@article {pmid41631832,
year = {2026},
author = {Biancheti, LM and Vilela, N and Gomes, E and Olsson, L},
title = {Whole-genome sequencing and annotation of Micrococcus luteus TG3.30 isolated from sugarcane plantation soil in São Paulo, Brazil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0107325},
doi = {10.1128/mra.01073-25},
pmid = {41631832},
issn = {2576-098X},
abstract = {We report the complete genome sequence of Micrococcus luteus TG3.30, isolated from sugarcane soil in Brazil. The 2.58 Mb genome (GC 72.92%) was assembled from hybrid Illumina-Nanopore sequencing with 99.96% completeness, providing a high-quality resource for taxonomic and comparative genomic studies of this versatile actinobacterium.},
}

@article {pmid41631824,
year = {2026},
author = {Gao, L and Qiu, Y and Lin, X and Zhou, Y and Lin, Y and Hong, K and Wang, L and Shen, W and Zhang, Q},
title = {Co-occurrence network analysis reveals novel associations between the neonatal airway microbiome and bronchopulmonary dysplasia risk: an observational, population-based study.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085725},
doi = {10.1128/msphere.00857-25},
pmid = {41631824},
issn = {2379-5042},
abstract = {UNLABELLED: To evaluate the association between respiratory tract microorganisms at birth and the subsequent development and severity of bronchopulmonary dysplasia (BPD) in preterm infants. This prospective cohort study enrolled 98 preterm infants (gestational age < 32 weeks, birth weight < 2,000 g). Tracheal aspirate samples were collected through endotracheal intubation within 2 h after birth. Using 16S rRNA sequencing, we characterized the airway microbiome and performed co-occurrence network analysis with compositionally robust methods. Among 98 preterm infants analyzed, the incidence of BPD was 68.4%, comprising 31 grade I, 20 grade II, and 16 grade III cases. Airway microbiota in infants with BPD exhibited distinct severity-stage patterns: Escherichia-Shigella and Streptococcus were significantly enriched in grade I, while Chryseobacterium increased markedly in grade III, accompanied by a significant reduction in Streptococcus. Microbial co-occurrence network analysis yielded three key insights. (i) Network complexity declined sharply with BPD severity, being sparsest in grade III. (ii) Distinct keystone taxa were identified across different groups: Acinetobacter and Fusobacterium in the non-BPD group; Brevundimonas and Fusobacterium in grade I; Fusobacterium and Acinetobacter at grade II and grade III. (iii) In a multivariable model adjusted for key clinical confounders, a higher microbial network density at birth was independently associated with a substantially reduced risk (OR = 0.12, P < 0.05). The ecological architecture of the neonatal airway microbiome at birth, defined by network complexity and keystone taxa, is associated with BPD severity. This highlights microbial network stability as a novel factor and ecological interactions as a target for future research.

IMPORTANCE: Bronchopulmonary dysplasia (BPD) remains the most common chronic lung disease in preterm infants. While its pathogenesis is incompletely understood, the role of the early respiratory microbe is increasingly recognized. Previous studies have largely focused on individual pathogenic taxa, overlooking the complex ecological interactions within microbial communities. Our analysis reveals that the architecture of microbial co-occurrence networks in the neonatal airway varies significantly with BPD severity. Notably, network complexity decreased markedly as BPD severity increased. We identified specific keystone taxa uniquely associated with disease outcomes, suggesting that microbial ecosystem stability rather than individual species may be a critical factor in BPD pathogenesis. These findings shift the focus from single microbes to the stability of the microbial ecosystem as a novel risk factor for severe BPD, offering new avenues for risk stratification and early intervention.},
}

@article {pmid41631397,
year = {2026},
author = {},
title = {Correction to "Polystyrene Microplastics Disrupt Vertical Transmission of the Breast Milk Microbiome, Impairing Early-Life Gut Colonization and Immune Development in Offspring".},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {3},
pages = {e71521},
doi = {10.1096/fj.202600412},
pmid = {41631397},
issn = {1530-6860},
}

@article {pmid41631341,
year = {2026},
author = {Gordon, N and Segal, LN and Wu, BG},
title = {Rethinking pneumonia in terms of the lung microbiome.},
journal = {Current opinion in pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCP.0000000000001247},
pmid = {41631341},
issn = {1531-6971},
abstract = {PURPOSE OF REVIEW: This review aggregates, analyzes, and summarizes the current understanding of the lung microbiome as it relates to pneumonia. We will review the composition and function of a healthy lung microbiome and conceptualize dysbiosis associated with pneumonia. Finally, we discuss how the lung microbiome impacts the diagnosis, prognostication and pathogenesis, and recovery from pneumonia.

RECENT FINDINGS: The most tangible benefit of studying the lung microbiome has been the identification of pathogenic organisms in suspected pneumonia; however, as there is a growing body of evidence that suggest the lung microbiome is critical to pneumonia. Generally, detection of potential pathogens such as Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Escherichia coli can be found even when sampling the lung microbiome of healthy individuals, yet it is unclear what determines the transition from potential pathogens present as bystanders to pathogens driving the development of pneumonia. Analysis of the lung microbiome suggests that the loss of "oral commensals" (bacteria found in the oral microbiome) in the lower airways is associated with the development of pneumonia and may provide diagnostic and prognostic insights.

SUMMARY: The lung microbiome is a rich and dynamic ecosystem comprised of numerous bacterial, fungal, and viral taxa that may contribute to pneumonia pathogenesis. There is increasing evidence that the lung microbiome may provide insight into factors that determine the pathogenicity of respiratory microbes and the susceptibility of individuals to those pathogens.},
}

@article {pmid41630848,
year = {2026},
author = {Klasek, SA and Crants, JE and Frost, KE and Schroeder, BK and Rosen, CJ and Kinkel, LL},
title = {Organic amendments to potato soils inconsistently enrich yield-associated soil microbiota across growing regions of the continental US.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20595},
pmid = {41630848},
issn = {2167-8359},
mesh = {*Solanum tuberosum/growth & development/microbiology ; *Soil Microbiology ; *Microbiota ; *Soil/chemistry ; United States ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Fumigation ; },
abstract = {Plant health is regulated by complex consortia of soil microbes with growth-promoting and pathogenic functions. In potato production, various soil management practices are undertaken to boost yields and suppress diseases, but connections between these practices, soil microbiomes, and tuber yields have not been characterized across diverse growing regions. To identify growing practices and microbes associated with increased yields, we established four-year field trials across eight US sites from Oregon to Maine that consisted of controls, fumigations, organic amendments, and mustard incorporations. Amplicon sequencing of 16S ribosomal RNA (rRNA) genes and intergenic transcribed spacer (ITS) regions was used to investigate bacterial and eukaryotic soil microbiomes, respectively. Fumigation and organic amendment treatments increased tuber yields in 23% and 29% of treatments relative to controls. While soil treatments influenced both microbiome types differently across all field sites, eukaryotes were more sensitive than bacteria to all treatments. Across field sites, soil treatments impacted relative abundances of amplicon sequence variants (ASVs) to varying degrees, even among ASVs belonging to the same genus. Associations between ASVs and tuber yields similarly varied within genera, highlighting the lack of consistent yield-associated taxa across US growing regions. Nevertheless, forty-five "target ASVs" across nine bacterial and three fungal phyla were identified as both treatment-impacted and yield-associated within any particular field site. Models identified three of thirteen organic amendment scenarios and one of thirteen fumigation scenarios where increased relative abundances of specific target ASVs accounted for up to a 23% increase in tuber yields compared to control treatments. These ASVs were largely site-specific and not influenced by treatment-associated changes in soil nutrients or organic matter, highlighting complex relationships within field sites that require further study to achieve the goal of implementing sustainable, microbiome-informed potato production techniques.},
}

*Solanum tuberosum/growth & development/microbiology
*Soil Microbiology
*Microbiota
*Soil/chemistry
United States
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Fumigation

@article {pmid41630783,
year = {2026},
author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS},
title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100544},
pmid = {41630783},
issn = {2666-5174},
abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.},
}

@article {pmid41630692,
year = {2026},
author = {Hu, X and Kong, F and Chen, J and Li, Z and Cai, Z and Kong, X},
title = {Microbiota in pancreatic ductal adenocarcinoma progression and therapy: The hidden players.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {41630692},
issn = {2542-5641},
abstract = {Pancreatic ductal adenocarcinoma (PDAC), the deadliest epithelial malignancy, is increasingly prevalent and contributes significantly to cancer-related mortality. Research over the past decade has demonstrated that microbiota may play a pivotal role in both PDAC oncogenesis and its resistance to chemotherapy. Emerging preclinical and clinical data highlight the impact of microbiota on therapeutic outcomes in PDAC patients. This review systematically explores the role and underlying mechanisms of microbiota in PDAC, with a particular focus on their clinical implications and translational potential in disease progression and therapeutic responses. Finally, this review addresses the potential of microbiome-based therapies to enhance the efficacy of PDAC treatments.},
}

@article {pmid41630319,
year = {2026},
author = {Yang, L and Li, L and Liang, B and Yu, J and Wang, J and Sun, F},
title = {Role of CD25 on resting Treg immune cell in mediating the effect of stearate biosynthesis microbiome pathway on lung adenocarcinoma.},
journal = {Medicine},
volume = {105},
number = {5},
pages = {e47505},
pmid = {41630319},
issn = {1536-5964},
support = {2020ZRQNB059//the fund of Southwest Medical University/ ; 2023ZD003//the fund of Southwest Medical University/ ; 2020LZXNYDJ44//the Luzhou City Science and Technology Bureau/ ; S202310632162//Provincial Innovation and Entrepreneurship Training Program for College Students/ ; },
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Interleukin-2 Receptor alpha Subunit/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; *Lung Neoplasms/immunology/microbiology/genetics ; *Adenocarcinoma of Lung/immunology/microbiology/genetics ; Mendelian Randomization Analysis ; },
abstract = {Gut microbiota (GM) often influences the development of diseases by regulating the immune system. The causal relationship between GM and lung adenocarcinoma (LUAD) and whether it can be mediated by immune cells remains unclear. We conducted two-step, two-sample Mendelian randomization (MR) analyses. The data of GM, LUAD and immune cells for analysis were derived from publicly available genetic data. The causal relationship between GM and LUAD, as well as the mediation effect of immune cells in the association between GM and LUAD were estimated using inverse variance weighted, MR-Egger and weighted median. Sensitivity analyses were implemented with Cochran Q test, MR-Egger intercept test, MR-PRESSO. MR analyses determined the protective effects of PWY-5989 (stearate biosynthesis II bacteria and plants) on LUAD. In addition, CD25 on resting regulatory T cell (Treg) was negatively correlated with LUAD. Of note, the mediation MR illustrated that in the presence of CD25 on resting Treg, PWY-5989 can promote the risk of LUAD by inhibiting the expression of CD25 on resting Treg. The study suggested a causal relationship between PWY-5989 and LUAD, which may be mediated by CD25 on resting Treg.},
}

Humans
*T-Lymphocytes, Regulatory/immunology/metabolism
*Interleukin-2 Receptor alpha Subunit/metabolism/immunology
*Gastrointestinal Microbiome/immunology
*Lung Neoplasms/immunology/microbiology/genetics
*Adenocarcinoma of Lung/immunology/microbiology/genetics
Mendelian Randomization Analysis

@article {pmid41630095,
year = {2026},
author = {White, P and Maybin, JA and Williams, EJ},
title = {Could the untapped potential of the reproductive tract microbiome hold the key to tackling heavy menstrual bleeding?.},
journal = {Reproduction (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/reprod/xaag018},
pmid = {41630095},
issn = {1741-7899},
abstract = {The well-studied role of the microbiome in gut physiology and pathology has led to revolutionary microbiome-targeted treatments, but the function of the reproductive tract microbiome is yet to be delineated. This underexplored avenue could shed light on historically neglected reproductive health symptoms such as heavy menstrual bleeding.},
}

@article {pmid41629888,
year = {2026},
author = {Luo, M and Xiao, X and Wu, Y},
title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-06531-0},
pmid = {41629888},
issn = {1471-2431},
support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; },
}

@article {pmid41629832,
year = {2026},
author = {Miyamoto, I and Shimizu, T and Hanamura, M and Tanaka, R and Kusahana, R and Nomoto, M and Sugaya, K and Nakagawa, Y and Gon, Y},
title = {Impact of proton pump inhibitor use on immune-related adverse events in patients with non-small cell lung cancer: a retrospective study.},
journal = {BMC cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12885-026-15646-7},
pmid = {41629832},
issn = {1471-2407},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICI) have revolutionized cancer therapy; however, immune-related adverse events (irAEs) remain a critical concern. Proton pump inhibitors (PPIs) are frequently co-administered to patients with advanced lung cancer and PPI-induced alterations in the gut microbiota may impair immune responses, potentially affecting ICI efficacy and prognosis. However, the association between PPI use and irAE development remains unclear.

METHODS: We retrospectively analyzed 228 patients with advanced non-small cell lung cancer who received first-line ICI therapy between April 2017 and December 2024. The impact of baseline PPI use on the incidence of irAEs, classified as checkpoint inhibitor pneumonitis (CIP) or irAEs without CIP (non-CIP irAEs), was evaluated.

RESULTS: Multivariate logistic regression analysis showed a non-significant association between PPI use and the incidence of overall irAEs. (odds ratio [OR] = 0.625; 95% confidence interval [CI], 0.348-1.120; p = 0.117). Notably, PPI exposure was significantly associated with a reduced incidence of non-CIP irAEs (OR = 0.510; 95% CI, 0.274-0.947; p = 0.033), whereas no significant association was observed with the incidence of CIP. Median overall survival (OS) was shorter in the PPI-exposed group than in the PPI-unexposed group, but the difference was not statistically significant (16.7 vs. 24.7 months; p = 0.065). In multivariate Cox regression analysis, PPI exposure was not identified as an independent prognostic factor for OS (hazard ratio [HR] = 1.120; 95% CI, 0.768-1.634; p = 0.556). In contrast, the occurrence of non-CIP irAEs (HR = 0.574; 95% CI, 0.368-0.895; p = 0.014) was significantly associated with improved OS.

CONCLUSIONS: PPI use was potentially associated with a lower incidence of non-CIP irAEs, whereas no significant effect was observed for CIP. In contrast, PPI use was not an independent prognostic factor, suggesting that irAE occurrence is influenced by multiple factors beyond PPI use. This study highlights the importance of investigating the interplay between PPI exposure, irAE occurrence, and gut microbiome alterations.},
}

@article {pmid41629813,
year = {2026},
author = {Astudillo-Guerrero, C and Garrido, Á and Masferrer, D and Sepúlveda, C and Olavarría, L and Del Campo, R and Bravo-Sagua, R and Cubero, FJ and Salech, F and Thumala-Dockendorff, D and Urrutia, PJ and Quera, R and Bunout, D and Espinoza, R and Jorquera, G},
title = {Randomized, double-blind, placebo-controlled trial of fecal microbiota transplantation from young physically active donors to promote resilient aging: clinical trial protocol (ARMOR study).},
journal = {BMC geriatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12877-025-06920-7},
pmid = {41629813},
issn = {1471-2318},
}

@article {pmid41629538,
year = {2026},
author = {Moore, ER and Rahman, MM and Galella, JG and Sena, M and Joshi, B and Yaculak, A and Peipoch, M and Kan, J and Inamdar, S},
title = {Distinct changes in riparian sediment microbial communities with depth and time since dam removal.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37708-3},
pmid = {41629538},
issn = {2045-2322},
support = {2023-67019-39835//U.S. Department of Agriculture/ ; },
abstract = {Microbes drive biogeochemical changes in ecosystems, including carbon (C) and nitrogen (N) cycling. Dam construction has altered riparian ecosystems worldwide, yet we know little about microbial community composition in riparian sediments and how it changes following dam removal and sediment/soil drainage. Here, we evaluate how riparian microbial communities change with increasing depth in the sediment profile for existing dams and over time following dam removal/breach and assess how various physico-chemical sediment properties influence microbial community composition. We studied microbial community structure for 12 riparian sites over a chronosequence of 0-234 years since dam breach. Sediment was collected every 0.3 m to a depth of 4 m. Aerobic taxa involved with N cycling (e.g., Nitrospirota) were dominant in surficial sediments, and increased in deeper sediments as time since dam breach increased. Anaerobic taxa implicated in C cycling (e.g., Bathyarchaeia, Anaerolineaceae) and iron reduction (e.g., Sva0485) were dominant in deeper, anoxic sediments, but declined the fastest post dam breach. These microbial trends provide insights into how riparian biogeochemical functions are impacted by dam inundation and the recovery and restoration of these ecosystems following dam removals.},
}

@article {pmid41629533,
year = {2026},
author = {Kaduwal, S and Stuart, EC and Auradkar, A and Washabaugh, S and Meyer, JR and Bier, E},
title = {A conjugal gene drive-like system efficiently suppresses antibiotic resistance in a bacterial population.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {8},
pmid = {41629533},
issn = {2731-8745},
abstract = {Antibiotic resistance (AR) is an escalating public health threat, necessitating innovative strategies to control resistant bacterial populations. One promising approach involves engineering genetic elements that can spread within microbial communities to eliminate AR genes. Previously, we developed Pro-Active Genetics (Pro-AG), a CRISPR-based gene-drive-like system capable of reducing AR colony-forming units (CFU) by approximately five logs. Here, we advance this technology by integrating Pro-AG into a conjugative transfer system, enabling efficient dissemination of an anti-AR gene cassette between two bacterial strains. Additionally, we characterize a complementary homology-based deletion (HBD) process, a CRISPR-driven mechanism that precisely removes target DNA sequences flanked by short direct repeats. Our findings reveal that Pro-AG and HBD are differentially influenced by the bacterial RecA pathway and that HBD components can be delivered via plasmids or phages to selectively delete Pro-AG cassettes. This built-in safeguard prevents uncontrolled spread of a gene cassette and mitigates unanticipated side effects. These refinements enhance the efficiency and flexibility of Pro-AG, expanding its potential applications in microbiome engineering, environmental remediation, and clinical interventions aimed at combating antibiotic resistance. More broadly, this work establishes a proof-of-principle for microbiome engineering strategies that could be leveraged to improve health and restore ecological balance.},
}

@article {pmid41629500,
year = {2026},
author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y},
title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38558-9},
pmid = {41629500},
issn = {2045-2322},
support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; },
}

@article {pmid41629499,
year = {2026},
author = {Saddik, JN and Naguib, MM and Labib, LM and El-Gendy, AO and Molham, F},
title = {Nano-chitosan modified restorative materials suppress Streptococcus mutans biofilm and virulence gene expression.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-02004-2},
pmid = {41629499},
issn = {2191-0855},
}

@article {pmid41629498,
year = {2026},
author = {O'Leary, K},
title = {Babies share microbiomes at nursery.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41591-026-00006-6},
pmid = {41629498},
issn = {1546-170X},
}

@article {pmid41629364,
year = {2026},
author = {Spörri, L and Studer, JM and Kreuzer, M and Rotzetter, J and Schärer, D and Largiadèr, CR and Jaggi, D and Zinkernagel, MS and Zysset-Burri, DC},
title = {Linking the microbiome to the complement system in geographic atrophy.},
journal = {NPJ genomic medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41525-026-00550-7},
pmid = {41629364},
issn = {2056-7944},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
abstract = {Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.},
}

@article {pmid41629309,
year = {2026},
author = {Jastrząb, R and Małecki, A and Kmiecik-Małecka, E and Gorzkowska, A and Krzystyniak, B and Kubas, K and Widłak-Kargul, J and Wolman, D and Matkiewicz, K and Nowacka-Chmielewska, M and Liśkiewicz, D and Grabowska, K and Grabowski, M and Pondel, N and Początek, G and Kłodowska, G and Mytych, J},
title = {Probiotic Lactiplantibacillus plantarum OL3246 supports healthy aging by enhancing quality of life, reducing inflammation, and modulating gut microbiota: a pilot study.},
journal = {npj aging},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41514-026-00338-0},
pmid = {41629309},
issn = {2731-6068},
abstract = {Aging is accompanied by low-grade intestinal inflammation, shifts in gut microbiota, and impaired oxidative balance. Probiotic supplementation has been proposed to mitigate these processes, yet evidence in elderly populations remains limited. In this pilot trial, older adults received oral Lactiplantibacillus plantarum OL3246 or placebo, with assessments including fecal calprotectin and zonulin as markers of intestinal inflammation, systemic oxidative stress parameters, self-reported quality of life and mood, and gut microbiome composition analyzed by sequencing and functional profiling. L. plantarum OL3246 supplementation was well tolerated and associated with consistent improvements across clinical, biochemical, and microbial measures. Participants reported enhanced quality of life and mood, while fecal calprotectin levels declined, indicating reduced intestinal inflammation. Moreover, oxidative stress markers improved with lower AOPP, stabilization of SOD, and restoration of redox balance. Microbiome analyses showed greater diversity and enrichment of health-associated taxa. These findings indicate that Lactiplantibacillus plantarum OL3246 may support healthy aging.},
}

@article {pmid41629169,
year = {2026},
author = {Liu, T and Lai, CH and Wu, YW and Lee, CH and Chen, PL and Wang, JY and Hsieh, MH and Hu, PH and Jeng, SL and Chuang, YC and Chuang, CH and Wang, JL and Kuo, CW},
title = {Comparative analysis of clinical outcomes and short-term treatment response of sputum microbiome between eosinophilic and non-eosinophilic COPD acute exacerbation.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2026.01.004},
pmid = {41629169},
issn = {1995-9133},
abstract = {BACKGROUND: Eosinophilic AECOPD is a specific phenotype; however, the clinical outcomes and the short-term changes in sputum microbiome remain unclear.

METHODS: We retrospectively included AECOPD patients admitted to National Cheng Kung Universal Hospital from January 2013 to December 2022. The primary outcome was respiratory failure rate. In addition, self-expectorated sputum was prospectively collected on days 1 and 5 of hospitalization between June 2020 and May 2021, and 16S rRNA gene segments (V3-V4) were amplified for sputum microbiome identification. Eosinophilic AECOPD were defined as blood eosinophils (bEOS) exceeding 2 % at admission.

RESULTS: From the analysis of 202 AECOPD hospitalizations, patients with bEOS ≥2 % had shorter hospital stays and respiratory failure days (β-coefficient: 2.98 and -3.86, P < 0.001 and = 0.049, respectively), a lower risk of respiratory failure and intensive care unit admission (odds ratio: 0.29 and 0.35, P = 0.007 and = 0.029, respectively). In a sub-cohort of 30 AECOPD patients undergoing sputum microbiome analysis, 12 had bEOS ≥2 %, a significant decrease in Shannon diversity at the phylum level after 5 days of treatment was observed only in the bEOS <2 % group. Moreover, the relative abundance of Proteobacteria increased after treatment in the patients with bEOS ≥ 2 % while a trend of decrease was observed in those with bEOS<2 %.

CONCLUSIONS: Patients with eosinophilic AECOPD demonstrate better short-term clinical outcomes. The sputum microbiota in the eosinophilic and non-eosinophilic patients also respond differently to the treatment for AECOPD.},
}

@article {pmid41629027,
year = {2026},
author = {Gao, Q and Wu, Y and Huang, J and Xu, S and Chen, R and Jiang, H and Huang, Y and He, Q and Wang, Y and Xiao, J and Cao, H},
title = {Chronic neonicotinoid exposure disrupts survival, development, digestive enzymes, and gut microbiome in honeybee queen larvae (Apis mellifera L.).},
journal = {Pesticide biochemistry and physiology},
volume = {218},
number = {},
pages = {106959},
doi = {10.1016/j.pestbp.2026.106959},
pmid = {41629027},
issn = {1095-9939},
mesh = {Animals ; Bees/drug effects/growth & development/microbiology ; *Neonicotinoids/toxicity ; *Gastrointestinal Microbiome/drug effects ; Larva/drug effects/growth & development/microbiology ; *Insecticides/toxicity ; Nitro Compounds/toxicity ; Guanidines/toxicity ; RNA, Ribosomal, 16S/genetics ; Thiazoles/toxicity ; },
abstract = {Honeybee queens (Apis mellifera L.) are essential for colony sustainability, most study mainly focused on the acute toxicity of chemical insecticides. This study investigated the chronic effects of three prevalent neonicotinoids on honeybee queen larvae development, digestive physiology, and gut microbiota. It was determined that exposure to elevated concentrations (10-40 mg/L) significantly increased larval mortality (up to 41.70%), which reduced both capping and emergence rates, with imidacloprid causing a 43.80% decline in emergence at 40 mg/L. Chronic exposure (1-25 mg/L) to clothianidin notably decreased birth weight by 11.40% and altered thoracic and abdominal morphometrics. Moreover, imidacloprid and clothianidin suppressed amylase activity by up to 94%, while acetamiprid enhanced it by nearly 60%. Additionally, 16S rRNA gene sequencing revealed significant shifts in gut microbiota composition, characterized by increased abundance of Firmicutes and decreased Bacteroidota, despite minor changes in overall diversity. Functional predictions indicated alterations in carbohydrate metabolism, amino acid metabolism, and membrane transport pathways. These findings demonstrate that chronic neonicotinoid exposure disrupts metabolic and microbial homeostasis in honeybee queen larvae, posing a serious threat to honeybee colony fitness, which is important and provides essential evidence for ecological risk assessment and the development of safer pesticide application strategies in apiculture and crop protection.},
}

Animals
Bees/drug effects/growth & development/microbiology
*Neonicotinoids/toxicity
*Gastrointestinal Microbiome/drug effects
Larva/drug effects/growth & development/microbiology
*Insecticides/toxicity
Nitro Compounds/toxicity
Guanidines/toxicity
RNA, Ribosomal, 16S/genetics
Thiazoles/toxicity

@article {pmid41629015,
year = {2026},
author = {Sun, L and Gao, J and Tan, Y and Xia, Y and Wang, R and Liu, R and Zhang, X and Yan, X and Huang, L},
title = {Biocontrol of Apple Valsa Canker by Bacillus sp. H12 and modulation of the apple seedlings microbiome.},
journal = {Pesticide biochemistry and physiology},
volume = {218},
number = {},
pages = {106946},
doi = {10.1016/j.pestbp.2026.106946},
pmid = {41629015},
issn = {1095-9939},
mesh = {*Malus/microbiology/growth & development ; *Plant Diseases/microbiology/prevention & control ; *Seedlings/microbiology/growth & development ; *Ascomycota ; *Microbiota ; *Bacillus/physiology ; Disease Resistance ; Soil Microbiology ; },
abstract = {Apple Valsa Canker (AVC), caused by the fungal pathogen Cytospora mali, is the most devastating stem disease in East Asia apple production systems. As an eco-friendly alternative to chemical control, biological control strategies have attained prominence for mitigating environmental pollution and preventing pathogen resistance. In this study, a soil-derived bacterial strain significantly inhibited AVC and promoted plant growth. The strain was identified as Bacillus amyloliquefaciens using combined morphological and molecular characterization and designated as H12. The bacterium directly induces abnormal branching of C. mali hyphae, cytoplasmic leakage, and cell wall rupture, ultimately leading to mycelia death. H12 exhibits strong control efficacy against AVC on in vitro branches and the leaves of tissue-cultured seedlings. Notably, H12 upregulates immune-related gene expression in apple, enhances reactive oxygen species (ROS) accumulation, and increases callose deposition. Microbiome sequencing indicates that H12 modulates the structure of the apple phyllosphere bacterial community, enriches beneficial microorganisms, and enhances host resistance. Furthermore, the strain achieves a 55.56% disease control efficacy in field trials, demonstrating its potential for practical application as a promising microbial agent. In summary, H12 has dual functions, directly inhibiting pathogenic fungi and inducing host resistance, providing theoretical and practical support for the green management of AVC.},
}

*Malus/microbiology/growth & development
*Plant Diseases/microbiology/prevention & control
*Seedlings/microbiology/growth & development
*Ascomycota
*Microbiota
*Bacillus/physiology
Disease Resistance
Soil Microbiology

@article {pmid41629012,
year = {2026},
author = {Zhou, X and Qing, Y and Wang, Y and Deng, H and Wang, J and Kuang, M and Luo, X and Zhao, C and Sun, Z and Wang, Y and Yang, L and Ding, W},
title = {Identification and validating native biocontrol bacteria Bacillus strain MZ3-12 against bacterial wilt.},
journal = {Pesticide biochemistry and physiology},
volume = {218},
number = {},
pages = {106943},
doi = {10.1016/j.pestbp.2026.106943},
pmid = {41629012},
issn = {1095-9939},
mesh = {*Bacillus/physiology/genetics/isolation & purification ; *Plant Diseases/microbiology/prevention & control ; Rhizosphere ; *Nicotiana/microbiology/growth & development ; Soil Microbiology ; *Ralstonia solanacearum/growth & development ; *Biological Control Agents ; Siderophores/metabolism ; Pest Control, Biological ; RNA, Ribosomal, 16S/genetics ; Microbiota ; },
abstract = {Tobacco bacterial wilt is a major threat to sustainable tobacco agriculture. To identify native biocontrol agents for managing this disease, this study integrated rhizosphere microbiome profiling with functional screening. Comparative 16S rDNA amplicon sequencing showed that disease-affected soils had higher abundances of pathogen-linked genera, while healthy soils were enriched in beneficial microbes such as Bacillus and Streptomyces. Then, we isolated thirty potential bacteria from healthy rhizospheres soil, and investigated the effect of screening potential bacteria on R. solanacearum growth, siderophore secretion, protease activity, and cellulase activity. Among these bacteria, four potential biocontrol bacteria were screened, including three Bacillus MZ3-12, MZ4-13, MZ9-28, and a Glutamicibacter MZ8-15. These strains significantly inhibited R. solanacearum growth and secreted highly active proteases, cellulases, and siderophores. They also promoted tobacco growth, increased plant dry weight and fresh weight, and enhanced the expression levels of genes related to the salicylic acid, jasmonic acid, and ethylene pathways. Furthermore, MZ3-12 displays considerable control effect on tobacco bacterial wilt in greenhouse and field conditions. Our results confirm that combining microbiome analytics with culture-based screening is an effective way to identify environment-friendly biocontrol agents, highlighting the role of Bacillus MZ3-12 in maintaining rhizosphere health and managing tobacco bacterial wilt.},
}

*Bacillus/physiology/genetics/isolation & purification
*Plant Diseases/microbiology/prevention & control
Rhizosphere
*Nicotiana/microbiology/growth & development
Soil Microbiology
*Ralstonia solanacearum/growth & development
*Biological Control Agents
Siderophores/metabolism
Pest Control, Biological
RNA, Ribosomal, 16S/genetics
Microbiota

@article {pmid41628857,
year = {2026},
author = {Theodosiou, A and Bogaert, D and Cleary, D and Fady, PE and Feehily, C and Gilbert, J and Greenhough, B and Guardabassi, L and Hall, L and Harman, T and Kuijper, E and Lebeer, S and Lorimer, J and Spector, T and Jones, C},
title = {Microbiome research in practice: priorities for clinical translation and impact.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.01.021},
pmid = {41628857},
issn = {1469-0691},
abstract = {BACKGROUND: Rapid advances in microbiome science have sparked clinical and commercial enthusiasm for interventions, yet translation into practice risks outpacing both mechanistic understanding and the infrastructure required for safe adoption.

OBJECTIVES: To outline a coordinated research, clinical, social, and policy agenda for advancing safe, effective, and equitable microbiome-based interventions.

SOURCES: We convened an interdisciplinary Royal Society-funded expert workshop (Leeds, UK, October 2024) with international leaders in microbiome science, clinical trials, regulation, and social science. Thematic analysis of workshop discussions and written contributions identified priority domains for translation.

CONTENT: Three intersecting priorities emerged: scientific credibility, practical viability, and stakeholder engagement. Scientific credibility demands investment in multiomic and strain-level characterisation of host-microbiome interactions on a large scale, benchmarking of clinical and microbiological endpoints, and harmonisation of trial conduct and reporting. Clinical adoption requires fit-for-purpose regulation, diversified investment to address funding bottlenecks, and coordinated capacity building. Meaningful stakeholder engagement with clinicians, patients, policymakers, and the public is essential to foster confidence, develop clinically relevant research questions, and ensure equitable implementation of any new technology.

IMPLICATIONS: To realise the clinical impact of microbiome interventions, sustained collaboration across disciplines is essential. This Review offers a translational roadmap and actionable priorities to accelerate safe, effective, and equitable microbiome-based interventions - ensuring the field fulfils its clinical potential and delivers real-world impact.},
}

@article {pmid41628782,
year = {2026},
author = {Majumdar, S and Samaiya, PK and Gupta, SK and Krishnamurthy, S and Prajapati, SK},
title = {Aging and neuropathic pain: Mitochondria-to-glia cascade, system mechanisms, and therapeutic strategies.},
journal = {Ageing research reviews},
volume = {116},
number = {},
pages = {103042},
doi = {10.1016/j.arr.2026.103042},
pmid = {41628782},
issn = {1872-9649},
abstract = {Neuropathic pain (NP) creates a severe pathological condition that primarily affects elderly people because of their accumulated neurobiological changes that make them more susceptible to persistent pain. The aging process leads to multiple mechanisms that combine neurodegeneration with immunosenescence and mitochondrial dysfunction with impaired autophagy and glial priming, and ion channel dysregulation to create a nociceptive environment. This review examines how mitochondrial breakdown and dysfunctional autophagy, and ion channel disturbances with glial cell activation form a interconnected system which makes older people more prone to NP. The review also examines how the neuro-immune-metabolic and gut-brain axis maintain persistent pain across the lifespan while discussing its cellular pathology. Preclinical research shows that aged models develop more severe NP symptoms, yet clinical evidence reveals distinct diagnostic and therapeutic challenges that affect older adults. The review presents current treatment strategies which include mitochondrial protectants and autophagy enhancers together with immunomodulators and microbiome-based interventions, and gene therapies to develop appropriate multimodal therapies for different age group. Further, it combines mechanistic knowledge with translational viewpoints to demonstrate the immediate requirement for treating NP as a geroscience challenge to develop better pain management strategies for older adults.},
}

@article {pmid41628747,
year = {2026},
author = {Vohra, V and Dhanawat, M and Chalotra, R and Bhushan, B and Garima, and Girdhar, J and Madar, IH and Singh, R and Fareed, M},
title = {Shaping immunotherapy through the tumor microenvironment: Translational perspectives.},
journal = {Critical reviews in oncology/hematology},
volume = {220},
number = {},
pages = {105169},
doi = {10.1016/j.critrevonc.2026.105169},
pmid = {41628747},
issn = {1879-0461},
abstract = {The tumour microenvironment (TME) is a simply orchestrator of cancer progression and a principal mediator of resistance to immunotherapy. This review explains the complex immunosuppressive ecosystem of the TME, highlighting mechanisms of immune evasion including the recruitment of regulatory T cells, myeloid-derived suppressor cells, and tumour-associated macrophages; metabolic competition via the Warburg effect and indoleamine 2,3-dioxygenase activity and hypoxia-driven upregulation of immune checkpoints such as PD-L1. We synthesize translational strategies designed to reprogram this hostile niche, moving beyond immune checkpoint inhibitor monotherapy. These approaches encompass metabolic targeting (e.g., MCT1/4, IDO inhibitors), stromal disruption (e.g., CAF inhibition, vascular normalization), and advanced cellular engineering, such as CAR-T cells resistant to exhaustion and cytokine-secreting constructs. We underline the synergy of combination therapies, integrating checkpoint blockade with chemotherapy, radiotherapy, oncolytic viruses, and adenosine pathway antagonists to augment immunogenic cell death and cytotoxic T lymphocyte infiltration. The predictive value of biomarkers including tumour mutational burden, microsatellite instability, and the spatial architecture of tumour-infiltrating lymphocytes is critically appraised. Furthermore, the review explores emerging frontiers such as neoantigen-based vaccines, microbiome modulation, and bispecific antibodies, underscoring their capacity to convert immunologically "cold" tumours into "hot", responsive lesions. By bridging preclinical insights with clinical trial evidence, this review speculates that the precise modulation of the TME is indispensable for unlocking durable, broad-spectrum antitumor immunity and defining the next generation of cancer immunotherapies.},
}

@article {pmid41628729,
year = {2026},
author = {Romeiro, K and Siqueira, JF and Rôças, IN and Gominho, LF and Villela, LB and Brisson-Suárez, K and Carmo, FL},
title = {Root Canal Microbiome in Patients Undergoing Antineoplastic Therapy: a Next-Generation Sequencing Study.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.01.020},
pmid = {41628729},
issn = {1878-3554},
abstract = {INTRODUCTION: This study compared the intracanal microbiome of teeth with apical periodontitis in oncological and healthy patients using 16S rRNA gene-based next generation sequencing.

METHODS: Root canal samples were taken from 46 teeth with pulp necrosis and primary apical periodontitis (23 from oncological patients and 23 from healthy controls). DNA was extracted and sequenced using the Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. Bioinformatics processing was conducted using QIIME2 and DADA2. Alpha and beta diversity analyses, genus-level abundance comparisons, and indicator species analyses were performed.

RESULTS: After quality filtering, 3,307,822 sequence reads were retained, averaging 68,912.96 reads/sample, and resulting in 3,241 unique amplicon sequence variants. Oncological patients exhibited significantly higher bacterial richness (p = 0.01), while Shannon diversity showed no significant difference between groups. Beta diversity analysis (Bray-Curtis, MDS stress = 0.14) did not reveal significant differences between groups. Indicator species analysis identified some specific taxa more associated with oncological patients, including the candidate endodontic pathogens Prevotella, Selenomonas, Alloprevotella, Rothia, and Fretibacterium.

CONCLUSIONS: The root canal microbiome of oncologic patients with apical periodontitis was broadly similar to that of healthy controls. The oncologic group showed higher species richness, but no significant differences in the overall bacterial diversity or community structure.},
}

@article {pmid41628665,
year = {2026},
author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM},
title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: a proof-of-concept placebo-controlled randomized trial.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2026.01.630},
pmid = {41628665},
issn = {1522-9653},
abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.

METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.

RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.

CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.

TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.},
}

@article {pmid41628518,
year = {2026},
author = {Aluisio, GV and Santagati, M and Stilo, G and Lentini, M and Sowerby, LJ and Mayo-Yáñez, M and Sedaghat, AR and Lechien, JR and Stefani, S and La Mantia, I and Maniaci, A},
title = {Can microbial profiles influence type II inflammation in chronic rhinosinusitis with nasal polyps?.},
journal = {American journal of otolaryngology},
volume = {47},
number = {2},
pages = {104786},
doi = {10.1016/j.amjoto.2026.104786},
pmid = {41628518},
issn = {1532-818X},
abstract = {OBJECTIVE: This study aimed to assess how different treatments - dupilumab vs surgery - influence the nasal microbiota, type 2 inflammation, and clinical outcomes in CRSwNP patients.

METHODS: This was a prospective observational study of 44 CRSwNP patients assigned to 6 months of biweekly dupilumab injections or functional endoscopic sinus surgery (FESS). Nasal microbiotas were analyzed at baseline and 6 months using culture techniques. Inflammatory biomarkers (IgE, eosinophils) and clinical endpoints (polyp score, SNOT-22, smell test) were measured. Patients were also stratified into groups based on which bacteria were cultured from their sinuses.

RESULTS: At baseline, the most prevalent bacteria were Staphylococcus aureus (43%), Stapylococcus epidermidis (36%), and Pseudomonas aeruginosa (16%). After 6 months, S. aureus and S. epidermidis significantly increased while P. aeruginosa decreased. Eosinophil counts were stable. IgE levels notably decreased in the S. aureus and S. epidermidis groups but increased with P. aeruginosa. All bacterial groups showed reduced polyp score and SNOT-22, and improved smell, but P. aeruginosa had smaller gains. Higher baseline S. aureus and S. epidermidis correlated with more significant IgE decrease.

CONCLUSIONS: Dupilumab and surgery-induced favourable microbiota changes by reducing pathogenic bacteria. Nasal microbiota composition may be associated inflammatory and clinical treatment responses in CRSwNP. S. aureus and S. epidermidis correlated with a greater improvement of IgE levels, whereas P. aeruginosa correlated with worse IgE outcomes. Analyzing each patient's nasal microbiome could enable more personalized, microbiome-directed treatment approaches for optimal CRSwNP management.},
}

@article {pmid41628253,
year = {2026},
author = {Abdalla, A and Padhi, P and Bakes, N and Thyer, R and Zenitsky, G and Jin, H and Anantharam, V and Kanthasamy, A and Ellington, AD and Phillips, GJ and Kanthasamy, AG},
title = {Preclinical Evaluation of Synthetic Biology-Driven Engineered Escherichia coli Nissle 1917 as a Living Therapeutic for Sustained L-DOPA Delivery.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00786},
pmid = {41628253},
issn = {2161-5063},
abstract = {Dopamine deficiency resulting from nigrostriatal dopaminergic neuronal damage manifests as extrapyramidal motor symptoms of Parkinson's disease (PD). Oral tablet dosing of levodopa, administered 3-4 times a day, remains the standard of care due to its tolerability and effectiveness; however, it is prone to deleterious side effects, including off-periods and levodopa-induced dyskinesia after long-term use. Herein, using synthetic biology approaches, we developed and systematically evaluated the feasibility of a probiotic-based live-biotherapeutic system to continuously deliver L-DOPA stably, thereby relieving motor symptoms. Our data demonstrate that our engineered plasmid-based L-DOPA-expressing Escherichia coli Nissle 1917 probiotic strain (EcN[2]LDOPA-P3) efficiently produced up to 12,000 ng/mL L-DOPA in vitro. In mouse model systems, EcN[2]LDOPA-P3 readily colonized for up to 48 h, achieved steady-state plasma L-DOPA concentrations, and increased brain L-DOPA and dopamine levels by 1- to 2-fold. Lastly, EcN[2]LDOPA-P3 significantly diminished motor and nonmotor behavioral deficits in a mouse model of PD compared to traditional chemical L-DOPA therapy. These findings support the therapeutic feasibility of a noninvasive, orally administered bioengineered bacterial therapy for the chronic delivery of L-DOPA, which may address limitations associated with current treatment alternatives.},
}

@article {pmid41627741,
year = {2026},
author = {Castañeda, S and Ramírez, JD and Poveda, C},
title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {265-297},
pmid = {41627741},
issn = {1940-6029},
mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.},
}

*Chagas Disease/microbiology/parasitology
Animals
Mice
Trypanosoma cruzi
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
*Microbiota
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid41627479,
year = {2026},
author = {Zhou, ZY and Liu, X and Gao, F and Wang, ML and Wang, JH and Cui, JL},
title = {Composition characterization of the culturable endophytic fungi in roots and their antagonistic activity against root rot of Astragalus mongholicus.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {178},
pmid = {41627479},
issn = {1432-072X},
support = {2025ZYYA021//Research Project on Traditional Chinese Medicine of the Health Commission of Shanxi Province/ ; },
mesh = {*Plant Roots/microbiology ; *Endophytes/isolation & purification/classification/physiology/genetics ; *Astragalus Plant/microbiology ; *Plant Diseases/microbiology/prevention & control ; Fusarium ; *Antibiosis ; *Fungi/classification/isolation & purification/genetics/physiology ; Ascomycota/isolation & purification/classification/genetics/physiology ; Phylogeny ; Alternaria ; },
abstract = {This study investigates the spatiotemporal distribution, diversity, and biocontrol potential of culturable endophytic fungi in the healthy roots of cultivated and wild Astragalus mongholicus (CA and WA), aiming to develop a microbiome-driven strategy for sustainable root rot management. A total of 304 endophytic fungal strains were isolated from roots of CA and WA, with 61 morphologically distinct representative strains identified via ITS sequencing. These strains belonged predominantly to Ascomycota (98.36%) and included 21 genera, with Fusarium (43.28%), Paraphoma (25.25%), and Alternaria (12.46%) as dominant genera. WA exhibited higher fungal diversity and evenness than CA, with community composition varying significantly by host age and cultivation status. Among the isolates, 177 strains (53 genera) showed antagonistic activity (≥ 30% inhibition rate) against root rot pathogens (F. acuminatum, F. solani, and F. oxysporum). Notably, Penicillium chrysogenum CA4-3 exhibited 78.96% inhibition against F. solani, while Paraphoma radicina CA3-15 displayed 70.23% inhibition against F. oxysporum. Bioactive strains were concentrated in 2 to 4-year-old CA roots, with Fusarium, Paraphoma, and Alternaria being the primary contributors. Mechanistic studies revealed that these fungi inhibited pathogens via secreted metabolites (causing mycelial deformation) or niche competition. The composition of endophytic fungi in A. mongholicus roots is dynamic and influenced by host development and cultivation practices. The antifungal active strain P. chrysogenum CA4-3 and P. radicina CA3-15 may possess potential value in controlling pathogenic fungi.},
}

*Plant Roots/microbiology
*Endophytes/isolation & purification/classification/physiology/genetics
*Astragalus Plant/microbiology
*Plant Diseases/microbiology/prevention & control
Fusarium
*Antibiosis
*Fungi/classification/isolation & purification/genetics/physiology
Ascomycota/isolation & purification/classification/genetics/physiology
Phylogeny
Alternaria

@article {pmid41627465,
year = {2026},
author = {Kumar, N and Das, J and Vanangamudi, M and Mojgani, N and Islam, A and Sridhar, SB and Sharma, H and Kumar, S and Panigrahy, UP and Mantry, S and Sharma, M and Ramzan, M and Chaudhary, P and Ashique, S},
title = {Modulating drug response through the gut microbiome: pathways to precision therapy.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {163},
pmid = {41627465},
issn = {1432-072X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Precision Medicine ; Pharmaceutical Preparations/metabolism ; Bacteria/metabolism/drug effects/genetics/classification ; Metabolomics ; Animals ; },
abstract = {The mutual association formed between the gut flora and the biological host is pivotal, mainly for drug action. Various examination has spotlighted the potential consequences of the gut microbiome on drug efficacy, revealing its role in controlling metabolism in the body. Furthermore, reciprocal engagement has been examined to investigate how pharmaceutical agents influence the composition of the gut microbiome. This paper emphasizes the intricate relationship between pharmacology and environmental microbiology, directing the extensive significance of pharmaceutical agents on health by controlling the gut microbial consortium. One main highlight of this review is to determine the differences observed in populace as a result of drugs, which is a crucial component in boosting personalized treatment approaches and intensifying therapeutic findings. Apart from their function in drug metabolization, the gut microbiota is disclosed as a source of metabolic products that can alter drug action. These microbially-derived metabolites could notably effect drug results and changes the body's physical mechanisms. The investigation suggests utilizing metabolomics to disclose the complications of gut microbiota-drug interactions. Several latest analytical strategies provide an effective tool for deciphering the complicated association among microbiome-generated fragments and pharmaceutical products, providing detailed understanding into this interesting connection.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Precision Medicine
Pharmaceutical Preparations/metabolism
Bacteria/metabolism/drug effects/genetics/classification
Metabolomics
Animals

@article {pmid41627460,
year = {2026},
author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT},
title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {167},
pmid = {41627460},
issn = {1432-072X},
support = {DTDLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification/virology ; *Bacteriophages/genetics/isolation & purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; },
abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.},
}

Humans
Infant
Vietnam
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification/virology
*Bacteriophages/genetics/isolation & purification/classification
Child, Preschool
Male
Female
Metagenome
Diarrhea/microbiology
Southeast Asian People

@article {pmid41627458,
year = {2026},
author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T},
title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {53},
pmid = {41627458},
issn = {1432-0614},
support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; },
abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.},
}

Animals
*Deer/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Forests
DNA, Bacterial/genetics
Endangered Species
Conservation of Natural Resources
Time Factors
Sequence Analysis, DNA

@article {pmid41627442,
year = {2026},
author = {Jay, M and Eskander, A and Lipscombe, L and Sutradhar, R},
title = {Clarifying the Interpretation of Subdistribution Hazard Ratios in Competing-Risk Analyses: Comment on Riis et al., Eur Thyroid J. 2024;13: e230181.},
journal = {European thyroid journal},
volume = {},
number = {},
pages = {},
doi = {10.1530/ETJ-25-0359},
pmid = {41627442},
issn = {2235-0802},
}

@article {pmid41627406,
year = {2026},
author = {Salvi, M},
title = {What has changed in Thyroid Eye Disease in the last five years (2020-2025).},
journal = {European thyroid journal},
volume = {},
number = {},
pages = {},
doi = {10.1530/ETJ-25-0363},
pmid = {41627406},
issn = {2235-0802},
abstract = {BACKGROUND: Significant progress has been made in the management of Thyroid eye disease (TED), based on the elucidation of important pathogenic mechanisms. This has led to novel therapeutics validated in randomized clinical trials. Autoreactive antigens that elicit specific orbital immune reactions have not yet been identified, although it has been shown that fibrocytes, circulating stem cells which differentiate into fibroblasts, are expressing the thyroid-stimulating hormone receptor (TSHR) and insulin-like growth factor-1 receptor (IGF-1R) and may be stimulated in the orbit by a cascade of inflammatory reactions inducing adipogenesis.

TED CLINICAL ASSESSMENT: Moderate-severe forms of TED are the target for immune suppressive therapy. Improvement in the assessment of the active and progressive phase of disease is becoming compelling, as the outcome of a treatment depends on how early during the progressive phase the disease is treated. The clinical activity score may not always help define the right time for treating.

THERAPY: In 2020 teprotumumab, an anti-IGF-1 receptor blocker, has been FDA approved for the treatment of TED. Since then other drugs were studied or are under investigation and will seek regulatory approval.

MICROBIOME AND TED: A series of studies have investigated the role of microbiome in thyroid autoimmunity and TED more in detail, based on the observation that treatment with antibiotics may modify the disease phenotype in a murine model of TED.

ARTIFICIAL INTELLIGENCE: This approach is being studied for the assessment of TED, especially trying to standardize the use of orbital and facial images for improving the diagnosis of the disease in the early, progressive phase. In the future these applications will allow the use of synthetic data, in addition to training on real patient images and data.},
}

@article {pmid41627377,
year = {2026},
author = {Fan, D and Wu, Y and Bao, Y and Xie, H},
title = {Effects of montelukast combined with inhaled corticosteroids on the airway-gut microbiome and immune regulation in children with asthma.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02777},
pmid = {41627377},
issn = {1588-2640},
abstract = {To evaluate the effect of montelukast combined with inhaled corticosteroids (ICS) on the microbiome-metabolism-immunity axis in children with asthma and to quantify the mediating role of short-chain fatty acids, this single-center, randomized controlled trial enrolled 100 asthmatic children (aged 6-11) who received inhaled corticosteroids with or without montelukast for 12 weeks (n = 50 in the combination group and n = 50 in the ICS-alone group). Microbiome profiles from nasal and fecal samples were assessed via 16S sequencing, and short-chain fatty acids (SCFAs) were quantified by LC-MS/MS. Immune markers (Tregs, cytokines) were measured by flow cytometry and Bio-Plex. Efficacy analyses employed linear mixed-effects models, and SCFA mediation was tested using bootstrap analysis. The combination group demonstrated significantly greater improvements in clinical outcomes including fractional exhaled nitric oxide (FeNO) (β_int = -10.24 ppb, 95% CI -16.37 to -4.11, P = 0.001), Childhood Asthma Control Test (C-ACT) score (β_int = +1.83, P < 0.05) and FEV1% (β_int = +1.87, P < 0.05) compared to ICS alone. Microbiome analysis revealed enhanced α-diversity in both nasal and fecal samples (interaction P < 0.01) with significant community structure changes (PERMANOVA interaction P_perm < 0.01). Specific genus-level alterations included reduced nasal Moraxella and Haemophilus (logFC < 0, q < 0.10) and increased fecal SCFA-producing taxa including Faecalibacterium, Roseburia, Subdoligranulum, Agathobacter, and Eubacterium hallii group (logFC > 0, q < 0.10). The combination therapy also led to elevated fecal and serum SCFA levels (β_int > 0, P < 0.01), enhanced regulatory T cell (Treg) and IL-10 responses, and suppressed Th2 cytokines (IL-4/IL-5/IL-13). Mediation analysis confirmed SCFAs partially mediated FeNO improvement, with proportions of 30.0% for total SCFAs and 37.5% for butyrate (ACME and ADE both negative, P < 0.01). The combination of montelukast and inhaled corticosteroids was superior to inhaled corticosteroids alone, providing clinical benefits that were linked to favorable remodeling of the airway-gut microbiome and enhanced Treg/IL-10 immunity. This improvement was partially mediated by short-chain fatty acids, with a comparable safety profile.},
}

@article {pmid41627349,
year = {2026},
author = {Cheng, X and Pu, S and Wang, Z and Zhang, X and Zuo, M and Ao, Q and Wu, Z},
title = {Gut microbiota dysbiosis and bone mineral density in hemodialysis patients: The mediating role of immune-metabolic pathways and clinical implications for nursing care.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02826},
pmid = {41627349},
issn = {1588-2640},
abstract = {The relationship between gut microbiota dysbiosis and bone mineral density (BMD) in hemodialysis patients, mediated through immune-metabolic pathways, remains to be fully elucidated. In this single-center prospective cross-sectional study, 165 maintenance hemodialysis patients were included to evaluate the independent association between gut microbiota composition and BMD, quantify the mediating roles of immune markers and gut-derived metabolites, and assess the effect modification by nursing-modifiable factors. Fecal samples underwent 16S rRNA sequencing and functional prediction. Inflammatory cytokines (IL-6, TNF-α), gut-derived metabolites (indoxyl sulfate, butyrate), and BMD via dual-energy X-ray absorptiometry (DXA) were measured. Gut microbiota community structure significantly differed across BMD tertiles (R2 = 0.033, P = 0.003). After full adjustment, principal coordinate 1 (PCoA-PC1, beta-diversity) was negatively associated with femoral neck BMD, while the Shannon diversity index showed a positive association (both P < 0.05). We identified 15 differentially abundant genera between high and low BMD groups. Functional prediction revealed short-chain fatty acid pathways were positively associated with BMD, while indole/p-cresol pathways showed negative associations. Mediation analysis demonstrated that immune markers and gut-derived metabolites collectively explained 45.71% of the microbiota-BMD relationship. Nursing factors significantly modified this association, with the negative relationship strengthened by low fiber intake, severe constipation, proton pump inhibitor use, and inadequate dialysis (Kt/V < 1.4). In conclusion, gut microbiota dysbiosis is independently associated with lower BMD in hemodialysis patients, partially mediated through immune-inflammatory pathways and gut-derived metabolites. Dietary fiber optimization, constipation management, prudent proton pump inhibitor prescribing, and dialysis adequacy represent actionable nursing targets to mitigate gut-mediated bone loss in this vulnerable population.},
}

@article {pmid41627982,
year = {2025},
author = {Berryman, MA},
title = {Impact of Cetylpyridinium Chloride and Zinc Mouthwash on Oral Health and the Microbiome.},
journal = {Compendium of continuing education in dentistry (Jamesburg, N.J. : 1995)},
volume = {46},
number = {Suppl 2},
pages = {5-8},
pmid = {41627982},
issn = {2158-1797},
mesh = {*Cetylpyridinium/pharmacology/therapeutic use ; *Mouthwashes/pharmacology/therapeutic use ; Humans ; *Microbiota/drug effects ; *Anti-Infective Agents, Local/pharmacology/therapeutic use ; *Zinc Compounds/pharmacology ; *Oral Health ; *Mouth/microbiology ; Dental Plaque/prevention & control ; *Zinc/pharmacology ; Biofilms/drug effects ; Halitosis/prevention & control/drug therapy ; },
abstract = {The widespread use of antimicrobial mouthwashes highlights the importance of understanding their impact on both clinical outcomes and the oral microbiome. This literature review seeks to critically evaluate the current academic knowledge regarding the clinical efficacy of mouthwash containing cetylpyridinium chloride (CPC) and zinc lactate in reducing plaque, gingivitis, and oral malodor, with a particular focus on its interactions with the oral microbiome. Clinical trials have validated the efficacy of CPC and zinc lactate in enhancing oral health metrics, although the long-term impact of their combined use on the oral microbiome warrants further exploration. CPC and zinc lactate in a mouthwash is particularly effective against oral biofilms. While bacteria has the potential to develop resistance against antiseptics, there is no evidence at this time to suggest that CPC and zinc lactate influences resistance in the oral cavity. However, there is evidence that CPC and zinc lactate in combination may be superior to other antibacterial mouthwashes at controlling periodontal pathogens while promoting a healthy and balanced oral microbiome. Future research should prioritize longitudinal, multi-omics investigations to elucidate the nature and extent of these interactions across diverse bacterial communities. The capacity of CPC and zinc lactate to support a healthy oral microbiome, without promoting antimicrobial resistance, underscores their combined potential as a safe and effective oral hygiene solution.},
}

*Cetylpyridinium/pharmacology/therapeutic use
*Mouthwashes/pharmacology/therapeutic use
Humans
*Microbiota/drug effects
*Anti-Infective Agents, Local/pharmacology/therapeutic use
*Zinc Compounds/pharmacology
*Oral Health
*Mouth/microbiology
Dental Plaque/prevention & control
*Zinc/pharmacology
Biofilms/drug effects
Halitosis/prevention & control/drug therapy

@article {pmid41627051,
year = {2026},
author = {Shoemaker, WR and Grilli, J},
title = {The macroecological dynamics of sojourn trajectories in the human gut microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0122125},
doi = {10.1128/msystems.01221-25},
pmid = {41627051},
issn = {2379-5077},
abstract = {The human gut microbiome is a dynamic ecosystem. Host behaviors (e.g., diet) provide a regular source of environmental variation that induces fluctuations in the abundances of resident microbiota. Despite these displacements, microbial community members remain highly resilient. Population abundances tend to fluctuate around a characteristic steady-state over long timescales in healthy human hosts. These temporary excursions from steady-state abundances, known as sojourn trajectories, have the potential to inform our understanding of the fundamental dynamics of the microbiome. However, to our knowledge, the macroecology of sojourn trajectories has yet to be systematically characterized. In this study, we leverage theoretical tools from the study of random walks to characterize the duration of sojourn trajectories, their shape, and the degree that diverse community members exhibit similar qualitative and quantitative dynamics. We apply the stochastic logistic model as a theoretical lens for interpreting our empirical observations. We find that the typical timescale of a sojourn trajectory does not depend on the mean abundance of a community member (i.e., carrying capacity), although it is strongly related to its coefficient of variation (i.e., environmental noise). This work provides fundamental insight into the dynamics, timescales, and fluctuations exhibited by diverse microbial communities.IMPORTANCEMicroorganisms in the human gut often fluctuate around a characteristic abundance in healthy hosts over extended periods of time. These typical abundances can be viewed as steady states, meaning that fluctuating abundances do not continue towards extinction or dominance but rather return to a specific value over a typical timescale. Here, we empirically characterize the (i) length (i.e., number of days), (ii) relationship between length and height, and (iii) typical deviation of a sojourn trajectory. These three patterns can be explained and unified through an established minimal model of ecological dynamics, the stochastic logistic model of growth.},
}

@article {pmid41626790,
year = {2026},
author = {Barati, S and Ghoflchi, S and Nakhaei, A and Yazdi, MP and Hosseinzadeh, P and Hosseini, H and Jalili-Nik, M},
title = {Gut Microbiome Strategies for Enhancing ICI Delivery Across the BBB in Glioblastoma.},
journal = {BioFactors (Oxford, England)},
volume = {52},
number = {1},
pages = {e70077},
doi = {10.1002/biof.70077},
pmid = {41626790},
issn = {1872-8081},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Glioblastoma/drug therapy/immunology/microbiology/pathology ; *Blood-Brain Barrier/drug effects/metabolism/immunology ; *Immune Checkpoint Inhibitors/administration & dosage/therapeutic use ; *Brain Neoplasms/drug therapy/immunology/microbiology/pathology ; Animals ; Tumor Microenvironment/drug effects ; Fecal Microbiota Transplantation ; },
abstract = {Glioblastoma (GB) is highly malignant with a median survival of 14 months despite conventional treatments like surgery, radiotherapy, and temozolomide. Resistance to these therapies necessitates innovative approaches, such as immune checkpoint inhibitors (ICIs) targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), programmed cell death protein 1 (PD-1), and programmed death ligand 1 (PD-L1) to enhance T-cell-mediated tumor destruction. However, clinical trials have shown limited ICI efficacy in GB due to its immunosuppressive microenvironment and the blood-brain tumor barrier (BBTB), which impairs drug delivery. Emerging evidence highlights the gut microbiota as a pivotal modulator of ICI response, enhancing CD8[+] and CD4[+] T-cell function, antigen presentation, and immune modulation via the gut-brain axis in cancers. In addition, studies showed that gut-derived metabolites, including short-chain fatty acids, modulate immune responses and support blood-brain barrier integrity by regulating inflammatory signaling and tight junction proteins. Future GB research should prioritize clinical trials, mechanistic studies, and interventional strategies like fecal microbiota transplantation and probiotics to enhance ICI efficacy.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Glioblastoma/drug therapy/immunology/microbiology/pathology
*Blood-Brain Barrier/drug effects/metabolism/immunology
*Immune Checkpoint Inhibitors/administration & dosage/therapeutic use
*Brain Neoplasms/drug therapy/immunology/microbiology/pathology
Animals
Tumor Microenvironment/drug effects
Fecal Microbiota Transplantation

@article {pmid41626630,
year = {2026},
author = {Lin, L and Neves, ALA and Ominski, KH and Guan, LL},
title = {Metatranscriptomics uncovers diet-driven structural, ecological, and functional adaptations in the rumen microbiome linked to feed efficiency.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf251},
pmid = {41626630},
issn = {2730-6151},
abstract = {The rumen microbiome plays a pivotal role in modulating feed efficiency in ruminants, yet the ecological mechanisms mediating the active interactions among microbial adaptations, dietary inputs, and host feed efficiency within the rumen remain poorly understood. To address this gap, we analyzed 120 metatranscriptomic datasets obtained from 30 purebred Angus bulls (each sampled four times) classified as high-feed-efficiency or low-feed-efficiency based on feed conversion ratio, and fed either forage-based (n = 15) or grain-based (n = 15) diets. We constructed a comprehensive active gene catalog comprising 1 744 067 non-redundant genes and compiled a reference set of 25 115 ruminant microbial genomes. Using integrated Neutral Community Model analysis and carbohydrate-active enzyme profiling, we examined how ecological processes and functional capacities differed across host phenotypes and diets. Neutral Community Model fits revealed that stochastic processes broadly governed rumen microbial community structures (R[2] = 0.779 for high-feed-efficiency; R[2] = 0.781 for low-feed-efficiency). Within the predominantly stochastic processes, however, high-feed-efficiency bulls exhibited strong positive selection for diet-responsive microbial lineages: Fibrobacter spp. (positively selected species-level genome bins: 61.3%-76.0%; negatively selected: 0%-1.3%), Butyrivibrio spp. (positively selected: 13.3%-46.0%; negatively selected: 1.0%-11.2%) under forage feeding, and UBA1067 spp. (positively selected: 33.3%-48.5%; negatively selected: 0%-8.3%) under grain feeding. These lineages encoded catalytic domains appended with carbohydrate-binding modules, such as tandem carbohydrate-binding modules linked to glycoside hydrolases, thereby enhancing substrate adhesion and degradation. In contrast, low-feed-efficiency bulls showed more random community structures and reduced functional specialization. Therefore, these suggest that cattle hosts with higher feed efficiency promote microbial populations functionally aligned with dietary inputs, a process we define as efficient host-mediated microbial amplification. These findings offer new insight into how ecological assembly and functional adaptation of the microbiome contribute to feed efficiency and lay the foundation for microbiome-informed strategies to enhance ruminant production sustainability.},
}

@article {pmid41626616,
year = {2026},
author = {Zhang, X and Lv, X and Zhang, L and Jia, T and Zhao, S},
title = {Association between a novel Dietary Index for Gut Microbiota and periodontitis: a cross-sectional study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1714913},
pmid = {41626616},
issn = {2296-861X},
abstract = {BACKGROUND: The gut microbiota and periodontitis have attracted increasing research interest. The Dietary Index for Gut Microbiota (DI-GM), a novel metric for assessing gut microbiome diversity, has not yet been investigated in relation to periodontitis.

METHODS: This cross-sectional study analyzed data from the 2009-2014 National Health and Nutrition Examination Survey including 9,978 participants aged 30-80 years who had periodontal examination records. Participants were categorized into two groups: no periodontitis (n = 4,879) and periodontitis (mild, moderate, or severe; n = 5,099). The DI-GM was calculated using dietary recall data, incorporating both beneficial and unfavorable components for gut microbiota. Multivariable logistic regression was applied to examine the association between DI-GM and periodontitis, with body mass index (BMI) evaluated as a potential mediator. Secondary analyses included subgroup evaluations, restricted cubic spline (RCS) modeling, and multivariable imputation.

RESULTS: A higher DI-GM score was inversely associated with periodontitis (odd ratio [OR] = 0.94, 95% confidence interval [CI]: 0.91-0.97). Similarly, a higher beneficial microbiota score was linked to a lower prevalence of periodontitis (OR = 0.90, 95% CI: 0.87-0.94). After adjustment, DI-GM remained inversely associated with moderate (OR = 0.94, 95% CI: 0.91-0.97) and severe periodontitis (OR = 0.89, 95% CI: 0.85-0.94; both p < 0.001). Likewise, higher beneficial microbiota scores correlated with reduced odds of moderate (OR = 0.91, 95% CI: 0.87-0.95) and severe periodontitis (OR = 0.84, 95% CI: 0.79-0.90; all p < 0.001). The RCS model indicated a linear association between DI-GM and periodontitis. BMI showed a significant mediating effect (4.9, 95% CI: 0.96-11.05%; p = 0.014).

CONCLUSION: The newly proposed DI-GM demonstrated an inverse association with the prevalence of periodontitis, with BMI acting as a significant mediator in this relationship.},
}

@article {pmid41626567,
year = {2026},
author = {Wang, J and Qu, J and Ye, M and Feng, R and Hui, X and Yang, X and Jin, J and Tong, Q and Zhang, X and Wang, Y},
title = {Beyond conventional therapies: Gut microbiota modulation and macromolecular drugs in the battle against cardiometabolic diseases.},
journal = {Journal of pharmaceutical analysis},
volume = {16},
number = {1},
pages = {101416},
pmid = {41626567},
issn = {2214-0883},
abstract = {Cardiometabolic diseases (CMDs) represent an ongoing major global health challenge, driven by complex interactions among genetic, environmental, microbiome-related, and other factors. While small-molecule drugs and lifestyle interventions can provide clinical benefits, they are possible to be constrained by the limited druggability of key target proteins, the potential risks of off-target effects, and difficulties in maintaining long-term adherence. In recent years, gut microbiota modulation and macromolecular drugs have emerged as promising therapeutic strategies. Gut microbiota modulation (e.g., probiotics, synbiotics, or natural products) exerts systemic metabolic and immune effects, supporting a therapeutic approach targeting multiple diseases. Meanwhile, macromolecular drugs (e.g., peptides, antibodies, and small nucleic acids) offer precise, pathway-targeted interventions. Despite advancements, limitations remain in addressing ethical considerations in microbiota modulation and optimizing targeted delivery systems, all of which may hinder clinical translation. Here, we provide a comprehensive overview of therapeutic approaches for CMDs, with a focus on obesity, type 2 diabetes mellitus (T2DM), and atherosclerosis (AS). The review is structured around three key aspects: i) conventional therapies, including small-molecule drugs and lifestyle interventions; ii) emerging therapies encompassing gut microbiota modulation, macromolecular drugs, and their interactions; and iii) challenges and opportunities for comorbidity management, microbiota ethics, and artificial intelligence (AI)-driven therapeutic optimization. We hope this review enhances the understanding of small-molecule drugs, lifestyle interventions, gut microbiota modulation, and macromolecular drugs in the management of CMDs, thereby fostering medical innovation and contributing to the development of system-based comprehensive therapeutic paradigms.},
}

@article {pmid41626521,
year = {2026},
author = {Al-Khatib, A and Naous, A and Sokhn, ES},
title = {Prevalence and characterization of bacterial rectal colonization patterns in pediatric patients: A cross-sectional study.},
journal = {New microbes and new infections},
volume = {70},
number = {},
pages = {101707},
pmid = {41626521},
issn = {2052-2975},
abstract = {BACKGROUND: Antimicrobial resistance is a major public health concern requiring ongoing surveillance to determine its extent and associated factors. This study evaluates bacterial isolates from pediatric patients in terms of distribution, resistance mechanisms, and demographic/clinical correlations.

METHODS: In this cross-sectional study, after obtaining parental assent, rectal swabs were aseptically collected from children by pediatric doctors at Healthcare Centers in Beirut. Necessary data were collected through validated questionnaires provided to parents. Bacterial identification was performed using standard culture, isolation, and biochemical techniques. Susceptibility of bacterial strains was studied using antimicrobial susceptibility testing. Finally, Polymerase Chain Reaction (PCR) was used to characterize resistance genes. Associations between resistance phenotypes and sample characteristics were assessed using chi-square or Fisher's exact test, as appropriate.

RESULTS: Among 118 rectal isolates, Escherichia coli predominated (75.4 %), followed by other Enterobacterales and Staphylococci. Overall, 31.36 % of isolates harbored a major resistance mechanism (ESBL, AmpC, CRE, or MRSA), with ESBL-producing E. coli being the most frequent (22 %) and blaCTX-M detected in the majority of ESBL isolates. Previous antacid intake was the only characteristic significantly associated with resistance phenotypes (p = 0.03). AmpC, CRE, and MRSA remained relatively infrequent but represented clinically important resistance mechanisms.

CONCLUSION: Rectal colonization with multidrug-resistant organisms was frequent, driven mainly by ESBL-producing, blaCTX-M-positive E. coli, while AmpC, CRE, and MRSA were less common but remained important resistance mechanisms. The association between resistance phenotypes and prior antacid use highlights the need for larger pediatric surveillance studies and careful evaluation of antacid and antibiotic use in this population.},
}

@article {pmid41626182,
year = {2025},
author = {Yao, B and Hou, C and Zhang, W and Bao, Z and Li, Y and Zhang, Z},
title = {Research progress on the impact and mechanisms of helicobacter pylori infection on the efficacy of immunotherapy for gastric cancer.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1674814},
pmid = {41626182},
issn = {2234-943X},
abstract = {BACKGROUND: Helicobacter pylori (H. pylori), recognized as a Group I carcinogen by the World Health Organization, is a key etiological agent in gastric cancer (GC). The majority of GC patients, particularly in China, present at advanced stages with constrained therapeutic options. Tumor immunotherapy, especially immune checkpoint inhibitors targeting the PD-1/PD-L1 axis, has emerged as a promising strategy. However, immunotherapy benefits only a subset of patients. Notably, H. pylori infection plays a significant role in GC and may also influence the efficacy of immunotherapy.

MAIN CONTENT: This review systematically summarizes the role and mechanisms of H. pylori in GC development, progression, and immunotherapy, focusing on the following aspects. Pathogenic mechanisms: H. pylori drives GC development through virulence factors (e.g., CagA, VacA, urease), which induce chronic inflammation, epithelial damage, immune evasion, and remodeling of the tumor microenvironment. Impact on immunotherapy and underlying mechanisms: The clinical efficacy is conflicting, some studies associate H. pylori infection with poor prognosis following immunotherapy, while others to better responses. Proposed mechanisms include PD-L1 upregulation via multiple signaling pathways, modulation of immune cells within the tumor microenvironment, and gut microbiota alterations affecting PD-1/PD-L1 inhibitor efficacy.

CONCLUSION: H. pylori has a complex influence on GC immunotherapy. Further research is needed to clarify the underlying mechanisms and assess the predictive value of H. pylori testing in clinical practice. Combining microbiome-based strategies with immunotherapy may enable more personalized and effective treatment.},
}

@article {pmid41625959,
year = {2026},
author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR},
title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100344},
pmid = {41625959},
issn = {2666-5662},
abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.},
}

@article {pmid41625945,
year = {2026},
author = {Larionova, E and Moran, GP},
title = {The role of Fusobacterium nucleatum in the tumour microenvironment and carcinogenesis of oral and colonic malignancies.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag002},
pmid = {41625945},
issn = {2633-6685},
abstract = {The intra-tumoural microbiome is an increasing area of research with potential benefits in cancer diagnostics and treatment development. Numerous studies have implicated Fusobacterium nucleatum, a member of the oral microbiota, in the development, immune evasion, and dissemination of oral and colorectal tumours. Although F. nucleatum is yet to be classified as a cause or consequence of cancer, reports indicate the microorganism's involvement in DNA damage, pathologic glucose uptake, and cellular proliferation. This accumulation of genetic instability is consistent with the multistep nature of malignant neoplasm progression. Virulence factors of F. nucleatum were shown to maintain an unresolved inflammatory state and impair the normal function of immune cells. The accompanying pro-inflammatory conditions facilitate vasculature remodelling, expediting tumour expansion, through a range of mechanisms. Pro-metastatic epithelial-to-mesenchymal transition and changes in gene expression have been observed in cancer cells upon F. nucleatum infection, suggesting an association with poorer prognosis. As a frequently encountered microorganism in the oral and colorectal intra-tumoural microbiome, F. nucleatum represents an intriguing, yet cautious research prospect with opportunities for novel prevention and therapeutic strategies. The objective of this work is to review the relevant evidence, taking into account the complexity of the tumour microenvironment.},
}

@article {pmid41625836,
year = {2025},
author = {Matsukawa, M and Sakai, Y and Aoki, K and Ishii, Y},
title = {Urinary Microbiome Profiling by Shotgun Metagenomic Sequencing in Women Having Acute Cystitis-Like Symptoms With Negative Urine Cultures.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e100451},
pmid = {41625836},
issn = {2168-8184},
abstract = {BACKGROUND: Women presenting with typical symptoms of acute cystitis but with negative urine cultures, termed acute cystitis-like symptoms with negative urine cultures (ACNCs) in this study, are not uncommon. Despite previous attempts to detect bacterial DNA in urine, the etiology remains unclear. Although alterations in the urinary microbiome have been linked to other urological disorders, its involvement in ACNC has not been thoroughly investigated.

METHODS: Between September 2016 and December 2017, midstream urine samples were collected from women aged ≥16 years who had at least one typical symptom of acute cystitis and a negative urine culture. Samples were obtained at the initial (V1) and follow-up (V2) visits. Shotgun metagenomic sequencing (SMG) was performed via an Illumina MiSeq system. Taxonomic analysis at the genus level included taxa with ≥10 assigned reads in samples with ≥10,000 human-subtracted reads (HSRs).

RESULTS: Of 206 eligible women, 15 (7.3%; median age, 65 years) met the ACNC criteria and were enrolled. SMG was conducted for 15 samples at V1 and nine samples at V2. At V1, the HSR varied widely, and only five samples met the criteria for reliable interpretation. Seven samples, particularly those with high-grade pyuria, contained fewer than 1,000 HSRs, indicating potentially very low microbial loads or technical limitations. ACNC microbiomes demonstrated marked interindividual variation in taxonomic composition. The predominant taxa most frequently observed were Lactobacillus spp., Gardnerella spp., and JC polyomavirus. Conventional uropathogens, such as Escherichia spp., were not identified at interpretable levels. At V2, microbial diversity remained heterogeneous, but eight samples yielded sufficient read counts for interpretation.

CONCLUSIONS: While conventional uropathogens below interpretable criteria are unlikely to be responsible for most ACNCs, it is not necessarily recommended to regard the leading taxon in each case as the cause or to exclude microbiological involvement simply due to a low HSR because no validated metagenomic signature distinguishes pathogens from commensals. However, the observed diversity in ACNC microbiome profiles may reflect a heterogenous group of microbial conditions, including potentially viral, and nonmicrobial etiologies.},
}

@article {pmid41625766,
year = {2025},
author = {Zhao, H and Liu, Y and Su, L and Cui, P and Sai, J and Li, S and Wang, N and He, P},
title = {Gut-liver-muscle axis: linking gut microbiota dysbiosis to malnutrition and sarcopenia in liver disease.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1727270},
pmid = {41625766},
issn = {2296-858X},
abstract = {Nutritional disorders and muscle wasting associated with liver disease are key determinants of poor prognosis in patients with chronic liver disease. The formation of these conditions involves multiple factors, including impaired energy metabolism, enhanced protein degradation, and gut microbiota imbalance. In recent years, with the deepening of microbiome research, the concept of the "gut-liver-muscle axis" has gradually emerged to explain the more systematic interaction between gut microbiota, liver metabolism, and skeletal muscle homeostasis. Gut dysbiosis can promote liver inflammation and metabolic disorders through various pathways, further weakening muscle energy utilization and protein synthesis, ultimately leading to malnutrition and sarcopenia. This review systematically explores the crucial role of gut microbiota in liver disease-related malnutrition and muscle wasting, elucidates its potential mechanisms in influencing host metabolism and nutritional status through the "gut-liver-muscle axis," and discusses the prospects of microbiome interventions in improving nutritional outcomes in liver disease.},
}

@article {pmid41625367,
year = {2025},
author = {He, S and Li, Z and Huang, W and Peng, Y and Niu, L and Wen, H and Xv, Y and Li, S and Li, Z},
title = {Functional phyto-nanozymes for dual regulation of microbial metabolism and overinflammation microenvironment in diabetic wound.},
journal = {Materials today. Bio},
volume = {35},
number = {},
pages = {102293},
pmid = {41625367},
issn = {2590-0064},
abstract = {Chronic wound management demands multifunctional therapeutic strategies that simultaneously address excessive inflammation and oxidative stress. To meet this challenge, we engineered a three-dimensional biomimetic scaffold (CSSTF) by integrating collagen-based thermosensitive hydrogel, a SiO2-supported copper single-atom catalyst (Cu-SAC-SE), and tea tree oil-encapsulated liposomes (TTO@Lpo). This composite design enables sustained release of bioactive components, achieving synergistic ROS scavenging, mitochondrial protection, and suppression of NLRP3 inflammasome-mediated pyroptosis. Notably, CSSTF exhibits dual immunomodulatory effects by attenuating neutrophil extracellular trap (NET) formation and shifting macrophage polarization from pro-inflammatory M1 to anti-inflammatory M2 phenotype, thereby mitigating inflammation-associated tissue damage. Parallelly, TTO@Lpo orchestrates microbial remodeling by selectively inhibiting pathogenic bacteria while enriching beneficial commensals, coupled with elevated production of anti-inflammatory metabolites (e.g., short-chain fatty acids), establishing a self-reinforcing "microbiota-metabolism-inflammation" regulatory loop. In diabetic murine models, CSSTF significantly accelerated wound closure through coordinated mechanisms: (1) enhanced angiogenesis via VEGF upregulation, (2) NETosis suppression that dampens cytokine storms, and (3) ECM reconstruction facilitated by fibroblast activation. Beyond material innovation, this work pioneers a phyto-bionic therapeutic platform leveraging enzymatic catalysis and microbiome reprogramming, offering a paradigm shift in chronic wound treatment through simultaneous physical barrier restoration and dynamic biological modulation.},
}

@article {pmid41625355,
year = {2026},
author = {Ling, X and Peng, Y and Zhang, Y and Yim, CC and Chan, HN and Yang, Y and Sun, Q and Zhang, XJ and Kam, KW and Chu, WK and Ip, P and Young, AL and Hammond, CJ and Tsui, SKW and Tham, CC and Pang, CP and Chen, LJ and Yam, JC},
title = {Associations between Ocular Surface Microbiome and Refractive Status in Children and Adolescents.},
journal = {Ophthalmology science},
volume = {6},
number = {3},
pages = {101042},
pmid = {41625355},
issn = {2666-9145},
abstract = {PURPOSE: To identify the compositional and functional alterations in the ocular surface microbiome (OSM) which are associated with myopia in children and adolescents.

DESIGN: A population-based, cross-sectional study.

PARTICIPANTS: Eight hundred forty-seven children and adolescents aged 3 to 17 years were included.

METHODS: Conjunctival swab samples were collected from the participants and processed via 16S ribosomal RNA gene sequencing.

MAIN OUTCOME MEASURES: Microbial profiles of participants were processed with QIIME2. Alpha (species diversity) and beta diversity (community structure) metrics were calculated. Microbial functional profile was predicted using PICRUSt2.

RESULTS: Shannon (P < 0.001) and observed (P = 0.010) indexes were different among samples from myopic eyes (n = 432), as compared with those from emmetropic (n = 214) and hyperopic (n = 201) eyes. They were correlated with spherical equivalent (Shannon P = 0.0036, observed P = 0.0129) and axial length (Shannon P = 0.0057, observed P = 0.012). Beta diversity with distinct microbial signatures was unique (P < 0.05) among the eyes with myopia (Haemophilus, Aquabacterium, Anaerococcus), emmetropia (Sphingobium, Clostridium sensu stricto 1, and Fusobacterium) and hyperopia (Streptococcus, Kocuria, and Gemella). Functional profiling found enrichment of several Kyoto Encyclopedia of Genes and Genomes pathways, including oxidative phosphorylation, in the myopic ocular surface, suggesting a distinct energy utilization pattern in the myopic microbiome.

CONCLUSIONS: This study reveals distinct compositional and functional profiles in the OSM of myopic children and adolescents. These findings demonstrate an association between refractive status and the OSM; however, causality has not been established, highlighting the need for further research.

FINANCIAL DISCLOSURES: The author has no/the authors have no proprietary or commercial interest in any materials discussed in this article.},
}

@article {pmid41625281,
year = {2026},
author = {Nieto Fernandez, FE and Roccanova, P and Fantal-Pinckombe, B and Catapano, R},
title = {Soil microbiome analysis of a northeastern deciduous forest in SUNY Old Westbury, Long Island, New York.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {41625281},
issn = {2578-9430},
abstract = {We studied spatial changes in soil bacterial microbiome composition and diversity in a 111 acres old growth mixed hardwood forest plot in Long Island, NY. Forty soil samples were collected from four forest transects across the forest plot representing various soil features, and dominant vegetation. Three phyla account for 91% of the bacteria in the samples, Acidobacteriota (43%), Proteobacteriota (30%), and Actinobacteriota (18%). We also found 16 different classes and 33 orders. Sites dominated by black birch, Betula lenta were significant more diverse than all other sites. We also found significant differences in microbiome composition based on pH and vegetation.},
}

@article {pmid41624431,
year = {2026},
author = {Shahzad, M and Ismail, M and Islam, MJU and Yumna, S and Irum, T and Malalai, K and Sara, I and Al Nabhani, Z and Andrews, SC},
title = {The oral microbiome profile of Pakistani infants characterized by 16S rRNA amplicon sequencing.},
journal = {Data in brief},
volume = {64},
number = {},
pages = {112449},
pmid = {41624431},
issn = {2352-3409},
abstract = {The oral microbiome is the second most complex and diverse ecosystem in the human body. A number of longitudinal studies assessing oral microbiome development in diverse populations has been reported recently. However, oral microbiome development in vulnerable populations such as infants who are at risk of malnutrition is rarely explored. The current study aims to assess oral bacterial community development and associated factors in Pakistani infants residing in malnutrition endemic areas of Pakistan. Data and oral swab samples were collected from infants (n = 71) at baseline (age <28 days) and 3-months follow-up (n = 65) followed by DNA extraction, PCR amplification and 16S rRNA amplicon sequencing on a DNBSEQ-G400 platform. Of the total 136 samples, 119 samples were successfully sequenced and analyzed further. Bioinformatics and statistical analyses were performed using Cutadapt, FLASH and R. Overall, the Bacillota (formerly known as Firmicutes) was the predominant bacterial phylum, accounting for 87.6 % relative abundance at baseline and 84.3 % at 3-months. The Streptococci and Veillonella were the predominant bacterial genera with 66.9 % and 13.4 % relative abundance at baseline and 55.4 % and 26.1 % at 3-months, respectively. This study provides the first comprehensive insights into oral bacterial community development of vulnerable infants at risk of malnutrition. The data can be used to longitudinally assess oral microbiome develop during early infancy and associated maternal, infant and environmental factors. Sequencing data are deposited in the NCBI Sequence Read Archive as BioProject PRJNA1303979.},
}

@article {pmid41624250,
year = {2026},
author = {Si, M and Yan, S and Ding, S and Liu, R and Xiong, X and Qiao, J and Qi, X},
title = {Changes in Metabolites and Microbial Communities in Follicular Fluid Associated With Ovarian Function in Patients With Polycystic Ovary Syndrome.},
journal = {MedComm},
volume = {7},
number = {2},
pages = {e70622},
pmid = {41624250},
issn = {2688-2663},
abstract = {Polycystic ovary syndrome (PCOS) is a well-documented endocrine disorder associated with metabolic abnormalities. Research has indicated potential links between PCOS and the gut microbiome, and the presence of microbial communities in follicular fluid (FF) has been demonstrated; however, their functional interplay with metabolites has not been elucidated. This case-control study involved 40 patients with PCOS and 40 controls matched for age. A comprehensive analysis of FF metabolites and microbial communities by means of metabolomics analysis and 16S rDNA sequencing was performed. Twelve metabolites and 15 microbial communities were significantly different between the PCOS and control groups. AMH and AFC were significantly associated with the majority of the differentially abundant metabolites and bacteria, suggesting a potential association between FF components and ovarian function. In this study, we found that D-glucose and Alicyclobacillus were the most important variables in the metabolite model and microbial model, respectively. Mechanistically, Alicyclobacillus acidoterrestris, Terrimonas ferruginea, or Terrimonas pekingense can efficiently utilize glucose thereby reducing FF glucose levels, which provides insights into the microbiome-metabolite connection. These findings suggest a potential link among bacteria-metabolite-ovarian function, which could have implications for understanding the pathophysiology of PCOS and developing novel diagnostic and therapeutic strategies targeting metabolic and microbial aspects.},
}

@article {pmid41624197,
year = {2025},
author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M},
title = {Effects of NatureKnit™ organic, a blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols, on the metabolic activity and community composition of the human gut microbiome using the M-SHIME[®] gastrointestinal model.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1740906},
pmid = {41624197},
issn = {2296-861X},
abstract = {OBJECTIVES: The effects of a proprietary blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially known as NatureKnit™ Organic) on the human gut microbiome were assessed.

METHODS: Short-term (48 h) in vitro colonic simulations using the validated Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME[®]) platform, with fecal inoculum from nine individual healthy human donors, were performed. Purified organic fibers (inulin and psyllium) were evaluated as comparators and a negative control was included. Primary measures included pH, gas pressure, short-chain fatty acid (SCFA) production, and microbial community composition.

RESULTS: All test products were well fermented with NatureKnit™ Organic showing slower fermentation kinetics than the purified fibers. SCFAs were significantly increased with all test products versus the negative control (p < 0.0001 for all) and NatureKnit™ Organic reached significance versus both purified fibers (p < 0.0001 for both). While relative abundances in the mucosal compartment were similar among all test conditions, luminal bacterial abundance increased with NatureKnit™ Organic and psyllium versus the negative control. The latter was mainly associated with statistically increased abundance (p < 0.05) of the genera Eisenbergiella and Monoglobus, with an additional strong enrichment of Bacteroidaceae. Furthermore, bacterial species richness was significantly increased with NatureKnit™ Organic versus the negative control (p = 0.0495), which was not observed for the purified organic fibers (p = 0.0567 and p = 0.4285 for inulin and psyllium, respectively).

CONCLUSION: Overall, the obtained results indicate that NatureKnit™ Organic may have a greater and gentler prebiotic effect compared with established purified prebiotic fibers.},
}

@article {pmid41624190,
year = {2025},
author = {Betancur, D and Jara, EL and Lima, CA and Victoriano, M},
title = {Diet type and the oral microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1691952},
pmid = {41624190},
issn = {2296-861X},
abstract = {BACKGROUND: The oral microbiome changes across the lifespan and is modulated by behavioral and metabolic exposures. Tobacco consumption, suboptimal hygiene, and frequent sugar intake disrupt microbial homeostasis, thereby increasing vulnerability to chronic oral diseases. While diet influences systemic metabolic and inflammatory health, evidence describing persistent, direct ecological effects on oral microbial communities remains limited.

OBJECTIVE: The objective of this study is to synthesize mechanistic insights on how dietary patterns shape the oral microbiome and influence systemic inflammatory or metabolic risk.

METHODOLOGY: A narrative, non-systematic review was conducted through expansive literature exploration. Peer-reviewed original and clinical studies reporting defined dietary exposures caloric restriction, plant-based diets, inorganic nitrate and fiber intake, and high-fat or high-sugar processed diets, were qualitatively evaluated for mechanistic relevance.

KEY FINDINGS: Plant-enriched, high-fiber diets, nitrate intake, and caloric restriction were associated with reduced oxidative stress, lower pro-inflammatory cytokines, and greater diversity of commensal taxa, suggesting improved ecological stability. In contrast, processed diets promote metabolic conditions that indirectly remodel the oral habitat, favoring dysbiosis and a niche permissive to periodontitis.

CONCLUSION: The diet-oral microbiome-systemic inflammation axis is bidirectional and clinically relevant. Understanding both direct ecological regulation and indirect metabolic effects is essential to support precision nutrition strategies aimed at maintaining oral microbial balance and systemic inflammatory risk mitigation.},
}

@article {pmid41624188,
year = {2025},
author = {Ohmi-Shimizu, N and Takano, C and Tsuji, NM and Iwama, M and Okamura, N and Komine-Aizawa, S and Hayakawa, S and Ogawa, E and Morioka, I and Ishige, M},
title = {Sibling-controlled study of the impact of dietary therapy on the gut microbiota in children with phenylketonuria.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1662634},
pmid = {41624188},
issn = {2296-861X},
abstract = {BACKGROUND: Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by a deficiency of phenylalanine hydroxylase activity. Due to intolerance to the dietary intake of phenylalanine (Phe), the patients need to take a low-protein diet alongside immediate utilization of Phe-free medical formula upon diagnosis to maintain optimal plasma Phe concentrations. While dietary influences on gut microbiome composition are well-established, the potential alterations in microbiota and their impact on the immune function of children with PKU remain underexplored. We therefore conducted a pilot, sibling-controlled study to assess how dietary therapy for PKU affects gut microbiota and whether these changes are associated with food allergy incidence.

MATERIALS AND METHODS: A questionnaire-based survey was conducted across multiple institutions to determine the prevalence of food allergies in children with PKU. Four children with PKU who have unaffected siblings were recruited to investigate their dietary intake and immunological profiles. Stool samples from both groups were collected and analyzed for gut microbiota composition and short-chain fatty acid (SCFA) profiles.

RESULTS: The survey indicated a notably low prevalence of food allergies in children with PKU (approximately 1%). The four children with PKU strictly adhered to a low-protein diet and maintained their blood phenylalanine levels within the target therapeutic range. Among the PKU group, only one child had an egg allergy, while the remaining children showed no allergic tendencies. Although no adverse immunological effects were observed, the gut microbiota composition of the PKU group significantly differed from that of the unaffected siblings, as indicated by the weighted UniFrac distance (p = 0.027). In the PKU group, the abundance of Faecalibacterium prausnitzii was significantly reduced (p = 0.002), that of Bifidobacterium was increased, and Akkermansia muciniphila was detected. No overall decrease in total SCFA levels was observed in the PKU group, although the acetate/butyrate ratio significantly increased.

DISCUSSION: This study is the first to characterize the gut microbiota of children with PKU using their unaffected siblings as genetically and environmentally matched controls. Our findings suggest that the distinctive dietary management in PKU results in a characteristic gut microbial profile. We further propose a novel hypothesis that these compositional shifts may establish a unique intestinal microenvironment in diet-adherent PKU, which could be negatively associated with the development of food allergy. Larger cohort studies incorporating host metabolomic profiling are needed to determine causal links between dietary therapy and immunological background, ultimately contributing to improved nutritional management.},
}

@article {pmid41624179,
year = {2026},
author = {Rana, MS and Shamsuzzaman, M and Shin, JH and Lee, YJ and Kim, B and Seo, MG and Seo, SM and Kim, SH and Lee, JC and Kim, J and Kim, S},
title = {Bentonite-Based Functional Nanoclay Enhances Bacteriophage Therapy against Enteric Infections via Toxin Adsorption and Microbiome Recovery.},
journal = {Biomaterials research},
volume = {30},
number = {},
pages = {0310},
pmid = {41624179},
issn = {1226-4601},
abstract = {Diarrheal infections caused by antibiotic-resistant Escherichia coli pose a serious threat to human and animal health, driving the need for innovative therapeutic strategies. This study introduces a dual-action strategy that integrates bacteriophage EC.W2-6 with bentonite to enhance bacterial clearance and macromolecular toxin removal. Phage EC.W2-6 demonstrated high specificity against enterotoxigenic E. coli (ETEC) H10407, achieving nearly 100% adsorption to host cells within 15 min and a moderate burst size of approximately 80 plaque-forming units per infected cell. Bentonite exhibited substantial dose-dependent binding of ETEC-secreted proteins and outer membrane vesicles (OMVs), with the 30-g treatment showing the highest efficiency. Nanoparticle tracking analysis confirmed a 3.56-fold reduction in OMVs at 5 g bentonite and near-complete removal at 30 g. Physicochemical analysis indicated a stabilizing effect of bentonite, showing that bentonite-phage association partially neutralized the phage surface charge (from -34.2 to -13.4 mV), forming a more stable colloidal complex with an approximately 2-fold decrease in colloidal size. In a murine diarrheal model, single therapy with either EC.W2-6 (multiplicity of infection = 0.1) or 8% bentonite conferred 60% survival, whereas combination treatment provided 100% protection with a synergistic effect. Microbiome analysis revealed that dual therapy restored gut microbial diversity and suppressed Proteobacteria expansion, closely resembling healthy controls. These findings highlight the therapeutic potential of combining bentonite with phage therapy as an integrated macromolecular intervention against ETEC-induced diarrhea and intestinal dysbiosis.},
}

@article {pmid41623987,
year = {2026},
author = {Ren, H and Fan, J and Guo, X and Zhang, B and Zhao, H and Ma, D and Liu, S and Mao, J and Zhang, B and Qiao, J and Jia, C and Ding, X},
title = {Deciphering the characteristics of strong-flavor Daqu at different grades through integrated microbiome and metabolome analysis.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103526},
pmid = {41623987},
issn = {2590-1575},
abstract = {In strong-flavor Baijiu production, Daqu quality is crucial, yet grading often relies on subjective evaluation. This study compares physical and chemical properties, metal content, microbial composition, and metabolic profiles of three Daqu grades (P90, F90, S90) using a multi-omics approach. P90 exhibits superior esterification power and is dominated by Bacillus, Thermoactinomyce, and Thermomyces, with enhanced ester formation and aromatic precursor accumulation. Although S90 has higher microbial diversity, its lower abundance of key functional strains may limit fermentation efficiency and flavor compound production. PICRUSt analysis reveals grade-specific differences in carbohydrate, amino acid, and nucleotide metabolism pathways. Metabolomic profiling identifies 23 amino acids and derivatives enriched in Daqu, primarily mapping to tryptophan, phenylalanine, and arginine-proline pathways. These likely contribute to aroma precursor synthesis and microbial stability. Overall, these findings elucidate the microbiome-metabolome interactions underlying Daqu quality grading and inform strategies for Daqu quality evaluation and improvement in Baijiu fermentation.},
}

@article {pmid41623644,
year = {2025},
author = {Chang, Y and Wang, J and Xu, C and Qu, F and Sun, X and Quan, Z and Yin, L and Fang, Y and Wang, C},
title = {Niche-specific maize microbiomes enhance productivity and nitrogen uptake under intercropping.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711988},
pmid = {41623644},
issn = {1664-302X},
abstract = {Intercropping is widely used to improve crop yield, but the microbial mechanisms driving biomass and nitrogen (N) gains remain unclear. In a maize-soybean intercropping system, we compared intercropped and monocultured maize to investigate niche-specific microbial processes. At the tasseling stage, bacterial and fungal communities were profiled across above- and belowground maize compartments and linked to organ-level biomass and N content. We found that intercropping significantly enhanced maize total biomass and nitrogen uptake, due to the greater increase in roots and leaves. The intercropping also restructured bacterial and fungal communities in a niche-specific manner: bacterial diversity declined in the phylloplane and root, leaf endospheres, whereas fungal diversity increased in the leaf endosphere and stem episphere. Moreover, higher bacterial diversity was associated with lower biomass and N content, while higher fungal diversity showed the opposite trend. Shifts in microbial composition, particularly enrichment of Proteobacteria, Bacteroidota, and Ascomycota, better predicted plant performance than diversity metrics alone. Overall, our findings suggest that intercropping enhances maize growth and N acquisition by steering niche-specific microbial assemblies, highlighting cross-compartment microbiome organization as a promising target for microbiome-informed crop management.},
}

@article {pmid41623642,
year = {2025},
author = {Kuang, HF and Jiang, XY and Tie, SY and Lian, K and Hao, MY and Xu, H and Huang, X and Yang, Y and Guo, Q and Li, J and Chen, LL},
title = {Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1738456},
pmid = {41623642},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.

METHODS: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.

RESULTS: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.

CONCLUSION: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.},
}

@article {pmid41623622,
year = {2025},
author = {Li, Y and Cheng, Y and Liu, W and Li, J and Li, S and Suriguga, and Ma, T and Kwok, LY and Cai, Z and Sun, Z},
title = {Gut microbial and functional signatures in breast cancer: an integrated metagenomic and machine learning approach to non-invasive detection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722632},
pmid = {41623622},
issn = {1664-302X},
abstract = {INTRODUCTION: Breast cancer is associated with significant restructuring of the gut ecosystem. Gut microbial composition and function may influence cancer development and progression through immune modulation, metabolic regulation, and inflammation-related pathways.

METHODS: Using shotgun metagenomic sequencing of fecal samples from 38 stage I-III breast cancer patients and 36 age- and body mass index-matched healthy controls. Machine learning models were constructed to evaluate the diagnostic potential of integrated microbial and metabolic features.

RESULTS: Significant alterations were observed in gut microbiota composition, including depletion of beneficial taxa (Limosilactobacillus fermentum, Blautia sp.) and enrichment of Prevotella copri. Pathways involved in short-chain fatty acid and purine metabolism were reduced. The gut phageome exhibited structural changes and altered correlations with bacterial hosts. Predictive analysis revealed depletion of short-chain fatty acids (butyrate, propionate), purine intermediates (hypoxanthine, xanthine), and nicotinate in patients. A machine learning model integrating microbial and predicted metabolic features achieved an area under the curve values of 0.78 in the discovery cohort and 0.73 (recall = 0.74) in an independent validation cohort.

DISCUSSION: Coordinated gut microbiome, phageome, and metabolome alterations characterize breast cancer, offering potential non-invasive biomarkers and mechanistic insights for disease detection and intervention.},
}

@article {pmid41623619,
year = {2025},
author = {Wei, T and Qian, N and Wang, H and Song, Y and Wang, W and Li, Y and Zhao, Z and Xu, F and Yang, W},
title = {Wilson's disease-associated gut dysbiosis: novel insights into microbial functional alterations, virulence changes, and resistance markers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714276},
pmid = {41623619},
issn = {1664-302X},
abstract = {BACKGROUND: Although the gut microbiota is associated with a variety of metabolic, inflammatory, and neurological disorders through microbial dysbiosis, current studies on the gut microbiota in Wilson's disease (WD) remain limited. Critical gaps exist in understanding the roles of key functional microbial factors in WD pathogenesis, which hinders the acquisition of mechanistic insights into this disease.

OBJECTIVE: This study aims to characterize alterations in the gut microbiome associated with WD, with a particular emphasis on virulence factors (VFs) and antibiotic resistance genes (ARGs), as well as functional mobile genetic elements (MGEs), in order to elucidate their potential roles in disease progression and clinical manifestations.

METHODS: We analyzed fecal samples from 37 patients with WD and 33 healthy controls (HCs) using metagenomic sequencing, with a specific focus on examining virulence gene profiles and antibiotic resistance patterns and MGE composition in relation to liver function markers.

RESULTS: Beta diversity analysis revealed significant differences in the gut microbial community structure between patients with WD and HCs, and a distinct set of microbial taxa was identified that showed significant associations with clinical indicators. A gut microbial co-occurrence network identified key species playing central roles in the microbial community structure, including Prevotella stercorea, Firmicutes bacterium CAG 110, Bacteroides salyersiae, Lactococcus petauri, Streptococcus cristatus, Actinomyces sp. HMSC035G02, and Streptococcus viridans. Widespread functional dysbiosis was detected across multiple biological levels in patients with WD, with significant correlations identified between these microbial alterations and clinical indicators. Significant disruptions were identified in key metabolic pathways, including the Pentose Phosphate Pathway, Pyruvate Metabolism, and Starch and Sucrose Metabolism, which were associated with the dysregulation of carbohydrate-active enzymes (CAZymes). These alterations showed significant correlations with clinical markers of liver dysfunction (e.g., procollagen III N-terminal peptide PIIINP, aspartate transaminase/alanine transaminase AST/ALT). A total of 54 virulence factor (VF) genes exhibited differential abundance in WD, with 36 genes depleted and 18 enriched. Notably, these included colibactin genes (clbB, clbH) from Escherichia coli and type IV secretion system genes (aec19, pilB). These VFs were significantly associated with indicators of liver function (e.g., bilirubin levels) and coagulation abnormalities. Among the detected antibiotic resistance genes (ARGs), 21 exhibited disease-specific patterns in WD, notably tetQ (encoding tetracycline resistance), ErmB (conferring macrolide resistance), and cfxA6 (mediating cephamycin resistance). Furthermore, ARG profiles were associated with Bifidobacterium enrichment and showed significant correlations with lipid metabolism markers [e.g., triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)]. Critically, we identified significant enrichment of 60 functional mobile genetic elements (MGEs) in WD, spanning categories involved in DNA replication/repair, phage activity, and conjugative transfer, indicating heightened genomic plasticity and horizontal gene transfer potential. Strikingly, correlation network analysis revealed strong and specific co-occurrence between key ARGs (e.g., ErmX) and defined suites of MGEs, suggesting MGE-facilitated dissemination of resistance determinants.

CONCLUSION: Wilson's disease (WD) patients exhibit significant alterations in gut microbial community structure and functional dysbiosis, wherein the enrichment of virulence genes (such as colibactin genes clbB/clbH) and the specific antibiotic resistance genes (such as tetQ and ErmB), and the activation of mobile genetic elements are closely associated with clinical indicators including liver function impairment, coagulation abnormalities, and lipid metabolism disorders.},
}

@article {pmid41623616,
year = {2025},
author = {Zheng, Y and Zhao, W and Hu, X and Li, Z and Gao, K and Jiao, N},
title = {Phosphorus fertilization and maize intercropping with peanut synergistically reshape rhizosphere microbiome and enhance crop yield.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1732662},
pmid = {41623616},
issn = {1664-302X},
abstract = {INTRODUCTION: Optimizing nutrient cycling in diversified cropping systems is essential for sustainable agriculture. While intercropping legumes with cereals can enhance complementary resource use, the interaction between phosphorus (P) fertilization and such systems in restructuring rhizosphere microbiomes and driving synergistic productivity gains in alkaline soils remains unclear.

METHODS: We conducted a long-term field experiment, integrating amplicon sequencing with comprehensive agronomic and soil analyses to investigate this interaction in a maize-peanut intercropping system under P fertilization.

RESULTS: Phosphorus fertilization significantly increased the yields of intercropped maize (by 52.12%) and peanut (by 43.60%), while simultaneously enhancing the intercropping yield advantage (IYA; +60.77%) and land equivalent ratio (LER; +2.54%). Soil P availability was the dominant environmental driver, explaining 73.46% and 84.39% of the variance in bacterial and fungal community structure, respectively. Phosphorus addition and intercropping selectively enriched keystone functional taxa, including the nitrifying bacterium Nitrospirae and the saprophytic fungus Mortierellomycota, whose abundances correlated strongly with improved soil nutrient availability and crop performance. Concurrently, intercropping suppressed the pathogen-rich phylum Ascomycota.

DISCUSSION: Our findings demonstrate that the synergy between P fertilization and intercropping enhances crop productivity through a microbiome-mediated mechanism. This synergy restructures the rhizosphere community into a functionally beneficial state, fostering a self-reinforcing plant-microbe-soil feedback loop. This study provides a mechanistic framework for developing integrated, microbiome-informed management strategies to support sustainable agricultural intensification.},
}

@article {pmid41623615,
year = {2025},
author = {Lai, X and Hou, S and Liu, S and Zhang, W and Peng, Z and Yang, J and Yan, L and Wang, X},
title = {Mixed application of microbial fertilizers reshapes the tobacco rhizosphere microbiome and enhances metabolic coordination to improve crop quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1726681},
pmid = {41623615},
issn = {1664-302X},
abstract = {Sustainable management of flue-cured tobacco requires a careful balance among productivity, chemical composition, and soil ecological function, which are often disrupted by excessive chemical fertilization. This study aimed to elucidate how microbial fertilization regulates plant performance, chemical coordination, and rhizosphere microbial structure under field conditions. A two-year factorial field experiment was conducted in Sichuan, China, using a Bacillus-based plant growth-promoting microorganism (PGPM) and a commercial microbial consortium (Xi⋅Weifeng), applied individually or in combination at gradient doses. Agronomic traits, cured-leaf chemical composition, secondary metabolites, and rhizosphere bacterial communities were comprehensively analyzed using multivariate statistics, network correlation analysis, and structural equation modeling (SEM). Moderate PGPM application (27 kg⋅ha[-1]) significantly increased plant height (8.6%), internode length (15.3%), and leaf width (7.8%) at the vigorous growth stage. Co-application further enhanced leaf expansion (9.7%) and improved chemical coordination, maintaining optimal sugar/nicotine (8-12) and N/nicotine (0.7-1.0) ratios. Chlorogenic acid (18.8 mg⋅g[-1]) and neochlorogenic acid (2.7 mg⋅g[-1]) were markedly elevated under the A27B54 treatment. Rhizosphere bacterial diversity peaked under co-application, with Bacillus, Rhizobiales, and Sphingomonas emerging as key taxa positively associated with both metabolic and agronomic improvements. SEM demonstrated that fertilization effects on leaf quality were mediated indirectly through microbial community restructuring and metabolite modulation. Microbial fertilizer co-application enhances tobacco performance by promoting rhizosphere microbial diversity and functional coordination, which in turn improves metabolic balance and nutrient-use efficiency. These findings highlight a soil microbiome-mediated pathway linking fertilization strategy to crop physiological and chemical responses, providing mechanistic insights for sustainable fertilization management.},
}

@article {pmid41623467,
year = {2026},
author = {Bisht, A and Ahn-Jarvis, J and Corbin, K and Harris, S and Troncoso-Rey, P and Olupot-Olupot, P and Calder, N and Walsh, K and Maitland, K and Frost, G and Warren, FJ},
title = {Gut microbial diversity impacts carbohydrate fermentation by children with severe acute malnutrition.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114640},
pmid = {41623467},
issn = {2589-0042},
abstract = {African children suffering from severe acute malnutrition (SAM) have a disrupted gut microbiome and low short-chain fatty acids (SCFAs). These are linked to persistently high mortality and morbidity rates. Supplementing recovery feeding regimes with suitable fermentable carbohydrate may improve outcomes in SAM. We adapted in vitro colon models to investigate the ability of children with SAM to utilize four carbohydrate substrates: milk powders (with and without human milk-like oligosaccharides), chickpea-enriched feed, and inulin. All substrates, except inulin, were fermented to produce SCFAs. The inability to utilize inulin ex vivo, a widely used prebiotic, is attributed to low microbial diversity, enriched with Proteobacteria. Stool samples obtained after partial anthropometric recovery showed increased microbial diversity and higher levels of GH32 enzyme family, responsible for inulin metabolism. These findings can inform the design of future therapeutic feeds for the treatment of SAM, where inulin has been found ineffective during initial hospitalization. Alternative carbohydrates appear to be more effective in supporting gut recovery during both the initial and later treatment phases.},
}

@article {pmid41623087,
year = {2026},
author = {Perucca, P and Perucca, E},
title = {Novel pharmacological therapies in development.},
journal = {Current opinion in neurology},
volume = {},
number = {},
pages = {},
pmid = {41623087},
issn = {1473-6551},
abstract = {PURPOSE OF REVIEW: To review progress in developing new pharmacological treatments for epilepsy, focusing on agents in clinical development.

RECENT FINDINGS: Over 30 different treatments are currently in clinical development, including novel small molecules, nucleic acid-based therapies, stem cells, microbiome-targeting bacteria, and repurposed drugs originally approved for other indications. Most of these treatments target rare epilepsies, particularly the developmental and epileptic encephalopathies, reflecting a development shift from common epilepsies to rare drug-resistant syndromes where unmet therapeutic needs are greatest. Most compounds are still in early development, and publicly accessible data consist mainly of conference reports and congress abstracts. For only two compounds (the Kv7 activator azetukalner and the inhaled emergency treatment Staccato alprazolam) has evidence of efficacy been obtained from relatively large, well designed randomized placebo-controlled trials.

SUMMARY: New paradigms in drug discovery have brought to development innovative treatments with diverse targets and mechanisms of action. Many of these treatments are etiology-targeting and have the potential for disease-modifying effects. Although high-quality evidence is awaited, there is hope that over the next few years, much needed life-changing therapies will be widely available for millions of people with disabling, drug-resistant epilepsies.},
}

@article {pmid41622839,
year = {2026},
author = {Wei, G and Zhang, H and Zhao, S and Jiang, J and Liu, C and Li, P and Ni, Y and Dai, H and Fan, L and Wei, H and Xi, J},
title = {Polysaccharide Engineered Nanozymes Target Inflammation for Alleviating Colitis-Associated Mental Disorders via Microbiome-Gut-Brain Axis.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e22010},
doi = {10.1002/adma.202522010},
pmid = {41622839},
issn = {1521-4095},
support = {22472146//National Natural Science Foundation of China/ ; BK20231329//Natural Science Foundation of Jiangsu Province/ ; YZLYJFJH2024YXBS164//Yangzhou "Lvyang Jinfeng" Talent Program/ ; YZ2024084//Yangzhou Key Research, Development Program (Social Development)/ ; 2025M782949//China Postdoctoral Science Foundation/ ; 25KJD416004//Natural Science Foundation of Jiangsu Higher Education Institution/ ; YZ2025125//Natural Science Foundation of Yangzhou Municipality/ ; },
abstract = {Molecular therapies for colitis-associated mental disorders show limited efficacy because they usually focus on a single pathway and exhibit substantial off-target toxicity toward healthy tissues. To tackle this limitation, bioinformatic approaches are employed to predict that inflammation and metabolism may be potential targets for Fucoidan. Guided by this prediction, we develop oral polysaccharide engineered nanozymes, Fucoidan-cerium nanocomplexes (FucCeNCs), which are capable of targeting the inflamed colon through electrostatic interactions, exerting anti-inflammatory effects, and concurrently regulating gut microbiota-derived metabolism. In a murine model of ulcerative colitis-associated mental disorders, FucCeNCs show anti-inflammatory and gut barrier-protective effects, thereby suppressing microglial/astrocytic overactivation and preserving neuronal integrity through the transmission of anti-inflammatory cytokines via gut-brain axis. Importantly, FucCeNCs restore gut microbial homeostasis through increasing the relative abundance of probiotics and reducing proportions of pathogens. This shift results in a marked attenuation of abnormal amino acid biosynthesis and metabolism in fecal metabolites, which in turn leads to elevated levels of bioactive metabolites such as homovanillic acid and γ-aminobutyric acid. These metabolites ultimately attenuate neuroinflammation via the microbiome-gut-brain axis, ameliorating depression- and anxiety-like behaviors. These results identify microbiome-gut-brain axis as pivotal therapeutic target for colitis-associated mental disorders therapy, which can be addressed by polysaccharide engineered nanozymes.},
}

@article {pmid41622714,
year = {2026},
author = {Weinberg, F and Achreja, A and Roy, A and Animasahun, O and Meghdadi, B and Mittal, A and Yang, F and Davis, M and De La Torre, KM and Mohamed, O and Barnett, SL and Mohan, A and Choppara, S and Kaur, G and Hulbert, A and Weinberg, SE and Dickson, RP and Tripathi, A and Reddy, RM and Ramnath, N and Nagrath, D},
title = {Integrative Analysis of Multi-omic Pathways Predict Cancer-Affected Lobes in Lung Cancer.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-25-0141},
pmid = {41622714},
issn = {1940-6215},
abstract = {Lung cancer is the leading cause of cancer-related deaths. The human microbiome plays an important role in regulating response to cancer therapeutics, outcomes, and biological processes. However, little is known regarding the interplay between the lung microbiome and other biological processes in cancer. In an exploratory pilot study, we collected bronchoalveolar lavage fluid and brushings from 20 patients with early-stage lung cancer and performed microbial sequencing, untargeted metabolomics, and cytokine analysis. In addition, we employed computational and machine-learning approaches to identify integrated microbial-immunometabolic pathways. Finally, we performed preliminary mechanistic studies to confirm our findings. Previously, we published that upper airway microbiota were selectively enriched in tumor-affected lobes. In the present study we demonstrate that enrichment of pro-tumorigenic cytokines and specific fatty acids are associated with tumor-affected lobes. Finally, we find that long-chain fatty acid stimulation of macrophages leads to neoplastic transformation of lung epithelial cells. Therefore, the findings of this study identify a perturbed fatty acid-macrophage axis that is a potential biomarker of early-stage lung cancer and will lead to development of novel therapeutic agents.},
}

@article {pmid41622628,
year = {2026},
author = {Yamada, T and Tateishi, R and Fujishiro, M},
title = {Post-Transplant Hepatocellular Carcinoma: Balancing Immunosuppression and Immune Checkpoint Inhibitors.},
journal = {Clinical and molecular hepatology},
volume = {},
number = {},
pages = {},
doi = {10.3350/cmh.2025.1179},
pmid = {41622628},
issn = {2287-285X},
abstract = {Liver transplantation (LT) is a life-saving treatment for patients with end-stage liver disease and hepatocellular carcinoma (HCC). Advances in surgical techniques and immunosuppressive regimens have markedly improved early post-transplant survival. However, long-term outcomes remain compromised by HCC recurrence, chronic rejection, metabolic complications, and de novo malignancies. Recurrence of HCC after LT remains a major clinical challenge, with available prognostic models providing limited accuracy in risk stratification. Simultaneously, systemic therapies for unresectable HCC have rapidly advanced, particularly with immune checkpoint inhibitors (ICIs), providing new opportunities and unique challenges in transplant settings. With ICIs carrying a risk of acute and potentially fatal rejection and lacking controlled data on efficacy or safety in the post-transplant setting, tyrosine kinase inhibitors currently represent a standard option for post-transplant recurrence. Novel biomarkers, such as donor-derived cell-free DNA and the gut microbiome, are emerging as potential tools to refine risk stratification and guide immunosuppression. Furthermore, innovative immunotherapies, including oncolytic viruses and mRNA vaccines, are being explored as tumor-specific approaches. Collectively, these advances may reshape future management of LT recipients.},
}

@article {pmid41622615,
year = {2026},
author = {Wang, J and Cheng, L and Zhang, J and Qin, Y and Fu, Q and Bai, X and Qi, F and Wu, F and Yang, J and Pan, Y},
title = {Comprehensive Evaluation of Body Lotion in Alleviating Xerosis: A Multi-Omics Approach to Lipid Metabolism and Microbial Community Modulation.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {2},
pages = {e70711},
pmid = {41622615},
issn = {1473-2165},
mesh = {Humans ; *Lipid Metabolism/drug effects ; *Microbiota/drug effects ; Female ; Ceramides/administration & dosage ; *Skin Cream/administration & dosage/pharmacology ; Lipidomics ; Adult ; Skin/microbiology/drug effects/metabolism ; Middle Aged ; Male ; *Skin Diseases/drug therapy/microbiology ; Water Loss, Insensible/drug effects ; Treatment Outcome ; Multiomics ; },
abstract = {BACKGROUND: Xerosis, marked by a compromised skin barrier and disrupted lipid metabolism, leads to dryness, scaling, and itching. Ceramide and natural oil-based moisturizers can improve skin hydration and barrier repair, but their effects on lipid networks and microbiome interactions have not been well understood.

METHODS: A multicenter, randomized, self-controlled study was conducted to assess the efficacy of a body lotion formulated with ceramides and natural oils in the management of xerosis. The lotion was applied daily to one leg for 4 weeks, with the other leg as a control. Skin radiance, skin scaliness, skin smoothness, stratum corneum hydration, transepidermal water loss, and pH were measured at various intervals. Lipidomics and microbiomics analyses evaluated changes in lipid metabolism and microbial structure.

RESULTS: The body lotion enhanced skin hydration, radiance, and smoothness, while decreasing TEWL and scaling. Lipidomics showed higher levels of essential lipids in the treatment group. Microbiome analysis revealed increased diversity, with more Firmicutes and Cutibacterium and less Proteobacteria, indicating improved skin barrier and microbial balance.

CONCLUSION: This body lotion effectively alleviates dryness, significantly improving skin hydration, barrier function, and texture. It achieves these benefits by restoring the skin's lipid balance and optimizing the microbial community, with lipid-microbiome crosstalk identified as a key mechanism. This multi-omics insight provides a foundation for the targeted management of dry skin.},
}

Humans
*Lipid Metabolism/drug effects
*Microbiota/drug effects
Female
Ceramides/administration & dosage
*Skin Cream/administration & dosage/pharmacology
Lipidomics
Adult
Skin/microbiology/drug effects/metabolism
Middle Aged
Male
*Skin Diseases/drug therapy/microbiology
Water Loss, Insensible/drug effects
Treatment Outcome
Multiomics

@article {pmid41622331,
year = {2026},
author = {Geraldi, MV and Brättemark, E and Lorentzon, M},
title = {Longitudinal associations of dietary intake, physical activity, and short-chain fatty acids with bone development in early postmenopausal women.},
journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
volume = {},
number = {},
pages = {},
pmid = {41622331},
issn = {1433-2965},
abstract = {UNLABELLED: Bone loss accelerates in early menopause, increasing fracture risk. In 223 women followed for 2 years, higher fiber and energy intake were linked to better bone structure, while higher fat intake and some physical activity domains were inversely associated. Specific short-chain fatty acids showed positive associations, highlighting diet-microbiome interactions in bone health.

BACKGROUND: The early postmenopausal period is characterized by accelerated loss of bone mineral density (BMD), underscoring the importance of modifiable lifestyle factors as potential targets for prevention.

METHODS: This study is a secondary analysis of the ELBOW trial, a 2-year longitudinal study of early postmenopausal Swedish women. We investigated the association between dietary intake, physical activity, and short-chain fatty acids (SCFAs) with bone outcomes in 223 early postmenopausal Swedish women aged 50-60 years. Assessments were conducted at baseline, 1 year, and 2 years. Diet and physical activity were assessed using validated questionnaires, and SCFAs were measured in plasma. Bone parameters, including total hip BMD, tibial volumetric BMD (vBMD), and bone microarchitecture, were evaluated using dual-energy X-ray absorptiometry (DXA) and high-resolution peripheral quantitative computed tomography (HR-pQCT). Associations were analyzed using linear mixed models for repeated measures.

RESULTS: Higher baseline fiber intake was positively associated with trabecular bone volume fraction, while total fat was inversely associated with total hip BMD, total vBMD, and cortical area. Greater energy intake during follow-up was positively associated with cortical area. No associations were observed between bone characteristics and calcium or vitamin D intake. Baseline transport-related and changes in domestic/gardening activity were inversely associated with bone measurements. Among SCFAs, baseline levels of acetic acid, formic acid, and isovaleric acid were positively associated with bone outcomes, while changes in caproic acid levels were negatively associated.

CONCLUSION: These findings suggest that specific dietary components and gut microbiota-derived metabolites may play a role in maintaining bone health during early postmenopause and highlight the need for further investigation into their preventive and therapeutic potential.},
}

@article {pmid41622302,
year = {2026},
author = {Li, S and Zhang, J and Han, L and Yu, Y and Mousa, AA and Zhu, W and Leng, J and Xie, F and Mao, S},
title = {Comparative metagenomic and metatranscriptomic analyses reveal the role of the gayal rumen and hindgut microbiome in high-efficiency lignocellulose degradation.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {18},
pmid = {41622302},
issn = {1674-9782},
support = {U2202203//Joint Funds of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gayal (Bos frontalis), a semi-domesticated bovine species, demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo, suggesting the presence of a specialized gastrointestinal microbiome. However, the functional mechanisms underlying this host-microbiome interaction remain poorly understood. Here, we conducted integrated metagenomic and metatranscriptomic analyses of rumen, cecum, and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.

RESULTS: The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle, evidenced by significantly higher (P < 0.05) fiber digestibility, cellulase and xylanase activities, and increased volatile fatty acids production despite identical feed intake. Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle, with notable enrichment of taxa specialized in lignocellulose degradation. Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes, particularly AA6, AA2, and AA3, primarily encoded by Prevotella, Cryptobacteroides, Limimorpha, and Ventricola. These enzymes are known to modify lignin structure to increase polysaccharide accessibility. These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade, especially effective in dismantling lignin barriers.

CONCLUSIONS: This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.},
}

@article {pmid41621781,
year = {2026},
author = {Wang, E},
title = {Deciphering Plant-Microbe Symbioses: A Molecular Blueprint for Precision Agriculture.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169668},
doi = {10.1016/j.jmb.2026.169668},
pmid = {41621781},
issn = {1089-8638},
abstract = {Symbioses between plants and microbes such as mycorrhizal fungi and rhizobia, provide critical advantages in plant nutrient acquisition and stress resilience, and thereby underpin agricultural sustainability. However, plants coexist with a myriad of soil microbes, including mutualists, pathogens and commensals, and so must accurately differentiate between beneficial, detrimental, and neutral partners to optimize tradeoffs between growth and defense. Since 2013, our research group has been dedicated to addressing fundamental questions in plant-microbe symbioses. Our work encompasses the exchange of nutrients and signals between symbionts, and the differentiation between mutualistic and pathogenic microbes within the rhizosphere microbiome. We first discovered fatty acids as the main carbon source supplied by plants to arbuscular mycorrhizal (AM) fungi and later revealed the phosphate starvation response-centered regulatory network that controls the root and AM fungi phosphorus uptake pathways. In addition, we identified the receptors that recognize Myc factors and have made inroads on revealing the mechanisms underlying how plants distinguish symbiotic and immune signals. The legume-rhizobium symbiosis is understood to have evolved from arbuscular mycorrhizal symbiosis. Related to this, our group identified the Nod factor co-receptor, MtLICK1/2, and revealed that a SHR-SCR module specifies legume cortical cell fate to enable root nodulation. Collectively, our work has provided fundamental insights into the two most agriculturally important plant-microbe symbioses, thereby paving the way for innovative strategies that harness these interactions to advance sustainable agriculture.},
}

@article {pmid41621544,
year = {2026},
author = {Aragón-Barroso, AJ and González-Martínez, A and González-López, J and Osorio, F},
title = {Impact of operational conditions and microbial dynamics on expanded granular sludge bed reactor performance: A comprehensive review.},
journal = {Bioresource technology},
volume = {445},
number = {},
pages = {134118},
doi = {10.1016/j.biortech.2026.134118},
pmid = {41621544},
issn = {1873-2976},
abstract = {Expanded granular sludge bed (EGSB) reactors have emerged as promising high-rate anaerobic treatment systems for industrial wastewater (WW) with increasing organic loads and complex compositions. This review provides a systematic overview of the main operational parameters, including organic loading rate (OLR), volatile fatty acids (VFA), pH, temperature, influent solids, upflow velocity (Vup), extracellular polymeric substances (EPS) production and solids retention time (SRT), focusing on their effects on granule formation and process performance. EGSB stability is governed by defined operational limits, with optimal performance at OLRs of 10-30 kg COD m[-3] d[-1], VFAs below 500-1000 mg L[-1], and moderate Vup (3-6 m h[-1]). Exceeding critical thresholds in VFA, Vup, or influent solids (>5000 mg L[-1]) induces washout and granulation failure, while protein-rich EPS enhance the cohesion and shear resistance of granular biomass under high hydraulic and organic loads. Special attention is paid to microbial community dynamics, emphasizing how substrate characteristics, operational conditions, height-to-diameter ratio, and microbial kinetics jointly shape community shifts, syntrophic interactions, and overall process stability in EGSB reactors. Furthermore, the insights derived from these analyses are used to provide a more robust explanation of anaerobic granulation mechanisms, integrating conceptual models, key physicochemical drivers, and the role of quorum sensing (QS). Based on this integrated framework, this review identifies existing knowledge gaps and proposes future directions to support the development of robust and efficient EGSB systems for the sustainable treatment of complex industrial WW.},
}

@article {pmid41519896,
year = {2026},
author = {Domańska, M and Kuśnierz, M and Charazińska, S and Gawor, J and Kamińska, J},
title = {Similarity of activated sludge and treated wastewater with special reference to nitrifiers and their seasonal variability.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4375},
pmid = {41519896},
issn = {2045-2322},
support = {2022/06/X/ST10/01775//National Science Centre/ ; },
abstract = {UNLABELLED: While the research into the activated sludge (AS) microbiome using next-generation sequencing (NGS) are increasingly being published, they still apply to a few wastewater treatment plants (WWTPs). Little information can be found in the scientific literature on the microbial composition of treated wastewater (TW) and bacterial activity in real WWTPs facilities. In this study, AS and TW are compared in terms of their physico-chemical parameters and bacterial community composition, with particular emphasis on nitrifying bacteria, based on the results from 16S rRNA amplicon sequencing using DNA and complementary DNA (cDNA) data and fluorescence in situ hybridization (FISH). Using a 24-h composite sample of TW rather than a grab sample yields highly representative microbial community profiles. The research revealed a decrease in biodiversity in months with lower sludge temperatures both in AS and TW. Differences among groups of nitrifying bacteria were observed during the monitoring of WWTP, suggesting that their presence in TW may not be a random occurrence but could serve as an indicator of physicochemical and operational changes within biological reactors.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34503-4.},
}

@article {pmid41485070,
year = {2026},
author = {Chen, JM and Zhang, C and Yu, LL and Sun, JX and Zhang, JH and Chen, L and Zhu, F and Shi, G and Yang, L and Guo, AC and Wu, JP and Tang, TS and Wang, Q},
title = {Microbiota-derived IPA mitigates post-stroke neuroinflammation by inhibiting TREM2-dependent pyroptosis.},
journal = {Journal of neuroinflammation},
volume = {23},
number = {1},
pages = {47},
pmid = {41485070},
issn = {1742-2094},
support = {82501758//National Natural Science Foundation of China/ ; U24A20695 and 82371449//National Natural Science Foundation of China/ ; 20221060//Hebei Province Medical Science Research Project/ ; 13000023P002DB4102678//the Introduction of Foreign Intelligence Program of Hebei Province/ ; K1297701, J.W//Faculty Development grants from Hubei University of Medicine/ ; 2023YFA1801904 and 2025YFA1805102//National Key Research and Development Program of China/ ; 2022YFC2503800//National Key Research and Development Program of China/ ; 7232045 and Z200024//Natural Science Foundation of Beijing Municipality/ ; 2024-1-2041//Capital Health Research and Development of Special grants/ ; },
abstract = {UNLABELLED: Ischemic stroke remains the leading cause of long-term disability globally, underscoring the urgent need for novel therapeutic strategies. Here, we explore a microbiota-gut-brain axis that provides valuable insights for achieving this objective. Utilizing a distal middle cerebral artery occlusion (dMCAO) mouse model, we observed a marked reduction in Duncaniella muris (D. muris) post-stroke, alongside dysregulated tryptophan metabolism, characterized by elevated levels of indole-3-lactic acid (ILA) and decreased indole-3-propionic acid (IPA). D. muris supplementation restored metabolic balance by converting ILA to IPA, leading to significant improvements in neurological recovery. Mechanistically, IPA exerted neuroprotective effects by attenuating neuroinflammation through TREM2-dependent modulation of microglial activation, promoting an anti-inflammatory phenotype and inhibiting NLRP3 inflammasome-mediated pyroptosis. These findings highlight the therapeutic potential of the D. muris-IPA-TREM2-pyroptosis axis as a novel target for ischemic stroke treatment, providing a basis for future microbiome-based interventions aimed at improving stroke outcomes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12974-025-03660-8.},
}

@article {pmid41455033,
year = {2025},
author = {Liu, Y and Eirin, A and Lerman, LO},
title = {Novel Therapeutic Strategies for Obesity-Related Glomerulopathy.},
journal = {Current hypertension reports},
volume = {28},
number = {1},
pages = {3},
pmid = {41455033},
issn = {1534-3111},
support = {DK122734/DK/NIDDK NIH HHS/United States ; HL158691/HL/NHLBI NIH HHS/United States ; AG062104/AG/NIA NIH HHS/United States ; },
abstract = {PURPOSE OF REVIEW:: Conventional management primarily focuses on weight reduction and renin-angiotensin-aldosterone blockade; however, these approaches are often insufficient to halt disease progression.

RECENT FINDINGS:: Recent advances have identified novel therapeutic targets and strategies aimed at addressing the metabolic, inflammatory, and hemodynamic abnormalities, as well as gut microbiome dysbiosis, driving obesity-related glomerulopathy (ORG). Pharmacological agents like sodium-glucose cotransporter-2 inhibitors, glucagon-like peptide-1 receptor agonists, finerenone, mitochondrial transfer, and fecal microbiota transplantation have demonstrated renoprotective effects through improving weight, insulin sensitivity, blood pressure, inflammation, and gut microbiome. The potential direct renoprotective effects of these medications in ORG, independent of weight loss, warrant further investigation. Additionally, artificial intelligence and emerging biomarkers represent promising strategies for personalized and precise management, early non-invasive diagnosis, and prognostic evaluation of ORG.},
}

@article {pmid41621408,
year = {2026},
author = {Mesto, G and Al Atrash, E and Rawat, D and Elzayat, H and Miqdady, M and Al-Marzooq, F},
title = {Multispecies Signatures and Driving Factors of Oral Microbiome Dysbiosis in Pediatric Crohn's Disease in the United Arab Emirates.},
journal = {Archives of medical research},
volume = {57},
number = {4},
pages = {103389},
doi = {10.1016/j.arcmed.2026.103389},
pmid = {41621408},
issn = {1873-5487},
abstract = {PURPOSE: Despite the recognized impact of the gut microbiome, research on the oral microbiome is limited, particularly in pediatric patients with Crohn's disease (CD). This study aims to explore salivary microbiome signatures in pediatric patients with CD from the United Arab Emirates (UAE), compared to healthy controls (HC), by analyzing early-life, lifestyle, and disease-specific factors driving dysbiosis.

METHODS: Salivary samples from 52 pediatric patients with CD and HC (n = 26/group) were subjected to 16S rRNA sequencing using Oxford Nanopore technology. Bioinformatics and biostatistical analyses were employed to compare groups and identify microbiota signatures correlated with clinical data.

RESULTS: Enrichment of several species, including Veillonella parvula, Veillonella dispar, and Prevotella denticola, with depletion of beneficial bacteria was observed in CD. Machine learning-based composite biomarker analysis identified 36 species distinguishing CD from HC, most of which are opportunistic pathogens, raising concerns about their potential impact on vulnerable pediatric patients with CD. Multifactorial analysis revealed significant oral microbiome dysbiosis in patients with CD across all 15 analyzed factors, with unique CD-specific biomarkers. The strongest associations with microbial alterations were demonstrated by disease duration, diet, exercise habits, early antibiotic exposure, and delivery method. Among the 19 species analyzed, Capnocytophaga gingivalis demonstrated multifactorial associations, emerging as an integrative biomarker of disease burden. The α-diversity was significantly lower in patients with CD, with distinctive β-diversity patterns.

CONCLUSION: This is the first comprehensive multifactorial analysis of the oral microbiome in pediatric patients with CD from the Middle East, employing novel machine learning approaches for composite biomarker discovery. Core dysbiotic species in CD may serve as potential diagnostic and prognostic biomarkers requiring validation in larger-scale studies.},
}

@article {pmid41621364,
year = {2026},
author = {Valenzisi, B and Gaston, TF and Parsons, M and Huggett, MJ},
title = {Effect of noise on the behaviour and microbiome of a common temperate estuarine fish.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119347},
doi = {10.1016/j.marpolbul.2026.119347},
pmid = {41621364},
issn = {1879-3363},
abstract = {Underwater noise pollution is an increasing stressor in marine and estuarine environments, with anthropogenic activity altering natural soundscapes and adversely affecting animal behaviour, which is often an early indicator of environmental stress with broader physiological implications. Host-associated microbiomes, particularly the gut, are central to organism health, influencing digestion, immunity, metabolism, and stress regulation. The gut microbiome also plays a key role in linking environmental disturbances with physiological condition and behavioural changes, yet the impacts of noise on these microbial communities remain poorly understood. We examined the behavioural and gut microbial response of Pelates sexlineatus exposed to three acoustic treatments: continuous white noise (i.e. urban hum), short-pulsed white noise (i.e. intermittent boat noise), and ambient control (no added noise), under controlled aquarium conditions. Fish in ambient tanks spent the most time swimming, while fish exposed to noise exhibited increased resting and erratic movements. Microbial communities in fish and water samples, characterised using 16S rRNA gene amplicon sequencing, identified 44 phyla in the fish microbiome and 11 comprised the core microbiome. Strong differentiation was observed between fish and water communities with fish dominated by Firmicutes, Proteobacteria and Actinobacteriota, and water dominated by Bacteroidota and Proteobacteria. Although short-term acoustic exposure did not significantly alter overall microbial diversity, subtle compositional shifts and strong host-environment distinctions highlight the complexity of microbiome responses to environmental stress. This study provides novel insights into the short-term stability of the gut microbiome in estuarine fish and highlights the need for integrated research assessing behavioural and microbial responses to noise pollution.},
}

@article {pmid41621269,
year = {2026},
author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L},
title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.},
journal = {Water research},
volume = {293},
number = {},
pages = {125448},
doi = {10.1016/j.watres.2026.125448},
pmid = {41621269},
issn = {1879-2448},
abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.},
}

@article {pmid41621204,
year = {2026},
author = {Leong, C and Scanlon, R and Kyne, A and Sharpton, TJ and Kent, ML},
title = {Pseudocapillaria tomentosa infections in laboratory larval and Adult Zebrafish (Danio rerio): Development and advances in an in vivo anthelmintic drug discovery model.},
journal = {Veterinary parasitology},
volume = {343},
number = {},
pages = {110704},
doi = {10.1016/j.vetpar.2026.110704},
pmid = {41621204},
issn = {1873-2550},
abstract = {Zebrafish (Danio rerio) are a widely used biomedical model and offers powerful high-throughput screening capabilities for assessing chemical bioactivity. We have previously employed adult zebrafish infected with the intestinal nematode Pseudocapillaria tomentosa to investigate nematode-microbiome interactions, nematode-promoted intestinal neoplasia, and anthelmintic drug discovery. Here we transition this model to a larval zebrafish infection infection to enable larger-scale experimentation and ultimately accelerate anthelmintic discovery. Infection conditions were optimized across 5-30 days post fertilization (dpf). The 30 dpf larvae exhibited the most robust and reproducible infections in multi-well formats, as well as the highest survival relative to younger stages. We described worm development from hatching through larval progression and maturation, addressing a major gap in foundational data with fish capillarids. Using in vitro-hatched larvae and infected larval and adult zebrafish, we documented developmental trajectories from 1 to 37 days post-exposure. Change-point analysis identified putative ecdysis transitions at the following worm lengths (mm): L1/L2 = 0.220, L2/L3 = 0.571, L3/L4 = 1.174, and L4/L5 = 1.584. Finally, we demonstrated proof-of-concept for anthelmintic screening by exposing fish to larvated eggs in the presence of emamectin benzoate (macrocyclic lactone) or fenbendazole (benzimidazole). Both compounds reduced worm burdens after 3 days, with the strongest effects at higher concentrations (0.7 µM emamectin benzoate; 0.3 µM fenbendazole). Together, these findings establishes a proof of concept for larval zebrafish infection platform which bridges the gap between in vitro and mammalian in vivo assays, enabling scalable, efficient, and biologically relevant screening for anthelmintic drug discovery.},
}

@article {pmid41620752,
year = {2026},
author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M},
title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02325-1},
pmid = {41620752},
issn = {2049-2618},
support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; },
abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.

RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.

CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.},
}

@article {pmid41620643,
year = {2026},
author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R},
title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623356},
doi = {10.1080/19490976.2026.2623356},
pmid = {41620643},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Socioeconomic Factors ; Bacteria/classification/genetics/isolation & purification ; *Social Class ; },
abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.},
}

*Gastrointestinal Microbiome
Humans
*Socioeconomic Factors
Bacteria/classification/genetics/isolation & purification
*Social Class

@article {pmid41620634,
year = {2026},
author = {Du, H and Lin, Q and He, X and Yang, B and Huang, Y and Li, Q and Wang, Y and Wen, R and Lin, W and Li, S and Zheng, L and Ou, Z},
title = {Dynamic involvement of the core gut microbiome XNP_Guild1 in the evolution of gestational diabetes mellitus.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623353},
doi = {10.1080/19490976.2026.2623353},
pmid = {41620634},
issn = {1949-0984},
mesh = {Humans ; *Diabetes, Gestational/microbiology ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Prospective Studies ; China ; Infant, Newborn ; Infant ; },
abstract = {Integrated large-scale maternal microbiome cohort analyses are critical for understanding the development of gestational diabetes mellitus (GDM) and its impact on maternal and offspring health. Here, we analyzed the microbiomes of 2,717 mothers and infants from 9 global cohorts, including both public datasets and a prospective cohort in China, using high-throughput sequencing and multilayer network modeling. We systematically identified and characterized a group of "predicted grey zone" individuals whose gut microbial network features fell between those of healthy and GDM subjects, which represent dynamic ecological transition states in disease development. Notably, we identified and validated across cohorts a core gut microbial guild (XNP_Guild1) that remained highly stable and functionally cohesive across healthy, grey zone, and GDM states, and was significantly associated with both disease progression and early pregnancy risk. In an exploratory intergenerational network analysis, we estimated the vertical transmission effect of the core guild and its potential influence on neonatal growth outcomes. These findings highlight the tight interconnection among core functional gut microbes, transitional ecological states, disease evolution, and maternal-infant health, providing a foundation for future targeted interventions and mechanistic studies of the maternal-offspring microecosystem in GDM.},
}

Humans
*Diabetes, Gestational/microbiology
Female
Pregnancy
*Gastrointestinal Microbiome
Adult
*Bacteria/classification/genetics/isolation & purification
Prospective Studies
China
Infant, Newborn
Infant

@article {pmid41620582,
year = {2026},
author = {Mei, LN and Shen, JS and Duan, Y and Shi, ZQ and Peng, HZ and Luo, XD},
title = {Dietary ellagic acid inhibiting gastrointestinal pathogens by modulation of microbiome-metabolite-immune axis.},
journal = {Natural products and bioprospecting},
volume = {16},
number = {1},
pages = {21},
pmid = {41620582},
issn = {2192-2195},
support = {2022SCP003//the High-level Talent Promotion and Training Project of Kunming/ ; No. U2202212//the National Natural Science Foundation of China/ ; 2022YKZY001//Project of Yunnan Characteristic Plant Screening and R&D Service CXO Platform/ ; },
abstract = {Antibiotic-induced depletion of the gut microbiota facilitated the colonization of vancomycin-resistant Enterococci (VRE) in the gastrointestinal tract, and then increased patients' susceptibility to secondary infections. Ellagic acid, a major constituent of fruits and nuts, showed various bioactivities except for antibacterial. Interestingly, it promoted the recovery of gut microbiota, enhanced microbial diversity and stimulated the proliferation of probiotic gut microbes, and then ameliorated the overgrowth of pathogens in vivo in our experiment. Moreover, ellagic acid activated Gpr41 and Gpr43 mainly by promoting the production of short chain fatty acids (SCFAs) such as acetic acid and propionic acid to inhibit the NF-ĸB signaling pathway. Then the dietary supplement with ellagic acid might treat infected gut to avoid antibiotic-associated intestinal diseases, and the finding also provided a novel strategy for exploring antibacterial agent besides screening in vitro.},
}

@article {pmid41620525,
year = {2026},
author = {Yang, Y and Qiu, K and Zhang, Y and Cui, Q and Liu, W and Guo, Y and Liu, H and Xie, Y},
title = {Rhizosphere microbial functions drive ecological stoichiometry in soils across an elevational gradient of a temperate mountain ecosystem.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09553-7},
pmid = {41620525},
issn = {2399-3642},
support = {42001095//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The soil microbiome plays a vital role in maintaining soil nutrient levels and ecological stoichiometry balance. However, the relationships between rhizosphere microbiomes and soil ecological stoichiometric characteristics, including organic carbon (SC), total nitrogen (SN), total phosphorus (SP), and their ratios, remain poorly understood. Here, we used a temperate mountain ecosystem as a natural laboratory along a ~ 2190 m elevational gradient spanning a desert steppe-alpine meadow transition. We investigated rhizosphere microbiomes from 20 dominant plant populations across 17 sites by integrating environmental factors, microbial community structure, functional genes, microbial biomass, and ectorhizosphere soil stoichiometric characteristics. Ectorhizosphere soil stoichiometric characteristics were significantly associated with microbial biomass stoichiometric characteristics, rhizosphere community composition, and C-, N-, and P-cycling genes, with functional genes emerging as the strongest predictors. Structural equation modeling further identified the composition and diversity of functional genes as key drivers of soil stoichiometric characteristics. Geographic and edaphic factors exerted primarily direct effects, whereas climatic influences were indirect and mediated through the rhizosphere microbiome. These findings highlight the rhizosphere microbiome as a critical biological filter linking climate to soil nutrient stoichiometry at the root-soil interface.},
}

@article {pmid41620213,
year = {2026},
author = {Pope, CE and Jones, RM and Rashied, AA and Nagy, T and Hanson, WH},
title = {Evaluating the Impact of Prophylactic Administration of Ivermectin on the Fecal Microbiome of Healthy C57BL/6J Mice (Mus musculus).},
journal = {Journal of the American Association for Laboratory Animal Science : JAALAS},
volume = {},
number = {},
pages = {1-8},
doi = {10.30802/AALAS-JAALAS-25-139},
pmid = {41620213},
issn = {2769-6677},
abstract = {Upon importation, laboratory mice may undergo prophylactic antiparasitic treatment during quarantine to prevent the introduction of parasites into established colonies. While quarantine protocols vary across institutions, ivermectin is commonly used, administered either orally or topically. However, the impact of these practices on the fecal microbiome remains poorly understood, raising concerns about unintended consequences for experimental outcomes. This study investigated the effects of ivermectin on fecal microbiome composition in naïve, healthy male and female C57BL/6J mice. Animals received either ivermectin-impregnated feed (12 ppm, ad libitum for 4 weeks), weekly topical ivermectin solution (2.0 mg/kg for 4 weeks), or no treatment (controls). Fecal samples were collected for 16S rRNA-based microbiome analysis before ivermectin treatment, immediately posttreatment, and 4 weeks after treatment cessation. Weekly body weights were recorded, and histopathologic evaluation of the small intestine and colon was performed at study completion. Both oral and topical ivermectin treatments resulted in significant alterations in microbiome α and β diversity at the end of treatment, with more pronounced effects observed in female mice. Some of these changes persisted for up to 4 weeks after treatment cessation. Furthermore, the findings indicate a sex-specific effect of ivermectin on specific bacterial orders, with Bacillales predominantly affected in male mice, whereas Coriobacteriales and Bacteriodales were primarily impacted in female mice. During treatment, males receiving topical ivermectin weighed significantly less than controls, while females receiving dietary ivermectin weighed significantly more. Histopathological analysis revealed no abnormalities in intestinal tissues across all groups at 4 weeks posttreatment. These findings demonstrate that ivermectin administration induces measurable and persistent changes in the fecal microbiome of healthy mice. Researchers should consider these effects when designing experiments, and institutions must weigh the benefits of colony protection against potential microbiome-related confounding variables.},
}

@article {pmid41619875,
year = {2026},
author = {Mathias, K and Petronilho, F and Danielski, LG},
title = {Nose-to-brain axis: mechanistic links between nasal microbiome dysbiosis, neuroinflammation, and brain disorders.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.039},
pmid = {41619875},
issn = {1873-7544},
abstract = {The nasal microbiome has emerged as a previously underrecognized modulator of neuroinflammation and central nervous system (CNS) homeostasis. Beyond its role in respiratory host defense, this microbial niche is anatomically positioned to directly influence brain physiology through olfactory neuronal pathways, systemic immune signaling, and inter-organ communication within the gut-lung-brain axis. Accumulating evidence indicates that nasal microbiome dysbiosis contributes to blood-brain barrier (BBB) dysfunction, microglial activation, and propagation of neurotoxic protein aggregates, processes implicated in neurodegenerative and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, and major depressive disorder. This review synthesizes experimental and clinical studies elucidating key mechanisms by which nasal microbial imbalance may impact CNS pathology, including microbial translocation along olfactory neurons, release of pathogen-associated molecular patterns and inflammatory mediators, extracellular vesicle-mediated signaling, and peripheral immune crosstalk. We further highlight clinical observations linking nasal microbiome signatures with olfactory dysfunction, cognitive decline, and altered inflammatory profiles, particularly in systemic conditions such as sepsis. Despite rapid advances in this field, significant knowledge gaps persist, including the limited availability of longitudinal human cohorts capable of establishing causality, incomplete mechanistic validation in translational models, and insufficient characterization of how environmental exposures and aging reshape the nasal microbiome-brain interface. By integrating current evidence and defining these unmet needs, this review positions the nasal microbiome as a promising source of diagnostic biomarkers and a therapeutic target for modulating neuroinflammation and mitigating neurodegenerative progression.},
}

@article {pmid41619780,
year = {2026},
author = {Saiz-Gonzalo, G and O'Connell, O and Joy, S and McSweeney, S and Kia, NV and Brodkorb, A and Bleiel, SB},
title = {New Insights into Probiotic Enumeration in a Complex Food Matrix: Flow Cytometry and Plate Count Correlation.},
journal = {Journal of AOAC International},
volume = {},
number = {},
pages = {},
doi = {10.1093/jaoacint/qsag009},
pmid = {41619780},
issn = {1944-7922},
abstract = {BACKGROUND: Accurate probiotic enumeration ensures the dose delivered to the mammalian host. Plate counting (PC) detects only culturable cells and can underestimate the total number of viable cells, particularly when some cells are injured or dormant and do not form colonies.

OBJECTIVE: To qualify a flow cytometry assay reporting active fluorescent units (AFU) and to compare counts with the plate-count (PC) method for micro-encapsulated Lacticaseibacillus rhamnosus GG in a snack product.

METHODS: Following AOAC/ICH/USP principles, precision, accuracy, ruggedness, specificity, and robustness of plate count and flow cytometry methods were evaluated for the first time in a commercial yogurt-bite snack product.

RESULTS: Both methods fulfilled the pre-specified performance targets (%RSD ≤ 15; AFU recovery 100-104%; live/dead R2 ≥ 0.95). Analyst to analyst differences were not significant. Flow cytometry spike recoveries were 100-104% across targets. Live/dead mixtures tracked linearly (R2 ≥ 0.95). Across matched samples, AFU and CFU values were equivalent within a pre-specified ± 0.5 log band; batch means typically differed by ≤ 0.2 log with no systematic bias.

CONCLUSIONS: The qualified flow cytometry method provides same-day counts and enumerates all membrane-intact cells, complementing plate counts while meeting analytical performance criteria. Findings endorse the use of AFU in tandem to CFU assessment for probiotic quantification, label accuracy and estimation of microbiome-relevant dose in snack and finished-product matrixes.

HIGHLIGHTS: Flow-cytometry provided same-day results and enumerated all membrane-intact cells for label verification in snack matrixes.s.},
}

@article {pmid41619561,
year = {2026},
author = {Inoki, L and Toyoda, S and Fukuokaya, W and Yanagisawa, T and Inamoto, T and Nukaya, T and Takahara, K and Tsujino, T and Maenosono, R and Komura, K and Bekku, K and Araki, M and Iwata, T and Fujita, K and , },
title = {Impact of Proton Pump Inhibitor Use on the Efficacy of IO-IO Versus IO-TKI Therapy in Metastatic Renal Cell Carcinoma.},
journal = {Clinical genitourinary cancer},
volume = {24},
number = {2},
pages = {102500},
doi = {10.1016/j.clgc.2025.102500},
pmid = {41619561},
issn = {1938-0682},
abstract = {BASCKGROUND: Immune checkpoint inhibitor (ICI)-based combination therapies have become the standard first-line treatment for metastatic renal cell carcinoma (mRCC). Proton-pump inhibitors (PPIs), frequently used to treat gastrointestinal conditions, have been implicated in modulating ICI efficacy, potentially through gut microbiome dysbiosis. However, the impact of PPIs on ICI-based therapies for mRCC remains unclear.

METHODS: This multicenter retrospective cohort study analyzed 427 patients with mRCC classified as intermediate or poor risk according to the IMDC criteria treated with first-line IO-IO (ipilimumab plus nivolumab) or IO-TKI (ICI plus tyrosine kinase inhibitor) therapies. Patients were stratified by PPI use during the 30 days before and including the day of ICI initiation. Overall survival (OS), progression-free survival (PFS), and objective response rate (ORR) were compared between PPI users and nonusers.

RESULTS: PPI use was significantly associated with shorter OS in patients receiving IO-IO therapy (median OS, 23.34 months vs. not reached; P = .002), but not in those receiving IO-TKI therapy (P = .909). Multivariate analysis confirmed PPIs as an independent prognostic factor for OS in the IO-IO group (HR, 1.647; 95% CI, 1.007-2.693; P = .046). No significant differences in PFS or ORR were observed between PPI users and nonusers in either group, although the complete response rate was notably lower in PPI users treated with IO-IO (1.6% vs. 10.3%; P = .025).

CONCLUSIONS: PPI use was associated with inferior survival in mRCC patients receiving IO-IO therapy, potentially through microbiome modulation and other immunologic or clinical mechanisms; however, these findings are based on retrospective data and should be regarded as hypothesis-generating. Caution is advised when prescribing PPIs to patients undergoing ICI-based therapy, particularly IO-IO regimens, and prospective studies are needed to confirm whether avoiding unnecessary PPI use can improve clinical outcomes.},
}

@article {pmid41619552,
year = {2026},
author = {Lian, Y and Chen, X and Shen, X and Gan, Z and Sun, J and Li, Q and Li, M and Li, J and Luo, J and Liu, X and Feng, W and Jiang, G},
title = {Spatial metabolomics combined with MALDI-MSI unveils gut-brain axis mechanisms of angelica dahurica radix in migraine rats.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {152},
number = {},
pages = {157815},
doi = {10.1016/j.phymed.2026.157815},
pmid = {41619552},
issn = {1618-095X},
abstract = {BACKGROUND: Migraine is a highly disabling neurological disorder characterized by recurrent headaches and complex metabolic disturbances, affecting approximately 15% of the global population. Angelica dahurica Radix (Baizhi), a classic traditional Chinese medicine documented in Shennong Bencao Jing, has been used for millennia to treat migraine, but its underlying mechanism remains unclear.

PURPOSE: This study aimed to explore the gut-brain axis mechanisms underlying Baizhi's anti-migraine effects by integrating multi-omics approaches to clarify its regulatory effects on intestinal barrier function, gut microbiota, and cerebral metabolism.

STUDY DESIGN: A nitroglycerin (NTG)-induced migraine rat model was used, with 48 male Sprague-Dawley rats randomized into four groups (n=12 each): Control (CON, 10 mL/kg water p.o.), Migraine model (NTG, water + NTG 10 mg/kg s.c.), Positive control (SS+NTG, sumatriptan succinate 260 mg/kg p.o. + NTG), and Baizhi aqueous extract (CBZ) group (7.2 g/kg crude drug + NTG). Migraine-like behaviors and biological samples were assessed after 22 days of intervention.

METHODS: The study combined MALDI mass spectrometry imaging (MALDI-MSI)-based spatial metabolomics (to analyze brain metabolic changes), fecal metabolomics (to identify systemic metabolic perturbations), and 16S rRNA sequencing (to profile gut microbiota composition). Additionally, histopathological staining (H&E) and immunohistochemistry (for Occludin and ZO-1) was used to evaluate intestinal barrier function, and ELISA(Enzyme-linked immunosorbent assay) was applied to detect pain-related biomarkers (5-HT, CGRP, TNF-α) in plasma and brain.

RESULTS: CBZ alleviated migraine-like behaviors (reduced head-scratching frequency) and normalized levels of pain-related biomarkers (5-HT, CGRP, TNF-α) in plasma and brain. It repaired intestinal barrier dysfunction by upregulating tight junction proteins (Occludin, ZO-1). 16S rRNA sequencing showed that CBZ reversed NTG-induced gut microbiota dysbiosis, specifically enriching Lactobacillus and reducing pro-inflammatory taxa (e.g., Blautia). Fecal metabolomics indicated restoration of key pathways, including lipid metabolism, glutathione metabolism, and short-chain fatty acid synthesis. MALDI-MSI visualized spatial metabolic normalization in the brain, with CBZ correcting abnormal glucose accumulation, restoring energy metabolism (e.g., ATP/GTP ratios), and regulating lipid signaling (e.g., phosphatidylinositol 4,5-bisphosphate) in specific brain regions.

CONCLUSION: Baizhi alleviates migraine through multi-target regulation of the gut-brain axis, including intestinal barrier repair, gut microbiota remodeling, and cerebral metabolic restoration. Notably, this study on Baizhi represents the first integration of spatial metabolomics (MALDI-MSI) with gut microbiome and systemic metabolomics to elucidate migraine mechanisms, providing a novel multi-omics strategy for understanding the holistic therapeutic effects of traditional Chinese medicine. These findings provide a mechanistic basis for its clinical application in migraine treatment.},
}

@article {pmid41619271,
year = {2026},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Functional Pathways of the Gut Microbiome Associated with SCFA Profiles in Preclinical Alzheimer's Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1539},
pmid = {41619271},
issn = {2152-5250},
abstract = {Functional activities of the gut microbiome, particularly those contributing to short-chain fatty acid (SCFA) metabolism, play a central role in host-microbe interactions and are linked to neuroinflammatory mechanisms underlying Alzheimer's disease (AD). How microbial metabolic functions relate to SCFA concentrations and cerebral amyloid-β (Aβ) burden during the preclinical stage of AD remains poorly understood. In this study, faecal metagenomes from 87 cognitively unimpaired adults were profiled using HUMAnN3 to generate MetaCyc pathway abundance data, normalised and filtered to retain pathways present in at least 30% of participants. A keyword-based search identified 362 SCFA-related pathways spanning acetate, propionate, butyrate, isobutyrate, valerate and isovalerate metabolism. Associations between microbial functions, SCFA concentrations and Aβ status were evaluated using Spearman correlations, Kruskal-Wallis tests across SCFA quartiles, and multivariable linear regression with false discovery rate correction, supported by canonical correspondence analysis and network modelling. A total of 38 significant SCFA pathway correlations were identified. Acetate, butyrate and total SCFA levels showed positive associations with biosynthetic pathways, including L-arginine biosynthesis II, peptidoglycan biosynthesis and flavin biosynthesis, whereas fermentative pathways such as pyruvate fermentation to acetone and lysine fermentation to butanoate were negatively correlated. Butyrate quartiles demonstrated dose-dependent increases in biosynthetic functions and declines in fermentative routes. Canonical Correspondence Analysis (CCA) confirmed a significant multivariate association, and network analysis revealed enhanced fermentative and methanogenic connectivity among Aβ High participants. These findings indicate that amyloid burden is associated with a shift from anabolic to fermentative microbial metabolism and may inform future studies examining potential mechanistic links in preclinical AD.},
}

@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}

Humans
Malaysia/epidemiology
*Pediculus/genetics/classification
Animals
*Microbiota
Male
*Lice Infestations/epidemiology/parasitology
Female
Child
Child, Preschool
*Genetic Variation
RNA, Ribosomal, 16S/genetics
Vulnerable Populations
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid41619222,
year = {2026},
author = {Hilger, E and Chan, K and Yip, A and Wang, XM and Broderick, C and Arents, B and van Bart, K and Eyerich, K and Rastrick, J and Weidinger, S and Flohr, C and , },
title = {Biomarkers for therapeutic response and adverse outcomes in atopic dermatitis: A systematic review.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70330},
pmid = {41619222},
issn = {1468-3083},
support = {821511//Innovative Medicines Initiative 2 Joint Undertaking (JU)/ ; },
abstract = {INTRODUCTION AND OBJECTIVES: Atopic dermatitis (AD) is a chronic, inflammatory cutaneous disease characterized by intense itch that affects approximately 20% of children and up to 10% of adults. Our systematic review aims to identify biomarkers with clinical significance for predicting response to systemic therapies and treatment-related adverse events (AEs) for AD patients.

MATERIALS AND METHODS: A systematic search was conducted across the electronic databases Embase and MEDLINE from database inception to September 2024. All records were independently screened at both the title/abstract and full-text stages. Included articles were randomized controlled trials, cohort studies or case-control studies that reported relevant data for investigating associations between biomarkers and disease progression and/or change in disease activity over time. All discrepancies at any stage were resolved through adjudication by a senior reviewer.

RESULTS: We identified 28 papers evaluating biomarkers for treatment response and 11 for AEs. Across treatment response studies, biomarkers investigated included IgE, eosinophils, LDH, TARC, cytokines, genetic variants and the skin microbiome. Most studies investigated the association between biomarkers and dupilumab, while studies reporting associations between biomarkers and AEs were limited to dupilumab-related conjunctivitis and ocular surface disease (DAOSD). The primary findings on treatment response were inconsistent, demonstrating that while elevated LDH was associated with poorer response to dupilumab, neither IgE nor eosinophil count showed consistent predictive value. Regarding the association between biomarkers and AEs, IgE was identified as the most promising predictor of DAOSD.

CONCLUSION: Predicting therapeutic responses and identifying patients at risk of developing AEs will be increasingly important with an expanding range of treatment options for AD. Finding robust predictive biomarkers for AD, however, is complicated by its clinical heterogeneity and multifactorial aetiology. Collaborative projects, such as BIOMAP, hold great potential to advance precision medicine and enhance individualized care.},
}

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units). Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

@article {pmid41618640,
year = {2026},
author = {Salehimoghaddam, Z and Hynes, AP and Doyle, RT},
title = {From bacterial predators to partners: phages in agriculture.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70959},
pmid = {41618640},
issn = {1469-8137},
support = {2018-05996//Natural Sciences and Engineering Council of Canada (NSERC)/ ; //Farncombe Family Chair in Phage Biology/ ; //McMaster University - Department of Biology/ ; 2023-05144//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
abstract = {Bacteriophages, viruses that infect bacteria, are critical players for shaping the taxonomic and functional composition of plant-associated microbiomes. Yet, their roles in plant health remain overlooked, along with their implications for sustainable agriculture. While phages are recognized as bacterial predators, they can also promote bacterial survival and competitiveness. Here, we highlight the roles phage play in shaping soil microbiomes and promising phage-based applications for sustainable agriculture. Ongoing research highlights the diverse roles of phages in regulating bacterial populations, enhancing nutrient cycling, improving stress tolerance, and suppressing soil-borne pathogens - microbial traits that directly link to plant health. Additionally, emerging applications such as bioremediation, phage-based biosensors, and microbiome engineering underscore phages' potential to revolutionize sustainable farming and optimize agricultural productivity.},
}

@article {pmid41618562,
year = {2026},
author = {Shelake, RM and Waghunde, RR and Kim, JY},
title = {Coevolution of plant-microbe interactions, friend-foe continuum, and microbiome engineering for a sustainable future.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2026.01.010},
pmid = {41618562},
issn = {1752-9867},
abstract = {The coevolution of plant-microbe (PM) associations over approximately 450 million years has been a fundamental driver of terrestrial life, giving rise to mutualistic, commensal, and pathogenic relationships along a dynamic friend-foe continuum. The need to adapt to the host environment has driven the convergent evolution of common strategies among mutualists and pathogens, enabling them to evade or modulate the plant immune system. This review synthesizes PM coevolution within a deep-time, three-pillar framework: organellogenesis, root evolution, and immune gatekeeping, linking ancient endosymbiotic events (mitochondria, chloroplast, and nitroplast) to contemporary holobiont-level phenotypes and biotechnological applications. We organize the friend-foe continuum around a coevolution-guided cost-benefit and tipping-point framework, using identified molecular switches and evolutionary constraints to derive actionable design rules for engineering PM associations. Moving beyond a descriptive toolbox of technologies, we integrate recent breakthroughs to analyze how four principal axes: host and microbial genetics, evolutionary dynamics, environmental and ecological conditions, and metabolic switches define the thresholds that govern microbial lifestyle transitions. Finally, we propose specific, testable strategies for PM coevolution-informed crop improvement, distinguishing near-term feasible targets from long-term speculative goals in nitrogen utilization, synthetic microbial communities, immune receptor engineering, modulation of plant memory, and microbiome-integrated breeding through genome editing, synthetic biology, AI, and microbiome engineering. Together, these approaches extend existing syntheses into a predictive, evolution-informed framework that transforms coevolutionary principles into a functional blueprint for sustainable and resilient agriculture.},
}