009) and Porphyromonas (r = 0.45 and P = 0.008). For pentose phosphate pathway, Sedoheptulose 7-phosphate, an intermediate in the pentose phosphate pathway, showed significantly positive correlations with Haemophilus (r = 0.42 and P = 0.02) and Porphyromonas (r = 0.43 and P = 0.01).

CONCLUSIONS: Our study provided new evidence that alteration in respiratory tract microbiome could be associated with RW in infants. By elucidating the microbiome and metabolite profile, we identified novel biomarkers potentially useful for personalized management of RW in infants. The future studies should validate the underlying mechanisms in longitudinal cohorts and explore interventions targeting metabolic-microbial crosstalk.},
}

Humans
Male
Female
Infant
*Respiratory Sounds/etiology
*Microbiota
Case-Control Studies
RNA, Ribosomal, 16S/genetics
Bronchoalveolar Lavage Fluid/microbiology
Metabolome
Metabolomics
Recurrence
DNA, Bacterial/genetics
Bacteria

@article {pmid42115865,
year = {2026},
author = {Huang, J and Chen, Z and Chen, M and Zeng, Z and Zhuang, X},
title = {Specific alterations in the gut microbiome and metabolome across disease locations of Crohn's disease: a systematic review.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-04898-z},
pmid = {42115865},
issn = {1471-230X},
support = {82200605//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Crohn's disease (CD) exhibits substantial heterogeneity in disease behavior and therapeutic outcomes across distinct disease locations. Specific alterations in the gut microbiota and metabolites may drive this variation. This review aims to characterize the distinctive microbial and metabolic signatures across CD phenotypes based on disease location.

METHODS: Electronic databases were searched from inception to December 2025 for studies that observed alterations in gut microbiota and metabolites in CD patients with different disease locations.

RESULTS: Forty-eight studies including 3,577 CD patients and 2,916 healthy controls (HCs) were analyzed. Ileal Crohn's disease (ICD) was characterized by significant dysbiosis compared with HCs, featuring enrichment of Enterobacteriaceae (especially adherent-invasive Escherichia coli [AIEC]), Fusobacterium and Shigella, alongside depletion of Faecalibacterium prausnitzii, Roseburia and Coprococcus. Patients with colonic Crohn's disease (CCD) exhibited increased levels of Proteobacteria, pro-inflammatory families (Actinomycetaceae, Micrococcaceae) and opportunistic pathogens (Streptococcus, Klebsiella). In contrast, a decrease in short-chain fatty acid (SCFA)-producing families (Lachnospiraceae, Ruminococcaceae) and F. prausnitzii was observed in CCD. Ileocolonic Crohn's disease (ICCD) displayed features combining ICD and CCD elements, with specific depletion in Alistipes communis and enrichment of Shigella flexneri. More pro-inflammatory bacteria were observed in ICD compared with CCD. In terms of metabolic alterations, ICD showed impaired enterohepatic bile acid circulation with excessive fecal loss of conjugated bile acids, while CCD exhibited defective conversion of primary to secondary bile acids. ICCD exhibited both impaired ileal reabsorption and defective colonic transformation.

CONCLUSIONS: Our results identified disease location-specific alterations in the microbiome and metabolome of CD, which might be associated with the clinical manifestations and prognosis of different phenotypes.},
}

@article {pmid42115921,
year = {2026},
author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F},
title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05117-1},
pmid = {42115921},
issn = {1471-2180},
abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.},
}

@article {pmid42115936,
year = {2026},
author = {Dalgic, A and Yet, I},
title = {Identifying gut microbiome signatures of type 1 diabetes using machine learning and evolutionary feature selection.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05113-5},
pmid = {42115936},
issn = {1471-2180},
abstract = {BACKGROUND: Type 1 Diabetes Mellitus (T1D) has been increasingly associated with alterations in the gut microbiome. However, the impact of taxonomic resolution, feature selection strategies, and machine learning methods on microbiome-based prediction remains incompletely understood.

METHODS: We analyzed publicly available 16S rRNA gene sequencing datasets from two geographic cohorts to evaluate microbiome-based prediction of T1D. Microbial features were constructed at multiple taxonomic levels and as full hierarchical taxonomic paths preserving phylogenetic structure. Machine learning models were trained using stratified cross-validation and cross-cohort validation frameworks. Feature selection was performed using Binary Particle Swarm Optimization (BPSO) to identify compact and predictive microbial signatures. Model performance was evaluated using AUC, Accuracy, F1 score, and Matthews Correlation Coefficient. Differential abundance analysis using the LinDA framework was used to support biological interpretation of selected taxa.

RESULTS: Tree-based models, particularly Random Forest and XGBoost, achieved the strongest predictive performance across taxonomic representations. Taxonomic resolution influenced model behavior, with family-level features providing strong performance with compact feature sets, while higher-resolution representations did not consistently improve performance despite increased complexity. BPSO identified consistently selected taxa across validation frameworks, suggesting stable predictive signatures. Several of these taxa have been linked to inflammatory or metabolically altered gut environments. Cross-cohort validation showed reduced performance compared with within-study models, highlighting challenges in generalization.

CONCLUSION: Machine learning combined with BPSO-based feature selection provides an effective framework for identifying predictive microbial signatures associated with T1D. Our findings highlight the importance of taxonomic resolution, feature stability, and cross-cohort validation in microbiome-based predictive modeling. Integrating evolutionary feature selection with machine learning and biological validation may improve the robustness and interpretability of candidate microbial signatures.},
}

@article {pmid42116047,
year = {2026},
author = {Choi, JW and Kim, H and Ham, SH and Han, YJ and Kim, SE and Sung, MK},
title = {Probiotic Bifidobacterium bifidum BGN4 supplementation modulates gut microbiome composition and reduces circulating zonulin, TNFα, and insulin in adults with excess adiposity: a randomized, double-blind, placebo-controlled trial.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01124-1},
pmid = {42116047},
issn = {1743-7075},
support = {2023R1A2C1005313//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2022R1A2C1004626//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; },
abstract = {BACKGROUND: Obesity, characterized by excess body fat accumulation, is closely linked to the alteration of gut microbiota, which contribute to systemic inflammation. Probiotics intervention has emerged as a promising strategy favorably modulating gut microbiota composition in obese individuals accompanied by improvements in metabolic parameters. The objective of this study was to evaluate whether supplementation with Bifidobacterium bifidum BGN4 alters gut microbiota composition and to assess its associated effects on circulating zonulin, a marker of intestinal permeability, as well as metabolic parameters in individuals with excess adiposity.

METHODS: This randomized, double-blind, placebo-controlled trial involved 60 adults with excess body fat (body fat percentage ≥ 20% for males and ≥ 28% for females). A total of 60 adults were enrolled, and sex- and age-stratified randomization allocated 30 participants to each group. Participants received one capsule of B. bifidum BGN4 (9 × 10[9] colony forming unit) or matched placebo for 8 weeks. Blood samples were analyzed for zonulin, TNFα, hs-CRP, glucose, insulin, lipid profiles, and total antioxidant capacity. Fecal samples were analyzed to determine alterations in gut microbiota composition.

RESULTS: A total of 58 participants, with 29 individuals in each group, successfully completed the 8-week intervention. Supplementation with B. bifidum BGN4 did not result in significant changes in BMI, body fat percentage, or the primary outcome, hs-CRP. In contrast, significant improvements were observed in serum zonulin (between-group differences: -1.61 ± 2.69 ng/mL), TNFα (between-group differences: -0.17 ± 0.26 pg/mL), and fasting insulin (between-group differences: -3.52 ± 10.25 μIU/mL). The probiotic intervention modulated the enrichment of several taxa, including Bacteroides coprocola, Bifidobacterium catenulatum group, Lactiplantibacillus plantarum group, and Prevotella stercorea. In addition, several microbial taxa demonstrated correlations with metabolic and inflammatory parameters. No adverse effects were observed, as indicated by stable liver enzyme concentrations, blood pressure, and gastrointestinal symptoms.

CONCLUSION: The results indicate that B. bifidum BGN4 may serve as a preventive strategy for metabolic disorders in individuals with excess adiposity through the maintenance of gut microbial balance and intestinal barrier integrity thereby potentially mitigating inflammation and metabolic stress.

TRIAL REGISTRATION: Clinical trial registration number: KCT0010817. Date of registration: July 28, 2025.},
}

@article {pmid42116157,
year = {2026},
author = {Li, S and Lin, L and Zhang, M and Liu, J and Lu, E and Cao, Z},
title = {Nanoengineered bile acid-mediated orchestration of versatile immuno-microbial cues for treating periodontitis.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04495-y},
pmid = {42116157},
issn = {1477-3155},
support = {82401198//National Science Foundation of China/ ; 52171075//National Science Foundation of China/ ; 22575146//National Science Foundation of China/ ; 2022M710748//China Postdoctoral Science Foundation/ ; 22YF1439400//the Youth Science and Technology Talents-the Sailing program of Shanghai/ ; 25ZR1401224//Natural Science Foundation of Shanghai/ ; },
abstract = {Periodontitis, a globally prevalent inflammatory disease, is propelled by a vicious cycle involving microbial dysbiosis, hyperactive host immune responses, excessive oxidative stresses, and chronic inflammations. Current treatments largely focus on reducing microbial pathogens, yielding limited therapeutic efficacy. Here, we report a polydopamine-based taurolithocholic acid (TLCA) nanotherapeutic (PDCA) that reprograms versatile immuno-microbial cues to ameliorate periodontal inflammation and restore tissue homeostasis. Leveraging the dual function of polydopamine in drug delivery and redox capacity, after cellular uptake, PDCA scavenges reactive oxidation species, and releases TLCA to interact with its nuclear receptors in various target cells, exerting multifaceted regulatory effects. In inflamed human gingival fibroblasts, PDCA reduces the oxidative stress and enriches intracellular accumulation of TLCA to assist its interaction with vitamin D receptor, thus attenuating the expression of pro-inflammatory cytokines. Furthermore, PDCA modulates hyperactive immune responses, including suppressing the maturation of dendritic cells, inhibiting osteoclast differentiation of monocytes, downregulating pro-inflammatory CD4[+] lymphocytes, and upregulating regulatory T cells. Concomitantly, this immunomodulation is associated with the restoration of periodontal microbiome homeostasis, contributing to a reduction in pathogens and an enrichment of beneficial flora. In addition, PDCA not only rescues inflammatory tissue destructions in both therapeutic and prophylactic mouse models of periodontitis, but also elicits robust decrement in pro-inflammatory cytokine production in ex vivo human periodontitis tissues. This work highlights polydopamine-based bile acid nanomedicine as a microenvironment-targeting platform for immuno-microbial rebalance, offering a transformative strategy to treat oral inflammatory diseases.},
}

@article {pmid42116193,
year = {2026},
author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS},
title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00909-4},
pmid = {42116193},
issn = {2524-6372},
support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; },
abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.

METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.

RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.

CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.},
}

@article {pmid42116194,
year = {2026},
author = {Buetas, E and Conde-Pérez, K and Concha, Á and Celeiro, C and Noguera, JF and Bou, G and Pardiñas-López, S and Vallejo, JA and Poza, M and Carda-Diéguez, M and Mira, A},
title = {Metatranscriptomic analysis of the microbiota of tumor tissue in colon cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02372-2},
pmid = {42116194},
issn = {2049-2618},
abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, accounting for more than 900,000 deaths a year worldwide. Microbial dysbiosis, including the presence of oral bacteria in the gut, has been linked to CRC. Some mechanisms by which specific microorganisms potentially drive tumorigenesis have been described, but there is a lack of studies elucidating whole microbiota activity in the tumor and their implication for the development of the disease. Here, the metatranscriptomic data of tumor and control tissue-associated microbiota (n = 18 pairs), as well as from subgingival sulcus (n = 15) of CRC patients, was analyzed.

RESULTS: We confirmed that Fusobacterium nucleatum was more active in the tumor tissue than in the control gut mucosa. In addition, the activity of this species was positively correlated with other oral bacteria in the tumors, including Parvimonas micra, Peptostreptococcus stomatis, and Granulicatella adiacens, along with gut bacteria like Hungatella hathewayi, suggesting a potential relationship among them. Regarding bacterial gene expression, a change in the functional profile was observed, including a higher expression of genes associated with carbon metabolism in control in contrast to an increase of amino acid-related genes in tumor. Furthermore, genes implicated in the biosynthesis and transport of lipopolysaccharide were increased in tumors. Interestingly, a significantly higher expression in tumor than control tissue of potential virulence factors from F. nucleatum was found, supporting their relevance in niche colonization and tumorigenesis. Correlation analysis of the bacterial activity with the host transcriptional profile showed significant correlations of the Fusobacterium-Peptostreptotoccus-Hungatella cluster with human genes involved in inflammation and metastasis, confirming the association of this microbial consortium with tumor development. For the first time, the gene expression profiles of oral bacteria in the gut and the oral cavity were compared. The cluster of co-active bacteria identified in tumors was partially found in the oral samples, suggesting a stable interaction and potential synergy. Although there were thousands of differentially expressed genes between subgingival sulcus and tumor tissue, the expression of key virulence factors was not significantly different.

CONCLUSIONS: In short, this study discovered new traits about tumor microbial-associated composition and activity and its connection with the oral composition that would be essential to unravel the translocation, colonization, and tumorigenesis of the CRC.},
}

@article {pmid42116227,
year = {2026},
author = {Hron, BM and Zhang, YJ and Golden, C and Chalmers, C and Nemec, G and Delaney, E and Ozcan, E and Kim, M and Jalali, L and Solari, T and Brezsny-Feldman, J and Alm, EJ and Bry, L and Rosen, R},
title = {Association between blenderized tube feeds and differential oropharynx, stomach, and stool microbiome signatures relative to conventional formula feeds in children fed via enteral tube: A cross-sectional study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.70097},
pmid = {42116227},
issn = {1941-2444},
support = {//Supported by National Institutes of Health R01 DK097112 (PI: Rosen) and K23 DK133679 (PI: Hron), NASPGHAN Astra- Zeneca Research Award (PI: Hron), NIH K12 5K12HD052896 (PI: Fleisher, awarded to Zhang); NASPGHAN Foundation/Reckitt/Mead Johnson Nutrition Young Investigator Development Award (PI: Zhang); AGA Research Scholar Award (PI: Zhang); Harvard Digestive Diseases Center Grants P30 DK034854 (NIH) and Massachusetts Life Sciences Center Capital Grant./ ; },
abstract = {BACKGROUND: Blenderized gastrostomy tube feeds are associated with reduced gastrointestinal symptoms. We hypothesize that patients receiving blenderized tube feeds, compared with standard formula, will have less gastric-oropharyngeal microbial overlap, a possible biomarker of less gastroesophageal refluxate, and differences in beta diversity in the oropharynx, stomach, and stool.

METHODS: Children requiring enteral tube feeds for >3 months were prospectively recruited to provide saliva via posterior tongue swabs, gastric aspirates, and stool samples. Exclusion criteria were history of cystic fibrosis or solid organ transplant or antibiotic treatment course within 4 weeks. The primary exposure was diet category (formula vs. blenderized feeds). The primary outcome was Jaccard similarity between the gastric and oral microbiomes. Relationships of diet to Jaccard and relative bacterial abundance were analyzed by multivariate linear regression models adjusting for age, sex and proton pump inhibitor use.

RESULTS: Sixty (60.6%) children received blenderized tube feeds and 39 (39.4%) received formula. Beta diversity in the oral and rectal samples differed significantly between patients on blenderized versus formula feeds. Importantly, gastric and tongue microbiomes had significantly less overlap (by Jaccard distance) in patients receiving blenderized feeds, adjusting for covariates. Several key oral, gastric and stool commensal organisms were present in higher relative abundance in the blenderized versus formula group.

CONCLUSION: Oropharyngeal microbiomes are more distinct from the gastric microbiomes in patients receiving blenderized feeds, and the oropharyngeal and stool microbiomes demonstrated differential bacterial abundance compared with formula. Overall, these findings suggest a highly favorable microbial profile with blenderized feeds.},
}

@article {pmid42116335,
year = {2026},
author = {Nie, Y and Lin, X},
title = {Analysis of oral microbiome characteristics and their correlation with oral health diseases.},
journal = {Medicine},
volume = {105},
number = {19},
pages = {e48600},
pmid = {42116335},
issn = {1536-5964},
mesh = {Humans ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; Middle Aged ; *Oral Health ; *Mouth Diseases/microbiology/epidemiology ; Adult ; *Mouth/microbiology ; Aged ; },
abstract = {To investigate the relationship between oral microbiome characteristics and oral health status, examining microbial diversity and the prevalence of specific bacterial genera. We conducted a cross-sectional study of 154 patients who underwent oral examinations at our hospital from January 2023 to December 2023. Based on routine oral examinations and medical history inquiries, patients were divided into oral health group (n = 71) and oral health disease group (n = 83). Oral samples were collected and analyzed using next-generation sequencing and bioinformatics to assess microbial diversity and abundance. Key demographic and behavioral factors were recorded, and statistical analyses determined oral microbiome characteristics with oral health. The oral health disease group had significantly higher average age, smoking rates, body mass index, alcohol use, family history of oral diseases, and worse oral health indicators (e.g., plaque, gum inflammation, calculus, periodontal status, decayed/missing teeth, and decayed, missing, and filled teeth scores). They also showed lower microbial diversity (Shannon, Chao1, and evenness indices) and reduced levels of protective bacteria (Streptococcus and Actinomyces). In contrast, the oral health group had higher flossing rates, more caries-free individuals, and greater microbial diversity. The Shannon, Chao1, and evenness indices were inversely linked to oral disease, while the Simpson Index (measuring dominance) was positively correlated. Protective bacteria were negatively linked to disease, whereas harmful bacteria (Fusobacterium and Prevotella) were positively correlated. Our findings highlight decreased microbial diversity as a significant factor in oral diseases, suggesting that maintaining a diverse oral microbiome was crucial for oral health.},
}

Humans
Female
Male
Cross-Sectional Studies
*Microbiota
Middle Aged
*Oral Health
*Mouth Diseases/microbiology/epidemiology
Adult
*Mouth/microbiology
Aged

@article {pmid42116339,
year = {2026},
author = {Han, GY and Wang, ZJ and Wang, DX and Wang, CY and Yang, MQ},
title = {Forging new insights in forensic microbiome studies: A 2000 to 2024 bibliometric analysis redefining the landscape.},
journal = {Medicine},
volume = {105},
number = {19},
pages = {e48661},
pmid = {42116339},
issn = {1536-5964},
mesh = {*Bibliometrics ; Humans ; *Microbiota ; *Forensic Sciences ; *Forensic Medicine ; RNA, Ribosomal, 16S ; Machine Learning ; },
abstract = {BACKGROUND: Microbial diversity has been extensively studied across various fields, including medicine and therapeutics. Its application in forensics is rapidly expanding due to its effectiveness. This study aimed to conduct a comprehensive bibliometric analysis of global research on forensic microbiome, providing a foundational knowledge framework for this emerging field.

METHODS: A comprehensive literature search was performed using the Web of Science Core Collection database to identify publications related to the forensic microbiome. Annual publication output, research collaborations, research hotspots, and developmental trends in this field were analyzed using bibliometric software (VOSviewer and CiteSpace).

RESULTS: In total, 709 articles published between 2000 and 2024 were selected. The first study in this field was published in 2000. Recently, the number of publications and citations has grown significantly. Cooperation network analysis revealed that the United States of America contributes the most to forensic microbiome research, with the highest publication volume. Michigan State University emerged as the most prolific institution. Forensic Science International is the most productive journal in this field. Carter David O. contributed the most to the articles and is the most co-cited authors. Keywords cluster analysis identified 4 major research clusters: bacteria, forensic medicine, 16s ribosomal ribonucleic acid, and machine learning. Machine learning, human microbiome, and forensic microbiology have attracted increasing attention from researchers.

CONCLUSION: This bibliometric analysis provides a data-driven and objective overview of forensic microbiome research currently, offering readers a valuable reference for future research. Our review provides insights into contemporary trends, global patterns of collaboration, fundamental knowledge, high-interest research areas, and emerging frontiers in the forensic microbiome.},
}

*Bibliometrics
Humans
*Microbiota
*Forensic Sciences
*Forensic Medicine
RNA, Ribosomal, 16S
Machine Learning

@article {pmid42116498,
year = {2026},
author = {Wang, L and Liang, C and Yu, J and Zhang, Y and Li, H and Hu, Y and Liu, W and Qu, X and Xie, W and Wang, X and Yuan, H},
title = {Timing matters in type 2 diabetes: Early high-Fiber nutrition enhances glycemic control and reshapes gut microbiota.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119257},
doi = {10.1016/j.foodres.2026.119257},
pmid = {42116498},
issn = {1873-7145},
mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy/microbiology/blood ; *Dietary Fiber/administration & dosage ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Over Studies ; Middle Aged ; *Glycemic Control/methods ; Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism/analysis ; Aged ; Obesity/diet therapy ; Time Factors ; Adult ; Overweight/diet therapy ; },
abstract = {Early, intensive dietary intervention may open a therapeutic window for type 2 diabetes (T2D) remission. We conducted a randomized, 2:1 crossover trial in 34 newly diagnosed overweight or obese patients with T2D. Participants were assigned to receive either high-fiber nutritional therapy (HFNT)-a 7-day very-low-calorie, high-fiber diet followed by a 23-day standard diabetes diet-or conventional diabetes treatment (control condition). Each treatment was administered for 90 days before crossover. Compared with the control condition, early HFNT led to greater reductions in HbA1c [-9.45% (-18.04, -4.63) vs 1.44% (-7.73, 3.08); P = 0.010] and fasting plasma glucose [-12.70% (-24.51, -6.01) vs 3.46% (-8.14, 0.94); P = 0.005], while changes in BMI and HOMA-IR were not significant (P > 0.05). Gut microbiome profiling revealed enrichment of short-chain fatty acid-producing taxa (Eubacterium ruminantium group, Blautia, Roseburia, Akkermansia muciniphila, Oscillospira) and depletion of pathogenic genera (Escherichia-Shigella) after HFNT, with compositional shifts correlating with improved glycemic control. Notably, glycemic benefits in participants receiving HFNT first persisted after crossover, whereas participants receiving conventional care first did not achieve full metabolic recovery after switching. These findings suggest that in newly diagnosed T2D, early, fiber-enriched, intermittent energy restriction can induce durable glycemic improvements, potentially mediated by gut microbiota remodeling. This trial highlights a narrow but impactful nutritional intervention window that may alter the trajectory of T2D progression.},
}

Humans
*Diabetes Mellitus, Type 2/diet therapy/microbiology/blood
*Dietary Fiber/administration & dosage
*Gastrointestinal Microbiome
Male
Female
Cross-Over Studies
Middle Aged
*Glycemic Control/methods
Blood Glucose/metabolism
Glycated Hemoglobin/metabolism/analysis
Aged
Obesity/diet therapy
Time Factors
Adult
Overweight/diet therapy

@article {pmid42116511,
year = {2026},
author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W},
title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119274},
doi = {10.1016/j.foodres.2026.119274},
pmid = {42116511},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; },
abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.},
}

*Fermentation
*Microbiota
*Metabolome
Food Microbiology
Taste
Volatile Organic Compounds/analysis
Bacteria/metabolism/classification/genetics
*Wine/microbiology/analysis
Fungi/metabolism/classification
Metabolomics
Flavoring Agents
China

@article {pmid42116975,
year = {2026},
author = {Latt, TS and Aye, TT and Ko, K and Win, SS and Chit, TT and Myint, KNS},
title = {Restructuring the Obesity Paradigm: Molecular Etiologies, Clinical Complexities, and the Future of Precision Intervention.},
journal = {Cureus},
volume = {18},
number = {4},
pages = {e106767},
pmid = {42116975},
issn = {2168-8184},
abstract = {Obesity is a complex, chronic, and relapsing disease affecting adults globally and continues to rise across all age and socioeconomic groups. Once regarded as a lifestyle issue, obesity is now recognized as a multifactorial condition influenced by multiple factors. This review consolidates current evidence on the dynamic pathophysiology of obesity, highlighting advances in understanding its genetic foundations, hormonal imbalances, gut microbiome disruptions, and the influence of early-life exposures, and emphasizing the systemic impact of obesity through its associations with cardiometabolic diseases, certain cancers, and mental health disorders. Emerging treatment paradigms include glucagon-like peptide-1 and dual agonists, endoscopic and surgical interventions, and microbiota-directed therapies. Advances in artificial intelligence and precision medicine are also redefining individualized care. Despite these developments, obesity remains underdiagnosed and undertreated in many healthcare systems. In high-income regions, the uptake of advanced therapies is limited by fragmented care pathways, in which obesity management is spread across multiple uncoordinated providers, and by affordability barriers due to high costs. In low-resource settings, constrained infrastructure and competing health priorities continue to hinder timely diagnosis and treatment. A shift toward holistic, patient-centered, and equity-driven models of care is essential for effectively addressing the global burden of obesity and improving long-term health outcomes.},
}

@article {pmid42117346,
year = {2026},
author = {Nguyen, HKD and Jones, PJ and Kendal, D and Powell, SM and Raspin, K and Dickinson, J and Flies, EJ},
title = {A Comparison of the Gut Microbiome of Two Sympatric Macropods Along an Urbanisation Gradient in Tasmania.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70359},
pmid = {42117346},
issn = {1758-2229},
support = {//Holsworth Wildlife Research Endowment/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Tasmania ; *Macropodidae/microbiology ; Urbanization ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Sympatry ; Feces/microbiology ; Parks, Recreational ; Cities ; Animals ; },
abstract = {This study investigates the gut flora of the red-necked wallaby (Notamacropus rufogriseus rufogriseus) and the Tasmanian pademelon (Thylogale billardierii) in the small city of Hobart, Tasmania, Australia. Faecal samples were collected from greenspaces across the Greater Hobart region. These greenspaces were chosen in areas with different human population densities. DNA was extracted from these samples, and targeted sequencing of the bacterial 16S ribosomal RNA gene was performed to understand the bacterial community. Our results showed that despite the many shared ecological traits between the two species, their gut microbiome displayed different responses to urban living. Alpha and beta diversity were significantly different across the urban gradient for Bennett's wallaby, but not for Tasmanian pademelon. Relative composition for both species was different across the urbanisation gradient. Some bacterial taxa associated with nutrient processing showed the clearest changes. The conclusion of this research is that living in cities can affect the gut microbiome of these two marsupial herbivores. More studies are needed to determine whether this has implications for the health of these species.},
}

*Gastrointestinal Microbiome/genetics
Tasmania
*Macropodidae/microbiology
Urbanization
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Sympatry
Feces/microbiology
Parks, Recreational
Cities
Animals

@article {pmid42117437,
year = {2026},
author = {Tumelty, M and Patel, K and Petersen, H and Delaney, C and Lappin, D and Gibson, J and Ramage, G and van der Gast, C and Smith, A and Nile, CJ},
title = {Investigations into the aetiopathogenesis of orofacial granulomatosis using multiple omics technologies reveal a potential role for B cells.},
journal = {Clinical and translational medicine},
volume = {16},
number = {5},
pages = {e70689},
doi = {10.1002/ctm2.70689},
pmid = {42117437},
issn = {2001-1326},
support = {//Royal College of Surgeons of England/ ; //Royal College of Physicians and Surgeons of Glasgow/ ; //Tenovus Scotland/ ; //University College London Hospitals Biomedical Research Centre/ ; //NIHR Newcastle Biomedical Research Centre/ ; },
}

@article {pmid42117804,
year = {2026},
author = {Zalila-Kolsi, I and Al-Barazie, R},
title = {Probiotics and the Human Microbiome: Classical Functions, Emerging Systemic Roles, and Future Therapeutic Frontiers.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090665},
pmid = {42117804},
issn = {2079-7737},
abstract = {Probiotics, live microorganisms that confer health benefits when administered in adequate amounts, are increasingly recognized as modulators of interconnected microbiome-host networks that extend beyond gastrointestinal function. This review synthesizes evidence on classical probiotic roles in maintaining gut homeostasis, immune regulation, and infection prevention, while integrating emerging systemic effects across the gut-brain, gut-skin, gut-oral, and metabolic axes. Rather than presenting isolated outcomes, we adopt a systems-level framework that links probiotic actions to shared mechanisms, including microbial metabolite signaling (e.g., SCFAs), competitive exclusion of pathobionts, barrier reinforcement, and immune-neuroendocrine pathway modulation. We further discuss translational advances that enable rational probiotic design, including targeted delivery platforms (encapsulation and protective matrices), engineered/next-generation strains, and postbiotic-inspired strategies, alongside sustainability considerations and regulatory/labeling challenges. Finally, we outline future directions emphasizing precision microbiome-centered interventions, synthetic biology, and AI-assisted multi-omics analysis to support strain- and context-specific probiotic strategies. Collectively, this review provides an integrated, systems-oriented synthesis to guide future research and accelerate safe clinical and industrial applications of probiotics.},
}