@article {pmid42567128,
year = {2026},
author = {Thaitumu, M and Gallou, D and Begou, O and Theodoridis, G and Gika, H},
title = {Quantifying the aromatic amino acid metabolome: UPLC-MS/MS analysis of aromatic amino acids and their host and co-metabolites in plasma.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1282},
number = {},
pages = {125242},
doi = {10.1016/j.jchromb.2026.125242},
pmid = {42567128},
issn = {1873-376X},
abstract = {Aromatic amino acids (AAAs), tryptophan, phenylalanine, and tyrosine along with their pathway metabolites have been implicated in the pathogenesis of diseases ranging from cardiovascular, neurological, inflammatory, and cancer diseases, among others. As such, the measurement of the primary AAAs, their host pathway metabolites, and microbiome derived co-metabolites in blood can provide a sensitive reflection of systemic health. The aim of the study was to develop a method for the quantification of 17 metabolites, the three AAAs and various of their metabolites in plasma using a high-throughput ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method. The method demonstrated a dynamic range (1 to 16,700 ng/mL), with detection limits (LOD) as low as 0.05 ng/mL. Quantification limits ranged from 3 to 5019 ng/mL (LLOQ) and up to 16,700 ng/mL (ULOQ). Recovery at LQC, MQC, and HQC was satisfactory and consistent across most metabolites, with significant matrix effects observed only for 4-ethylphenol sulfate. Furthermore, intra and inter-day accuracy and precision met all acceptance criteria at all quality control concentrations for most of the metabolites. Measurement of NIST SRM 1950 showcased the method's accuracy for most of the metabolites. Finally, the method was applied on the analysis of plasma samples from 55 individuals (13 males and 42 females) providing information on AAAs and their pathway metabolites relevant concentrations in human plasma.},
}

@article {pmid42567235,
year = {2026},
author = {Ma, HC and Wang, DJ and Yuan, ZJ and Shi, B and Chen, ZH and Zhuo, M and Zeng, JY and Aqib, AI},
title = {Systematic approach for revealing biomarkers of diarrheal microbiome of yaks through Metagenomics sequencings.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108700},
doi = {10.1016/j.micpath.2026.108700},
pmid = {42567235},
issn = {1096-1208},
abstract = {Yaks are important food ruminants on the Plateau, but the presence of a diarrhea disease is seriously threatening the yak sector. To detect bacterial biomarkers of diarrhea in this animal, metagenomics sequencing of fecal samples from diarrhea (group D) and normal (group H) yaks was performed. The results showed 61963 936 432 and 63 972 070 354 clean samples in the diarrheal and normal yaks, respectively. Genotyping in group D (20 000) was statistically lower than that in group H (80 000) (p<0.05). Firmicutes and bacteroides levels in diarrheal yaks (1.03) were lower than in normal animals. There were 23 phyla and 696 species significantly different between the two yak groups including species of pathogenic Bacteroides fragilis, Alloprevotella tannerae, Parabacteroides merdae, Anaerococcus marasmi, and beneficial Methanobrevibacter millerae, Elusimicrobium minutum, Adlercreutzia equolifaciens. Our results may contribute to the prevention and treatment of diarrheal in yaks in the cold plains areas.},
}

@article {pmid42567258,
year = {2026},
author = {Eubank, T and Msdi, AS and Garey, KW},
title = {Microbiome Stewardship: re-defining high-risk antibiotics.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103072},
doi = {10.1016/j.anaerobe.2026.103072},
pmid = {42567258},
issn = {1095-8274},
abstract = {Healthy human gut microbiomes are essential for overall wellness and must be safeguarded by incorporating preservation into clinical decision-making processes and policies. Given the paradigm shift of single-acting bacteria causing infectious diseases to a new understanding of interacting communities of bacteria that build up stable network structures and functions to prevent diseases, a One-Health umbrella has emerged that interconnects all life through their respective microbiota. The preservation of this homeostasis is a term coined Microbiome Stewardship. Although multi-causal, antimicrobial use has the most disruptive effect on the microbiome, quickly changing microbiome structure and function as well as promoting antimicrobial resistant gene (ARG) generation and abundance. Clinically, Microbiome Stewardship could lead to new strategies around antimicrobial administration route and enhanced consideration of whether anaerobic coverage is required, especially routine empiric coverage. Antimicrobial resistance (AMR) and perturbation of the microbiome effect short- and long-term patient outcomes and should drive the drug development process and repurposing of current antimicrobials. In the new scientific era of systems biology providing increasingly accessible and cost-effective studies, evaluation of the microbiome during the antimicrobial drug development process should become the new standard. Microbiome Stewardship incorporation into clinical practice and drug development will advance patient outcomes and AMR prevention on an individual and public health platform.},
}

@article {pmid42567327,
year = {2026},
author = {Li, S and Chu, X and Deng, R and Zheng, W and Suo, X and Sun, G and Liu, H and Geng, M and Tian, J and Zhang, Y},
title = {Akkermansia muciniphila gavage alleviates depression-like behaviors in female A53T α-synuclein transgenic mice.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {116413},
doi = {10.1016/j.bbr.2026.116413},
pmid = {42567327},
issn = {1872-7549},
abstract = {Parkinson's disease (PD) is characterized not only by progressive motor deficits but also by non-motor symptoms, such as depression, which often emerge during the prodromal stage and significantly impair quality of life. While Akkermansia muciniphila (AKK) has shown potential in modulating neuroinflammation, its specific role and underlying mechanisms in alleviating PD-associated non-motor symptoms remain unclear. In this study, we investigated the effects of AKK intervention in 16-month-old female A53T α-synuclein (α-syn) transgenic mice. Behavioral assessments revealed that oral administration of AKK significantly ameliorated depression-like behaviors, evidenced by reduced immobility in the forced swim test and increased sucrose preference, without affecting motor function, spatial memory, or gastrointestinal motility. Mechanistically, the intervention exhibited genotype-specific effects: AKK significantly increased plasma 5-HT levels in C57 mice. This increase was associated with an enrichment of Lactobacillus taiwanensis and metabolic pathways favoring peripheral tryptophan conversion. Conversely, in A53T mice, the treatment specifically elevated hippocampal 5-HT levels without altering plasma concentrations. This central effect correlated with distinct microbial remodeling, characterized by the enrichment of butyrate/propionate-producing Lachnospiraceae and the activation of purine degradation. Collectively, these findings provide novel mechanistic insights into the therapeutic potential of AKK for managing non-motor symptoms in PD. While limited to a female cohort, our results suggest that AKK ameliorates depression-like behaviors in PD through sex-specific remodeling of the gut microbiome and serotonergic signaling.},
}

@article {pmid42567746,
year = {2026},
author = {Deande, ST and Leeds, SG and Fair, L and Wang, CY and Buckmaster, BA and Cantrell, CG and Aladegbami, B and Ogola, G and Ward, MA},
title = {First insights into the microbiome of leaks following foregut surgery.},
journal = {Surgery},
volume = {},
number = {},
pages = {110428},
doi = {10.1016/j.surg.2026.110428},
pmid = {42567746},
issn = {1532-7361},
abstract = {BACKGROUND: Anastomotic leaks are a devastating complication of foregut surgery that can be managed surgically or endoscopically. Studies show that the pathogenesis of leaks is influenced by gut microbiomes. We seek to delineate outcome differences in patients who were successfully managed endoscopically versus those who required surgery and compare differences in microbiome composition.

METHODS: An institutional review board-approved, prospectively maintained database was retrospectively reviewed for patients with foregut leaks from 2021 to 2024. Primary end points were endoscopic-only management or surgery. Other variables include readmissions, interventions, bloodwork, and American College of Surgeons surgical risk. During therapeutic interventions, microbial and host samples were collected. For the first 16 patients, the DNA samples were extracted, amplified, sequenced, and clustered into operational units for analysis.

RESULTS: Of the 38 patients with leaks, 92% were managed endoscopically, whereas 8% required surgery. Of the endoscopic group, 26% healed with endoluminal vacuum therapy, 9% with stent, 23% with an endoluminal drain, and 42% with a combination. The surgery group had a lower albumin level (P = .04) and longer preoperative predicted length of stay (P = .03). Bacterial composition shifted with each intervention. There were 4 main bacteria-Firmicutes, Bacteroides, Actinobacteria, and Proteobacteria. In the endoscopic-only group, Bacteroides and Firmicutes predominated. One surgical patient had a comparatively higher ratio of Proteobacteria.

CONCLUSION: Patients who failed endoscopic management had poorer nutrition and higher preoperative risk factors, which may contribute to an unfavorable microbial composition that inhibits wound healing. Understanding the gut microbiome in gastrointestinal leaks could lead to more effective prevention and treatment strategies.},
}

@article {pmid42567842,
year = {2026},
author = {Iqbal, MZ and Sharma, P and Shafi, Z and Shahid, M and Debnath, A and Rasool, A and Ali, S},
title = {The Gut Microbiome in Foodborne Microplastic Toxicity: Mechanistic Insights and Human Health Risk Assessment.},
journal = {Journal of applied toxicology : JAT},
volume = {},
number = {},
pages = {},
doi = {10.1002/jat.70387},
pmid = {42567842},
issn = {1099-1263},
support = {KFU264174//Deanship of Scientific Research, King Faisal University/ ; },
abstract = {Microplastics (MPs) are emerging foodborne contaminants with increasing implications for gastrointestinal health. However, the mechanistic basis linking dietary MP exposure to gut dysbiosis and intestinal dysfunction remains poorly resolved, limiting robust human health risk assessment. This review critically synthesizes current evidence on foodborne MPs, dietary exposure, and the physicochemical determinants of gastrointestinal fate, bioavailability, and toxicity. We examine the molecular and microbiome-mediated mechanisms linking MPs exposure to intestinal dysbiosis, barrier dysfunction, oxidative stress, immune activation, and metabolic reprogramming. Particular attention is given to the role of MPs as vectors for co-contaminants, which can amplify toxicity through synergistic interactions and reshape host-microbiome responses. We highlight advances in dynamic colon simulation and integrated multi-omics that unravels the mechanism underlying MP-induced intestinal toxicity. Current evidence indicates that gut microbiome dysregulation is a key mechanism driving foodborne MP-induced intestinal dysfunction and systemic toxicity. This review integrates multidisciplinary evidence to identify critical knowledge gaps and guide future research on the mechanisms, exposure, and health risks of foodborne microplastics.},
}

@article {pmid42567864,
year = {2026},
author = {Buyanbadrakh, B and Baland, E and Lambeck, P and Pérez Jiménez, L and Holmberg, SM and Puértolas-Balint, F and Toh, E and Wai, SN and Schroeder, BO and Ramstedt, M and Zhu, S and Mateus, A},
title = {Systematic profiling of growth interactions in human gut microbiome species.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42567864},
issn = {2041-1723},
mesh = {Humans ; Hydrogen-Ion Concentration ; *Gastrointestinal Microbiome/physiology ; Clostridium perfringens/physiology/growth & development ; *Microbial Interactions/physiology ; Veillonella/growth & development ; Bacteria/growth & development/classification/genetics ; Eubacteriales/growth & development ; },
abstract = {Microbial interactions shape the composition and stability of the human gut microbiome. Yet, few studies have systematically investigated species-species growth interactions and the mechanisms behind these. Here we show that among 36 representative gut bacterial strains, when two species interact, the interactions are mostly inhibitory. To provide biological insight into specific interactions, we further investigate the basis of a positive interaction, showing that Clostridium perfringens promotes the growth of Mediterraneibacter gnavus through extracellular vesicles. Additionally, we identify Veillonella parvula as a species capable of modulating environmental pH, thereby enabling the growth of Parabacteroides merdae, a strain highly sensitive to acidic conditions. This pH-increasing effect is enhanced by guanine supplementation and persists in multi-species communities containing different pH-lowering strains from diverse bacterial phyla. Although V. parvula is commonly present in human gut microbiomes, it is generally found at low levels. Given the spatial organization of bacteria in the gut, the local pH modulation by V. parvula might support the growth of acid-sensitive strains. Overall, the comprehensive dataset and mechanistic insights presented here provide a starting point to predict microbiome composition by integrating growth interactions.},
}

Humans
Hydrogen-Ion Concentration
*Gastrointestinal Microbiome/physiology
Clostridium perfringens/physiology/growth & development
*Microbial Interactions/physiology
Veillonella/growth & development
Bacteria/growth & development/classification/genetics
Eubacteriales/growth & development

@article {pmid42567900,
year = {2026},
author = {Sevi, S and Romeggio, S and Dinatale, G and Alfonsi, F and Fiorini, E},
title = {Precision periodontology in clinical practice: bridging omics and clinical decision-making.},
journal = {Clinical oral investigations},
volume = {30},
number = {9},
pages = {},
pmid = {42567900},
issn = {1436-3771},
mesh = {Humans ; *Clinical Decision-Making ; *Precision Medicine ; *Periodontics/methods ; Biomarkers/analysis ; *Genomics ; Microbiota ; },
abstract = {BACKGROUND: Precision periodontology integrates molecular diagnostics, genomics, and advanced imaging into clinical decision-making. Despite major advances in microbiome characterisation, host genetics, and inflammatory biomarkers, their translation into routine care remains limited.

OBJECTIVES: To critically appraise current evidence on microbiome-based profiling, genetic and epigenetic markers, host-response biomarkers, and three-dimensional imaging in periodontology, and to propose a conceptual decision-support framework linking diagnostic outputs to potential therapeutic actions and future implementation research.

MATERIALS AND METHODS: A narrative review searching PubMed/MEDLINE, Scopus, Embase, and the Cochrane Library (2010-2025) using terms related to precision periodontology, subgingival microbiome, periodontitis genetics and epigenetics, salivary and GCF biomarkers, aMMP-8, CBCT, risk assessment, and artificial intelligence. Priority was given to meta-analyses, systematic reviews, longitudinal studies, and guideline documents.

RESULTS: Microbiological testing has defined but narrow indications; single-SNP genotyping has not demonstrated clinical utility commensurate with cost; aMMP-8 point-of-care testing is among the most extensively investigated host-response tools and may have adjunctive value in selected monitoring and peri-implant scenarios; however, current evidence remains insufficient to support routine diagnostic implementation. CBCT may directly influence surgical decision-making through defect morphology characterisation. AI-based models show promise but lack prospective clinical validation. These conclusions are consistent with the 20th EFP Workshop Consensus Report.

CONCLUSIONS: Precision periodontology currently operates in addition to, rather than in replacement of, conventional staging and grading. We propose a conceptual decision-threshold framework for the selective consideration of molecular and advanced imaging tools when their additive contribution may meaningfully inform management. This framework should be regarded as a research-oriented decision-support model rather than a validated clinical algorithm.

CLINICAL RELEVANCE: Clinicians are provided with a structured, evidence-based framework that identifies specific clinical scenarios where molecular diagnostics, host-response biomarkers, and three-dimensional imaging may meaningfully modify periodontal treatment decisions, supporting the operationalisation of precision approaches in daily practice.},
}

Humans
*Clinical Decision-Making
*Precision Medicine
*Periodontics/methods
Biomarkers/analysis
*Genomics
Microbiota

@article {pmid42568234,
year = {2026},
author = {Bahadoran, E and Babaei, A and Shahbazi, S and Badri, M and Nikkhahi, F and Sabzi, S},
title = {Insights Into Infections and Inflammation in Prostate Cancer Development and Management: An Overview.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e7584584},
pmid = {42568234},
issn = {2314-6141},
mesh = {Humans ; Male ; *Prostatic Neoplasms/pathology/therapy/microbiology/epidemiology ; *Inflammation/pathology/complications ; Prostatitis/pathology ; Signal Transduction ; Risk Factors ; Prostatic Hyperplasia/pathology ; },
abstract = {Prostate cancer (PCa) represents a major public health concern and continues to be one of the leading causes of cancer-related mortality among men worldwide. Current epidemiological projections suggest that the incidence and associated burden of PCa are likely to increase, emphasizing the importance of advancing preventive measures, improving early diagnostic approaches, and refining targeted therapeutic strategies. While established risk factors, including age, genetic predisposition, lifestyle-related factors, ethnicity, and androgen signaling, have been extensively studied, these factors alone do not fully explain the observed patterns of PCa development. Increasing evidence suggests that infection-associated chronic inflammation plays a central role in prostate tumor initiation and progression. Chronic inflammation of the prostate, arising from conditions such as prostatitis, benign prostatic hyperplasia (BPH), lower urinary tract infections (UTIs), sexually transmitted infections (STIs), and prolonged or repeated catheterization, has been associated with histological and molecular changes that may predispose prostate tissue to malignant transformation. Moreover, emerging evidence suggests that alterations in the prostate microbiome may sustain inflammatory signaling, thereby influencing tumor initiation and progression. This review synthesizes current epidemiological findings and experimental evidence linking infection-associated inflammation to the development of PCa. Particular focus is placed on inflammatory signaling pathways implicated in prostate tumorigenesis, including nuclear factor kappa B (NF-κB), signal transducer and activator of transcription 3 (STAT3), cyclooxygenase-2/prostaglandin E2 (COX-2/PGE2), interleukin-6 and interleukin-8 signaling, Toll-like receptor (TLR) pathways, and activation of the NLRP3 inflammasome. In addition, we discuss therapeutic strategies that are aimed at modulating these pathways and their potential relevance in PCa management. A more comprehensive understanding of the interactions between infection, chronic inflammation, and PCa development may facilitate the identification of novel biomarkers and therapeutic targets. Such advances could ultimately contribute to improved risk stratification, earlier detection, and more effective treatment of PCa.},
}

Humans
Male
*Prostatic Neoplasms/pathology/therapy/microbiology/epidemiology
*Inflammation/pathology/complications
Prostatitis/pathology
Signal Transduction
Risk Factors
Prostatic Hyperplasia/pathology

@article {pmid42568240,
year = {2026},
author = {Cuervo-Zanatta, D and Balasubramanian, HB and Pasokh, A and Zille, M},
title = {Microbiome-blood-brain barrier interactions in aging - mechanisms and therapeutic potential.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70412},
pmid = {42568240},
issn = {1873-3468},
support = {Hochschuljubiläumsfonds / H-506512/2024//Hochschuljubiläumsstiftung der Stadt Wien/ ; SECTEI/070/2024//Secretaría de Estado de Ciencia, Tecnología e Innovación/ ; DOC Fellowship #27097//Österreichische Akademie der Wissenschaften/ ; },
abstract = {Age-related decline in neurovascular integrity is an increasingly recognized contributor to cognitive impairment and neurodegenerative vulnerability. A central feature is blood-brain barrier (BBB) dysfunction arising from endothelial senescence, altered barrier regulation, and chronic low-grade inflammation. In parallel, aging remodels the gut microbiota, with reduced diversity, loss of short-chain fatty acid-producing commensals, and expansion of pro-inflammatory taxa. Converging evidence indicates that age-related shifts in the gut microbiota alter microbiome function and can modulate BBB physiology through microbial metabolites, immune-endothelial signaling, and systemic metabolic pathways. These data position the gut-brain axis as an important, but not sole, modulator of neurovascular aging. Preclinical and emerging human data suggest that dysbiosis lowers the threshold for BBB dysfunction, and microbiome-targeted interventions in experimental models can improve barrier-relevant features. Notably, no human trial has yet demonstrated that microbiome modulation prevents or reverses BBB impairment using validated neuroimaging or fluid biomarkers. This review synthesizes mechanisms of microbiota-BBB crosstalk in aging, distinguishes correlation from causation, and outlines translational opportunities and limitations of dietary, probiotic, and fecal microbiota-based strategies for preserving neurovascular health in older adults.},
}

@article {pmid42568471,
year = {2026},
author = {Witkowski, M and Przybyciński, J and Wojciuk, B and Czaja, W and Gołembiewska, N and Gołembiewska, E},
title = {The role of gut microbiome disruption in the development of metabolic dysfunction-associated kidney disease.},
journal = {Acta biochimica Polonica},
volume = {73},
number = {},
pages = {16436},
pmid = {42568471},
issn = {1734-154X},
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; *Renal Insufficiency, Chronic/microbiology/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Metabolic Diseases/microbiology/complications/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; },
abstract = {Metabolic dysfunction-associated kidney disease (MDAKD) is increasingly recognised as a major clinical consequence of the global rise in obesity, type 2 diabetes, hypertension, and cardiovascular disease. Accumulating evidence suggests that the gut microbiota may contribute to the development and progression of metabolic and renal disorders through complex mechanisms involving microbial metabolites, immune activation, and disruption of the intestinal barrier. This review provides an overview of current knowledge regarding the role of the gut microbiota and gut-derived metabolites in the pathogenesis of chronic kidney disease (CKD) associated with metabolic disorders. Special attention is given to short-chain fatty acids, bile acids, N-trimethylamine oxide, branched-chain amino acids, indoxyl sulfate, p-cresol sulfate, and lipopolysaccharides. Accumulating experimental and clinical evidence suggests that dysbiosis may contribute to chronic low-grade inflammation, insulin resistance, endothelial dysfunction, lipotoxicity, and profibrotic signaling pathways associated with kidney injury and cardiovascular complications. The review also identifies significant limitations in current microbiome research, such as the predominance of animal studies, methodological challenges in metabolite quantification, and difficulties in establishing causality in humans. Emerging therapeutic strategies targeting the gut microbiota, including dietary interventions, prebiotics, probiotics, sodium-glucose cotransporter 2 inhibitors, glucagon-like peptide-1 receptor agonists, and faecal microbiota transplantation, may offer novel approaches to slowing CKD progression and improving metabolic health. However, further mechanistic and clinical studies are required to determine the efficacy of microbiota-targeted therapies in MDAKD.},
}

Humans
*Gastrointestinal Microbiome
Animals
*Renal Insufficiency, Chronic/microbiology/metabolism
*Dysbiosis/microbiology/metabolism/complications
*Metabolic Diseases/microbiology/complications/metabolism
Diabetes Mellitus, Type 2/microbiology/metabolism

@article {pmid42568521,
year = {2026},
author = {Tang, H and Zheng, S and Lai, Y and Wang, Q and Yang, N and Luo, N and Cai, L and Liu, Y and Chen, X and Yang, Y and Wan, H and Liu, Z and Li, Y and Yang, F and Yang, W and Ren, Y and Li, J},
title = {Geographic origin and wheat variety shape microbial and functional profiles of brewing wheat for Daqu fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1879363},
pmid = {42568521},
issn = {1664-302X},
abstract = {INTRODUCTION: Wheat is the primary raw material for traditional Baijiu Daqu fermentation, yet its role as a carrier of functional microbiota and its contribution to Daqu quality remain poorly understood.

METHODS: A total of 135 wheat samples representing five geographic regions and nine cultivars were subjected to sensory evaluation, physicochemical analysis, and 16S rRNA gene and ITS amplicon sequencing. Microbial community composition, predicted functional potential, and their associations with wheat quality traits were analyzed using PICRUSt2, Mantel tests, and correlation analyses.

RESULTS: Sensory evaluation indicated that the cultivation environment had a greater impact on Daqu quality than wheat cultivar, with wheat from the Dayi region and the MM916 cultivar exhibiting the most favorable characteristics. Sequencing identified 1,732 bacterial and 484 fungal amplicon sequence variants (ASVs), revealing significant geographic and varietal differences in microbial communities, while core taxa dominated by Pseudomonadota and Basidiomycota were consistently detected across all samples. Functional prediction suggested that microbial communities were primarily enriched in metabolic pathways, particularly carbohydrate metabolism, energy metabolism, and cofactor and vitamin metabolism. Spatial variation was observed in starch and sucrose metabolism, acetoin biosynthesis, and enzymes such as β-glucosidase and alcohol dehydrogenase. Wheat quality traits, especially protein, starch, and wet gluten content, were significantly associated with microbial composition and predicted functions. Thirty-two genera, including Sphingomonas, Pedobacter, and Martelella, showed strong correlations with these quality traits.

DISCUSSION: Geographic origin and wheat cultivar jointly shape the microbial communities and functional potential of brewing wheat, providing pre-existing microbial resources that may influence early Daqu fermentation and flavor formation. These findings offer a microbiome-based framework for evaluating and selecting high-quality wheat for Baijiu production.},
}

@article {pmid42568523,
year = {2026},
author = {Emiliani, G and Barberini, S and Della Rocca, G and Bigazzi, F and Moricca, S and Schicchi, R and Danti, R},
title = {Habitat conditions shape the phyllosphere mycobiome of the critically endangered Abies nebrodensis.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1876158},
pmid = {42568523},
issn = {1664-462X},
abstract = {The phyllosphere harbors diverse fungal communities that influence tree health, adaptation, and growth. This study investigated the phyllosphere mycobiome of the critically endangered Abies nebrodensis, using ITS2 metabarcoding. Samples were collected from 10 trees distributed across three sites during a single sampling campaign. Influence of tissue health state (green vs. blighted twigs) and variation of habitat conditions on diversity and composition of the mycobiome was evaluated. The 4,501 amplicon sequence variants (ASVs) detected were dominated by Ascomycota, particularly Dothideomycetes and Sordariomycetes. The endospheric community showed reduced diversity compared to the full phyllospheric community; however, both were dominated by Valsaceae and Phaeosphaeriaceae and by the genera Phaeosphaeria and Lachnellula. Tissue health and site conditions significantly affected diversity and composition of the full phyllospheric but not of endospheric communities. Valsaceae were consistently detected within the core mycobiota of Sicilian fir, together with melanized and extremotolerant genera such as Knufia, Perusta, Cladosporium, Alternaria, and Sarcinomyces. Despite the study was based on a single spring snapshot, our findings indicate habitat variation as a major driver of the phyllosphere mycobiome of A. nebrodensis. The occurrence of Valsaceae and extremotolerant fungi in the core mycobiome suggests that these taxa may play a functional role potentially contributing to the holobiont adaptation to a harsh environment.},
}

@article {pmid42568550,
year = {2026},
author = {Sonnauer, F and Fries, FL and Druzenko, M and Kastner, UW and Mühle, C and Kornhuber, J},
title = {Clinical relevance of loneliness in the treatment of depression: study protocol for a naturalistic prospective longitudinal study.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1827062},
pmid = {42568550},
issn = {1664-0640},
abstract = {BACKGROUND: Loneliness and depression are widespread and severely debilitating health conditions. Notably, loneliness and depression are closely intertwined, with individuals suffering from depression being particularly vulnerable to loneliness and vice versa. However, little is known regarding the clinical significance of loneliness in the treatment of depression and the biopsychosocial mechanisms underlying this association.

METHODS: This protocol presents a naturalistic longitudinal study on the clinical significance of loneliness in inpatient and post-inpatient treatment outcomes of adults with depression. The design includes three main assessment points with comprehensive diagnostics (including clinical interviews, questionnaires, and optional biospecimen collection for biomarker and microbiome analyses), as well as interim assessments and the integration of routine clinical data. The primary outcomes include depressive symptom severity and perceived loneliness across the course of treatment and follow-up. Secondary outcomes and covariates are analyzed to identify other clinically relevant indicators, such as life satisfaction and suicidality, and to better understand the biopsychosocial interplay between loneliness and depression. Descriptive and inferential statistical analyses, including (generalized) linear mixed model analyses and mixed analyses of variance (ANOVA), will be conducted following both hypothesis-driven and exploratory approaches.

DISCUSSION: By employing a clinical sample and longitudinal design, this study advances the understanding of the role of loneliness in the treatment and maintenance of depression. In addition to evaluating primary outcomes, analyses of secondary outcomes can provide information on shared and distinct biopsychosocial pathways, thereby identifying potential correlates of mental health outcomes that may inform future research. Limitations include the possible inflation of Type I errors in exploratory analyses and potential biases such as selection bias and cognitive distortions in self-reported data. Nevertheless, this study can provide an important foundation for subsequent clinical trials and translational research. This study was prospectively registered at ClinicalTrials.gov on 31[st] December 2025 before patient enrollment (Identifier: NCT07333027, Study Details | NCT07333027 | Lonely in Depression | ClinicalTrials.gov).

STUDY PROTOCOL REGISTRATION: https://clinicaltrials.gov/study/NCT07333027?cond=NCT07333027&viewType=Card&rank=1, identifier NCT07333027.},
}

@article {pmid42568762,
year = {2026},
author = {Hong, L and Wang, Y and Li, M and Li, J and Zhang, Q and Qiu, M and Jia, X and Su, Q and Lin, W and Wang, H and Wu, Z},
title = {Continuous Planting Reshapes Root Endophytic Microbes and Drives Growth Decline in Casuarina equisetifolia.},
journal = {Indian journal of microbiology},
volume = {66},
number = {4},
pages = {1081-1097},
pmid = {42568762},
issn = {0046-8991},
abstract = {UNLABELLED: Continuous planting barrier limits the growth of Casuarina equisetifolia (C. equisetifolia), an ecological and economic tree species, yet its microbial mechanism remains unclear. This study revealed microbial-driven barriers by examining the impact of continuous planting on root endophyte communities in C. equisetifolia. The results showed that continuous planting significantly reduced the antioxidant enzyme activities, root activity, and nutrient accumulation in the root system of C. equisetifolia, and inhibited root length and plant height growth. Microbial community analysis revealed that continuous planting led to a significant decrease in the abundance of Nitrobacter, a key endophytic bacterium in the root system, which may weaken the nitrogen metabolism functions mediated by nitrate reduction, nitrogen respiration, and nitrate respiration, and to some extent undermine the nitrogen conversion efficiency of the root system. At the same time, continuous planting promoted the enrichment of pathogenic endophytic fungi (Phomopsis, Pseudocercospora and Diaporthe) in the root system, which may be accompanied by enhanced plant pathogen functions, and this may be associated with a reduction in the antioxidant and nutrient uptake capacities of the C. equisetifolia root system. It was shown that continuous planting inhibited C. equisetifolia growth through a dual microbial mechanism: on the one hand, it reduced functional flora, which may in turn weaken nitrogen metabolism and stress tolerance; on the other hand, it increased pathogenic fungi, which may intensify disease impact. This study offers a new perspective on the microecological mechanism of continuous planting disorder and a theoretical basis for its mitigation via root microbiome regulation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-026-01561-9.},
}

@article {pmid42568814,
year = {2026},
author = {Chen, Y and Sun, Y and Huang, R and Li, S and Liu, Y and Yuan, X and Chen, X and Li, J and Yin, L and Ma, C and Zhang, F},
title = {Stochasticity dominated adaptive assembly of benthic microbiota across oasis-to-desert sections of an arid inland river.},
journal = {iScience},
volume = {29},
number = {8},
pages = {117003},
pmid = {42568814},
issn = {2589-0042},
abstract = {Sediment microbial communities in arid inland rivers are important for biogeochemical cycling, but the assembly mechanisms and network responses across the transition from irrigated oases to desert margins remain unclear. We investigated bacterial and fungal communities in Yarkand River sediments along salinity and nutrient gradients using 16S rRNA and ITS sequencing, sediment chemistry, iCAMP null-model analysis, and co-occurrence networks. Downstream increases in electrical conductivity, total nitrogen, and pH were associated with reduced bacterial α-diversity and turnover from nutrient-responsive Pseudomonadota in the oasis midstream to stress-tolerant Chloroflexota and Actinomycetota in the desert downstream. Fungal diversity showed high inter-site variability without a linear decline. Despite strong physicochemical gradients, ecological drift dominated assembly in both kingdoms, while desert networks showed higher connectivity. These findings support a hierarchical assembly model in which salinity filters community composition, but stochastic processes and network densification shape benthic microbiota in arid river sediments.},
}

@article {pmid42568886,
year = {2026},
author = {Muigano, MN},
title = {Functional genetic signatures of the gut microbiome in cardiometabolic diseases: mechanisms and translational opportunities.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1847345},
pmid = {42568886},
issn = {2813-4338},
abstract = {The human gut microbiome plays a very important role in the regulation of host metabolism and overall physiological homeostasis. Disruptions in microbial community function have been increasingly implicated in cardiometabolic diseases, including obesity, type 2 diabetes, cardiovascular disease, and metabolic dysfunction-associated liver disease. Advances in metagenomic sequencing have identified functional genetic signatures within the gut microbiome for short-chain fatty acid biosynthesis, bile acid metabolism, lipopolysaccharide (LPS) production, amino acid metabolism, trimethylamine N-oxide (TMAO) generation, and carbohydrate-active enzymes (CAZymes). Across cardiometabolic conditions, a consistent pattern emerges of depletion of beneficial metabolic functions and enrichment of pro-inflammatory and metabolically disruptive pathways. These findings point to the importance of microbial functional capacity, rather than taxonomic composition alone, in shaping disease risk and progression. This review explores the functional genetic signatures for cardiometabolic diseases and translational potential of these signatures including their potential roles as diagnostic biomarkers, therapeutic targets, and tools for precision therapy. This understanding of microbiome-derived functional pathways may inform the development of targeted strategies aimed at restoring metabolic balance and improving cardiometabolic health.},
}

@article {pmid42569238,
year = {2026},
author = {Dolkar, P and Themchuirin, L and Sonia, N and Atri, A and Yadav, P and Siwach, S and Modeel, S and Negi, RK},
title = {Fish gut-water interface as a hotspot for the dissemination of antibiotic resistance genes across natural and aquaculture systems.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100646},
doi = {10.1016/j.crmicr.2026.100646},
pmid = {42569238},
issn = {2666-5174},
abstract = {Freshwater ecosystems are important reservoirs and transmission pathways for antibiotic resistance genes (ARGs), yet host-mediated microbial selection and anthropogenic pressure on fish gut resistome remain poorly characterised, especially in major South Asian river systems. We performed shotgun metagenomics and genome-resolved binning from 194 fish representing four species, along with host-associated water samples, collected from six geographically distinct sites spanning two major river systems (the Yamuna and the Indus) and two aquaculture farms. The fish gut nurtures distinct microbial communities from the surrounding water, revealing strong host-mediated filtering of environmental microbiota. Across all samples, 1108 ARG subtypes conferring resistance to 14 antibiotic classes were detected, including extended-spectrum β-lactamases (blaTEM and blaCTX-M) and WHO critical-priority carbapenemases (blaIMP and blaOXA). Fish from the Indus River maintained diverse but comparatively stable resistomes dominated by intrinsic chromosomal efflux mechanisms, whereas fish from the urbanized Yamuna River, particularly Labeo boggut, exhibited noticeable enrichment of clinically important ARGs. The prevalence of mobile genetic elements (MGEs) and virulence factors (VFs) were consistently more abundant in the fish gut microbiome than in the host's surrounding water, indicating an increased potential for horizontal gene transfer and microbial persistence. A total of 19 metagenome-assembled genomes (MAGs) carrying multiple ARGs, VFs, and plasmid-associated markers were detected, identifying bacterial populations capable of maintaining and disseminating antimicrobial resistance. These outcomes confirm that fish inhabiting anthropogenically influenced river systems can serve as important reservoirs of clinically relevant resistance determinants, highlighting potential risks for environmental dissemination, aquaculture and human exposure through aquatic ecosystems.},
}

@article {pmid42569308,
year = {2026},
author = {Fan, G and Wang, K and Qi, X and Shi, Y and Li, J and Zhang, Y and Yang, B and Wang, K and Lv, J},
title = {Integrative multi-omics analysis identifies microbial dysbiosis and functional metabolic reprogramming in acute kidney injury.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1781145},
doi = {10.3389/fmed.2026.1781145},
pmid = {42569308},
issn = {2296-858X},
abstract = {BACKGROUND: Acute kidney injury (AKI) is a life-threatening syndrome with high morbidity and mortality, yet its early diagnosis and underlying mechanisms remain poorly defined. Emerging evidence implicates gut dysbiosis and microbial metabolic dysfunction in AKI pathogenesis via the gut-kidney axis, yet a comprehensive, multi-omics characterization of microbial functional alterations in general AKI populations remains lacking.

METHODS: We conducted a prospective multi-omics study including 16 patients with acute kidney injury (AKI) and 16 age- and sex-matched healthy controls (HCs). Plasma metabolomic profiling was performed using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). Gut microbiome composition and function were characterized through whole-metagenome sequencing of stool samples. Differential taxonomic and metabolite features were identified using multivariate and univariate statistical analyses. Microbial functional potential was assessed across four hierarchical layers: Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologs (KOs) genes, pathways, gut-metabolite modules (GMMs), and gut-brain modules (GBMs), to achieve high-resolution mapping of metabolic pathways and taxon-specific functional contributions. Integrated microbe-metabolite-phenotype relationships were evaluated using Spearman correlation analysis.

RESULTS: Metabolomic profiling identified 65 differentially abundant metabolites between AKI patients and healthy controls (HCs), including 53 upregulated and 12 downregulated metabolites. These metabolites were mainly enriched in carbohydrate metabolism (e.g., starch and sucrose metabolism, fructose and mannose metabolism) and amino acid metabolism pathways. Among them, Maltol (C11918, AUC = 0.961), D-Quinovose (C02522, AUC = 0.926), and L-fucose (CO1019, AUC = 0.926) demonstrated the most robust diagnostic potential. Further feature selection using a random forest model identified an optimal panel of three metabolites, which achieved good discriminative performance (AUC = 0.859, 95% CI: 0.7073-1). Metagenomic analysis revealed significant gut microbiota dysbiosis in AKI, characterized by reduced α-diversity and distinct β-diversity compared to HCs. Taxonomic profiling showed depletion of key short-chain fatty acid-producing bacteria, including Faecalibacterium prausnitzii, along with enrichment of taxa such as Phocaeicola and Bifidobacterium pseudocatenulatum, as well as Phocaeicola vulgatus at the species level. Functional analysis indicated that AKI was associated with enhanced amino acid and carbohydrate metabolism, increased xenobiotic degradation, and alterations in neuroactive metabolic pathways. Integrated analysis further revealed significant correlations between altered microbial taxa, metabolic pathways, and clinical indicators. Specifically, health-associated taxa were negatively correlated with systemic inflammation markers (IL-6, IL-8) and renal injury markers (SCr, BUN), whereas Bacteroides uniformis showed positive associations with metabolic alterations in AKI.

CONCLUSION: This multi-omics study reveals coordinated gut microbial dysbiosis and systemic metabolic reprogramming in AKI. The depletion of key commensals, rather than pathogen overgrowth, appears central to AKI-associated functional disruption. These findings highlight potential microbial and metabolic biomarkers and offer mechanistic insights into AKI pathogenesis.},
}

@article {pmid42569327,
year = {2026},
author = {Meng, L and Zhang, X and Zhuang, X and Cui, W},
title = {Oral microbiome diversity and mortality in metabolic syndrome: a cohort study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2712017},
doi = {10.1080/20002297.2026.2712017},
pmid = {42569327},
issn = {2000-2297},
abstract = {BACKGROUND: Metabolic syndrome (MetS) is associated with a higher risk of mortality. Oral microbiome diversity is related to health outcomes, but its role in forecasting MetS prognosis and the relevant pathogenic mechanisms is still largely unexplored.

METHODS: Data from 1,769 MetS patients were extracted from the National Health and Nutrition Examination Survey (NHANES) 2009-2012 cycle. To evaluate alpha diversity, the Shannon index, Faith's phylogenetic diversity (PD), observed operational taxonomic units (OTUs), and the Inverse Simpson index were determined. ALDEx2 was employed for differential abundance analysis in the high-diversity subgroup. Co-occurrence network analysis was subsequently conducted, followed by partitioning around medoids (PAM) clustering for community typing. Prognostic associations were validated through Cox regression.

RESULTS: Both the Shannon index (hazard ratio [HR] = 0.78, 95% confidence interval [CI]: 0.63-0.96) and the Inverse Simpson index (HR = 0.84, 95% CI: 0.74-0.96) were inversely associated with mortality. In the high-diversity subgroup, differential abundance analysis did not identify any OTU whose relative abundance differed significantly by survival status. According to network analysis, the deceased group exhibited a higher density of positive co-occurrences (283 vs. 224 edges) alongside a notable expansion of negative interactions (71 vs. 15 edges), which was a hallmark of declining community stability. Two clusters were identified through community typing, yet this classification was not significantly related to survival outcomes (CType_2 vs. CType_1: HR = 1.05, 95% CI: 0.73-1.49).

CONCLUSIONS: Oral microbiome diversity exhibits a negative association with mortality among MetS patients. However, in the high-diversity subgroup, ecological network disruption, rather than alpha diversity or differential taxonomic richness, differentiates the deceased patients from the alive counterparts. This suggests that community structure is a promising risk marker with a higher sensitivity than diversity alone.},
}

@article {pmid42569339,
year = {2026},
author = {Xue, K and Hu, C and Lin, Z and Mao, X and Zhu, H and Xie, Y and Luo, Q and Zhu, F},
title = {Multi-omics profiling of oral microbial functional signatures and systemic immune-metabolic features in perinatal depression.},
journal = {Brain, behavior, & immunity - health},
volume = {56},
number = {},
pages = {101300},
doi = {10.1016/j.bbih.2026.101300},
pmid = {42569339},
issn = {2666-3546},
abstract = {BACKGROUND: Perinatal depression (PND) occurs during a period marked by profound endocrine, metabolic, and immune adaptation. Although alterations in immune-metabolic regulation have been reported in PND, how such changes manifest across distinct biological compartments remains unclear. The oral mucosal ecosystem represents an immunologically active interface with direct connections to systemic circulation, yet its functional characteristics in PND have been insufficiently explored. In this study, we examined whether PND is characterized by differences in oral microbial functional profiles alongside systemic immune-metabolic features.

METHODS: We performed an integrated multi-omics analysis combining salivary shotgun metagenomics and untargeted serum metabolomics in 31 women with PND and 32 healthy controls. Oral microbial taxonomic composition and inferred functional profiles were analyzed together with circulating metabolites related to endocrine and immune processes. Cross-omics analyses were used to evaluate overall concordance as well as pathway- and feature-level associations between microbial functional signals and host metabolic features.

FINDINGS: The oral microbiome of women with PND showed largely preserved community structure and diversity, while differences were observed at the level of inferred functional pathways, including enrichment of lipopolysaccharide biosynthesis and virulence-associated functional categories. Concurrently, the serum metabolome exhibited differences in steroid-related metabolites, bile acid profiles, and lipid mediator-associated features involved in immune modulation, including putatively annotated resolvin D5. Global concordance between oral microbial functional profiles and systemic metabolomic patterns was limited; however, reproducible associations were observed at the pathway and feature levels, such as an inverse association between the relative abundance of the genus Abiotrophia and the bile acid taurochenodeoxycholate-7-sulfate.

INTERPRETATION: Together, these findings describe concurrent differences in oral microbial functional signatures and systemic immune-metabolic features in women with PND, occurring in the context of minimal changes in microbial community composition. The limited global concordance and selective pathway-level correspondence across omic layers are consistent with asynchronous patterns of biological variation during the perinatal period. These observations support the potential relevance of the oral-systemic axis as a non-invasive perspective for characterizing biological heterogeneity associated with perinatal depression.},
}

@article {pmid42569366,
year = {2026},
author = {Niu, X and Nur, Z and Xie, W and Sun, Y and Wang, L and Zheng, Y},
title = {Immunosenescence shapes the tumor immune microenvironment and limits PD-1/PD-L1 blockade efficacy in older patients with cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1781004},
doi = {10.3389/fimmu.2026.1781004},
pmid = {42569366},
issn = {1664-3224},
mesh = {Humans ; *Immunosenescence/immunology ; *Tumor Microenvironment/immunology/drug effects ; *Neoplasms/immunology/drug therapy/metabolism ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; *B7-H1 Antigen/antagonists & inhibitors/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; Animals ; T-Cell Exhaustion ; Aged ; },
abstract = {As the global population ages, immunosenescence is emerging as a critical determinant of cancer outcomes in older adults. Although programmed cell death protein 1/protein programmed death-ligand 1 (PD-1/PD-L1) blockade has significantly improved the treatment of multiple malignancies, its efficacy in older patients is highly heterogeneous, and the biological basis for this variability remains incompletely understood. Current evidence indicates that immunosenescence reshapes antitumour immunity through thymic involution, reduced T cell receptor diversity, chronic low-grade inflammation, and expansion of immunosuppressive cell populations, thereby impairing antigen presentation, weakening T cell activation and effector function, promoting terminal T cell exhaustion, and reinforcing suppressive tumour microenvironments. Together, these changes form an important mechanistic basis for the limited benefit of PD-1/PD-L1 blockade in older patients. Meanwhile, potentially targetable processes, including metabolic dysregulation, mitochondrial dysfunction, defective autophagy-mitophagy, redox imbalance, and gut microbiota dysbiosis, are increasingly recognized as modifiable contributors to age-associated resistance to immunotherapy. In this Review, we discuss how immunosenescence remodels antitumour immunity and constrains responses to PD-1/PD-L1 blockade in older patients, and we summarize potential strategies to improve immunotherapeutic efficacy in this population. These insights may inform future mechanistic studies, biomarker discovery, and the development of age-adapted therapeutic strategies.},
}

Humans
*Immunosenescence/immunology
*Tumor Microenvironment/immunology/drug effects
*Neoplasms/immunology/drug therapy/metabolism
*Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology
*B7-H1 Antigen/antagonists & inhibitors/immunology
*Immune Checkpoint Inhibitors/therapeutic use
Animals
T-Cell Exhaustion
Aged

@article {pmid42569432,
year = {2026},
author = {Murphy, EF and Templeman, I and Rimmer, J and Harding, SV},
title = {Gut microbiome modulation for military resilience and performance.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1828981},
doi = {10.3389/frmbi.2026.1828981},
pmid = {42569432},
issn = {2813-4338},
abstract = {A range of technologies are being developed to modulate the human gut microbiome, aimed at resolving gut dysbiosis and restoring normal host function. Although limited, a subset of studies have begun to evaluate these technologies within healthy human populations. This could provide approaches to mitigate the impact of occupational stressors on military personnel to ensure their operational effectiveness and resilience is maintained, and could also extend to enhancing the physical or cognitive performance of an individual beyond their baseline potential. Research using in vivo models and healthy human populations suggest that cognition, mineral absorption, muscle resilience, endurance and structural integrity, and injury recovery are modified by the gut microbiome. However, the regulations that govern the use of these technologies are largely focused on their use in treating disease and promoting health, which could hinder such applications. Therefore, whilst the use of gut microbiome modulation could present opportunities to enhance resilience and performance in military personnel, more research in healthy human cohorts is needed, alongside the development of effective regulatory frameworks supporting wider applications.},
}

@article {pmid42569838,
year = {2026},
author = {Wang, Z and Shang, D and Zhao, C and Song, T and He, C},
title = {Neuro-Immune-Skin Axis: The Role of Neuropsychological Factors in Atopic Dermatitis.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {},
number = {},
pages = {17103568261475840},
doi = {10.1177/17103568261475840},
pmid = {42569838},
issn = {2162-5220},
abstract = {The understanding of atopic dermatitis (AD) pathogenesis is evolving beyond the barrier-immune dichotomy, with neuropsychological factors gaining prominence as a central component. This review systematically decodes the multi-level crosslink within the "brain-skin axis" in AD, encompassing recent advances in peripheral sensory neuron sensitization, central neural remodeling, and neuro-immune interactions. We elaborate on the roles of neuropeptides, cytokines, the autonomic nervous system, and the hypothalamic-pituitary-adrenal axis in the itch-scratch cycle, inflammation amplification, and mood disorders. Furthermore, we examine the influence of novel therapeutic strategies, including biologics, Janus kinase inhibitors, psychological approaches, and microbiome modulation, on these neuropsychological components. Finally, we outline future research directions, such as elucidating the molecular mechanisms of neuro-immune crosstalk, identifying relevant biomarkers, and establishing interdisciplinary diagnostic and treatment models. A deeper understanding of the role of neuropsychological factors in AD not only drives innovation in treatment strategies but also offers new perspectives for breaking the vicious cycle of "pruritus-inflammation-psychological distress."},
}

@article {pmid42569868,
year = {2026},
author = {Zhao, Z and Yue, S and Yang, M and Zhang, J and Li, F and Li, Y and Wang, P and Zhan, S},
title = {A Universal Fenton-Like Strategy for Selective Generation of [1]O2 in Mixed Industrial Wastewater Treatment and Green Chemical Synthesis.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e4329489},
doi = {10.1002/anie.4329489},
pmid = {42569868},
issn = {1521-3773},
support = {//Haihe Laboratory of Sustainable Chemical Transformations/ ; 22225604//Natural Science Foundation of China/ ; U24A20518//Natural Science Foundation of China/ ; 22422605//Natural Science Foundation of China/ ; 24YFZCSN00050//Tianjin Commission of Science and Technology as key critical technologies R&D projects/ ; 63181206//Frontiers Science Center for New Organic Matter/ ; QN20230206//Young Scientific and Technological Talents/ ; 25JCYBJC01450//Tianjin Natural Science Foundation Project/ ; 63261159//Fundamental Research Funds for the Central Universities, Nankai University/ ; },
abstract = {Sustained and selective generation of singlet oxygen ([1]O2) in Fenton-like catalytic systems is highly desirable for diverse applications, from freshwater resource management to green chemical synthesis. Despite advances in advanced oxidation processes, there remains a lack of generalizable methods that reliably modulate [1]O2 selectivity. Here, we propose a descriptor-assisted coordination modulation strategy, in which machine-learning analysis identifies the d-band center as an important electronic descriptor associated with [1]O2 selectivity. Through N-coordination modulation, the CoN5 catalyst exhibited near-complete [1]O2 selectivity among the quantified reactive oxygen species (ROS) with a steady-state concentration of 394 µM, outperforming recent reports. As an internal-circulation pre-oxidation module, the CoN5/peroxymonosulfate (CoN5/PMS) system continuously raised wastewater biochemical oxygen demand/chemical oxygen demand (BOD/COD) to above 0.5 over 192 h, increased bioavailable dissolved organic matter (DOM), and showed high microbiome compatibility, evidenced by reduced Vibrio fischeri inhibition and microbial diversity ordination clustering near the background with greater shared-taxa overlap. This system also enabled selective thioanisole oxidation, achieving 90.6% conversion and 99.5% selectivity, with green synthesis potential demonstrated in a three-chamber continuous single-pass reactor. These results establish a generalizable coordination principle for steering ROS pathways and provide a deployable, low-ecological-risk route for both mixed wastewater treatment and green chemical synthesis.},
}

@article {pmid42569915,
year = {2026},
author = {Lin, CP and Geroldi, A and Selem, N and Liti, G and Tsai, IJ},
title = {A Global Synthesis of Yeast in Microbiomes.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.70039},
pmid = {42569915},
issn = {1097-0061},
support = {Impulscience 2024 - SMIC//Fondation Bettencourt Schueller/ ; AS-IA-113-L04//Academia Sinica/ ; 114-2628-B-001-014-//National Science and Technology Council, R.O.C/ ; },
abstract = {Yeasts are widespread members of microbial communities across terrestrial, aquatic, and host-associated environments, yet they remain underrepresented in microbiome studies due to low abundance and methodological biases. By combining a literature review with a meta-analysis of ~44,000 fungal metabarcoding samples from the GlobalFungi database, we show that yeasts occur in over 90% of samples, confirming their global ubiquity. Basidiomycetous lineages-especially Agaricomycotina-were most frequently detected, whereas Saccharomycotina showed stronger signals in anthropogenic, aquatic, host-associated, and food-related settings depending on the dataset. Although yeasts typically comprised only ~0.1% of fungal reads, their distributions were structured rather than uniform and reflected distinct habitat associations across environments. In ~3% of samples, yeasts exceeded 25% of reads, with genera such as Aureobasidium, Hanseniaspora, and Saccharomyces episodically dominating nutrient-rich or human-influenced environments. Cosmopolitan genera including Vishniacozyma, Solicoccozyma and Rhodotorula were broadly distributed but remain underreported in microbiome surveys. Shotgun metagenomic data further confirmed yeast presence across diverse microbiomes, with yeast-derived reads being a small fraction of total metagenomic sequences, reflecting the 'curse of low abundance'. Despite their rarity, yeasts are likely to contribute to nutrient cycling, plant growth, and host interactions. We recommend inclusive multi-kingdom approaches-improved primer design, optimised fungal DNA recovery, long-read sequencing, and quantitative tools-to better integrate yeasts into microbiome research.},
}

@article {pmid42570071,
year = {2026},
author = {Sumi, MSA and Islam Rahat, MT and Resma, MNJ and Ahmed, MF and Mollah, MNH and Kibria, MK},
title = {Identification of hypertension-associated bacterial key genes as potential targets and therapeutic agents through integrated bioinformatics approach.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42570071},
issn = {1618-1905},
abstract = {Hypertension (HTN) is a major global health burden and a leading risk factor for cardiovascular morbidity and mortality. Although numerous studies have explored host genetic factors and molecular mechanisms underlying HTN, increasing evidence indicates that gut microbiota dysbiosis also contributes to disease development. However, the specific microbial genes involved in HTN pathogenesis and their potential therapeutic targeting remain largely unexplored. This study aimed to identify HTN-associated differentially abundant bacterial genes (DAGs), prioritize bacterial key genes (bKGs) from among them, and repurpose potential therapeutic agents targeting these bKGs using an integrated bioinformatics framework. A total of 167 stool (fecal) microbiome samples, comprising 72 samples from HTN patients and 95 samples from HCs, were analyzed using publicly available 16 S rRNA sequencing data. After quality processing and clustering at 97% similarity, 95,361 representative operational taxonomic units were obtained. Microbial diversity analysis revealed significant alterations in community composition between HTN and HC groups. Differential abundance analysis identified 24 significantly altered bacterial genera associated with HTN. Functional prediction analysis further revealed 28 differentially abundant metabolic pathways and 631 differentially abundant bacterial genes (DAGs) potentially involved in HTN pathogenesis. From these DAGs, protein-protein interaction network analysis prioritized ten hub genes as bKGs (alsB, ampC, gsiB, araC, coaA, dnaB, fruA, ssuA, minE and tsx) representing potential microbial therapeutic targets. Structure-based molecular docking identified five approved drugs, namely Azilsartan, Eplerenone, Candesartan, Conivaptan, and Telmisartan, as top-ranked compounds exhibiting strong binding affinities toward the proposed targets. ADMET evaluation suggested favorable pharmacokinetic and safety profiles for Azilsartan, Eplerenone, and Candesartan. Furthermore, molecular dynamics simulation analyses confirmed that Eplerenone and Candesartan exhibited greater structural stability and sustained binding interactions, suggesting their potential as promising therapeutic candidates for HTN management. Therefore, this study identifies microbial gene signatures potentially involved in HTN and proposes a microbiome-guided drug repurposing strategy targeting bacterial functional pathways. These findings provide novel insights into microbiota-host interactions in HTN and highlight promising therapeutic candidates that warrant further experimental and clinical validation.},
}

@article {pmid42570167,
year = {2026},
author = {Al Srouji, N and Ismaiel, A and Puia, A and Ismaiel, M and Abosheisha, M and Popa, SL and Puia, IC},
title = {Beyond the biopsy: the new era of non-invasive staging and biomarkers in colorectal cancer.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {42570167},
issn = {1699-3055},
abstract = {Colorectal cancer (CRC) management is increasingly challenged by shifting demographics, notably the rise in aggressive early-onset CRC, and the limitations of conventional anatomical staging. This comprehensive review explores the paradigm shift toward noninvasive and minimally invasive pre-operative biomarkers for CRC diagnosis, staging, and prognostic stratification. While traditional colonoscopy and radiological imaging often fail to capture intratumoral heterogeneity and micrometastatic dissemination, emerging biomarker modalities offer real-time, high-fidelity tumor phenotyping. Advanced fecal tests and microbiome profiling, highlighting enriched taxa like Fusobacterium nucleatum, provide crucial insights into the tumor microenvironment, disease progression, and localized immune evasion. Concurrently, accessible systemic immune-inflammatory scores, such as the pan-immune-inflammation value (PIV), systemic immune-inflammation index (SII), and the cancer-specific Glasgow prognostic score (C-GPS), demonstrate robust capabilities in predicting overall survival, disease recurrence, and pathological complete response. The clinical maturation of circulating tumor DNA (ctDNA) represents a cornerstone of this evolution, offering unparalleled sensitivity for detecting molecular residual disease (MRD) post-surgery and dynamically guiding adjuvant chemotherapy de-escalation or escalation protocols. Ultimately, the future of CRC precision oncology relies on multimodal convergence, synergistically integrating liquid biopsies, radiomics, and clinical scores into unified predictive models or "Digital Twins". Emphasizing the need for multi-center standardization and prospective validation, this integrated noninvasive biomarker landscape promises to overcome current diagnostic blind spots, optimize therapeutic interventions, and fundamentally individualize patient care.},
}

@article {pmid42570316,
year = {2026},
author = {Tilves, C and Holingue, C and Wanigatunga, SK and Chia, CW and Zhao, N and Wu, MN and Schrack, JA and Simonsick, EM and Ferrucci, L and Tanaka, T and Spira, AP and Mueller, NT},
title = {Associations of self-reported and actigraphic sleep with gut microbiome composition and diversity among older adults.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsag217},
pmid = {42570316},
issn = {1550-9109},
abstract = {STUDY OBJECTIVES: Poor sleep is linked to adverse health outcomes. Animal studies suggest the gut microbiome may influence sleep, but human findings remain inconsistent. We examined associations of self-reported insomnia symptoms, daytime sleepiness, and actigraphy-measured sleep with gut microbiome diversity and composition in older adults.

METHODS: We studied 869 Baltimore Longitudinal Study of Aging participants with self-reported sleep and shotgun metagenomic sequencing; 332 also had actigraphy. We tested associations of sleep with alpha diversity, beta diversity, and species composition using regression, PERMANOVA, and ANCOM-BC2, adjusting for age, sex, BMI, physical activity, education, and depressive symptoms.

RESULTS: Participants had mean age 70.7 years; 54.8% were female and 66.9% White. Trouble falling asleep ≥5 times/week was associated with higher Shannon diversity (β=0.41 SD; 95% CI: 0.09, 0.73) and Pielou's evenness, but not richness metrics. No actigraphy-measured sleep variables were associated with alpha or beta diversity. Beta diversity analyses suggested excessive sleepiness (1-2 o 3-4 times/week) was associated with different microbial composition, though variance explained was small. In species-level analyses, frequent insomnia symptoms or excessive sleepiness were associated with depleted or undetected Eubacterium sp. CAG:251. In exploratory actigraphy models, each doubling of sleep efficiency was associated with higher Eubacterium sp. CAG:251 prevalence (PR=2.15; 95% CI: 1.47, 3.14), while each 30-minute increase in wake after sleep onset was associated with lower prevalence (PR=0.49; 95% CI: 0.29, 0.81).

CONCLUSIONS: Global diversity findings were limited and inconsistent, whereas subjective and objective sleep disturbances converged on Eubacterium sp. CAG:251. Findings are exploratory and require longitudinal replication.},
}

@article {pmid42570323,
year = {2026},
author = {Watanabe, Y and Orihara, K and Tsukuda, N and Hara, T and Matsuki, T},
title = {Natural transformation drives large-scale genome mosaicism in human gut bifidobacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag208},
pmid = {42570323},
issn = {1751-7370},
abstract = {Although horizontal gene transfer drives bacterial diversification, its contribution to chromosome-scale variation in human gut commensals remains unclear. This study demonstrated that human-associated bifidobacteria undergo extensive chromosomal transfer through natural transformation. Comparative genomics of coexisting Bifidobacterium pseudocatenulatum isolates from a single individual revealed extensive recombination signatures between the lineages. We experimentally reproduced this recombination by co-culturing strains, resulting in the transfer of multiple chromosomal regions and generation of mosaic genomes. Individual recombination tracts reached up to 247 kb per site, with cumulative replacements accounting for up to 28.9% of the recipient chromosome. These transfers occurred with heat-killed donors or purified DNA and were abolished by DNase, thereby identifying natural transformation as the underlying mechanism. Furthermore, we observed that environmental factors strongly influenced transformation frequency, suggesting that gut environmental conditions play a role regulating this process. Using natural transformation, we established a simple markerless genome-editing method that enables efficient gene deletions. Deletions of the Tad pili, ComEA-ComEC, or DprA-ComM-YraN gene clusters abolished transformation, defining the core machinery. The conservation of these genes across the genus Bifidobacterium and experimental demonstration of natural transformation in Bifidobacterium longum and Bifidobacterium breve indicate that natural transformation capacity is widespread within the genus. Our findings establish natural transformation as a key mechanism that promotes genome plasticity and contributes to adaptive evolution in bifidobacteria, thereby expanding our current understanding of horizontal gene transfer in the human gut microbiota.},
}

@article {pmid42570388,
year = {2026},
author = {Malik, K and Iqbal, A and Du, M and Chen, T and Li, C},
title = {Impact of Epichloë endophyte on rhizosphere resistome dynamics in wild barley and bluegrass.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143115},
doi = {10.1016/j.jhazmat.2026.143115},
pmid = {42570388},
issn = {1873-3336},
abstract = {Fungal endophytes are universally present in plant tissues to enhance stress resilience and growth of plants. They can change the microbial communities and functional characteristics of the rhizosphere without harming the host. However, the effect of their colonization on the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in rhizosphere soil remains largely unexplored. In the present study, the impact of the Epichloë bromicola fungal endophyte on the rhizosphere resistome structure and environmental factors in wild barley (Hordeum brevisubulatum) and bluegrass (Poa pratensis) plants was investigated. The rhizosphere ARGs and MGEs communities were characterized through metagenome analysis. Simultaneously, their relationship with key rhizosphere environmental variables was evaluated using redundancy analysis (RDA) and Mantel tests. The results revealed that infection altered the taxonomic distribution of ARGs and MGEs-carrying bacteria. Besides, it reduced the prevalence of the predominant genera Sphingomonas and Nocardioides, while increasing the contribution of the less prevalent genera Bradyrhizobium and Rubrivivax to multidrug efflux and macrolide resistance mechanisms. Co-occurrence network analysis showed decreased modularity, indicating a less compartmentalized resistome-mobilome under infection. The findings revealed that endophyte infection fundamentally restructured the rhizosphere resistome by changing environmental pressures and favoring stress-response mechanisms. The study provides novel insights into how fungal endophytes influence microbial resistome assembly and HGT processes, their role in environmental antibiotic resistance dissemination, and One Health resistome dynamics in the rhizosphere.},
}

@article {pmid42570689,
year = {2026},
author = {Jiao, Y and Shen, R and Xu, M and Liang, H and Jiang, L and Wang, Y and Wu, Y and Wu, S and Jia, C and Wang, Y and Lv, B and Shen, L and Li, Y and Zhao, L and Yao, Z and Han, F and Zhu, X and Wang, Y and Yang, J},
title = {A least-input nitrogen fertilizer reduction strategy sustains peanut yield with lower nitrogen inputs.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.08.025},
pmid = {42570689},
issn = {2090-1224},
abstract = {INTRODUCTION: Synthetic nitrogen (N) fertilizers underpin global food security but drive escalating environmental costs, including greenhouse gas (GHG) emissions and soil degradation. Conventional N-reduction strategies face a fundamental trade-off: lowering fertilizer inputs typically compromises crop productivity and farmer income. Nanotechnology offers a pathway to decouple yield from N dependency, yet scalable, low-cost solutions remain elusive.

OBJECTIVES: This study aimed to develop a least-input foliar fertilization strategy using bio-derived nanocarbon (BNC) that enables a 30% reduction in synthetic N input in peanut (Arachis hypogaea L.) without sacrificing crop yield, nutritional quality, or economic returns, while elucidating the underlying physiological and microbiological mechanisms.

METHODS: Field trials were conducted with peanut (cv. Huayu 22) over two consecutive growing seasons (2024-2025) in Laixi, Shandong, China, under four treatments: N (conventional N, 100% urea), N-30 (reduced N, 70% urea), N + BNC (100% urea + foliar BNC), and N-30 + BNC (70% urea + 18 g ha[-1] foliar BNC). Photosynthetic parameters, oxidative stress markers, and [15]N isotope tracing were assessed. Transcriptomic, metabolomic, and 16S rRNA microbiome analyses characterized systemic signaling and rhizosphere responses. GHG emissions were modeled using the DNDC framework, and economic benefits were calculated based on yield and input costs.

RESULTS: BNC application under N-30% maintained yield parity with the N control by sustaining photosynthetic electron transport and reducing reactive oxygen species (ROS). This enhanced carbon status upregulated the transcription factor HY5, activating nitrate transporter AhNRT1.2 and ammonium transporter AhAMT1.1 and increasing [15]N uptake. Changes in root-exudate composition were accompanied by shifts in the rhizosphere bacterial community, including higher relative abundance of taxa associated with nitrification and nutrient turnover (Nitrospira and Gemmatimonas), and coincided with 21% and 14% higher root NO3[-]-N and NH4[+]-N contents, respectively. Nitrogen use efficiency (NUE) improved by 16.0%, total GHG emissions decreased by 34.8%, and net profit increased by 27.0%.

CONCLUSION: A micro-dosage of upcycled BNC (∼$0.02 ha[-1]) orchestrates HY5-mediated shoot-to-root signaling and rhizosphere microbiome restructuring to sustain crop productivity under reduced N inputs. This commercially viable, low-input framework offers a scalable route for climate-smart agriculture that reconciles food security with environmental sustainability.},
}

@article {pmid42562480,
year = {2026},
author = {Marotta, R and De Filippis, F and Valentino, V and Ercolini, D},
title = {Fermentation of legumes as a strategy to enhance nutritional and sensory properties and modulate gut microbiome and human health.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119704},
doi = {10.1016/j.foodres.2026.119704},
pmid = {42562480},
issn = {1873-7145},
mesh = {*Fabaceae/chemistry/metabolism ; Humans ; *Fermentation ; *Nutritive Value ; *Gastrointestinal Microbiome/physiology ; *Fermented Foods/microbiology ; },
abstract = {Legumes represent a valuable and vegetable source of proteins and fiber with a very low environmental footprint production, therefore, both dietary guidelines and international agencies suggest increasing their production and consumption. Despite their favorable nutritional composition, they also naturally contain antinutritional factors such as phytic acid, that limit the absorption of micronutrients. This, coupled with the lower bioavailability of proteins as compared with meat, diminishes the biological and economic value of legumes. However, recent studies have shed a light on the power of fermentation to improve the protein profile of pulse and neutralize antinutritional compounds. In this review, we explore the benefits of legumes fermentation in depth, focusing on the role of microorganisms in enhancing the nutritional and sensory enhancement of legumes. Furthermore, we describe the properties and the microorganisms involved in the production of several craft-based fermented legumes typically consumed by non-Westernized populations, particularly delving into their effects on the gut microbiome and on the human health.},
}

*Fabaceae/chemistry/metabolism
Humans
*Fermentation
*Nutritive Value
*Gastrointestinal Microbiome/physiology
*Fermented Foods/microbiology

@article {pmid42562482,
year = {2026},
author = {Doddabematti Prakash, S and Balyatanda, SB and Sytsma, J and Tenzin, K and Siliveru, K},
title = {Benchmarking a 16S rRNA sequencing protocol for microbiome analysis in low-moisture grain environments.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119710},
doi = {10.1016/j.foodres.2026.119710},
pmid = {42562482},
issn = {1873-7145},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Benchmarking ; *Edible Grain/microbiology ; Computational Biology ; Triticum/microbiology ; *Bacteria/genetics/classification ; *Food Microbiology ; Workflow ; },
abstract = {Microbial amplicon sequencing studies are an important tool in food and biomedical research. However, accurate interpretation of the 16S rRNA gene survey requires specialized software and an algorithm to convert raw sequencing data into reliable taxonomic profiles. Given the existence of multiple bioinformatics pipelines varying in sequence aggregation strategies, reference databases, and filtering parameters, there is little to no consensus on best practices for LMF processing systems. In this study, we systematically assessed discrepancies in taxonomic composition, alpha diversity, and beta diversity across 32 combinations of bioinformatics workflows, based on eight widely used 16S rRNA pipelines and four taxonomic databases, applied to 16S rRNA gene sequences extracted from wheat milling environments (n = 160). Weighted composite scores were used to select the top 10-performing workflow combinations for downstream analysis. Taxonomic assignments were broadly similar across workflows at the family and genus levels; however, genus-level diversity metrics were more sensitive to workflow choice. At the family level, diversity metrics were conserved across pipeline-database combinations (Chao1: 22.97 ± 2.20-24.92 ± 2.04; Shannon: 2.59 ± 0.19-2.74 ± 0.18; InvSimpson: 10.63 ± 1.25-11.27 ± 1.06; Bray-Curtis: 0.528-0.556; Jaccard: 0.557-0.582), whereas at the genus level both alpha and beta diversity exhibited wider ranges and larger dispersion (Chao1: 45.27 ± 5.68-50.20 ± 5.64; Shannon: 2.54 ± 0.24-2.73 ± 0.22; InvSimpson: 10.37 ± 1.4-11.03 ± 1.05; Bray-Curtis: 0.79-0.82; Jaccard: 0.79-0.80). Furthermore, ASV vs. OTU workflows were comparable across the evaluated metrics; however, ASVs showed numerically higher values for some genus-level measures than OTUs because they can resolve variation down to the single-nucleotide level, thereby retaining low-abundance features important for LMF safety. This work paves the way toward using bioinformatics and 16S pipelines to characterize sparse, low-density, and uneven samples in low-moisture environments.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Benchmarking
*Edible Grain/microbiology
Computational Biology
Triticum/microbiology
*Bacteria/genetics/classification
*Food Microbiology
Workflow

@article {pmid42562511,
year = {2026},
author = {Lee, JW and Kim, YM and Kim, YJ and Jeong, KC and Kim, SA},
title = {Wastewater irrigation reshapes the microbiome and resistome of radish sprouts: Insights from 16S rRNA and shotgun metagenomic sequencing.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119739},
doi = {10.1016/j.foodres.2026.119739},
pmid = {42562511},
issn = {1873-7145},
mesh = {*Raphanus/microbiology/growth & development ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Agricultural Irrigation/methods ; Animals ; Metagenomics/methods ; Shotgun Sequencing ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Swine ; },
abstract = {Water scarcity is increasing the reliance on treated wastewater in fresh produce production, yet its effects on the microbial and hygienic quality of fresh produce remain unclear. This study evaluated the influence of wastewater irrigation on the microbiome and antibiotic resistance gene (ARG) profiles of radish sprouts grown under commercially relevant conditions. Using culture-dependent methods and integrated sequencing (16S rRNA and shotgun metagenomics), we tracked microbial and resistome dynamics across the sprout production process under three irrigation regimes: swine wastewater, treated wastewater, and sterile distilled water. Wastewater irrigation markedly increased microbial loads, with aerobic plate counts exceeding 8.0 log CFU/g in final radish sprouts. Both wastewater treatments were dominated by Pseudomonas and Acinetobacter. Resistome profiling showed persistent multidrug, bacitracin, and polymyxin resistance genes in wastewater-irrigated sprouts, while sulfonamide resistance genes occurred exclusively under wastewater irrigation, suggesting wastewater-associated environmental transmission. Higher ARG subtype richness in wastewater treatments suggested that conventional wastewater treatment processes do not completely eliminate diverse ARGs. ARG-host linkage analysis suggested an elevated potential for horizontal gene transfer within edible plant tissues. Overall, wastewater irrigation altered the microbiological quality of radish sprouts and facilitated ARG persistence, underscoring the need for improved post-treatment and preventive water management to safeguard fresh produce safety.},
}

*Raphanus/microbiology/growth & development
*Wastewater/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Agricultural Irrigation/methods
Animals
Metagenomics/methods
Shotgun Sequencing
Bacteria/genetics
Drug Resistance, Microbial/genetics
Swine

@article {pmid42562512,
year = {2026},
author = {Murthy, N and Nayak, KN and Tanu, and Priya, S and Priyadarshini, P},
title = {Dual-stage assessment of Salmonella-specific bacteriophage formulation: Antibiofilm activity on food matrices and in vivo efficacy against the murine salmonellosis model.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119738},
doi = {10.1016/j.foodres.2026.119738},
pmid = {42562512},
issn = {1873-7145},
mesh = {Animals ; *Biofilms/growth & development ; *Salmonella Phages/physiology ; Mice ; Disease Models, Animal ; Humans ; *Salmonella Infections/microbiology/therapy/prevention & control ; *Food Microbiology ; Chickens/microbiology ; *Salmonella/virology ; *Salmonella Food Poisoning/prevention & control/microbiology ; HT29 Cells ; Meat/microbiology ; Female ; Fruit/microbiology ; },
abstract = {Foodborne infections caused by Salmonella infection remain a major global concern due to increasing multidrug resistance and biofilm formation, resulting in significant morbidity and mortality. Thus, the development of potential alternatives, including bacteriophage cocktail formulations, is emerging as a promising strategy. In this direction, we developed a Salmonella-specific phage formulation (BPF-Sal) and evaluated its stability, biocontrol efficacy, in vitro safety, antibiofilm activity and protective potential in an in vivo model. Interestingly, BPF-Sal remained stable across a wide range of pH values and temperatures while maintaining significant lytic activity. Further, it effectively reduced Salmonella contamination on chicken breast and mixed fruit matrices to below detection limits (<1 CFU/100 μL) within 6 h and 10 h, respectively, compared to conventional preservatives. In HT-29 cells, BPF-Sal (10[2]-10[1][0] PFU/mL) exhibited no cytotoxicity, preserved cellular morphology, and showed efficient phage internalization. It also displayed antibiofilm activity, reducing preformed Salmonella biofilms by 90-92% at MOI 100 and up to 98% at MOI 1000, as confirmed by crystal violet assay, scanning electron and fluorescence microscopy. In a murine salmonellosis model, oral administration of BPF-Sal conferred significant protection, preventing weight loss and reducing bacterial loads along with improved health status and histopathological outcomes. Metagenomic analysis revealed infection-induced gut dysbiosis, characterized by enrichment of Proteobacteria and depletion of beneficial taxa. BPF-Sal partially restored microbial balance, while combination therapy further improved microbiota normalization. Thus, our findings establish BPF-Sal as a safe, effective, multifunctional phage-based strategy for Salmonella biocontrol and other phage-based applications.},
}

Animals
*Biofilms/growth & development
*Salmonella Phages/physiology
Mice
Disease Models, Animal
Humans
*Salmonella Infections/microbiology/therapy/prevention & control
*Food Microbiology
Chickens/microbiology
*Salmonella/virology
*Salmonella Food Poisoning/prevention & control/microbiology
HT29 Cells
Meat/microbiology
Female
Fruit/microbiology

@article {pmid42562540,
year = {2026},
author = {Kong, F and Xu, J and Liu, Z and Ju, N and Guo, S},
title = {Ecological mechanisms and functional stability of lactic acid Bacteria in synthetic microbial communities: Competition, cross-feeding, and homeostasis maintenance.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119779},
doi = {10.1016/j.foodres.2026.119779},
pmid = {42562540},
issn = {1873-7145},
mesh = {*Lactobacillales/metabolism/physiology ; *Homeostasis ; Fermentation ; *Microbial Consortia/physiology ; *Microbiota/physiology ; Humans ; Microbial Interactions ; },
abstract = {Synthetic microbial communities (SynComs) play a pivotal role in advancing precision fermentation and microbiome engineering. Within these multispecies systems, lactic acid bacteria (LAB) function as ecological and metabolic cornerstones. However, the mechanisms underlying LAB-mediated community stability remain insufficiently understood. This review synthesizes current knowledge on microbial competition, cross-feeding, and community homeostasis to evaluate the ecological contributions of LAB. We compare the metabolic roles of LAB in SynComs and natural ecosystems, highlighting competitive strategies, including acidification and antimicrobial production, as well as lactate-centered syntrophic interactions. As central metabolic hubs, LAB facilitate the division of labor by transforming excess metabolic outputs into shared resources, thereby reducing metabolic inefficiencies. We further examine how functional redundancy and metabolic coupling contribute to community resilience and stability. The review also discusses emerging applications of SynComs in gut health, particularly inflammatory bowel disease (IBD), and industrial fermentation processes. We conclude that the integration of multi-omics approaches with predictive modeling will be critical for the rational design and programmable regulation of stable microbial consortia. Furthermore, this review proposes a unified hierarchical framework for understanding the stability of LAB-mediated SynComs. By integrating competition-driven colonization, cooperation mediated through cross-feeding interactions, and multidimensional homeostatic mechanisms, the framework bridges fundamental ecological theory with applied microbiome engineering. The proposed framework is primarily applicable to LAB-centered SynComs associated with food fermentation systems, acidic environments, and lactate-driven metabolic networks.},
}

*Lactobacillales/metabolism/physiology
*Homeostasis
Fermentation
*Microbial Consortia/physiology
*Microbiota/physiology
Humans
Microbial Interactions

@article {pmid42562772,
year = {2026},
author = {Xu, C and Xie, Q and Li, X and Li, W},
title = {RNAi-mediated knockdown of vitellogenin genes disrupts ovary development and alters ovarian bacterial composition in Zeugodacus tau (Diptera: Tephritidae).},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag239},
pmid = {42562772},
issn = {1938-291X},
support = {20252BAC200396//Jiangxi Provincial Natural Science Foundation/ ; GJJ210443//Foundation Project of Jiangxi Provincial Educational Committee/ ; },
abstract = {Zeugodacus tau Walker (Diptera: Tephritidae) is an invasive pest of global significance that inflicts substantial losses to the fruit and vegetable production sectors annually. Despite the availability of the Z. tau genome in public database, functional characterization of key genes remained limited. Vitellogenin (Vg) functions as a key precursor of yolk protein and exerts a pivotal part in the insect reproductive process. Here, we identified 3 Vg genes (Vg1, Vg2, and Vg3) based on genetic data from Z. tau. Analysis of amino acid sequences demonstrated that all ZtVgs contain conserved serine residues, a putative cleavage site, and putative N-linked glycosylation sites. Molecular phylogenetic reconstruction revealed that ZtVgs exhibited the closest evolutionary affinity to their homologs found in Zeugodacus cucurbitae and Bactrocera dorsalis. Spatiotemporal expression profiling indicated that all 3 ZtVgs exhibit pronounced expression in the female fat body. Treatments with the Methoprene and 20-hydroxyecdysone (20E) significantly upregulated ZtVgs expression 24 h post application at a dose of 1 μg. RNA interference (RNAi) bioassay revealed that the suppression of 3 ZtVgs delayed ovary development and impaired female fertility. Further microbiome analysis revealed that knockdown of the 3 Vg genes led to reduced abundance of bacterial taxa affiliated with the phylum Pseudomonadota and the genus Burkholderia in the ovary. These findings elucidate the important function of Vgs in ovary development and provide insights into the association between insect Vg genes and the ovarian bacteria, thereby establishing a groundwork for subsequent investigations on the molecular mechanisms underlying their interaction.},
}

@article {pmid42562802,
year = {2026},
author = {Cassey, J and Banati, R},
title = {The Benefits and Biological Risks in Breastfeeding and Sharing Human Milk: Have We Got it Right?.},
journal = {Journal of human lactation : official journal of International Lactation Consultant Association},
volume = {},
number = {},
pages = {8903344261451926},
doi = {10.1177/08903344261451926},
pmid = {42562802},
issn = {1552-5732},
abstract = {BACKGROUND: Implementation of the strong recommendation by the World Health Organization (WHO), the United Nations Children's Fund (UNICEF), and others, to increase use of donor human milk in cases where breastfeeding cannot be provided, requires a flexible, knowledge-based and risk-informed approach.

METHODS: Based on an extensive literature review, we present the evidence for potential biological risks of breastmilk in three scenarios: fresh, unmodified milk from breast to baby (breastfeeding and wet-nursing); expressed and unmodified milk stored at < 4 ºC until just before consumption; and milk modified by some form of pasteurization.

RESULTS: With the exception of contamination by some viruses and syphilis, breastfeeding is the safest way to feed a baby, despite its highly variable microbiome and virome-including organisms that, in other circumstances, can cause disease. Wet-nursing, where the donor has been appropriately screened, carries a similar risk profile to mother's own feeding. Whilst expression and storage of raw milk at < 4 °C adds a bacterial load, the additional risk, with knowledge and screening of the donor and careful attention to all steps in delivery, seems small and is smaller than using bovine-based formulae-especially in low resource circumstances. Donated milk from unknown donors carries additional risks. A decision to reduce these risks through thermal pasteurization must be weighed against the loss of breastmilk's natural protective components.

CONCLUSIONS: Not only have the biological risks of both informal and formal milk sharing for healthy infants been greatly exaggerated, but that they are often quoted without consideration of the overall risks of alternatives.},
}

@article {pmid42562842,
year = {2026},
author = {Lechleiter, N and Wedemeyer, J and Junker, J and Wilczek, M and Klich, D and Olech, W and Anusz, K and Homeier-Bachmann, T and Didkowska, A},
title = {Microbiome and resistome of the European bison (Bison bonasus).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42562842},
issn = {2045-2322},
mesh = {Animals ; *Bison/microbiology ; *Microbiota/genetics ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {After facing extinction in the early 20th century, populations of the two remnant genetic lines of European bison are now under continuous health monitoring. Faecal samples were taken from five Polish and one German herd of European bison over the course of several years. Through metagenomic sequencing, the bacterial and archaeal microbiome as well as the resistome of these samples could be characterized. Significant differences were mainly found between the bacterial microbiome of samples taken from droppings as opposed to rectal samples. Apart from this, the microbiome and resistome had low differentiation, showing no significant influence of individual factors or location. Oscillospiraceae, Lachnospiraceae and Bacteroidaceae were the dominant bacterial families, the archaeome was mostly made up by Methanobacteriaceae. Genes from resistance classes like Aminoglycosides and Macrolide, Lincosamide and Streptogramine were present. This study characterises the microbiome and resistome of the European bison with the help of metagenomics, providing novel insights into its biology.},
}

Animals
*Bison/microbiology
*Microbiota/genetics
Feces/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
Metagenomics
Anti-Bacterial Agents/pharmacology
Archaea/genetics/classification/isolation & purification
Phylogeny

@article {pmid42562890,
year = {2026},
author = {Murao, A and Aziz, M and Wang, P},
title = {Inflammatory gut-liver crosstalk: mechanisms and therapeutic targets.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42562890},
issn = {2092-6413},
support = {R35GM118337//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01HL076179//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The gut has a profound influence on the liver through their anatomical connection via the portal vein. During acute inflammation, gut tissue injury leads to increased barrier permeability, allowing the translocation of external contents that can affect hepatic function. Gut-liver crosstalk contributes to the pathophysiology of acute inflammatory disorders, such as sepsis, intestinal ischaemia-reperfusion, hepatitis and drug-induced liver injury. This organ-to-organ crosstalk is mediated by the microbiome, pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs) and various proinflammatory mediators. Different types of gut and liver resident cells as well as circulating cells also facilitate inflammatory gut-liver crosstalk. These cell types include intestinal epithelial and myeloid cells, Kupffer cells, sinusoidal endothelial cells, hepatic stellate cells, hepatocytes, lymphocytes and neutrophils. PAMPs and DAMPs activate pattern recognition receptors, such as Toll-like receptors, on various cells, leading to proinflammatory signal transduction, including NFκB activation, cytokine and chemokine production, and NETosis. Collectively, these soluble and cellular factors exacerbate acute inflammation and tissue injury via the gut-liver axis, leading to poor outcomes in critically ill patients. Potential therapeutic interventions for this deadly clinical condition include modulation of the microbiome and pharmacological inhibition of proinflammatory mediators and cellular interactions. In this article we review the pathophysiology of inflammatory gut-liver crosstalk and potential therapeutic interventions.},
}

@article {pmid42562892,
year = {2026},
author = {Li, XY and Xie, ZQ and Geng, MY},
title = {Gut microbiota modulation of gastrointestinal cancers: from dysbiosis signatures to therapeutic interventions.},
journal = {Acta pharmacologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {42562892},
issn = {1745-7254},
abstract = {The human gut microbiota constitutes the largest and most metabolically active microbial ecosystem in the body, and accumulating evidence links dynamic alterations in microbial composition and function to the initiation, progression, and treatment responses of multiple gastrointestinal (GI) cancers, including esophageal, gastric, hepatocellular, pancreatic, and colorectal malignancies. This review synthesizes current evidence on dysbiosis signatures, mechanistic pathways, and translational opportunities across major GI cancer types, with a focus on microbe-derived metabolites and microbe-associated molecular patterns that shape inflammation, epithelial barrier integrity, and antitumor immunity. Across GI cancers, recurrent patterns include enrichment of pro-inflammatory/pathobiont taxa, depletion of homeostasis-maintaining and butyrate-producing commensals, and perturbations in metabolic axes centered on bile acids and short-chain fatty acids. Mechanistically, these changes can remodel the tumor microenvironment via epithelial and immune signaling, epigenetic regulation, and metabolic reprogramming. Importantly, the gut microbiota is increasingly recognized as a modifiable determinant of the efficacy and toxicity of immune checkpoint blockade, adoptive cell therapies, chemotherapy, and radiotherapy. Despite rapid advances, key challenges persist in translating microbiome research into cancer care, including validation, standardization, variability, and safety. Future success likely depends on function-oriented, targeted modulation, supported by multi-omics, strong causal evidence, and clinical trials.},
}

@article {pmid42563165,
year = {2026},
author = {Richie, TG and Wiechman, H and Vogt, B and Ingold, C and Heeren, L and Kamke, A and Pogranichniy, S and Monk, K and Summers, T and Ran, Q and Sarkar, S and Plattner, BL and Sidebottom, AM and Chang, EB and Lee, STM},
title = {Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42563165},
issn = {2049-2618},
mesh = {*Oxidative Stress/drug effects ; Animals ; *Glutathione/metabolism/pharmacology ; Reactive Oxygen Species/metabolism ; Mice ; Colon/microbiology/metabolism ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; Nitric Oxide/metabolism ; Intestinal Barrier Function ; Gastrointestinal Microbiome ; Metagenomics ; Mice, Knockout ; Interleukin-10/genetics ; },
abstract = {BACKGROUND: Certain microbes inhabiting the gut have been implicated in maintaining gut homeostasis and promoting gut damage repair. Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment.

RESULTS: We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and reactive oxygen species (ROS) levels. Cell-free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells and colon organoids. CFSM-treated organoids showed reduced ROS accumulation, improved epithelial integrity, and partial recovery of barrier function compared to oxidatively stressed controls. We demonstrated through shotgun metagenomics, metabolomics, host RNA sequencing, and molecular techniques that glutathione (GSH) biosynthesized by E. rectale alleviated host ROS damage. We showed downregulation of cell stress and immune response genes, indicating recovery from ROS stress. Chemical depletion of GSH in CFSM confirmed the role of microbial derived GSH in alleviation of ROS in colon cells.

CONCLUSIONS: In this study, we identify E. rectale as a potential probiotic by lowering colon inflammation and ROS damage through production of reduced glutathione. Microbially derived GSH has not been well established in the Lachnospiraceae family which are a large member of the overall gut microbiota. Understanding more about the impacts of microbial functions including GSH on lowering inflammation is needed to develop potential probiotics or therapies for chronic inflammatory conditions. Video Abstract.},
}

*Oxidative Stress/drug effects
Animals
*Glutathione/metabolism/pharmacology
Reactive Oxygen Species/metabolism
Mice
Colon/microbiology/metabolism
*Intestinal Mucosa/metabolism/microbiology/drug effects
Nitric Oxide/metabolism
Intestinal Barrier Function
Gastrointestinal Microbiome
Metagenomics
Mice, Knockout
Interleukin-10/genetics

@article {pmid42563179,
year = {2026},
author = {Miyamoto, H and Takahashi, H and Suda, W and Yamano, H and Inabu, Y and Kodama, H and Nakanishi, Y and Moriya, S and Satoh, T and Kato, T and Shindo, C and Tsuji, N and Matsuura, M and Ishii, C and Nakaguma, T and Etoh, T and Shiotsuka, Y and Udagawa, M and Kurotani, A and Suzuki, K and Masuya, H and Wada, S and Fukuda, S and Tashiro, Y and Miyamoto, H and Kikuchi, J and Hattori, M and Nishiuchi, T and Yamamoto, N and Ohno, H},
title = {Gut-protective metabolic phenotype for diarrhoeal remission caused by an environmental probiotic thermophile.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42563179},
issn = {2049-2618},
mesh = {Animals ; *Probiotics/administration & dosage ; *Diarrhea/veterinary/microbiology/therapy ; Feces/microbiology ; Cattle ; *Gastrointestinal Microbiome ; Proteomics ; Butyrates/metabolism ; Bacteriocins/genetics/biosynthesis ; Administration, Oral ; Genomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {BACKGROUND: Controlling diarrhoea in humans and livestock is a global challenge with diverse aetiologies. However, the dynamics of the microbiome for diarrhoeal remission are not sufficiently understood, and effective intervention strategies based on environmental microorganisms have not been fully explored.

METHODS: We investigated the metabolic structure associated with diarrhoeal remission using a combination of statistical, genomic, and proteomic approaches in a cattle model. Oral administration of the compost-derived thermophile Caldifermentibacillus hisashii significantly ameliorated persistent diarrhoea. Faecal bacterial populations and metabolites were characterised by a multi-step statistical pipeline comprising difference-in-differences (DID) analysis, Cliff's delta effect size estimation with permutation-based validation. The functional importance of the selected feature components was validated through genomic and proteomic analysis of C. hisashii N11 (AP028807.1).

RESULTS: Oral administration of C. hisashii significantly ameliorated persistent diarrhoea in calves. Although no significant differences in faecal bacterial community composition were observed, integrated analysis of faecal metabolites identified butyrate and 2-aminoisobutyrate (AIB) as the most discriminative features associated with diarrhoeal remission. Genomic and proteomic analyses of C. hisashii confirmed biosynthetic gene clusters for butyrate and AIB-containing lantibiotics, supporting the structural importance of these metabolites in diarrhoeal remission.

CONCLUSION: These findings suggest that diarrhoeal remission observed in this study involves characteristic shifts in faecal metabolite profiles rather than marked changes in overall gut microbial community composition, highlighting a protective role of C. hisashii as an environmental probiotic against diarrhoeal dysbiosis through modulation of gut microbial metabolic output. This offers a perspective that bridges environmental microbiology and gut health within a One Health framework. Video Abstract.},
}

Animals
*Probiotics/administration & dosage
*Diarrhea/veterinary/microbiology/therapy
Feces/microbiology
Cattle
*Gastrointestinal Microbiome
Proteomics
Butyrates/metabolism
Bacteriocins/genetics/biosynthesis
Administration, Oral
Genomics
Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid42563207,
year = {2026},
author = {Abdel-Hady, DM and Sabry Zeid, M and Hamdy Mohamed, E and El Sayed Zaki, M and Mohamed Reda El-Lakany, R and Mohamed Reda Mahmoud El-Lakany, N and Ahmed Noureldin, M},
title = {Early-Life Antibiotic Exposure Disrupts Bifidobacterium in Infants: A qPCR-Based Cohort Study.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000005360},
pmid = {42563207},
issn = {1532-0987},
abstract = {BACKGROUND: Early infancy represents a critical window for establishing the gut microbiome, during which Bifidobacterium species dominate and play essential roles in metabolic, immune and intestinal maturation. Antibiotic exposure during this sensitive period may disrupt microbial development, yet quantitative data on its longitudinal impact remain limited. To evaluate the effect of systemic antibiotic exposure during the first 6 months of life on the abundance of Bifidobacterium using quantitative real-time polymerase chain reaction in a prospective infant cohort.

METHODS: Seventy healthy term infants were enrolled at birth and followed at 1, 3 and 6 months. Stool samples were analyzed using quantitative real-time polymerase chain reaction targeting genus-level Bifidobacterium. Infants were categorized into antibiotic-exposed (n = 27) and nonexposed (n = 43). Demographic and clinical variables were compared, and longitudinal and multivariate analyses were used to assess factors associated with Bifidobacterium abundance.

RESULTS: No significant baseline differences were observed between groups. Antibiotic-exposed infants demonstrated significantly lower Bifidobacterium levels at all measured time points (P < 0.001). Nonexposed infants showed the expected rise in Bifidobacterium from 1 to 3 months, whereas exposed infants exhibited a significant decline from 1 to 6 months (P = 0.009). Multivariate regression analysis indicated that clinical factors, such as delivery mode, feeding type, gestational age and maternal intrapartum antibiotics, were not significant predictors of Bifidobacterium levels among exposed infants.

CONCLUSIONS: Antibiotic exposure in the first 6 months leads to persistent suppression of Bifidobacterium, disrupting normal microbiome maturation. These findings underscore the importance of cautious antibiotic use in early infancy and highlight the need for strategies to restore microbial balance following antibiotic therapy.},
}

@article {pmid42563405,
year = {2026},
author = {Adil, M and Gul, I and Lu, S and Bashir, S and Razzaq, S and Lu, H and Daud, M and Iqbal, Y and Tao, Y},
title = {Crop Resilience to Combined Drought and Salinity Stress in Drylands: From Soil Processes to Genomic Solutions.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70804},
pmid = {42563405},
issn = {1365-3040},
support = {41871079//National Natural Science Foundation of China/ ; SKLECRA2023//Chinese Research Academy of Environmental Sciences/ ; //Open Foundation of State Key Laboratory of Environmental Criteria and Risk Assessment/ ; },
abstract = {Drought and soil salinization increasingly co‑occur, threatening global food security, particularly in dryland farming systems where these stresses can interact additively, synergistically or antagonistically to reduce crop yields. This review critically distinguishes these interaction types and moves beyond single‑stress frameworks to provide a multiscale synthesis of plant responses, soil water-salt dynamics, root‑system plasticity, rhizosphere microbiome modulation, emerging breeding modelling and agronomic tools. This review provides a detailed overview of the multilevel damage from these co-occurring stresses, including osmotic shock, ionic toxicity and systemic oxidative damage, and examines plant strategies such as ion homoeostasis, osmotic adjustment and antioxidant responses. Beyond plant-centric views, the review explores epigenetic reprogramming for stress memory and the potential of rhizosphere microbiome engineering with plant growth-promoting rhizobacteria as a biological stress-alleviation strategy. It critically examines how high-throughput multiomics techniques, combined with innovative breeding methods, provide a transformative approach to decode complex tolerance traits and accelerate cultivar development. These techniques cover genomics, epigenomics, transcriptomics, proteomics and metabolomics, while the breeding methods include genomic selection and CRISPR-Cas gene editing. Despite progress, key challenges remain: validating combined stress resilience under field conditions, harnessing epigenetic inheritance and integrating microbial solutions into breeding pipelines. We propose a unified framework that merges mechanistic discovery, microbiome-assisted breeding, soil and water management and systems-level predictive modelling. This integrative approach is essential for developing climate-resilient crops to sustain dryland agriculture.},
}

@article {pmid42563426,
year = {2026},
author = {Rivas, JA and Scieszka, DP and Peralta-Herrera, E and Madera Enriquez, C and Merkley, SD and Nava, AL and Gullapalli, RR and Guo, Y and Castillo, EF},
title = {Colonic metabolomic and transcriptomic alterations in a mouse model of metabolic syndrome.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00121.2026},
pmid = {42563426},
issn = {1522-1547},
support = {IRG-21-146-25//American Cancer Society (ACS)/ ; P30CA118100//Center for Strategic Scientific Initiatives, National Cancer Institute (CSSI)/ ; UL1TR001449//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; P20GM121176//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32 GM144834//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Metabolic syndrome (MetS), characterized by abdominal obesity, insulin resistance, dyslipidemia, and hypertension, affects a substantial proportion of the global population and increases the risk for cardiovascular disease, diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD). Despite its prevalence, there are currently no effective pharmacological therapies targeting MetS, highlighting the need to identify novel etiological mechanisms, particularly within the gastrointestinal (GI) tract. Using a mouse model of MetS and healthy lean controls, we assessed the colonic microenvironment through metabolomic, transcriptomic, and microbiome analyses. Colonic organoids were cultured to further explore epithelial alterations. Additionally, human MetS fecal metabolomics data were cross-compared with the mouse model to validate translational relevance. MetS mice exhibited upregulation of colonic anabolic pathways, including glycolysis, the pentose phosphate pathway, and the tryptophan/kynurenine pathway, without evidence of intestinal inflammation. Microbiome analysis revealed an increased abundance of the genus Lactobacillus in MS NASH mice. Colonic organoids from MetS mice showed altered goblet cell differentiation. Comparative analysis with human MetS fecal metabolomics demonstrated similar dysregulated pathways, underscoring the translational relevance of these findings. Our study reveals significant metabolic and microbial alterations in the colon of MS NASH mice, implicating a dysfunctional GI tract as a potential etiological factor in MetS. These findings highlight specific metabolic pathways and microbial signatures that could serve as future therapeutic targets for MetS.},
}

@article {pmid42563439,
year = {2026},
author = {Frye, RE and Rossignol, DA},
title = {Mechanistic pathways linking gut microbial metabolites, microbial structural products, and host-microbe co-metabolites to mitochondrial function.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694140},
doi = {10.1080/19490976.2026.2694140},
pmid = {42563439},
issn = {1949-0984},
mesh = {*Mitochondria/metabolism/physiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Bacteria/metabolism/classification ; *Host Microbial Interactions ; Butyrates/metabolism ; Organelle Biogenesis ; Propionates/metabolism ; Cresols ; Sulfuric Acid Esters ; },
abstract = {Gut-derived microbial metabolites modulate host mitochondrial function. To our knowledge, no prior systematic review has synthesized evidence linking these metabolites to direct mitochondrial endpoints across all major metabolite classes. PubMed, Scopus, and Web of Science were systematically searched through March 2026 for studies examining direct mitochondrial endpoints in relation to ten classes of gut-derived metabolites. Gut-derived microbial metabolites exert diverse effects on mitochondrial function, ranging from bioenergetic enhancement to direct toxicity. After contextual evidence was excluded from the certainty assessment, four metabolite-mitochondrial outcome groupings had moderate certainty: butyrate, propionate, indoxyl sulfate, and lipopolysaccharide. Evidence for p-cresyl sulfate, H2S, and urolithin A was rated low; evidence for the remaining metabolite classes was low or very low. Butyrate generally enhances mitochondrial biogenesis, ATP generation, and electron transport chain activity across multiple experimental models. Indoxyl sulfate generally impaired mitochondrial function, whereas p-cresyl sulfate produced concentration- and model-dependent effects. PGC-1α emerges as a central regulatory node, integrating microbial metabolic signals to control mitochondrial biogenesis and oxidative metabolism. Many microbial metabolites demonstrate concentration-dependent biphasic effects. These findings support a mechanistic microbiome-mitochondrial framework in which diverse gut-derived molecules converge on a limited set of mitochondrial control nodes: electron transport chain activity, reactive oxygen species handling, biogenesis, and mitophagy. The evidence base is predominantly preclinical; these insights should be considered hypothesis-generating.},
}

*Mitochondria/metabolism/physiology
*Gastrointestinal Microbiome/physiology
Humans
Animals
*Bacteria/metabolism/classification
*Host Microbial Interactions
Butyrates/metabolism
Organelle Biogenesis
Propionates/metabolism
Cresols
Sulfuric Acid Esters

@article {pmid42563483,
year = {2026},
author = {Hedström, AK},
title = {The gut microbiome plays a modifiable role in MS progression?-Commentary.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261471368},
doi = {10.1177/13524585261471368},
pmid = {42563483},
issn = {1477-0970},
}

@article {pmid42563487,
year = {2026},
author = {Afzal, S and Fox, RJ},
title = {The gut microbiome plays a modifiable role in MS progression-No.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261471355},
doi = {10.1177/13524585261471355},
pmid = {42563487},
issn = {1477-0970},
}

@article {pmid42563498,
year = {2026},
author = {Darbar, F and Priyadarshini, M and Wang, Y and Safdary, Z and Mahmoud, AM and DiDomenico, RJ and Rosas, P},
title = {From Gut to Heart: The Emerging Role of Dietary Fermentable Fiber in Heart Failure with Preserved Ejection Fraction.},
journal = {American journal of physiology. Heart and circulatory physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpheart.00177.2026},
pmid = {42563498},
issn = {1522-1539},
support = {K01HL155241//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Heart failure with preserved ejection fraction (HFpEF) is a multisystemic syndrome that accounts for more than half of all heart failure cases and causes a substantial burden of morbidity and mortality. In contrast to heart failure with reduced ejection fraction (HFrEF), few disease-modifying therapies exist for HFpEF, reflecting differences in pathophysiology. Low fermentable fiber (FF) intake, gut dysbiosis, and depletion of short-chain fatty acids (SCFAs), microbial metabolites central to immune, metabolic, and vascular homeostasis, are increasingly linked to the pathophysiology of HFpEF. Here, we synthesize preclinical and clinical evidence on FF and SCFAs and evaluate their therapeutic relevance to HFpEF. Preclinical studies demonstrate that FF supplementation or direct SCFA administration improves cardiometabolic function and attenuates cardiac remodeling through SCFA receptor signaling, enhanced nitric oxide bioavailability, reduced inflammation, and metabolic support of the energy-starved failing heart. Supporting the translational relevance of these findings, a systematic review of 27 human randomized controlled trials showed that FF interventions exert microbiome-mediated effects, enriching SCFA-producing taxa and augmenting fecal and circulating SCFA levels, while improving insulin sensitivity and reducing abdominal adiposity and LDL cholesterol. Direct SCFA supplementation increases SCFA availability and provides modest metabolic benefits, including reduced adiposity and liver fat. However, its effects are inconsistent. Collectively, these findings provide a mechanistic and translational rationale for FF-based interventions in HFpEF. To date, no clinical trials have evaluated the effects of FF on HFpEF-specific outcomes. Clinical studies are therefore needed to determine whether increasing FF intake can improve symptoms, cardiac function, and disease progression in HFpEF.},
}

@article {pmid42563687,
year = {2026},
author = {Liu, C and Wu, Q and Yuan, M and Liu, M and Wang, X and Shen, J and Cao, X},
title = {Multi‑omics insights into uveitis: From mechanisms to precision medicine (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {4},
pages = {},
doi = {10.3892/ijmm.2026.5947},
pmid = {42563687},
issn = {1791-244X},
mesh = {Humans ; Multiomics ; *Uveitis/genetics/metabolism/therapy/diagnosis ; *Precision Medicine/methods ; Biomarkers/metabolism ; Genomics/methods ; Metabolomics/methods ; Proteomics/methods ; Animals ; },
abstract = {Uveitis encompasses a group of intraocular inflammatory disorders that notably contribute to global visual morbidity. Persistent challenges include early diagnosis, accurate subtype classification and individualized treatment. Recent advances in omics technologies, including genomics, epigenetics, transcriptomics, single‑cell omics, proteomics, metabolomics, lipidomics and microbiome profiling, have reshaped the current understanding of uveitis pathogenesis by uncovering disease‑associated genetic variants, dynamic transcriptional landscapes, inflammatory proteins, metabolic alterations, and microbe‑host interactions. Notably, single‑cell RNA sequencing offers unprecedented insights into retinal immune cell heterogeneity and functional states, while radiomics is emerging as a valuable platform for imaging biomarkers. The present review summarizes key findings from multi‑omics studies in uveitis, described the sample sources and analytical strategies employed, and highlighted the transformative potential of integrative omics in precision ophthalmology. Multi‑omics approaches hold promise for identifying novel biomarkers and therapeutic targets, refining disease classification, and enabling tailored interventions for patients with uveitis.},
}

Humans
Multiomics
*Uveitis/genetics/metabolism/therapy/diagnosis
*Precision Medicine/methods
Biomarkers/metabolism
Genomics/methods
Metabolomics/methods
Proteomics/methods
Animals

@article {pmid42564041,
year = {2026},
author = {Jiang, W and Zhang, R and Wang, L and Xu, Y and Tan, Y},
title = {Clinical effects of a 0.5% selenium sulfide shampoo on dandruff and scalp microbiota in adolescents: a prospective single-arm clinical study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1866777},
pmid = {42564041},
issn = {2296-858X},
abstract = {INTRODUCTION: This prospective, exploratory single-arm pilot study evaluated the clinical efficacy, safety, and scalp microecological effects of a 0.5% selenium sulfide shampoo in adolescents with dandruff.

METHODS: Following a 2-week washout, 31 adolescents applied the shampoo three to four times weekly for 4 weeks. Investigator assessments, patient-reported pruritus scores, instrumental assessments (transepidermal water loss, stratum corneum hydration, sebum spot size), and scalp microbiome analysis were performed at baseline (week 0) and at week 4 (or week 2 for some measures).

RESULTS: Investigator assessments showed significant improvements: median dandruff scores declined from 16 to 6, erythema scores from 12 to 2, total scalp oiliness scores from 153 to 127, and total hair lift scores increased from 107 to 122 at week 4. Patient-reported pruritus scores decreased from 109 at baseline to 60, 48, and 37 at weeks 1, 2, and 4, respectively (P<0.001). Instrumental assessments demonstrated reduced transepidermal water loss (35.66 ± 8.18 to 31.12 ± 4.36 g/m[2]·h, P < 0.01), increased stratum corneum hydration (30.49 ± 10.28 to 35.01 ± 9.64 a.u., P < 0.001), and decreased sebum spot size at week 2 (953.65 ± 892.50 to 692.33 ± 456.19 pixels, P < 0.05). Genus-level microbiome profiling revealed significantly elevated Cutibacterium abundance (P < 0.001), alongside reduced levels of Staphylococcus and Malassezia (both P < 0.01). No adverse events were reported.

CONCLUSION: The 0.5% selenium sulfide shampoo significantly improved clinical symptoms of dandruff in adolescents, with favorable safety, barrier-protective effects, promoted beneficial compositional shifts in the scalp microbial community toward a healthier profile.},
}

@article {pmid42564062,
year = {2026},
author = {Huang, WZ and Huang, W and Jin, LZ and Yu, CH and Yu, MJ and Chen, WW and Wu, YH},
title = {Bryophytes in heavy metal-polluted environments: trait-based sensitivity, tolerance mechanisms, biomonitoring applications, and restoration potential.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1891423},
pmid = {42564062},
issn = {1664-462X},
abstract = {Heavy metal contamination remains a persistent environmental challenge due to its non-degradable nature, long residence time, and cumulative ecological impacts. Bryophytes have long been recognized as effective bioindicators because of their high sensitivity and strong metal accumulation capacity. However, current research on bryophyte-metal interactions remains fragmented, with limited integration between mechanistic understanding and ecological application. In this review, we develop a trait-informed, hypothesis-generating framework that links bryophyte characteristics to heavy metal exposure, physiological responses, and ecological functions. We first examine the structural, physicochemical, and ecological attributes that govern metal interception and exposure variability, and then synthesize current evidence for extracellular immobilization, intracellular detoxification, regulatory coordination, redox buffering, and metabolic reprogramming. We further evaluate bryophyte-associated microbiomes while distinguishing functional plausibility from direct causal evidence. On the applied side, we assess bryophytes as biologically interpretable biomonitoring systems and as realistic agents of ecological stabilization and engineered biosorption. Finally, we identify key limitations, including taxonomic bias, inconsistent trait parameterization, limited experimental validation, and challenges in translating laboratory findings to field conditions. This framework currently supports directional and testable expectations rather than universal quantitative prediction, and its predictive capacity will depend on standardized cross-species experiments and field validation.},
}

@article {pmid42564071,
year = {2026},
author = {Ying, H},
title = {Bacterial and gut microbiota-derived extracellular vesicles as emerging sources of cancer biomarkers: molecular mechanisms, diagnostic approaches, and therapeutic applications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1806945},
pmid = {42564071},
issn = {2235-2988},
mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Biomarkers, Tumor/metabolism ; *Neoplasms/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Bacteria/metabolism ; Animals ; },
abstract = {Extracellular vesicles (EVs) originating from bacteria and gut microbiota have recently been recognized as pivotal agents in the communication between host and microbes, exhibiting considerable promise as innovative biomarkers and therapeutic instruments in the realm of oncology. These nanoscale vesicles encapsulate a heterogeneous array of molecular constituents, including metabolites, proteins, nucleic acids, and toxins, which possess the capacity to influence tumor proliferation, apoptosis, immune responses, and metastasis. Recent investigations underscore their bifunctional nature: specific bacterial EVs can facilitate oncogenesis by altering signaling cascades such as BRCA1/EXO1/TP53BP1 or TGF-β1/Smad, while others may suppress tumor growth through the induction of oxidative stress, mitophagy, or the activation of antitumor immunity via STING or cGAS pathways. The metabolomic and molecular characterizations of bacterial and fecal EVs afford a distinctive, non-invasive perspective into tumor biology and the interactions between host and microbiome. Sophisticated diagnostic methodologies, encompassing targeted metabolomics, high-throughput sequencing, and flow cytometry-based characterization of EVs, have enabled the discovery of EV-derived cancer biomarkers with exceptional specificity and sensitivity. Moreover, engineered EVs that transport therapeutic agents, including prodrugs, microRNAs, or photosensitizers, exhibit significant anticancer efficacy in preclinical experimental models. This review consolidates contemporary understanding regarding the molecular mechanisms, diagnostic capabilities, and therapeutic implications of bacterial and gut microbiota-derived EVs in the context of cancer.},
}

Humans
*Extracellular Vesicles/metabolism
*Biomarkers, Tumor/metabolism
*Neoplasms/diagnosis/therapy
*Gastrointestinal Microbiome
*Bacteria/metabolism
Animals

@article {pmid42564172,
year = {2026},
author = {Rojas, L and Zuluaga, J and Cardona, AF},
title = {Microbiome as a prediction of immunotherapy response in lung cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1849553},
pmid = {42564172},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/drug therapy/microbiology/therapy ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology/drug effects ; Treatment Outcome ; Animals ; *Microbiota/immunology ; },
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of lung cancer (LC), offering durable responses in non-small cell lung cancer (NSCLC) and, to a lesser extent, small cell lung cancer (SCLC). Nevertheless, clinical outcomes remain highly heterogeneous, with many patients experiencing primary or acquired resistance and/or immune-related adverse events (irAEs) that impair their quality of life and treatment adherence. The human microbiome, particularly in the gut and oral compartments, has emerged as a critical modulator of systemic antitumor immunity and a promising noninvasive predictive biomarker for ICI efficacy and toxicity. This narrative review synthesizes the current evidence on microbiome composition, diversity, and function in patients with LC receiving ICIs as monotherapy, dual blockade, or in combination regimens, as well as clinically relevant biomarkers associated with treatment response and toxicity. Higher gut microbial alpha diversity and enrichment of beneficial taxa (e.g., Akkermansia muciniphila, Faecalibacterium prausnitzii, and certain Firmicutes) are consistently linked to improved progression-free survival (PFS) and overall survival (OS), mediated by microbial metabolites such as short-chain fatty acids and inosine, which enhance T-cell priming, tumor microenvironment remodeling, and gut-lung axis communication. Microbiome-disruptive exposures, particularly antibiotics and proton pump inhibitors (PPIs), induce dysbiosis and are strongly associated with poorer survival outcomes. Mechanistic insights from preclinical models and clinical cohorts, alongside clinical confounders, underscore the complementary role of the microbiome relative to established markers such as programmed death-ligand 1 (PD-L1) and tumor mutational burden. Prospective standardization of metagenomic profiling and microbiome-modulating interventions represents a key next step in translating these findings into personalized immunotherapy strategies for LC.},
}

Humans
*Lung Neoplasms/immunology/drug therapy/microbiology/therapy
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology/drug effects
Treatment Outcome
Animals
*Microbiota/immunology

@article {pmid42564309,
year = {2026},
author = {Akther, SM and Krakko, D and Shi, W},
title = {Rhizosphere microbiomes in drought-tolerant and drought-sensitive bermudagrass genotypes: root exudate association.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1868900},
pmid = {42564309},
issn = {1664-302X},
abstract = {INTRODUCTION: Plant-microbiome interactions in the rhizosphere are critical for plant adaptation to environmental stress; however, the coordinated roles of root exudates and microbiome dynamics remain poorly understood.

METHODS: Integrating untargeted metabolomics and shotgun metagenomics, we analyzed drought responses in drought-tolerant and drought-sensitive bermudagrass genotypes.

RESULTS: Drought stress shaped the root exudate chemistry, which likely reprogrammed microbiome functions, such as TccC toxins and the Type VI secretion system, without considerable broad taxonomic shifts. A few metabolites, including riboflavin and 1-carboxy-6-hydroxy-3,4-dihydro-beta-carboline, were associated with Massilia putida, particularly in the rhizosphere of the drought-tolerant genotype.

DISCUSSION: Our data suggest a potential explanation for a genotype-driven strategy of microbiome modulation via metabolite signaling.},
}

@article {pmid42564344,
year = {2026},
author = {Ruan, Z and Sheng, F and Lin, M and Wu, S and Hu, C and Shao, Z and Hu, H and Xu, L},
title = {Gut microbiota in asthma: mechanisms, clinical evidence, and therapeutic opportunities.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1842331},
pmid = {42564344},
issn = {2235-2988},
mesh = {Humans ; *Asthma/therapy/microbiology/immunology ; Animals ; *Gastrointestinal Microbiome ; Dysbiosis ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Disease Models, Animal ; Lung/immunology ; Prebiotics/administration & dosage ; },
abstract = {Asthma is a heterogeneous chronic airway inflammatory disease associated with high global prevalence and substantial clinical burden. Conventional therapies remain limited in controlling refractory phenotypes and preventing disease progression. The gut-lung axis has emerged as a fundamental regulatory network connecting intestinal homeostasis with pulmonary immune function, and mounting evidence has established a close mechanistic link between gut dysbiosis and the onset, persistence, and exacerbation of asthma. This review comprehensively integrates evidence from epidemiological investigations, animal models, clinical observational studies, and randomized controlled trials published between 2011 and 2025 to elucidate the crosstalk mechanisms of the gut-lung axis in asthma, characterize compositional and functional alterations of the gut microbiome, evaluate microbiota-targeted interventions such as probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplantation, and discuss current translational challenges. We highlight that the gut microbiota orchestrates airway inflammatory responses through fine-tuning immune cell differentiation, mediating microbial metabolite signaling, and maintaining intestinal barrier function, with discernible microbial signatures evident across allergic versus non-allergic and pediatric versus adult asthma phenotypes. Despite promising preclinical and preliminary clinical findings, causal evidence remains insufficient, and intervention heterogeneity limits clinical application. This review underscores the potential of microbiome-based precision strategies and identifies key directions for future mechanistic research and clinical translation.},
}

Humans
*Asthma/therapy/microbiology/immunology
Animals
*Gastrointestinal Microbiome
Dysbiosis
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Disease Models, Animal
Lung/immunology
Prebiotics/administration & dosage

@article {pmid42564438,
year = {2026},
author = {Diovu, EO and Nnadi, CO and Paul-Chima, UO},
title = {Pharmaceutical wastewater irrigation and metabolite-based environmental pharmacognosy: a perspective on quality and safety risks for medicinal plants.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1878168},
pmid = {42564438},
issn = {1663-9812},
abstract = {Medicinal plants are increasingly cultivated in agroecosystems irrigated with treated or untreated wastewater, biosolids and contaminated surface water. Pharmaceutical residues are recognised contaminants of emerging concern, but their implications for botanical-drug quality, therapeutic consistency and safety remain insufficiently characterised. This Perspective argues that pharmaceutical wastewater irrigation is a plausible yet underexamined driver of metabolite reprogramming in medicinal plants. Chronic exposure to antibiotics, non-steroidal anti-inflammatory drugs, antiepileptics, antidepressants, hormones and transformation products may alter secondary metabolism through oxidative stress, xenobiotic detoxification, rhizosphere microbiome disturbance and modified nutrient signalling. These processes may change phenolic, flavonoid, alkaloid, terpenoid, glycoside and volatile metabolites that underpin pharmacognostic quality and ethnopharmacological reliability. Medicinal plants may also accumulate parent pharmaceuticals, transformation products and, under some conditions, microbial signatures associated with antibiotic resistance. Building on Carter et al.'s source-pathway-receptor framework and Helmecke et al.'s regulatory risk synthesis, we shift attention from residue burden to how exposure history alters the medicinal metabolome. Evidence from antibiotic-induced metabolite changes in Pinellia ternata supports this proposition, while indicating compound- and context-specific effects. We advance a balanced position: metabolite reprogramming is biologically credible, but food-crop studies often report de minimis residue risks and inconsistent rhizosphere-resistome effects. Future work should integrate wastewater profiling, matched controls, targeted and untargeted metabolomics, transformation-product discovery, microbiome analysis, digestion and bioaccessibility testing, bioactivity assays and probabilistic mixture-risk assessment.},
}

@article {pmid42564505,
year = {2026},
author = {Goyal, A and Kaur, J and Chauhan, S},
title = {Faecal carriage of multidrug-resistant Enterobacterales in hospitalisaed and outpatient children in northern India: A cross-sectional study.},
journal = {African journal of laboratory medicine},
volume = {15},
number = {1},
pages = {3027},
pmid = {42564505},
issn = {2225-2002},
abstract = {BACKGROUND: Asymptomatic intestinal carriage of multidrug-resistant (MDR) Enterobacterales in children is increasingly recognised as an important reservoir for transmission and subsequent infection. However, data from northern India remain limited, warranting evaluation of its burden and associated risk factors.

OBJECTIVE: To determine the prevalence of MDR Enterobacterales carriage among children and to identify associated risk factors, including recent hospitalisation, antimicrobial exposure, and hygiene practices.

METHODS: This cross-sectional study was conducted at a tertiary care hospital in northern India from January to June 2025. Children aged ≤ 14 years were enrolled after obtaining informed consent from parents or legal guardians. A total of 340 stool samples were processed using standard microbiological methods. Bacterial identification was performed using conventional biochemical tests, and antimicrobial susceptibility testing was carried out according to Clinical and Laboratory Standards Institute guidelines, 2025 edition. Multidrug-resistant was defined as resistance to at least one agent in three or more antimicrobial classes. Demographic and clinical data were analysed using SPSS version 25.0; p < 0.05 was considered statistically significant.

RESULTS: Among 340 enrolled children, Enterobacterales were isolated from 309 (90.9%). Multidrug-resistant Enterobacterales were identified in 87 children, yielding a prevalence of 28.2% among Enterobacterales-positive children and 25.6% overall. Escherichia coli (66.7%) and Klebsiella spp. (33.3%) were the predominant MDR organisms. Extended-spectrum β-lactamase production was detected in 18.1% of isolates. Multidrug-resistant carriage was significantly higher among inpatients (p < 0.001).

CONCLUSION: Asymptomatic carriage of MDR Enterobacterales is common, particularly among hospitalised children, highlighting the importance of strengthened antimicrobial stewardship and infection prevention strategies in paediatric care.

WHAT THIS STUDY ADDS: This study demonstrates a high prevalence of asymptomatic multidrug-resistant Enterobacterales carriage among children in northern India, particularly among hospitalised children, highlighting the need for ongoing surveillance, infection prevention and antimicrobial stewardship.},
}

@article {pmid42564592,
year = {2026},
author = {Alexiev, A and Beaver, LM and Bouranis, JA and Wong, CP and Stevens, JF and Sharpton, TJ and Ho, E},
title = {The Gut Microbiome and Diet Interact to Dictate Personalized Response to Broccoli Sprout Consumption.},
journal = {Food science & nutrition},
volume = {14},
number = {8},
pages = {e72211},
pmid = {42564592},
issn = {2048-7177},
abstract = {Broccoli sprouts produce sulforaphane (SFN), a dietary isothiocyanate with anti-cancer and anti-inflammatory properties. Human intervention trials observe large variation in metabolite generation and bioactivity with broccoli sprout consumption across individuals. We hypothesize that interactions between pre-intervention diet and personalized gut microbiome composition contribute to this variation. This exploratory analysis leverages a small existing dataset to test novel mediation pathways, with the goal of identifying associations for future validation in larger, prospectively designed studies. In a trial of 38 healthy adults, we analyzed participant-recorded 7-day food diaries, profiled baseline gut microbiome compositions, and quantified urinary SFN metabolites over 72 h after broccoli sprout consumption. Using regression-based mediation analysis, we modeled two complementary predictions: (1) that specific gut bacterial genera mediate how pre-intervention diet composition influences SFN metabolism, and (2) that particular dietary components mediate how gut microbiome composition influences SFN metabolism. These analyses found that seven genera, including Collinsella, Ruminococcus, and Bifidobacterium, mediated relationships between pre-intervention diet and SFN metabolites, particularly the bioactive forms. Unsupervised clustering further revealed three distinct baseline gut microbiome community "types," each exhibiting differential production of SFN-nitrile, a biologically inert metabolite, with effects mediated by the consumption of specific carbohydrate classes. Together, these findings indicate that microbiome structure, in concert with diet, shapes individual SFN metabolic outcomes. Considering pre-intervention diet and gut microbiome may therefore enhance the design and personalization of cruciferous vegetable interventions.},
}

@article {pmid42565114,
year = {2026},
author = {Russell, AL and Olthoff, B and Zhang, C and Lutz, C and Franklin, CL and Ericsson, AC},
title = {Gut microbiota and pathobiont exposure influences disease incidence in non-obese diabetic mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844128},
pmid = {42565114},
issn = {1664-302X},
abstract = {While the non-obese diabetic (NOD) mouse is the most widely used animal model of type 1 diabetes (T1D), it suffers from poor reproducibility in disease incidence often attributed to variables in the environment, including the gut microbiota (GM). Prior research suggests a protective effect of segmented filamentous bacteria (SFB) on disease incidence, but it is unclear whether other pathobiont organisms or resident GM affect disease incidence. The objectives of the current study were to determine the effect of supplier-origin GMs and three different microbial challenges (SFB, Helicobacter hepaticus, and Mouse Hepatitis Virus [MHV]) on early-stage insulitis and lifelong disease incidence in NOD mice. The fecal microbiome was assessed pre- and post-disease onset to identify shifts in composition and predicted function of the GM. Results show that all three microbes influence T1D incidence and insulitis severity. Overall, SFB, MHV, and a high-richness microbiome were associated with lower disease incidence, while H. hepaticus and a low-richness microbiome were associated with higher disease incidence. H. hepaticus, but not SFB or MHV, was associated with significant changes in beta-diversity of the GM. While immune outcomes were not included, these findings provide guidance on microbes affecting disease incidence in NOD mice and evidence that such microbes may contribute to poor reproducibility in NOD mice or other mouse models.},
}

@article {pmid42565182,
year = {2026},
author = {Shen, Y and Choi, E and Kleinberg, S},
title = {Quantifying the Contributions of Food, Glucose, Sleep, and Microbiome Data to Personalized Glycemic Response Prediction.},
journal = {Current developments in nutrition},
volume = {10},
number = {8},
pages = {109429},
pmid = {42565182},
issn = {2475-2991},
abstract = {BACKGROUND: Individual glycemic responses to foods vary and can be predicted using microbiome, activity, and dietary data. However, these data are expensive and invasive to collect, and it is not known how much each modality contributes to accuracy.

OBJECTIVES: We aim to quantify the contributions of dietary, sleep, continuous glucose monitor (CGM), and microbiome features for glycemic response prediction; understand how much personal data are required for training; and evaluate how microbiome sample timing impacts model accuracy.

METHODS: We used data from 8334 participants in the Human Phenotype Project cohort study who provided demographic, anthropometric, dietary, and CGM data. Participants self-reported meals in a dietary tracking application for a mean of 10.78 d, during which they wore CGMs. We trained CatBoost models to predict postprandial glycemic response (PPGR) using 2-h incremental area under the curve and peak 2-h postprandial glucose rise (Glumax). We conducted ablation studies with varied feature combinations to assess the contribution of each data modality. We used 3 train/test splits (split-by-meal, 5-d personal training, and split-by-person) to assess the impact of personal training data. Lastly, we evaluated accuracy as a function of microbiome sample timing (from before meal logs to ≤60 d after).

RESULTS: The model combining all features performed best, and CGM was the most informative feature. Models trained with more personal data had the best performance (PPGR split-by-meal R = 0.731; split-by-person R = 0.590), and personal training data had a larger effect on accuracy than microbiome. Microbiome features improved predictions most when collected within 7 d of meal logs and did not improve performance without personal training data or for samples collected >14 d after meal logs.

CONCLUSIONS: Although CGM was the most important feature group, combining it with personal training data and timely microbiome samples led to the most accurate models in our analysis. These findings can help researchers understand the tradeoffs between the time and effort of data collection and how data types impact model performance.},
}

@article {pmid42565253,
year = {2026},
author = {Li, Y and Wu, Q and Zhang, X and Liu, L and Ding, L and Xu, J and Cheng, C and Peng, Y and Yu, K and Yao, W and Pi, Y and Li, J and Wu, D and Wei, J and Yu, Y and Chen, T},
title = {Conjunctival Sac-Derived Lactobacillus mucosae MM-1 Metabolite Indole-3-Lactic Acid Attenuates Lens-Induced Myopia in Mice via AHR Activation and TGF-β/Smad Inhibition.},
journal = {Microbial biotechnology},
volume = {19},
number = {8},
pages = {e70426},
doi = {10.1111/1751-7915.70426},
pmid = {42565253},
issn = {1751-7915},
support = {YC2024-B072//Graduate Innovation Special Fund of Jiangxi Province/ ; },
mesh = {Animals ; *Lactobacillus/metabolism/isolation & purification ; *Receptors, Aryl Hydrocarbon/metabolism ; Mice ; *Transforming Growth Factor beta/metabolism/antagonists & inhibitors ; *Myopia/metabolism/drug therapy ; *Smad Proteins/metabolism/antagonists & inhibitors ; *Conjunctiva/microbiology ; Humans ; *Probiotics/administration & dosage ; Signal Transduction/drug effects ; Male ; Disease Models, Animal ; *Indoles/metabolism ; Microbiota ; Collagen Type I/metabolism ; },
abstract = {Emerging research has revealed a diverse microbiota in the high myopia (HM) conjunctival sac, highlighting the therapeutic potential of modulating this community to influence disease outcomes. However, current research on targeted modulation of this microbiota for myopia intervention lacks in-depth investigation and definitive conclusions regarding its efficacy and underlying mechanisms. In this study, high-throughput sequencing and culturomics were first used to screen the conjunctival sac microbiota of healthy people, identifying Lactobacillus mucosae MM-1 as a potential probiotic for myopia control. Then, animal studies further confirmed that L. mucosae MM-1 significantly attenuated lens-induced myopia, improved COL1A1 expression and scleral integrity and elevated Lactobacillus abundance. Furthermore, untargeted metabolomics analysis suggested that indole-3-lactic acid (ILA) may be a key substance for L. mucosae MM-1 to exert its effects for myopia control. Mechanistically, pharmacological ILA supplementation supports the involvement of AHR in TGF-β/Smad pathway inhibition, accompanied by altered COL1A1 and α-SMA expression and attenuation of lens-induced myopia in mice. Therefore, these findings suggest that L. mucosae MM-1 may attenuate lens-induced myopia in mice, at least in part, through ILA-mediated regulation of the TGF-β/Smad pathway, and offer a theoretical foundation for future therapeutic strategies based on conjunctival sac microbiome manipulation.},
}

Animals
*Lactobacillus/metabolism/isolation & purification
*Receptors, Aryl Hydrocarbon/metabolism
Mice
*Transforming Growth Factor beta/metabolism/antagonists & inhibitors
*Myopia/metabolism/drug therapy
*Smad Proteins/metabolism/antagonists & inhibitors
*Conjunctiva/microbiology
Humans
*Probiotics/administration & dosage
Signal Transduction/drug effects
Male
Disease Models, Animal
*Indoles/metabolism
Microbiota
Collagen Type I/metabolism

@article {pmid42565380,
year = {2026},
author = {Yang, S and Guo, C and Zhang, J and Ma, M and Tian, J and Zhang, Y},
title = {The efficacy of microbiome transplantation in treating vaginosis and its impact on vaginosis recurrence: a meta-analysis of randomized controlled trials.},
journal = {Ginekologia polska},
volume = {},
number = {},
pages = {},
doi = {10.5603/gpl.106234},
pmid = {42565380},
issn = {2543-6767},
abstract = {OBJECTIVES: Bacterial vaginosis (BV) is a recurrent condition with significant health implications. Microbiome transplantation has emerged as a potential treatment strategy. This meta-analysis assesses its efficacy in treating vaginosis and preventing recurrence.

METHODS: A systematic review and meta-analysis of randomized controlled trials (RCTs) evaluating microbiome transplantation for vaginosis treatment were conducted. Pooled risk ratios (RRs) with 95% confidence intervals (CIs) were calculated for short- and long-term efficacy. Sensitivity and publication bias analyses were performed.

RESULTS: In the short-term follow-up, microbiome transplantation significantly reduced vaginosis recurrence (pooled RR = 0.628, 95% CI: 0.543-0.726, p < 0.001). However, heterogeneity was moderate (I² = 60.8%). Sensitivity analyses confirmed the robustness of findings. Long-term follow-up results showed a pooled RR of 0.746 (95% CI: 0.670-0.831, p < 0.001), though with higher heterogeneity (I² = 72.8%). After sensitivity adjustments, meta-analysis yielded a pooled RR of 0.865 (95% CI: 0.735-1.019, p = 0.083), suggesting reduced long-term efficacy. No significant publication bias was detected.

CONCLUSIONS: Microbiome transplantation effectively reduces short-term vaginosis recurrence. However, long-term efficacy diminishes upon sensitivity adjustment, necessitating further investigation.},
}

@article {pmid42565831,
year = {2026},
author = {Baker, JL and Tang, J and Guo, M and Farias-da-Silva, FF and Barbisan, M and Burnside, M and Crofton, K and Williams, S and Rao, S and Lee, M and Drucker, SG and Kim, D and Higashi, D and Merritt, J and Hirose, Y and Veening, J-W and Nizet, V},
title = {Monounsaturated fatty acid biosynthesis is critical for streptococcal envelope homeostasis and stress tolerance.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0002626},
doi = {10.1128/jb.00026-26},
pmid = {42565831},
issn = {1098-5530},
abstract = {The genus Streptococcus contains some of the most important commensals and pathogens of the human microbiome. To obtain the fatty acids required for cell membranes, Streptococcus either produce fatty acids de novo through the fatty acid biosynthesis (fab) pathway or uptake host fatty acids through the fatty acid kinase (fak) pathway. Although both the fab and fak pathways represent potential therapeutic targets to prevent or treat infection, progress is limited because of an incomplete understanding of taxon-to-taxon variability in streptococcal lipid metabolism. Here, we examined the role of de novo monounsaturated fatty acid (MUFA) synthesis in physiology and virulence-associated traits in Streptococcus mutans, Streptococcus pyogenes, and Streptococcus pneumoniae, three major pathogens that cause disease at distinct body sites. In all three species, deletion of fabM abolished MUFA production and caused severe growth defects, decreased stress tolerance, increased antibiotic susceptibility, and defects in cell viability, morphology, and division. In S. mutans, loss of fabM also markedly reduced competence signaling and production of the mutacin IV bacteriocin. Deletion of fabM increased susceptibility to killing by human neutrophils in S. mutans and S. pneumoniae, but not S. pyogenes. Together, these findings illustrate that MUFA synthesis is broadly important for streptococcal physiology and cell membrane homeostasis, while its contribution to pathogenesis is strongly species- and context-dependent, providing leads to guide the development of novel therapeutic and/or preventative strategies.IMPORTANCEStreptococcus spp. exert profound effects on human health, with several species causing significant morbidity and mortality. Although streptococcal fatty acid biosynthesis and utilization are attractive metabolic targets for development of therapeutics, this opportunity is vexed by an incomplete understanding of taxon-to-taxon variability in lipid metabolism. In this study, the role of de novo monounsaturated fatty acid (MUFA) synthesis in physiology and virulence-associated traits was examined in Streptococcus mutans, Streptococcus pyogenes, and Streptococcus pneumoniae, three major pathogens that cause disease at distinct body sites. MUFA synthesis was important for stress and antibiotic tolerance across all three species, while its impact on virulence was species- and context-dependent. Overall, these discoveries provide leads to guide the development of novel therapeutic and/or preventative strategies.},
}

@article {pmid42565868,
year = {2026},
author = {Abuelhaded, K and Mohamed, HH and Alam-ElDein, KM},
title = {Bacteria-nanoplastic interactions: mechanisms, ecological consequences, and advances in biodegradation technologies.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42565868},
issn = {1432-072X},
mesh = {Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; *Environmental Pollutants/metabolism ; *Microplastics/metabolism/chemistry ; Microbiota ; Gene Transfer, Horizontal ; Humans ; },
abstract = {Nanoplastics (< 1 μm) represent a pervasive class of environmental contaminants with unique physicochemical properties that profoundly influence microbial ecosystems. Their high surface-area-to-volume ratio, weathering-induced functionalization, and ability to adsorb chemical pollutants and biomolecules facilitate intricate interactions with bacterial communities. This review systematically examines nanoplastic-bacteria interactions, highlighting mechanisms such as oxidative stress induction, membrane perturbation, DNA damage, metabolic reprogramming, biofilm modulation, and enhanced horizontal gene transfer, which collectively reshape microbial structure and function. Emphasis is placed on the plastisphere microbiome as a dynamic hotspot for pollutant accumulation, pathogen enrichment, and resistance gene exchange. Bacterial biodegradation pathways, including enzymatic hydrolysis, oxidative processes, biosurfactant-mediated interactions, and multispecies consortia activity, are analyzed in detail. Advanced analytical tools, such as nanoscale imaging, spectroscopy, flow cytometry, meta-omics, and AI-assisted computational modeling, are discussed for their role in elucidating nanoplastic-microbe dynamics. Environmental and human health implications, including microbiome disruption, immunotoxicity, and ecological perturbations, are evaluated. Finally, emerging biotechnological strategies for enhancing biodegradation are explored, and critical research gaps are identified. This review provides a comprehensive framework for understanding nanoplastic-bacteria interactions, offering strategic insights for environmental monitoring, risk assessment, and bioremediation development.},
}

Biodegradation, Environmental
*Bacteria/metabolism/genetics
*Environmental Pollutants/metabolism
*Microplastics/metabolism/chemistry
Microbiota
Gene Transfer, Horizontal
Humans

@article {pmid42565884,
year = {2026},
author = {Chen, C and Song, W and Ai, C and Zhao, J},
title = {Optimization and application of probiotics complex for grouper based on dynamic model.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42565884},
issn = {1573-0972},
support = {3502Z20226031//Xiamen Science and Technology Program of China/ ; XMUPTI2024004//Xiamen University Pingtan Institute/ ; },
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; Bacillus/growth & development ; Vibrio ; *Bass/microbiology/growth & development ; Aquaculture/methods ; Bacillus subtilis/growth & development ; Bacillus megaterium/growth & development ; Animal Feed/microbiology/analysis ; Gastrointestinal Microbiome ; Fish Diseases/prevention & control/microbiology ; },
abstract = {This study applied systematic microecological method to develop multi-strain probiotics for grouper aquaculture, focusing on rational strain selection and interaction optimization. Five strains from marine source were initially screened through functional and safety assessments. Based on single-strain growth kinetics and pairwise interaction data, the generalized Lotka-Volterra model and multiple linear regression were employed to identify an optimal consortium consisting of Bacillus subtilis, Bacillus megaterium, and Bacillus velezensis (1: 1: 1), which exhibited significantly antagonism against Vibrio harveyi (p < 0.05) and higher digestive enzyme activities among thirty predefined combinations. In vitro tests using intestinal communities from the purebred grouper Epinephelus coioides (Ec) and the hybrid grouper E. fuscoguttatus ♀ × E. lanceolatus ♂ (Elf) revealed host-specific microbiome characteristics. The consortium exerted stronger effects in Elf than single-strain treatments. Supplementation of probiotic complex enhanced network stability, enriched beneficial genera (e.g., Bacillus), and suppressed opportunistic pathogens (e.g., Vibrio). Finally, in a 42-day feeding trial in juvenile Elf grouper, both single bacteria (B. velezensis at 10[7] CFU/g feed) and the multi-strain consortium (total 10[7] CFU/g feed) improved growth performance and disease resistance compared to the control. The consortium further increased weight-specific growth rate by 23.41% (p < 0.05), feed intake by 25.92% (p < 0.05), and survival rate after pathogenic challenge by 40.0% (p < 0.05). Both treatments reshaped gut microbiome correlation networks, reducing the dominance of Vibrio and Photobacterium while increasing the centrality of beneficial Cetobacterium in the consortium group. This work validated the effectiveness of the gLV model for screening and designing probiotic consortia, providing a promising solution for precision aquaculture of grouper.},
}

Animals
*Probiotics/administration & dosage/pharmacology
Bacillus/growth & development
Vibrio
*Bass/microbiology/growth & development
Aquaculture/methods
Bacillus subtilis/growth & development
Bacillus megaterium/growth & development
Animal Feed/microbiology/analysis
Gastrointestinal Microbiome
Fish Diseases/prevention & control/microbiology

@article {pmid42565949,
year = {2026},
author = {Temu, SG and Myovela, HH and Hussein, JM},
title = {Lichen biomonitoring revisited: a multi-level framework incorporating symbiotic response and microbiome dynamics as early-warning indicators.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42565949},
issn = {1614-7499},
abstract = {Lichens are among the most widely used biological indicators of environmental quality because they integrate atmospheric pollutants and respond sensitively to environmental change. However, recent advances in lichen biology have expanded biomonitoring beyond traditional measures of pollutant accumulation, physiological injury, and community composition, creating the need for an updated synthesis. This review integrates current evidence on the biological basis, response mechanisms, environmental applications, and emerging frontiers of lichen biomonitoring. Classical approaches have been successfully applied to monitor air pollution, heavy metals, nitrogen deposition, and other environmental stressors, while recent studies demonstrate that symbiotic interactions and lichen-associated microbiomes provide additional, potentially earlier indicators of ecosystem disturbance. Building on this evidence, we propose a multi-level framework integrating six complementary biological domains: pollutant accumulation, physiological responses, community dynamics, functional traits, symbiotic interactions, and microbiome dynamics. This framework links established and emerging response pathways into a unified biomonitoring concept while acknowledging remaining challenges, including environmental variability, species-specific responses, methodological standardization, and geographic bias. Integrating conventional and emerging biological endpoints provides a more comprehensive and mechanistic foundation for lichen biomonitoring in a rapidly changing environment.},
}

@article {pmid42566093,
year = {2026},
author = {Chaudhary, R and Bansal, N and Kaur, A and Gupta, S and Chopra, K and Bansal, S},
title = {Co-supplementation of fructooligosaccharide with soy isoflavone restores the gut-brain axis dysfunction via modulation of gut microbiome in estrogen-deprived rat model.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42566093},
issn = {1573-4978},
support = {ANRF/ECRG/2024/001702/LS//Anusandhan National Research Foundation (ANRF), Prime Minister Early Career Research Grant (PMECRG) Program/ ; },
mesh = {Animals ; *Oligosaccharides/pharmacology/metabolism ; Female ; *Isoflavones/pharmacology ; Rats ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Estrogens/deficiency/metabolism ; *Brain-Gut Axis/drug effects ; Glycine max/chemistry ; Disease Models, Animal ; Oxidative Stress/drug effects ; Ovariectomy ; Brain/drug effects/metabolism ; Hippocampus/drug effects/metabolism ; Apoptosis/drug effects ; Dietary Supplements ; },
abstract = {BACKGROUND: The gut-brain axis (GBA) plays a critical role in regulating neurocognitive and gastrointestinal functions through integrated neuronal, immune, endocrine, and microbial pathways. Estrogen deficiency causes gut dysbiosis and associated GBA dysfunction. Strategies that may modulate GBA dysfunction in the postmenopausal phase need to be explored. Our present research aimed to examine the synergistic effect of soy isoflavone (SIF) and fructooligosaccharide (FOS) in combination on GBA dysfunction in an estrogen-deprived rat model.

METHODS: To induce similar postmenopausal complications, female SD rats were bilaterally ovariectomized (OVX) and were orally administered a combination of FOS (50 mg/kg) & SIF (40 mg/kg) and 17β-estradiol (10 μg/kg) for 28 days. At the end, the uterus, hippocampus, & proximal colon health was measured.

RESULTS: Co-supplementation of FOS with SIF in estrogen-deprived rats synergistically improves body weight, neurobehavior, brain-derived neurotrophic factor levels, and monoamine neurotransmission. We also observed marked restoration of oxidative stress, inflammation, and apoptosis in the hippocampus and colon. With this, we also observed restoration of gut health as indicated by increased mucosal layer integrity, promoting tight junction (TJ) genes, and rebalancing the gut microbiome (GM). The combination approach also selectively activates ER-β expression in the hippocampus without affecting serum estradiol levels & uterine weight. Collectively, the combination approach acts as a selective estrogen receptor modulator and improves GBA functioning.

CONCLUSION: Thus, the combination approach may attenuate GBA dysfunction in estrogen-deprived rats by selectively activating the ER-β receptor and modulating oxidative stress, inflammation, and apoptosis while preserving the mucosal layer, TJ genes, and GM.},
}

Animals
*Oligosaccharides/pharmacology/metabolism
Female
*Isoflavones/pharmacology
Rats
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Estrogens/deficiency/metabolism
*Brain-Gut Axis/drug effects
Glycine max/chemistry
Disease Models, Animal
Oxidative Stress/drug effects
Ovariectomy
Brain/drug effects/metabolism
Hippocampus/drug effects/metabolism
Apoptosis/drug effects
Dietary Supplements

@article {pmid42566148,
year = {2026},
author = {Walczuk, U},
title = {Context Dependent Effects of Probiotics: A Systems Perspective on the Interpretation of Experimental Findings.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42566148},
issn = {1867-1314},
abstract = {Current definitions of probiotics emphasize their beneficial effects on the host but do not fully capture the complexity of their interactions within the host. Most experimental models remain reductionist, focusing on individual probiotic strains rather than the biological systems in which they operate. However, the effects of probiotics emerge within a dynamic context shaped by the resident microbiota, host metabolism, and immune responses. From this perspective, the present article discusses selected examples illustrating how commonly used experimental models may influence the interpretation of the mechanisms underlying observed probiotic effects. These examples include DSS induced colitis models, specific pathogen free (SPF) animal models, experimental design based on single endpoint measurements, assessment of microbial colonization, and probiotic dosing defined by colony forming units (CFU). The examples presented suggest that probiotic effects should be interpreted as properties emerging from the entire biological system, resulting from interactions among the host, the resident microbiota, and experimental conditions, rather than as direct effects of individual probiotic strains. This systems-oriented perspective may support more accurate interpretation of experimental findings and contribute to the further refinement of experimental models used in probiotic research.},
}

@article {pmid42566149,
year = {2026},
author = {Nomiri, S and Yazdani, F and Heidary, H and Sadeghi, A and Tarzemani, S and Sadeghloo, Z and Saeedi Niasar, M and Tillotson, G and Safarpour, H and Raeisi, H},
title = {Live Biotherapeutic Products (LBPs) as Promising Microbiome-Based Medicines for Colorectal Cancer (CRC): Mechanistic Basis, Therapeutic Applications, and Translational Challenges.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42566149},
issn = {1867-1314},
abstract = {Colorectal cancer (CRC) is the third most prevalent and second deadliest cancer worldwide. The gut microbiota profoundly influences this cancer by modulating immune responses and therapeutic efficacy. Recently, live biotherapeutic products (LBPs), comprising live resident microorganisms in the gut, have emerged as promising agents to reprogram host immunity and enhance treatment efficacy in preclinical CRC models. However, translation of these findings to clinical practice remains limited due to heterogeneous study designs, poorly defined mechanisms in human hosts, unresolved manufacturing and safety concerns, and lack of personalized treatment strategies. This review briefly introduces LBPs as a new class of medicines, categorize them as single strains, composite strains, and engineered strains, and details their multifaceted mechanisms against CRC, including direct immunomodulation to enhance anti-tumor activity, production of protective metabolites like short-chain fatty acids (SCFAs), and restoring gut microbiota. Additionally, the synergistic potential of LBPs with conventional chemo- and immunotherapies and current LBPs in clinical trials for CRC are summarized, highlighting their translational progress. We further address the manufacturing, regulatory, and safety barriers constraining clinical adoption and propose strategies for integrating preclinical and clinical evidence to meet patient needs. By consolidating current knowledge of LBPs as an emerging oncology drug class, this review offers a practical framework for advancing LBPs from preclinical promise to clinical practice, supporting the development of personalized medicine.},
}

@article {pmid42566244,
year = {2026},
author = {Garcia-Perez, E and Perrin, L and Malone, JG and Thompson, CMA and Guiziou, S},
title = {Engineering rhizobacterial communities for soil and plant health.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
doi = {10.1099/mic.0.001748},
pmid = {42566244},
issn = {1465-2080},
mesh = {*Soil Microbiology ; Rhizosphere ; *Plants/microbiology ; Synthetic Biology ; *Microbial Consortia ; Bacteria/genetics/metabolism ; Genetic Engineering ; *Microbiota ; },
abstract = {Rhizobacteria play a central role in supporting plant growth, contributing to nutrient acquisition, stress tolerance and disease suppression. Harnessing and improving rhizosphere microbial communities therefore represents a promising avenue towards more sustainable agriculture. Recent advances in microbiome ecology and synthetic biology have enabled the rational design of microbial consortia. Synthetic communities are widely used as tractable models to study ecological interactions and are increasingly explored as biofertilizers and biocontrol agents. Here, we define engineered microbial communities (EngComs) as microbial consortia augmented with strains carrying synthetic genetic circuits. These systems extend SynCom approaches by enabling programmable functions, such as intercellular communication, division of labour, biosensing and controlled nutrient mobilization, ultimately improving functional stability in complex environments. Beyond bacteria-bacteria interactions, we highlight emerging strategies to engineer plant-microbe interfaces through synthetic signalling pathways and multi-input genetic circuits that enable context-dependent responses. Despite this progress, the engineering of rhizobacteria for real soil environments remains at an early stage. Most systems are still characterized in simplified or artificial conditions, and key challenges persist, including environmental complexity, genetic stability, biocontainment and regulatory constraints. Addressing these limitations will be essential to translate engineered functions from laboratory settings to the field. Overall, continued integration of synthetic biology with ecological and biophysical understanding of the rhizosphere will pave the way for programmable plant-microbe systems, offering new opportunities to enhance crop productivity while reducing environmental impact.},
}

*Soil Microbiology
Rhizosphere
*Plants/microbiology
Synthetic Biology
*Microbial Consortia
Bacteria/genetics/metabolism
Genetic Engineering
*Microbiota

@article {pmid42566284,
year = {2026},
author = {Oláh, ÁA and Dudás-Györki, Z and Dunay, IR and Dunay, MP},
title = {Alterations in the feline oral microbiome in common oral diseases - A comprehensive review.},
journal = {European journal of microbiology & immunology},
volume = {},
number = {},
pages = {},
doi = {10.1556/1886.2026.00040},
pmid = {42566284},
issn = {2062-509X},
abstract = {The most prevalent diagnostic conditions in domestic cats (Felis catus) are oral diseases, affecting up to 90% of older cats. Periodontal disease (PD), feline chronic gingivostomatitis (FCGS), and tooth resorption (TR) are the principal clinically relevant entities, each with distinct histopathological and microbiological features. Certain molecular techniques, including 16S rRNA sequencing, shotgun metagenomics, and metatranscriptomics, have substantially advanced our understanding of the feline oral microbiome alterations. This review summarizes the findings of the healthy oral microbiome and its disease-associated shifts in PD, FCGS, TR, and feline immunodeficiency virus (FIV)-associated pathology. The healthy oral cavity is dominated by Proteobacteria, Bacteroidota, Bacillota, Fusobacteria, and Actinobacteria, notably Porphyromonas, Moraxella, Capnocytophaga, and Fusobacterium. Dental disease is characterised by expansion of Bacteroidota and Spirochaetota, enrichment of Treponema, Peptostreptococcus, Filifactor, and Fusobacterium nucleatum, and depletion of commensals. The contributions of fungi, viruses, and host immunity are critically evaluated, alongside the development of microbiome-based diagnostics and therapeutics. We argue that dysbiosis is a unifying (albeit not monocausal) feature of feline oral pathology and identify gaps in current knowledge that require further investigation.},
}

@article {pmid42566286,
year = {2026},
author = {Dhiman, NK and Ahmad, SR},
title = {From Dysbiosis to systemic health: Microbiome modulation as a unified therapeutic framework.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.03015},
pmid = {42566286},
issn = {1588-2640},
abstract = {The gut microbiome is a dynamic microbial ecosystem regulating gastrointestinal, metabolic, immune, and neurobehavioral physiology. Dysbiosis has been linked to irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and systemic disorders including metabolic syndrome, autoimmune conditions, and neurodegenerative diseases. This narrative review synthesizes mechanistic, clinical, and translational evidence to delineate molecular pathways of microbiome-targeted interventions, evaluates clinical outcomes in IBS and IBD, and proposes a unified framework linking gastrointestinal modulation to systemic health. A structured literature search across PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar (2012-2024) identified approximately 68 eligible sources, appraised using Cochrane Risk of Bias 2.0 and AMSTAR-2. Five principal molecular pathways were identified: competitive pathogen exclusion, epithelial barrier reinforcement, immune modulation, short-chain fatty acid (SCFA) production, and neurotransmitter signaling. Clinically, dietary strategies, biological agents (probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplantation [FMT]), advanced modalities (rifaximin, psychobiotics, bacteriophage therapy), and lifestyle interventions collectively engage these pathways. The same mechanisms underpin emerging applications in metabolic, autoimmune, neurological, and cardiovascular disease. We propose a three-tier model progressing from molecular mechanisms through gastrointestinal outcomes to systemic benefits, with precision medicine and standardized trial designs as prerequisites for therapeutic translation.},
}

@article {pmid42566294,
year = {2026},
author = {Tanveer, M and Ud Din Khan, W and Fotopoulos, V and Shabala, S and Wang, L and White, JC},
title = {Nanoscale Strategies for Improving Plant Salinity Tolerance.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01761},
pmid = {42566294},
issn = {1520-5118},
support = {NA//Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences/ ; },
abstract = {Soil salinity poses a major threat to global food security, impairing plant physiology through ionic toxicity, osmotic stress, and oxidative damage. However, conventional breeding and genetic engineering approaches face limitations due to the complexity of stress responses and regulatory hurdles. Nanotechnology, through the unique properties of nanomaterials (NMs), offers a promising alternative. This review synthesizes recent advances in nanoscale strategies for early salt stress sensing, the regulation of ion homeostasis, and reactive oxygen species scavenging. It further examines how NMs enhance nutrient use efficiency under saline conditions and discusses emerging applications in microbiome engineering and nontransgenic genetic improvements. The integration of machine learning to optimize NM design and application is also discussed. By synthesizing insights across these disciplines, this review provides a holistic framework for developing next-generation, nanotechnology-driven solutions to mitigate salinity stress, bridging the fundamental research with field-scale application for sustainable agriculture.},
}

@article {pmid42566596,
year = {2026},
author = {Cao, X and Guo, H and Wang, K and Wu, Q and Wang, X and Shao, J},
title = {The gut-immune-brain axis in CNS tumors: Causal roles of microbiota and inflammatory proteins unveiled by Mendelian randomization and single-cell transcriptomics.},
journal = {Medicine},
volume = {105},
number = {32},
pages = {e50109},
doi = {10.1097/MD.0000000000050109},
pmid = {42566596},
issn = {1536-5964},
support = {2020THRC-DJ-SNW//Wuxi Taihu Lake Talent Plan - Supports for Leading Talents in Medical and Health Profession/ ; ZD2022038//Key Project of the Jiangsu Provincial Health Commission/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/immunology/genetics ; *Central Nervous System Neoplasms/genetics/immunology/microbiology ; Genome-Wide Association Study ; Single-Cell Analysis ; Transcriptome ; *Brain ; Single-Cell Gene Expression Analysis ; Cytokines/genetics ; Inflammation ; },
abstract = {There is a growing number of research suggesting that there is an association between gut microbiota and central nervous system (CNS) tumor. However, the causal relationships and the mediation effects of inflammatory proteins in the associations are unclear. We extracted genetic variants associated with gut microbiota, inflammatory proteins, and 4 subtypes of CNS tumors from published genome-wide association studies and performed a Mendelian randomization analysis to identify potential causal effects. The inverse variance weighted method was used as the main method. Mediation analysis and single-cell RNA-seq analysis were performed to explore the mediation effects and the expression in cells. This study identified 73 gut microbial taxa and 11 inflammatory proteins that were significantly associated with CNS tumors. The inflammatory proteins may act as intermediate mediators in the potential causal association between gut microbiota and 4 CNS tumor subtypes. Mediation analysis suggested that CX3CL1 may partially mediate the relationship between gut microbiota and Glioblastoma, while Eotaxin, CSF-1, IL-15RA and the other 5 cytokines may serve as subtype-specific potential mediators for the remaining 3 tumor types. Our research supports a hypothesized "gut-immune-brain" axis that may mediate the effects of gut microbiota on different CNS tumor subtypes, with distinct immune proteins implicated for each. These findings strongly suggest potential targets for microbiome therapy and immune therapy, though the underlying mechanistic links require experimental validation.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/immunology/genetics
*Central Nervous System Neoplasms/genetics/immunology/microbiology
Genome-Wide Association Study
Single-Cell Analysis
Transcriptome
*Brain
Single-Cell Gene Expression Analysis
Cytokines/genetics
Inflammation

@article {pmid42566682,
year = {2026},
author = {Kiecolt-Glaser, JK},
title = {Four Decades of Stress, Depression, and Close Relationships: Lessons from Psychoneuroimmunology.},
journal = {Annual review of psychology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-psych-020226-033326},
pmid = {42566682},
issn = {1545-2085},
abstract = {Human psychoneuroimmunology research has demonstrated that stress, depression, and close relationships reliably shape immune and endocrine function in ways that matter for health. Across studies of examination stress, laboratory stressors, marital discord, cancer survivorship, and dementia caregiving, psychosocial adversity predicts more infections, weaker vaccine responses and faster erosion of vaccine protection, slower wound healing, heightened inflammation, and accelerated cellular aging. Depression also sensitizes immune function, producing larger inflammatory responses when individuals encounter stressors. Loneliness, low support, and distressed relationships can amplify stress reactivity and are linked to greater inflammatory and metabolic vulnerability, including postprandial inflammatory and endothelial responses. More recent work has extended these pathways to the gut microbiome and intestinal permeability (leaky gut), integrating microbial, neuroendocrine, and immune mechanisms. Collectively, the evidence supports a biobehavioral model in which social stress accelerates immune aging and increases risk for inflammation-related disease, while behavioral and nutritional interventions can modify these trajectories.},
}

@article {pmid42567032,
year = {2026},
author = {Wu, G and Li, AX and Gu, YW and Cheng, XL and Mao, RC and Wang, XJ and He, MY and Chai, QQ and Li, FN and Liu, HY and Zhang, WX and Zheng, XY and Wu, Z and Wu, X and Liu, JY},
title = {Biomimetic delivery systems for overcoming drug resistance in gastrointestinal cancers.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {89},
number = {},
pages = {101465},
doi = {10.1016/j.drup.2026.101465},
pmid = {42567032},
issn = {1532-2084},
abstract = {Gastrointestinal (GI) cancers remain a major cause of cancer-related mortality worldwide, and multidrug resistance (MDR) is a critical barrier to durable therapeutic response. In GI malignancies, MDR arises from multilayered and interdependent factors, including insufficient intracellular drug accumulation, altered drug activation and metabolic detoxification, target rewiring and phenotypic plasticity, apoptosis-autophagy-mediated stress adaptation, and extrinsic protection from the tumor microenvironment, cancer stem cells, metastatic niches, and microbiome-associated mechanisms. Biomimetic delivery systems (BDSs), including cell membrane-coated nanocarriers, extracellular vesicles, and living or virus-mediated platforms, provide biological interface functions that may improve drug circulation, tumor recognition, tissue penetration, membrane interaction, and active trafficking. However, their therapeutic value in MDR GI cancers should not be judged merely by improved delivery efficiency, but by whether they address defined resistance bottlenecks and generate evidence of genuine re-sensitization in resistant disease contexts. Current evidence indicates that many BDSs remain at the level of exposure enhancement or mechanism-aligned sensitization, whereas only a limited subset has demonstrated functional restoration of treatment response in established resistant models. This review organizes current BDS strategies according to their dominant mechanistic functions: enhancing drug accumulation and intratumoral delivery, reversing cellular drug resistance, remodeling resistance-supportive tumor microenvironment, targeting cancer stem cells (CSCs) and metastatic niches, and enabling site-directed intervention using living carriers and living therapeutics. By linking GI cancer-focused MDR biology to function-oriented biomimetic design, this review establishes an evidence-based framework for distinguishing delivery enhancement from true MDR reversal and outlines platform-specific requirements for clinical translation.},
}

@article {pmid42555106,
year = {2026},
author = {Luo, Z and Liu, Y and Wu, H and Xiao, Y and Li, Y and Liu, M and Li, C and Zhu, D and Jin, LN and Dong, T and Yan, W},
title = {Zoo gut plastispheres enable pathogen escape and adaptation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag207},
pmid = {42555106},
issn = {1751-7370},
abstract = {In zoos, intensive human contact and artificial feeding may create pathways for microplastic (MP) ingestion and gut colonization. We hypothesized that ingested MPs form intestinal plastispheres with elevated pathogenic potential and enhanced environmental persistence. To test this, we surveyed feces from 15 zoo-dwelling species and coupled particle characterization, feces-derived intestinal simulations, metagenomic sequencing, and a subsequent water-exposure experiment. Zoo feces contained more abundant MPs than reported for wild counterparts, with fragments predominating and polyethylene terephthalate (PET)/polystyrene (PS) dominating polymer profiles. MP burdens tracked human-animal interaction patterns, with human-fed species (e.g., Tiger, Elephant) carrying the highest loads (88-212 items/g). MPs supported dense biofilms whose composition diverged from bulk gut communities, exhibiting greater compositional variability and substrate-specific assembly. Metagenomic analyses revealed coordinated enrichment of potentially pathogenic taxa, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs), with ARG profiles dominated by efflux- and inactivation-related mechanisms and tightly associated with mobile genetic elements. Elevated Type II/III/IV/VI secretion systems and effector delivery-related VFGs occurred within extracellular polymeric substance-rich biofilms, suggesting enhanced potential for ARG retention and horizontal gene transfer. During the 35-day aquatic exposure, MP-associated communities persisted longer than non-plastic particle-associated communities and free gut microbiota, suggesting that plastic-specific properties promote microbial persistence. PET/PS plastispheres showed the slowest declines in bacterial activity and favored the persistence of Enterococcus, Enterobacter, and Clostridium. Overall, intestinal MPs in zoo animals may select, enrich, and export high-risk microbiomes, highlighting the need for MP mitigation and evidence-based management of zoos and adjacent ecosystems.},
}

@article {pmid42555112,
year = {2026},
author = {Timotej, TD and Ion, GA and Tinkara, R and Tinkara, T},
title = {Viral lysis accelerates microbial succession patterns resembling diatom senescence.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag206},
pmid = {42555112},
issn = {1751-7370},
abstract = {Diatom blooms influence carbon cycling through organic matter production and its deposition or remineralization - processes mediated by the microbial community. Viruses can influence diatom bloom dynamics and even terminate blooms, yet interactions between diatoms, their viruses, and associated bacteria remain poorly resolved. Here, we examined how infection of the toxigenic diatom Pseudo-nitzschia galaxiae by its ssRNA virus PnGalRNAV reshapes host physiology, microbiome structure, and organic-matter processing in non-axenic batch cultures. Using epi-fluorescence microscopy, 16S rRNA amplicon sequencing, and metatranscriptomics, we linked microbial composition, localisation, and functional activity during viral lysis. Infection rapidly collapsed diatom growth and induced a senescence-like host state, with broad repression of photosynthesis, silicon metabolism, and core biosynthetic pathways, alongside induction of heat-shock and other stress-related genes. Concurrently, phycosphere-associated bacteria declined, detritosphere-associated bacteria increased, and community composition shifted from Marinobacter (Gammaproteobacteria) dominated, towards Flavobacteriaceae (Bacteroidetes) dominated, especially by Polaribacter. In non-infected controls Alphaproteobacteria proved to benefit from the stable healthy phycospheres with a distinct DOM pool. Bacterial metatranscriptomes showed significant upregulation of polysaccharide-degradation-associated genes in infected cultures, indicating active utilisation of lysis-derived diatom glycans. Similar compositional and metabolic profiles in infected cultures and later-stage senescent controls suggest infection accelerated senescence-associated microbial processes. Overall, viral lysis converted a productive diatom culture into a detrital, DOM-rich environment that selects for specialised polysaccharide degraders, redirects carbon through the viral shunt and may accelerate nutrient recycling in coastal systems. Extending this approach to natural microbial communities and diverse diatom-virus systems will help determine whether these mechanisms are broadly conserved.},
}

@article {pmid42555374,
year = {2026},
author = {Palagiano, C and Potestio, L and Brescia, C and Napolitano, M},
title = {Pharmacotherapeutic strategies for the treatment of severe juvenile acne.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14656566.2026.2715706},
pmid = {42555374},
issn = {1744-7666},
abstract = {INTRODUCTION: Severe juvenile acne vulgaris represents a highly prevalent chronic inflammatory disorder that may significantly impair quality of life and lead to permanent scarring during adolescence. Increasing understanding of acne pathophysiology has progressively modified therapeutic approaches, with growing emphasis on early intervention, antimicrobial stewardship, and individualized systemic treatment strategies.

AREAS COVERED: This narrative review summarizes current evidence regarding pharmacotherapeutic strategies for severe juvenile acne, with particular focus on systemic therapies. A literature search was conducted in PubMed, Embase, Google Scholar, Cochrane Library, and ClinicalTrials.gov from database inception to March 2026. The pathogenic mechanisms underlying juvenile acne, including sebaceous hyperactivity, follicular hyperkeratinization, Cutibacterium acnes, dysbiosis, immune-inflammatory activation, and hormonal influences, are discussed.

EXPERT OPINION: Severe juvenile acne should not be underestimated as a physiologic condition of adolescence, as delayed or inadequate treatment may result in substantial physical and psychological sequelae. Oral isotretinoin remains the gold-standard therapy for severe nodulocystic, scarring, or treatment-resistant acne. Timely specialist assessment is essential in high-risk adolescents to avoid unnecessary delay when the licensed criteria for isotretinoin treatment are fulfilled; however, its use must remain consistent with applicable product information, regulatory requirements, and risk-minimization measures. Simultaneously, prolonged systemic antibiotic exposure should be minimized through stewardship-oriented approaches integrating benzoyl peroxide combinations and shorter treatment durations. Future therapeutic strategies will likely move toward increasingly individualized, microbiome-conscious, and inflammation-targeted approaches aimed not only at lesion clearance but also at prevention of long-term scarring and psychosocial burden.},
}

@article {pmid42555388,
year = {2026},
author = {Sun, W and Xiao, M and Ali, SL and Jin, C and Khan, A and Shakirullah, and Ni, R and An, Y and Zhang, M and Tian, Y and Kaushik, S and Zhang, Y and Gong, W},
title = {Harnessing the gut microbiome to combat tuberculosis: a technological and clinical review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1847443},
pmid = {42555388},
issn = {2235-2988},
mesh = {Humans ; *Tuberculosis/therapy/diagnosis/microbiology/prevention & control ; *Gastrointestinal Microbiome ; Artificial Intelligence ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Biomarkers ; Multiomics ; },
abstract = {Tuberculosis (TB), especially multidrug-resistant and extensively drug-resistant strains, remains a severe global health threat. Advances in high-throughput sequencing, omics technologies and artificial intelligence have revealed the critical involvement of the gut microbiome (GM) in TB pathogenesis, diagnosis and treatment via the gut-lung axis. The GM modulates host immunity and metabolism; TB patients typically show reduced microbial diversity and enriched pro-inflammatory taxa closely linked to disease severity and treatment responses. Omics research has identified promising biomarkers and pathways for early diagnosis and personalized management, while artificial intelligence improves diagnostic accuracy and treatment outcome prediction. GM-targeted interventions, including probiotics, dietary adjustment and fecal microbiota transplantation, can enhance therapeutic efficacy and relieve adverse drug reactions. Current limitations include insufficient validation of the gut-lung axis' causal mechanisms, lagged clinical translation of biomarkers, biases and errors in diagnosis and prediction, data privacy and security concerns, gaps in intervention research, and poor accessibility of related technologies in resource-scarce medical regions. Future studies need rigorous causal analyses, real-time monitoring tools and large-scale multicenter trials to validate microbiome-based strategies. This review highlights the translational potential of GM interventions to optimize personalized TB prevention, diagnosis and treatment and improve clinical outcomes.},
}

Humans
*Tuberculosis/therapy/diagnosis/microbiology/prevention & control
*Gastrointestinal Microbiome
Artificial Intelligence
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Biomarkers
Multiomics

@article {pmid42555404,
year = {2026},
author = {Hosen, MA and Rahman, T and Rahatuzzaman, and Kabir, RB and Ahsan, CR and Rahman, M and Yasmin, M and Jubair, M},
title = {Uncovering the Hidden Diversity and Antimicrobial Resistance of Uropathogens in a Tertiary-Care Hospital in Bangladesh.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {8327078},
pmid = {42555404},
issn = {1687-918X},
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections worldwide; however, their diagnosis in low- and middle-income countries often relies on conventional culture and biochemical methods with limited sensitivity. This study evaluated the limitations of routine diagnostic approaches and explored the microbial diversity and antimicrobial resistance (AMR) profiles of uropathogens in a tertiary-care hospital in Bangladesh using integrated culture-based and molecular methods. Among 30 patient urine samples collected in 2025, 10 were selected for detailed analysis due to funding and resource limitations; therefore, the findings should be interpreted as exploratory and may be subject to selection bias. Of these 10 samples, routine hospital diagnostics identified only eight isolates, whereas extended biochemical analysis detected 29 isolates, indicating substantial underestimation of microbial diversity in standard practice. Antibiotic susceptibility testing revealed a high prevalence of multidrug resistance, with 83% and 80% of isolates resistant to ampicillin and clindamycin, respectively. In contrast, nitrofurantoin and fosfomycin retained effectiveness against most isolates, supporting their continued clinical utility. 16S rRNA gene sequencing further revealed complex and heterogeneous microbial communities, with several samples dominated by Escherichia-Shigella, whereas others exhibited polymicrobial profiles including commensal and opportunistic genera. Despite taxonomic variability, microbial diversity did not differ significantly between inpatient and outpatient groups. Functional pathway prediction demonstrated a largely conserved metabolic profile across samples, including pathways associated with virulence, iron acquisition, and AMR. Overall, this study demonstrates that conventional diagnostic methods substantially underestimate uropathogen diversity and may contribute to misdiagnosis and inappropriate antibiotic use. Integrating molecular approaches into routine clinical workflows could improve pathogen detection, enhance AMR surveillance, and support more effective management of UTIs in Bangladesh and similar resource-limited settings.},
}

@article {pmid42555417,
year = {2026},
author = {Kamaljeet, and Vijukumar, A and Shahi, A and Kumar, A and Bhatia, R},
title = {AUTO-brewery syndrome and the human microbiome: Insights into endogenous ethanol production and human diseases.},
journal = {Food science and biotechnology},
volume = {35},
number = {9},
pages = {2415-2436},
pmid = {42555417},
issn = {2092-6456},
abstract = {Auto-Brewery Syndrome (ABS) is a metabolic condition where microbiota dysbiosis undergoes ethanolic fermentation within the gastrointestinal tract. Because the microbial ethanolic fermentation of dietary carbohydrates occurs entirely within the host's gastrointestinal tract, resulting ethanol is referred as "endogenous" while the gut dysbiosis in ABS can rise from multiple fungal or bacterial species. The pathophysiology of ABS is frequently linked to shifts in gut microbiota composition often arising from antibiotics use, high carbohydrate diets, or an underlying immunological or metabolic condition. In this review, the mechanisms behind microbial endogenous ethanol production, the connection between gut, liver, brain, and microbial ethanol-producing routes are examined. Treatments for ABS have been evaluated including antifungals, low-carbohydrate diets, probiotics, and faecal-microbiota transplantation. Lastly, the social, legal, and mental impacts of ABS have been discussed. It would be wise for future studies to develop customized microbiome approaches for detection and treatment guided by omics and AI technologies.},
}

@article {pmid42555451,
year = {2026},
author = {Singh, G and Lavika, and Nandini, and Abhay, and Deepika, and Thakur, N and Kaura, R and Kaur, S and Saini, HS and Khulape, S and Puniya, AK and Dhillon, HS},
title = {Rumen mycobiome dynamics and dairy productivity: functional contributions of fungi to milk yield in bovine ruminants.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1878257},
pmid = {42555451},
issn = {2673-6128},
abstract = {The rumen microbiome is a key factor influencing feed efficiency and milk production in ruminants. However, most studies have focused on the bacterial and archaeal components, with the fungal fraction of the rumen being relatively understudied. The unique ability of anaerobic rumen fungi of the phylum Neocallimastigomycota to colonize and degrade lignocellulosic biomass in the rumen through mechanical disruption of plant cell walls has now made them well known as important functional members of the rumen ecosystem. These fungi are armed with a plethora of carbohydrate-active enzymes degrading fiber and increase the availability of substrates for microbial fermentation. This leads to increased production of volatile fatty acids, especially acetate, which is a major precursor for milk fat production. Recent research evidence has indicated that rumen fungal communities are associated with feed efficiency, fermentation dynamics, and milk composition traits such as fat and protein content in bovine ruminants such as cattle and buffalo. However, most of the studies available are correlative, and the direct causal relationships between fungal activity and milk productivity are poorly delineated. High-throughput sequencing and multi-omics approaches have broadened our knowledge of fungal diversity and function; however, there are still limitations in reference databases and methodological biases. This review summarizes the current knowledge of the diversity, ecological roles, and functional contributions of anaerobic rumen fungi, with special reference to their association with milk production. It also highlights significant methodological and conceptual gaps and proposes future avenues for the integration of fungal ecology into microbiome-based approaches to improve dairy productivity. We need a holistic multi-kingdom view of the rumen microbiome to design efficient and sustainable dairy production systems.},
}

@article {pmid42555752,
year = {2026},
author = {Rachid, R and Martinez-Blanco, M and Kuziel, GA and Stephen-Victor, E and Groussin, M and Orakov, A and Russell, G and Nguyen, LTT and Poyet, M and Mukhatayev, Z and Yee, CSK and Albuhairi, S and Kteish, R and Rahman, EA and Farraj, FA and Wang, Z and Dahlberg, S and Ryan, M and Fitzgerald, M and Elverson, W and Lee, JJ and Schneider, L and MacGinnitie, A and Crestani, E and Queheillalt, D and Burke-Roberts, E and Watson, J and Elliott, RJ and Wong, WF and Osman, M and Voyksner, R and Hohmann, E and Huttenhower, C and Alm, E and Rakoff-Nahoum, S and Chatila, TA},
title = {Fecal microbiome transplant in food allergy in humans and mice identifies a role for bile acid metabolites in oral tolerance.},
journal = {Science translational medicine},
volume = {18},
number = {861},
pages = {eaee3263},
doi = {10.1126/scitranslmed.aee3263},
pmid = {42555752},
issn = {1946-6242},
mesh = {Animals ; Humans ; *Bile Acids and Salts/metabolism ; *Food Hypersensitivity/immunology/therapy/microbiology ; *Fecal Microbiota Transplantation ; Mice ; Adult ; T-Lymphocytes, Regulatory/immunology ; Administration, Oral ; Female ; *Immune Tolerance ; Male ; },
abstract = {The gut microbiome has been implicated in the pathogenesis of food allergy (FA), prompting microbiome-focused interventions. We evaluated, in a phase 1 open-label trial (NCT02960074), the safety and efficacy of oral encapsulated fecal microbiome transplantation (FMT) in 15 adults with peanut allergies. An increase in the peanut reactivity threshold was noted in 3 of 10 participants not pretreated with antibiotics and 3 of 5 participants pretreated with antibiotics, without safety issues. In responders, FMT increased tolerogenic RORγt[+] regulatory T cells (Treg cells) and decreased T helper 2 cells (TH2 cells). Mice transplanted with the microbiomes of post-FMT responders were protected from FA in association with increased RORγt[+] Treg cell percentages and increased colonization with members of the gut Bacteroides. In both humans and mice, protection by FMT was associated with increased bile acid metabolites. Deletion of a bile salt hydrolase in a candidate protective Bacteroides abrogated FA suppression in mice. These results suggest that FMT is a safe and potentially promising therapeutic modality for treating FA.},
}

Animals
Humans
*Bile Acids and Salts/metabolism
*Food Hypersensitivity/immunology/therapy/microbiology
*Fecal Microbiota Transplantation
Mice
Adult
T-Lymphocytes, Regulatory/immunology
Administration, Oral
Female
*Immune Tolerance
Male

@article {pmid42556070,
year = {2026},
author = {Wespiser, M and Rochefort, P and Gauduchon, T and Coste, C and Caux, C and Ray-Coquard, I and Perol, M and Blay, JY and Heudel, PE},
title = {Pharmacological prevention of second primary cancers: From chemoprevention to precision cancer interception.},
journal = {Cancer treatment reviews},
volume = {149},
number = {},
pages = {103200},
doi = {10.1016/j.ctrv.2026.103200},
pmid = {42556070},
issn = {1532-1967},
abstract = {BACKGROUND: The growing population of cancer survivors is increasingly exposed to the long-term risk of second primary cancers (SPCs), which represents a major source of morbidity and mortality. While current prevention mainly relies on surveillance and screening, pharmacological and immunological strategies may offer opportunities to reduce SPC incidence in selected high-risk populations.

METHODS: This narrative review synthesises current evidence on pharmacological prevention strategies for SPCs, including endocrine therapy, aspirin and non-steroidal anti-inflammatory drugs, PARP inhibitors, metformin, GLP-1 receptor agonists, statins, nicotinamide, immune checkpoint inhibitors, cancer vaccines, and microbiome modulation. Evidence from randomised trials, observational studies, translational research, and ongoing clinical trials was reviewed, with particular attention to SPC-specific endpoints, biological rationale, safety, and clinical applicability.

RESULTS: The strongest evidence currently supports endocrine therapy for reducing contralateral breast cancer in patients with hormone receptor-positive breast cancer, and aspirin in selected populations such as Lynch syndrome carriers or patients with molecularly defined colorectal cancer. Other repurposed agents, including metformin, statins, GLP-1 receptor agonists, and nicotinamide, remain investigational, with most available data addressing incident cancer, recurrence, or surrogate endpoints rather than SPC prevention specifically. Immunological approaches are emerging as particularly promising strategies. Retrospective studies and exploratory analyses of randomised trials suggest that immune checkpoint inhibitors may reduce the occurrence of new malignancies, while neoantigen-based vaccines, especially in Lynch syndrome, provide an early proof of concept for cancer immunoprevention.

CONCLUSIONS: Pharmacological prevention of SPCs is an expanding but remains a heterogeneous field. Current evidence supports a shift from broad chemoprevention toward biologically informed, risk-adapted prevention strategies. Future progress will depend on dedicated SPC-focused trials, biomarker-driven patient selection, long-term safety evaluation, and integration of pharmacological prevention into broader cancer interception programmes.},
}

@article {pmid42556158,
year = {2026},
author = {Sharmin, A and Zalbegi, S and Bhatia, M and Siddiquee, M and Thomas, AB and Yun, TS and Bishop, WM and Kang, DW and Seo, Y},
title = {Integrated management of cyanobacterial harmful algal blooms: Coupling algaecide treatment with bioaugmentation of toxin degraders.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {142970},
doi = {10.1016/j.jhazmat.2026.142970},
pmid = {42556158},
issn = {1873-3336},
abstract = {Cyanobacterial harmful algal blooms (CHABs) are a growing global concern, threatening drinking water safety and complicating water treatment through cyanotoxin release, operational disruptions and increased costs. Although chemical algaecides are widely applied for rapid bloom suppression, they frequently induce cyanobacterial lysis, releasing intracellular toxins that further challenge treatment and increase risks for smaller utilities lacking advanced infrastructure. Bioaugmentation with toxin-degrading bacteria has emerged as a complementary and sustainable strategy, however, the effects of algaecides on bioaugmented bacteria remain poorly understood. This study evaluated an integrated strategy combining algaecide application with bioaugmentation for simultaneous CHAB and cyanotoxin control. Two copper-based (SeClear® and Algimycin® PWF) and two hydrogen peroxide-based (PAK®27 and Oximycin®P5) algaecides were tested in combination with a microcystin (MC)-degrading bacterium, Sphingopyxis sp. IM1 under laboratory and mesocosm conditions. Among the four algaecides and tested concentrations, PAK®27 exhibited the highest compatibility with IM1, with substantial toxin removal observed only under low-dose conditions and after sufficient oxidant decay when IM1 was introduced 24 h post-treatment. Laboratory experiments showed that medium-dose PAK®27 followed by IM1 bioaugmentation reduced chlorophyll-a by 76.7% and dissolved MC-LR by 96.6%. In lake mesocosms, maximum-dose PAK®27 with IM1 achieved 77.6% chl-a reduction and 96% cyanobacterial suppression, lowering MC concentrations below 1 µg/L within 3 days. Microbiome profiling confirmed cyanobacterial collapse accompanied by the proliferation of green algae, diatoms, and heterotrophs, with IM1 abundance negatively correlated with toxin concentrations. These findings demonstrate that hydrogen peroxide-based algaecides combined with targeted bacterial bioaugmentation can provide an effective strategy for rapid toxin mitigation and microbial community recovery in CHAB-impacted waters.},
}

@article {pmid42556226,
year = {2026},
author = {Zhang, H and Shen, J and Bai, G and Ma, Y and Chu, R and Zhang, N and Zhang, G and Zuo, L and Li, L},
title = {Niche-driven microbial assembly across the soil-root continuum of Casuarina equisetifolia under a heavy metal pollution gradient.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120615},
doi = {10.1016/j.ecoenv.2026.120615},
pmid = {42556226},
issn = {1090-2414},
abstract = {Heavy metal pollution (HMP) threatens soil ecosystems and plant health. This study integrated 16S rRNA sequencing, network analysis, environmental mapping, and bacterial isolation to investigate how distinct ecological niches of Casuarina equisetifolia modulate microbial communities under metal stress. Results revealed a spatial pollution gradient, with Pb[2+], Zn[2+], and Cd[2+] decreasing with distance from the mine, while As[5+], Cr[3] [+], and Ni[2+] remained near background levels but displayed significant niche-dependent enrichment, especially for Cr[3] [+], and Ni[2+] in rhizosphere soil under medium and high pollution. Niche was the primary driver of microbial divergence, with only 0.56% of OTUs shared between the soil and root compartments. Rhizosphere soils harbored more unique OTUs and higher α-diversity than non-rhizosphere soils. Root endosphere and rhizosphere soil communities were consistently dominated by Actinobacteria across all pollution levels, whereas non-rhizosphere soil communities shifted from Proteobacteria (low pollution) to Actinobacteria (medium) and Chloroflexi (high). LEfSe identified niche-specific biomarkers from the phylum to genus levels, with high-pollution roots harboring the most diverse indicators. Heavy metals and soil properties (pH, CEC, and SOM) collectively shaped community assembly, with distinct drivers per niche: CEC and Enterobacter in non-rhizosphere soil, pH and Acidobacteriales in rhizosphere soil, and Zn as the central hub in the root endosphere network. Isolation yielded 63 metal-tolerant strains across eight genera, predominantly Bacillus cereus sensu lato group, whose niche origin shifted from the rhizosphere (low pollution) to the non-rhizosphere (medium) to the roots (high pollution), suggesting pollution-associated enrichment. These findings reveal niche-specific community assembly and pollution-driven enrichment of metal-tolerant Bacillus cereus s.l. in the root endosphere.},
}

@article {pmid42556260,
year = {2026},
author = {Dhilipkannah, P and Jiang, F},
title = {Coordinated microbial-inflammatory associations in never-smoking lung cancer.},
journal = {Lung cancer (Amsterdam, Netherlands)},
volume = {219},
number = {},
pages = {109561},
doi = {10.1016/j.lungcan.2026.109561},
pmid = {42556260},
issn = {1872-8332},
abstract = {BACKGROUND: While smoking is the leading cause of lung cancer, the increasing incidence among never-smokers is a growing concern, highlighting non-tobacco-related mechanisms of carcinogenesis. Emerging evidence suggests that respiratory microbial dysbiosis and associated inflammatory responses may contribute to lung tumorigenesis. We previously showed that elevated abundances of Selenomonas, Streptococcus, and Veillonella are correlated with lung cancer independent of smoking history. Here, we examine whether circulating microbial and inflammatory profiles are linked to lung cancer in never-smokers.

METHODS: Circulating bacterial DNA representing the three genera was quantified by droplet digital PCR, and seven systemic inflammatory cytokines were measured by ELISA in plasma of 56 ever-smoker lung cancer patients, 56 never-smoker lung cancer patients, and 78 healthy controls. Integrative statistical modeling was performed to evaluate relationships among bacterial DNA burden, inflammatory activation, smoking history, and cancer status.

RESULTS: Plasma DNA levels of Selenomonas, Streptococcus, and Veillonella, together with IL-6, TNF-α, IL-1β, IL-8, and IL-17A, were elevated in lung cancer patients compared with controls (all p < 0.05). No significant differences were observed between smoking and never-smoking lung cancer patients for bacterial DNA levels, IL-6, TNF-α, or IL-17A (all > 0.05), whereas modest but statistically significant differences were observed for IL-8 (P = 0.036) and IL-1β (P = 0.048). Bacterial DNA burden was correlated with systemic inflammatory cytokine activation independent of smoking history (all p < 0.05).

CONCLUSIONS: A smoking-independent microbial-inflammatory signature is associated with lung cancer and provides a foundation for future studies evaluating its biological significance and clinical utility for diagnosis and management.},
}

@article {pmid42556262,
year = {2026},
author = {Dai, W and Yang, F and Chen, W and Liu, C and Henawy, AR and Liu, X and Huang, F and Cai, M and Zheng, L and Yu, Z and Gong, Y and van Huis, A and Zhang, J and Cheng, W},
title = {Paenibacillus polymyxa drives root fatty acyl metabolites-rhizosphere Pseudomonas abundance interaction to suppress root-knot nematode disease in tomato.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128662},
doi = {10.1016/j.micres.2026.128662},
pmid = {42556262},
issn = {1618-0623},
abstract = {Root-knot nematodes (RKNs) pose a severe threat to global agricultural production, highlighting the urgent need for effective biocontrol agents. However, the mechanisms by which biocontrol agents suppress RKNs in complex soil environments remain poorly understood, which hinders the development and practical application of these agents. In the present study, the application of Paenibacillus polymyxa KM2501-1 significantly reduced RKN disease, with a control efficacy of 69.89%. Metabolomics analysis revealed that the biocontrol agent P. polymyxa altered the composition of tomato root exudates, leading to the identification of a key fatty acyl metabolite 8-methylnon-6-enoic acid. Specifically, P. polymyxa increased the abundance of 8-methylnon-6-enoic acid, which exhibited repellent activity against RKNs in vitro and suppressed RKN infection in situ. Metagenomic analysis further demonstrated that P. polymyxa reshaped the tomato rhizosphere microbial community and promoted the enrichment of Pseudomonas putida, particularly its representative strains PR035 and PR036. Both strains exhibited significant biocontrol efficacy against Meloidogyne incognita. A significant positive correlation was observed between the levels of key metabolite 8-methylnon-6-enoic acid and the abundance of P. putida, and their combined application exhibited effective control against M. incognita. Overall, this study demonstrates that the suppression of RKNs by P. polymyxa is associated with triggering the exudation of fatty acyl metabolites from tomato roots and enriching rhizosphere Pseudomonas populations. These findings provide valuable insights into the interplay between root metabolites and the rhizosphere microbiome in mediating synergistic plant disease control, offering a theoretical basis for the development of next-generation microbial nematicides.},
}

@article {pmid42556364,
year = {2026},
author = {Raes, J},
title = {Translating the gut microbiome: where are we?.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {11},
number = {9},
pages = {750-752},
doi = {10.1016/S2468-1253(26)00181-0},
pmid = {42556364},
issn = {2468-1253},
}

@article {pmid42556662,
year = {2026},
author = {Fan, Y and Xu, Z and Zheng, H and Han, J and Hu, S and Pan, X and Ma, R and Liu, C and Tian, Y},
title = {Dietary carboxymethyl starch improves glycemic control and enhances barrier function via Bifidobacterium-mediated galactose metabolism in vivo and in organoids.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153925},
doi = {10.1016/j.ijbiomac.2026.153925},
pmid = {42556662},
issn = {1879-0003},
abstract = {Etherified resistant starches (ERS), including hydroxypropyl starch (HPS), carboxymethyl starch (CMS), and hydroxyethyl starch (HES), are emerging as functional food ingredients with potential to modulate glycemic responses and gut health. However, their comparative efficacy and underlying gut-mediated mechanisms remain poorly defined. This study systematically evaluated their digestive properties and effects on gut microbiota. In vitro digestion demonstrated that etherification substantially increased resistant starch content, with CMS exhibiting approximately 70% resistant starch content and the lowest estimated glycemic index (GI = 53) among the tested starches. In vivo evaluation further showed that CMS significantly attenuated the peak postprandial glucose level (9.6 mmol/L) compared with native starch (17.4 mmol/L). Microbiome analysis revealed that CMS intervention was associated with specific remodeling of the gut microbiota, notably enriching beneficial Bifidobacterium pseudocatenulatum and Bifidobacterium adolescentis. Functionally, integrated KEGG pathway analysis and metabolomics consistently indicated that CMS markedly downregulated galactose metabolism, evidenced by reduced concentrations of galactose-related metabolites such as galactonic acid and galactitol. Furthermore, Spearman correlation analysis highlighted a strong mechanistic link between B. adolescentis abundance and galactose metabolic shifts. Crucially, utilizing, CMS-derived microbiota enhanced intestinal barrier function and galactose metabolism via co-culture model of gut microbiota and colonic organoids. Overall, CMS as a promising functional food ingredient that not only mitigates postprandial glycemia but also improves gut health by regulating microbiota-dependent galactose metabolism.},
}

@article {pmid42556710,
year = {2026},
author = {Simón-Vicente, L and Lafont, MO and Franch, MA and Menéndez-Trillo, P and Rivadeneyra-Posadas, J and Miguel-Pérez, I and Aguado, L and Siscart, IM and Piñeiro, DD and Mariscal, N and Megías-Lobón, G and Calvo, S and Cubo, E and Saiz-Rodríguez, M},
title = {Gut microbiome composition in Huntington's disease: Stage-dependent differences between premanifest and manifest patients.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124617},
doi = {10.1016/j.lfs.2026.124617},
pmid = {42556710},
issn = {1879-0631},
abstract = {BACKGROUND: Huntington's disease (HD) is a progressive neurodegenerative disorder with substantial clinical heterogeneity. The gut microbiome has been proposed as a potential modulator of neurodegeneration, but its role in HD and across disease stages remains unclear.

METHODS: This cross-sectional case-control study included 50 individuals with HD (35 manifest, 15 pre-manifest) and 36 age- and sex-matched cohabiting controls. Stool samples were analysed using 16S rRNA sequencing. Clinical, lifestyle, and dietary variables were recorded. Microbial diversity and differential taxonomic abundance were assessed, accounting for relevant covariates.

RESULTS: No significant differences in global microbial diversity were observed between HD and controls. Age was the main factor associated with both alpha and beta diversity. However, HD was associated with discrete taxonomic differences. More pronounced alterations were identified between manifest and pre-manifest stages, with exploratory genus-level compositional differences identified between disease stages. Antibiotic exposure significantly reduced microbial richness and influenced community structure.

CONCLUSIONS: Gut microbiome alterations in HD may differ across clinical stages rather than reflecting global dysbiosis. These exploratory findings suggest that microbiome composition may contribute to disease heterogeneity, although confirmation in larger longitudinal and independent cohorts is required before considering its potential as a biomarker or therapeutic target.},
}

@article {pmid42556887,
year = {2026},
author = {Mitrea, L and Martău, GA and Călinoiu, LF and Vodnar, DC},
title = {Microbiota, fermentation, and metabolite biotransformation: Pathways to functional foods and personalised nutrition.},
journal = {Advances in food and nutrition research},
volume = {121},
number = {},
pages = {79-130},
doi = {10.1016/bs.afnr.2026.02.001},
pmid = {42556887},
issn = {1043-4526},
mesh = {*Fermentation ; Humans ; *Functional Food ; *Biotransformation ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine ; },
abstract = {Fermentation is among the oldest biotechnological processes and a modern platform for precision metabolic engineering, enabling the targeted production of health-promoting metabolites. The human gut microbiota, with its complex enzymatic potential, converts dietary substrates into a wide range of bioactive molecules, including short-chain fatty acids, vitamins, neuroactive compounds, and polyphenol-derived metabolites that influence host metabolism, immunity, and neurological functions. Advances in microbial genomics, systems biology, and synthetic biology now allow the design of fermentation processes and engineered microbial strains capable of producing specific metabolites with improved bioavailability and tailored health effects. Precision fermentation integrates traditional microbial fermentation with genome editing, metabolic flux optimisation, and AI-assisted pathway design to achieve predictable yields of vitamins, polyphenols, bioactive peptides, and long-chain polyunsaturated fatty acids. These innovations create opportunities to develop functional foods, nutraceuticals, and personalized nutrition strategies that match metabolite profiles to an individual's microbiome composition. This chapter explores the mechanistic links between microbial metabolism and host health, reviews emerging fermentation technologies for targeted metabolite production, and highlights industrial case studies demonstrating the transition of precision fermentation from research to commercial applications.},
}

*Fermentation
Humans
*Functional Food
*Biotransformation
*Gastrointestinal Microbiome/physiology
*Precision Medicine

@article {pmid42557497,
year = {2026},
author = {Chen, E},
title = {First poo transplant to treat food allergy in people has 'exciting' results.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42557497},
issn = {1476-4687},
}

@article {pmid42557505,
year = {2026},
author = {Dos Santos, RAC and Hidalgo-Martinez, K and Muñoz-Perez, JM and Laspisa, DJ and Li, C and Mendes, LW and Riaño-Pachón, DM and Wallace, JG},
title = {Diurnal dynamics of maize gene expression is associated with phyllosphere microbiome composition.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42557505},
issn = {1618-1905},
abstract = {Bacterial communities play important roles in the plant phyllosphere. Both microbial communities and their hosts exhibit endogenous circadian rhythms while simultaneously responding to environmental changes across the diurnal cycle. However, the interaction between the host and microbiome is still poorly understood. Here, we exploit paired sequencing data of host transcriptome and microbiome derived from diverse maize genotypes in field conditions and under two contrasting diurnal periods. Expression patterns of known maize circadian clock genes were consistent with the expected sampling phases. Groups of co-expressed genes that responded to diurnal periods were associated with nucleic acid-binding, heat stress responses, and photosynthesis. Microbiome analysis revealed only modest differences in alpha diversity between midday and midnight samples. However, beta diversity indicated a significant shift in community composition. Co-occurrence network analysis identified keystone taxa specific to each time point, suggesting time-dependent ecological roles within the phyllosphere microbiome. Cross-correlation analyses between host gene expression and bacterial taxon abundance revealed a greater number of host-microbe associations during the night. Several canonical circadian clock genes significantly correlated with microbial taxa. Our findings provide initial evidence for diurnal associations between host gene expression and leaf-associated bacteriome, suggesting that maize diurnal transcriptional dynamics, including the activity of circadian clock genes, may contribute to shaping the composition and functional potential of the phyllosphere microbiome.},
}

@article {pmid42557545,
year = {2026},
author = {Rodríguez Del Río, Á and Cui, Y and Mansour, I and Rillig, MC},
title = {Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42557545},
issn = {1471-2164},
mesh = {*Soil Microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Genomics ; Phylogeography ; Phylogeny ; *Prokaryotic Cells ; *Archaea/genetics/classification ; },
abstract = {Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the genomic features and biogeography of uncultivated prokaryotic taxa at the large scale. Here, we analyze 40,039 genomic bins from cultivated and uncultivated soil taxa within the SMAG catalog, and examine the occurrence of uncultivated prokaryotes in 9,012 metagenomic samples from the Sandpiper resource. Compared to genera with cultivated representatives, uncultivated soil prokaryotes show smaller genomes, lower G + C content, tendency to acidophilic, non-alkaline, thermophilic and host-associated lifestyles, and slower growth rates, with the latter having the highest predictive power for cultivation status. Uncultivated soil microbes also show unique gene repertoires, characterized by a depletion of biosynthetic and motility genes. We also show that completely uncultivated genera are more abundant in tropical and arctic soils, indicating substantial hidden diversity in these regions. Our work emphasizes that current cultivation efforts systematically fail to capture a particular fraction of soil prokaryotic diversity, and provides guidelines for future cultivation strategies.},
}

*Soil Microbiology
Metagenomics
Metagenome
*Bacteria/genetics/classification
*Genome, Bacterial
*Genomics
Phylogeography
Phylogeny
*Prokaryotic Cells
*Archaea/genetics/classification

@article {pmid42557733,
year = {2026},
author = {Murillo-Herrera, AI and Eguiarte, LE and Acuña Gómez, EP and Castro, C and Acevedo, J and Castrillon, J and Oyarzún-Galaz, L and Valenzuela, P and Aguayo-Lobo, A and Pastene, LA and Souza, V},
title = {Temperature and Ultraviolet Radiation Influence the Skin Microbiome of Humpback Whales.},
journal = {Molecular ecology},
volume = {35},
number = {15},
pages = {e70500},
doi = {10.1111/mec.70500},
pmid = {42557733},
issn = {1365-294X},
support = {R20F0009//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {Animals ; *Ultraviolet Rays ; RNA, Ribosomal, 16S/genetics ; Female ; *Humpback Whale/microbiology ; *Skin Microbiome ; Male ; *Temperature ; *Bacteria/classification/genetics ; *Skin/microbiology ; Ecuador ; Ecosystem ; *Microbiota ; Seawater ; Sequence Analysis, DNA ; Seasons ; DNA, Bacterial/genetics ; },
abstract = {The skin microbiome of humpback whales harbours diverse microbial communities that play a crucial role in host skin protection and environmental interaction. However, studies on cetacean skin microbiomes in the Southern Hemisphere focus on feeding grounds, with limited information on microbiome dynamics at breeding grounds and during migration across contrasting habitats. We characterised the skin microbiome of 46 humpback whales from two seasonal habitats: the Magellan Strait feeding ground and the Ecuadorian coast breeding ground, comparing age, sex, environmental conditions, and seawater. Amplicon sequencing of the 16S rRNA gene revealed no differences in alpha diversity, but habitat-specific compositional shifts were found. Psychrobacter was detected in both regions, with higher abundance in the feeding ground, while Tenacibaculum remained abundant across sites. Additional taxa exhibited habitat-specific patterns, including bacteria associated with thermal sensitivity and ultraviolet radiation-tolerance in the Magellan Strait, and lactic acid bacteria in Ecuador. Skin microbiomes were similar between age classes and sexes, but distinct from seawater. Our findings show that geographic and environmental factors, such as superficial seawater temperature and maximum ultraviolet B radiation, shape the skin microbiome of humpback whales, with certain taxa reflecting migratory behaviour across seasonal habitats.},
}

Animals
*Ultraviolet Rays
RNA, Ribosomal, 16S/genetics
Female
*Humpback Whale/microbiology
*Skin Microbiome
Male
*Temperature
*Bacteria/classification/genetics
*Skin/microbiology
Ecuador
Ecosystem
*Microbiota
Seawater
Sequence Analysis, DNA
Seasons
DNA, Bacterial/genetics