@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.},
}

@article {pmid41618437,
year = {2026},
author = {Chong-Nguyen, C and Artiles, RF and Pilgrim, T and Yilmaz, B and Döring, Y},
title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00824-w},
pmid = {41618437},
issn = {2042-6410},
abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.

METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.

RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.

CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.},
}

@article {pmid41618422,
year = {2026},
author = {Wang, T and Gyori, B and Weiss, ST and Menichetti, G and Liu, YY},
title = {Revealing interactions between microbes, metabolites, and dietary compounds using genome-scale analysis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02312-6},
pmid = {41618422},
issn = {2049-2618},
support = {K25HL173665/HL/NHLBI NIH HHS/United States ; 24MERIT 1185447//American Heart Association/ ; R01AI141529, R01HD093761, RF1AG067744, UH3OD023268, U19AI095219, and U01HL089856/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The role of gut microbiome in predicting diet response and developing personalized dietary recommendations has been increasingly recognized. Yet, we still lack comprehensive, genome-based insights into which gut microbes metabolize specific dietary compounds.

RESULTS: Here, we leveraged the metabolic networks constructed from well-annotated microbial genomes to characterize the potential interactions between microbes and metabolites, specifically emphasizing the interactions between microbes and dietary compounds. We revealed a substantial, approximately fourfold variation in both the number of metabolites and dietary compounds in the microbial genome-scale metabolic networks across different genera, whereas species within the same genus showed a high metabolic similarity (mean coefficient of variation in microbial network degree CV¯ = 0.023 for metabolites and 0.015 for dietary compounds). We found that the number of species that can utilize a metabolite drastically varies, ranging from 1 to 818 species, with some metabolites being used by a wide range of species (211 out of 1390 metabolites used by more than 95% of species) and others only by a few species (435 metabolites used by less than 5% of species). Leveraging a longitudinal microbiome study, we observed that microbial taxa with similar metabolic capacity tend to have positively correlated abundances, and the gut microbiome's capacity to process dietary compounds is functionally stable. Finally, we propose a network-based method to identify the dietary compounds that are specific to no more than 10 microbial species, offering a new strategy for combining a dietary compound and its linked microbial species to design synbiotics.

CONCLUSIONS: Our results quantitatively reveal large-scale variation and redundancy in gut microbial metabolism and identify dietary compounds linked to only a few microbial species. These findings improve understanding of microbe-metabolite interactions and provide a foundation for the rational design of microbiome-based interventions for healthy benefits. Video Abstract.},
}

@article {pmid41618396,
year = {2026},
author = {Capparotto, A and Chesneau, G and Tondello, A and Orellana, E and Stevanato, P and Bonato, T and Squartini, A and Hacquard, S and Giovannetti, M},
title = {Plant phenotypic differentiation outweighs genetic variation in shaping the lettuce leaf microbiota.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00850-6},
pmid = {41618396},
issn = {2524-6372},
support = {DOT1471523//PON Ricerca e Innovazione 2014-2020 PhD fellowship/ ; NextGenerationEU 2021 STARS Grants@Unipd program P-NICHE//European Commission/ ; Progetti di Ricerca Dipartimentali - PRID, grant number BIRD214519 to MG//Dipartimento di Biologia, Università degli Studi di Padova/ ; },
abstract = {Lettuce, a widely consumed raw vegetable, harbors leaf-associated microbial communities whose understanding and prediction are crucial for plant and human health. While environmental factors are known to strongly influence plant leaf microbiomes, the role of plant-specific determinants in shaping microbial diversity remains unclear. In this study, we investigated how three key plant factors -genetic distance, plant variety and leaf micro- and macronutrient content- influence the composition and diversity of lettuce leaf bacterial communities, by analyzing 131 fully-sequenced Lactuca sativa genotypes via 16S rRNA amplicon sequencing. Our findings revealed that variety, as defined by breeders, exerts a greater influence on bacterial community diversity than genetic distance or variations in leaf nutrient levels. Together with available and detailed shoot traits they explained 13.4% of the observed bacterial diversity. Inspection of 9 specific leaf morphological traits, with further validation by MAGs analysis, showed that heart formation, head height, and venation types significantly shaped bacterial richness and evenness, mainly acting on non-hub members. These results highlight the strong relationship between leaf morphology and bacterial community structure, suggesting that phenotypic traits play an outsized but understudied role in shaping the leaf microbiota, a crucial aspect of the edible microbiome.},
}

@article {pmid41618136,
year = {2026},
author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX},
title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04750-0},
pmid = {41618136},
issn = {1471-2180},
support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41618101,
year = {2026},
author = {Park, SJ and Özdinç, BE and Coker, KG and Walsh, DM and Fox, DJ and Evans, S and Farahnik, J and Moffat, K and Boomgaarden, M and Mischley, LK},
title = {Metagenomics indicates an interplay of the microbiome and functional pathways in Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01271-5},
pmid = {41618101},
issn = {2373-8057},
abstract = {Previous studies suggest there are distinct gut microbial and functional variations in patients with Parkinson's disease (PwPD) that may reveal potential microbiome signatures or biomarkers to aid in early detection of the disease. In this case-control study, we used whole genome sequencing to compare the stool samples of 55 PwPD to 42 healthy controls (HC) from a public database (BioProject Accession PRJEB39223). For bacterial phyla, we observed a greater relative abundance in Firmicutes and Actinobacteria among PwPD, while that of Bacteroidetes was lower. For phages, PwPD had a greater relative abundance of Siphoviridae, Tectiviridae, and Podoviridae, while Microviridae was lower. Moreover, we described 10 functional pathways that most significantly differed between PwPD and HC (all P < 0.0001). In conclusion, significant differences were observed in gut bacteria, phages, and functional pathways between PwPD and HC that both support and conflict with previous case-control studies and warrant further validation.},
}

@article {pmid41617858,
year = {2026},
author = {Ma, A and Xun, W and Zhang, S and Liang, S and Wei, W and Huang, H and Shen, Q and Xu, G and Zhang, R},
title = {Amino-acid-transporter-mediated assembly of rhizosphere microbiota enhances soil organic nitrogen acquisition in rice.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {41617858},
issn = {2055-0278},
abstract = {Amino acids are plant-available organic nitrogen (N) that can be directly absorbed, but their availability relies on microbial decomposition of organic matter in the soil. Natural variation in Lysine-Histidine-Type Transporter-1 (OsLHT1) (NCBI Gene ID: 3974662) is associated with higher amino acid uptake in japonica rice than in indica. However, how this genetic variation influences rhizosphere microbiome assembly and its subsequent impact on amino acid acquisition remains unclear. In this study, we demonstrate that the OsLHT1a allele in japonica is prevalent in rice grown in high-organic-N soils, where it recruits a distinct rhizosphere microbiome to enhance amino acid acquisition. A synthetic microbiota composed of bacteria enriched by the OsLHT1a allele in japonica enhanced amino acid production in soil through organic matter decomposition and increased root amino acid uptake by upregulating OsLHT1 gene expression. The rhizosphere colonization of the synthetic microbiota was specifically driven by the function of OsLHT1. Notably, organic fertilization facilitated this colonization, thereby improving organic N use efficiency and rice yield. This root-rhizosphere microbiome functional synergy under organic fertilization presents a promising strategy to increase organic fertilizer use efficiency and demonstrates the potential for harnessing plant-gene-associated rhizosphere microbiomes for sustainable agriculture.},
}

@article {pmid41617724,
year = {2026},
author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG},
title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06624-6},
pmid = {41617724},
issn = {2052-4463},
abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.},
}

@article {pmid41617669,
year = {2026},
author = {Jiang, Y and Jiang, S and Wang, Z and Zhu, P and Zhang, J and Teng, F and Huang, S},
title = {Precise probiotic therapy: Advances, bottlenecks, and the road to microbiome-informed nutrition.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623359},
doi = {10.1080/19490976.2026.2623359},
pmid = {41617669},
issn = {1949-0984},
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Gastrointestinal Microbiome ; Precision Medicine/methods ; Host Microbial Interactions ; },
abstract = {The human gut microbiome is a cornerstone of health, yet conventional probiotic therapies often exhibit limited efficacy owing to heterogeneity in host-microbe-environment dynamics. This review dissects the biological and environmental drivers of such variability and highlights emerging frameworks that integrate cross-sectional and longitudinal multi-omics data to predict probiotic treatment outcomes and host metabolic responses. We further spotlight breakthroughs in methodological development in efficient mining and engineering of probiotic strains, which enable the rational design of functionally enhanced, personalized probiotics. By synthesizing these advances, the review underscores the transformative potential of combining data-driven models with precision-engineered microbial therapeutics to address current limitations and usher in a new era of future microbiome-informed nutrition and personalized interventions.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Gastrointestinal Microbiome
Precision Medicine/methods
Host Microbial Interactions

@article {pmid41617485,
year = {2026},
author = {Chang, YH and Hong, TC and Lin, KT and Hsiao, YJ and Hsu, HE and Waniwan, JT and Silva, RE and Lai, IR and Lee, PC and Lin, MT and Shun, CT and Hsieh, MS and Chen, YJ and Wang, SW and Hsu, WH and Wu, IC and Wang, YK and Li, CC and Wang, JY and Hsu, YC and Fang, H and Lin, ZS and Chang, WH and Lin, JH and Chen, YS and Ko, YC and Shen, CY and Chen, YM and Wang, CY and Jheng, YT and Liu, WY and Wang, YT and Yeh, CW and Huang, PR and Liou, JM and Chen, LT and Han, CL and Wu, DC and Chen, HY and Yu, SL and Wu, MS and Chen, YJ and , },
title = {Integrative proteogenomics maps multifactorial aetiology, progression and therapeutic vulnerabilities in gastric cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337247},
pmid = {41617485},
issn = {1468-3288},
abstract = {BACKGROUND: Gastric cancer, with disproportionately higher incidence in East Asia, arises from complex host-microbiome-environment interactions beyond Helicobacter pylori (HP) infection. However, the molecular architecture linking environmental carcinogens, microbial succession and host response remains unclear.

OBJECTIVE: To delineate multifactorial aetiologies and clinically actionable subtypes/biomarkers of gastric cancer through integrative proteogenomic, microbial and environmental exposure profiling.

DESIGN: We established a multiomics atlas of paired tumour, adjacent mucosa tissues and blood from 154 treatment-naïve Taiwanese patients, integrating whole-exome sequencing, RNA-seq, proteome and phosphoproteome profiling with carcinogen signatures, HP status, microbiome composition and refined anatomical mapping. Cell-based functional assays tested carcinogen effects. Microbial subtype was assessed in an independent cohort.

RESULTS: A polycyclic-aromatic-hydrocarbon signature, dibenz[a,h]acridine, emerged as a high-risk exposure promoting invasion, immune suppression and poor survival, significantly exceeding nitrosamine-linked risk in this cohort. Multilayer integration defined three initiation ecologies: HP-driven inflammatory, non-HP microbiome-enriched immune-silent and HP-free microbially depleted states. Among HP-negative tumours, a Streptococcus-enriched subtype associated with tight-junction (CLDN18.2/ZO-1/OCLN) disruption and epithelial-mesenchymal transition, whereas a subset of clinically aggressive cases retained CLDN18.2-high epithelial-stable subtype for therapeutic accessibility. An independent cohort revealed gastric juice-derived Streptococcus anginosus abundance inversely correlated with tight-junction proteins. Anatomical mapping reveals location-specific, sex-specific, subtype-specific oncogenic networks and kinase activity, including CDK4 activation in clinical biomarker-negative tumours. Decision-tree models combining exposure and proteome-immune states refined recurrence and survival prediction beyond stage.

CONCLUSION: This proteogenomic framework defines exposure-informed and microbiome-informed gastric cancer subtypes, providing a molecular schema for patient stratification, prevention and actionable therapeutic vulnerabilities.},
}

@article {pmid41617205,
year = {2026},
author = {Størdal, K and Andersen, S and Mårild, K and Larsson, V and Imberg, H},
title = {Systematic review and meta-analysis of childhood exposure to antibiotics and the subsequent risk of IBD.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf324},
pmid = {41617205},
issn = {1536-4844},
abstract = {BACKGROUND: Antibiotic use in early childhood may alter the developing microbiome and has been proposed as a risk factor for inflammatory bowel disease (IBD). We conducted a systematic review to examine the association between childhood antibiotic use and subsequent risk of IBD.

METHODS: In a systematic literature search, we identified cohort and case-control studies reporting the association between antibiotic use (exposure age <1 to 17 years) and development of IBD. MEDLINE and EMBASE databases were searched from inception through December 31, 2024. Studies reporting a hazard ratio, odds ratio, or risk ratio (RR) were included. To account for heterogeneity, pooled estimates were calculated using the DerSimonian-Laird random-effects model. Estimates were adjusted for potential confounding as reported in the original studies.

RESULTS: We identified 10 studies, of which 8 (n = 2783 cases) reported associations between childhood antibiotics and IBD risk. Additionally, 2 studies on Crohn's disease (CD) and 1 on ulcerative colitis were included in disease-specific analyses. In pooled analyses, antibiotic exposure compared with no exposure was associated with increased risk of IBD (RR, 1.42; 95% confidence interval [CI], 1.23-1.66), CD (RR, 1.59; 95% CI, 1.39-1.81), and ulcerative colitis (RR, 1.23; 95% CI, 1.08-1.40). Heterogeneity was low to moderate (I2 = 0%-35%), and funnel plots did not indicate publication bias (Egger's test, P = .12-.43). Adjustment for infections did not attenuate the association between childhood antibiotic exposure and IBD development.

CONCLUSIONS: While causal interpretation should be cautious, childhood exposure to antibiotics was associated with an increased risk of later IBD, particularly for CD.},
}

@article {pmid41617030,
year = {2026},
author = {Picking, J and Li, Y and Ticak, T and Ferguson, DJ and Hao, B and Krzycki, JA},
title = {Delineation of the Active Site of MtgB, a Cobalamin-dependent Glycine Betaine Methyltransferase.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111216},
doi = {10.1016/j.jbc.2026.111216},
pmid = {41617030},
issn = {1083-351X},
abstract = {The MttB superfamily member MtgB catalyzes the methylation of a cognate corrinoid protein with glycine betaine and representatives have been described from both bacteria and archaea. Here we focused on MtgB from Desulfitobacterium hafniense, a protein for which a crystal structure had been previously obtained. We employed different programs to predict the binding of glycine betaine and identified a consensus binding site. The modelled binding site consisted of two aromatic residues, Y97 and a F356, which are both proposed to interact with the quaternary amine portion of glycine betaine via pi:cation interactions. Additionally, two basic residues, H348 and R312, were proposed to interact with the carboxylate group. We carried out site directed substitutions and subsequently tested the necessity of these residues for glycine betaine:cob(I)alamin methyltransferase activity. These experiments supported a role in catalysis for each residue, presumably in placement of glycine betaine at proper position for nucleophilic attack by the Co(I) ion of cobalamin. Subsequently, the structure of the glycine betaine bound enzyme was obtained and confirmed the interaction of these residues with glycine betaine. Other MttB superfamily members with specificity for different quaternary amines were modeled and compared with the glycine betaine bound structure of MtgB. The nitrogen of each quaternary amine was brought within an average value of 1.8 Å to each other, suggesting that members of the superfamily bring their methyl groups into nearly the same space within the TIM barrel prior to methyl group transfer to cob(I)alamin.},
}

@article {pmid41616776,
year = {2026},
author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W},
title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.01.006},
pmid = {41616776},
issn = {1934-6069},
abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.},
}

@article {pmid41616767,
year = {2026},
author = {Dhariwala, MO and Carale, RO and DeRogatis, AM and Rodriguez-Valbuena, H and Okoro, JN and Ekstrand, CA and Weckel, A and Tran, VM and Habrylo, I and Barrere-Cain, R and Ojewumi, OT and Tammen, AE and Tsui, J and Shaikh, S and Yellamilli, S and Aladhami, AK and Schwartz, R and Leech, JM and Merana, GR and Hiam-Galvez, KJ and Mack, M and Halkias, J and Gardner, JM and Rutishauser, RL and Fragiadakis, GK and Spitzer, MH and Combes, AJ and Scharschmidt, TC},
title = {Commensal-myeloid crosstalk in neonatal skin regulates interleukin-1 signaling and cutaneous type 17 inflammation.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.01.005},
pmid = {41616767},
issn = {1097-4180},
abstract = {Early-life microbe-immune interactions at barrier surfaces have lasting impacts on the trajectory toward health versus disease. Monocytes, macrophages, and dendritic cells are primary sentinels in barrier tissues, yet the salient contributions of commensal-myeloid crosstalk during tissue development remain poorly understood. Here, we identify that commensal microbes facilitate accumulation of a population of monocytes in neonatal skin. Transient post-natal depletion of these monocytes resulted in heightened interleukin (IL)-17A production by skin T cells, which was particularly sustained among CD4[+] T cells and was sufficient to exacerbate inflammatory skin pathologies. Neonatal skin monocytes were enriched in expression of negative regulators of the IL-1 pathway. Functional in vivo experiments confirmed a key role of excessive IL-1R1 signaling in T cells as contributing to the dysregulated type 17 response in neonatal monocyte-depleted mice. Thus, a commensal-driven wave of monocytes into neonatal skin critically facilitates immune homeostasis in this prominent barrier tissue.},
}

@article {pmid41616716,
year = {2026},
author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM},
title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.},
journal = {Journal of environmental management},
volume = {400},
number = {},
pages = {128747},
doi = {10.1016/j.jenvman.2026.128747},
pmid = {41616716},
issn = {1095-8630},
abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.},
}

@article {pmid41616707,
year = {2026},
author = {Wasim, I and Mondal, NS and Dey, J and Saikia, L and Law, D and Sen, S and Gautam, MK and Dutta, PP},
title = {Seborrheic dermatitis and dandruff: An overview of pathogenesis, role of Malassezia spp., and natural treatment approaches.},
journal = {Journal de mycologie medicale},
volume = {36},
number = {1},
pages = {101604},
doi = {10.1016/j.mycmed.2026.101604},
pmid = {41616707},
issn = {1773-0449},
abstract = {Seborrheic Dermatitis (SD) and dandruff are prevalent dermatological disorders that primarily affect the sebaceous glands and have significant implications for adults and children. While chronic skin lesions characterise SD, dandruff is characterised by excessive scalp flaking, pruritus, and erythema. Despite their overlapping clinical manifestations, these conditions differ in their underlying pathophysiology, with overgrowth of Malassezia species (spp.) emerging as a central pathogenic factor in both. Malassezia, a commensal yeast naturally residing on the skin, has been implicated in exacerbating inflammation and triggering immune responses, thereby contributing to the initiation and progression of SD and dandruff. In this comprehensive review, we systematically evaluated the role of natural and plant-derived ingredients in managing SD and dandruff, with a particular focus on their effects on Malassezia spp. The literature search was conducted using Google Scholar, Google Patents, PubMed, and SciFinder until December 2025. The extracted data were qualitatively synthesised to identify key findings and highlight existing research gaps. The results indicate that Malassezia spp., particularly Malassezia furfur, play a pivotal role in SD and dandruff by overgrowing, leading to excessive sebum production, yeast colonisation, and subsequent inflammation. M. furfur has been shown to stimulate the release of proinflammatory cytokines and activate the NLRP3 inflammasome, further promoting the inflammatory cascade associated with these conditions. Plant-derived ingredients, such as antimicrobial and anti-fungal compounds, have garnered attention for their potential therapeutic effects. Several studies suggest that substances like tea tree oil, aloe vera and various herbal extracts may reduce Malassezia load and mitigate the inflammation associated with these disorders. However, there remains a lack of clarity regarding the precise mechanisms by which these natural agents influence the skin's microbiome and immune system. Further clinical investigations are essential to assess the efficacy, safety, and optimal formulations of these plant-based treatments. Despite promising evidence supporting their use, additional well-designed studies are needed to clarify their roles and to establish standardised treatment protocols for SD and dandruff management.},
}

@article {pmid41616686,
year = {2026},
author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ},
title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103436},
doi = {10.1016/j.copbio.2026.103436},
pmid = {41616686},
issn = {1879-0429},
abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.},
}

@article {pmid41615983,
year = {2026},
author = {Gin, TE and Moore, CO and Tomlinson, T and Wilson, G and Gray, A and Sutherland, C and Miller, K and Li, K and Canfield, M and Herrin, B and Lashnits, E and Callahan, B},
title = {Pathogenic bacterial species and the microbiome of cat fleas (Ctenocephalides felis) inhabiting flea-infested homes.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0341824},
pmid = {41615983},
issn = {1932-6203},
mesh = {Animals ; Cats ; *Ctenocephalides/microbiology ; *Microbiota/genetics ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Flea Infestations/veterinary/parasitology/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Cat Diseases/parasitology ; Bartonella/genetics/isolation & purification ; },
abstract = {BACKGROUND: Ctenocephalides felis is a common ectoparasite of dogs and cats and can transmit a variety of pathogens including Bartonella and Rickettsia species. These bacteria, along with the known endosymbiont Wolbachia, are well-documented members of the C. felis microbiome, but species-level information is limited. Additionally, little is known about the variation in the C. felis microbiome in fleas from different sources and when different sequencing methods are applied to the same samples.

OBJECTIVE: This study aimed to characterize the flea microbiome using both short-read (V3/V4) and long-read (full-length) 16S rRNA gene sequencing, determine whether long-read sequencing improves species-level identification especially in known pathogenic genera, and evaluate differences in microbial composition between fleas collected from cats, dogs, and environmental traps.

METHODS: Fleas were collected from cats, dogs, and traps in flea-infested homes in Florida, pooled by source, and sequenced using short- (V3/V4) and long-read (full-length) 16S rRNA gene sequencing. Microbial prevalence and abundance were compared across sequencing approaches. Community composition was evaluated for differences between sources and houses. Candidate members of the flea microbiome were identified based on a combination of prevalence, abundance, and statistical signatures of potential contaminant origin. For Rickettsia and Bartonella, species-level taxonomic assignments were refined using a phylogenetic approach.

RESULTS: Wolbachia, Rickettsia, and Bartonella were the most prevalent and abundant taxa. Spiroplasma was identified as a fourth core member of the flea microbiome. Long-read sequencing enabled better, but not perfect, species-level classification of Bartonella and Rickettsia compared to short-read sequencing. Important relationships between specific ASVs and flea sources were identified, for example fleas from cats harbored higher abundances of B. clarridgeiae and B. henselae than fleas from traps.},
}

Animals
Cats
*Ctenocephalides/microbiology
*Microbiota/genetics
Dogs
RNA, Ribosomal, 16S/genetics
*Flea Infestations/veterinary/parasitology/microbiology
*Bacteria/genetics/classification/isolation & purification
Phylogeny
Cat Diseases/parasitology
Bartonella/genetics/isolation & purification

@article {pmid41615917,
year = {2026},
author = {Shokoohi, E and Masoko, P},
title = {Morphological traits and microbiome diversity in the free-living nematodes Acrobeles complexus and Zeldia punctata.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0341018},
pmid = {41615917},
issn = {1932-6203},
mesh = {Animals ; *Microbiota ; *Nematoda/microbiology/anatomy & histology ; Bacteria/classification/genetics ; Biodiversity ; },
abstract = {Morphological adaptations play a key role in shaping the feeding behavior and microbiome associations of Cephalobidae nematodes. To investigate how morphology influences nematode-associated microbiomes, we selected two widely distributed species: Acrobeles complexus, exhibiting elaborated oral structures, and Zeldia punctata, with simpler oral morphology. Unlike earlier studies that reported the microbiomes of A. complexus and Z. punctata independently, this study is the first to directly compare the two species. By integrating in silico re-analysis of our previously published microbiome datasets with new light microscopy and scanning electron microscopy (SEM) observations, we demonstrate how morphological adaptations, such as labial probolae and cuticle structures, shape associated bacterial communities. Our results revealed that A. complexus harbored a more diverse bacterial community than Z. punctata. Morphology showed that the complex oral structures of A. complexus facilitated selective bacterial capture, supporting greater microbial diversity compared to the simpler morphology of Z. punctata. Although statistical significance was not observed, the two species showed distinct patterns of microbial richness and diversity. Principal Coordinate Analysis (PCoA) revealed clearly separated bacterial community structures between the species. Linear discriminant analysis effect size identified potential microbial biomarkers at the genus level, including Firmicutes and Clostridium in A. complexus and Actinobacteria and Pseudomonas in Z. punctata. Predicted functional pathway analysis revealed notable differences in microbial metabolism, such as enrichment of bacterial secretion systems in A. complexus and amoebiasis and lipid metabolism pathways in Z. punctata. This study highlights the role of morphological adaptations in shaping microbiome composition in Cephalobidae nematodes and provides insights into the contribution of free-living bacterivorous nematodes to soil microbial balance. These findings lay the groundwork for further studies on nematode-mediated microbial interactions in soil ecosystems.},
}

Animals
*Microbiota
*Nematoda/microbiology/anatomy & histology
Bacteria/classification/genetics
Biodiversity

@article {pmid41615721,
year = {2026},
author = {Vásquez-Dean, J and Canales, A and Orellana, CA and Garrido, D},
title = {Bifidobacterium as Keystone Species Driving Microbial Interactions in the Infant Digestive Tract.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-052924-065321},
pmid = {41615721},
issn = {1941-1421},
abstract = {Bifidobacterium plays a keystone role in the ecological assembly of the infant-gut microbiome and in shaping host immune and metabolic development. These anaerobic bacteria possess specialized transporters and glycosyl hydrolases that enable the degradation of human milk oligosaccharides (HMOs), driving early microbial succession through coexistence, competition, and priority effects. Their fermentation products, mainly acetate and lactate, acidify the gut environment, inhibit pathogens, and sustain cross-feeding with butyrate-producing microbes, whereas aromatic lactic acids contribute to immune modulation. Ecological and clinical evidence indicates that loss of Bifidobacterium perturbs community structure and increases disease risk. Understanding these interactions has guided the design of HMO-based and synbiotic strategies that aim to restore healthy colonization patterns. Ongoing efforts now integrate ecological, metabolic, and computational approaches to better predict and replicate the health-promoting functions of Bifidobacterium throughout life.},
}

@article {pmid41615587,
year = {2026},
author = {Zhu, B and Chen, YE and Guo, Y},
title = {Emerging Mechanisms of Abdominal Aortic Aneurysm.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {17},
pmid = {41615587},
issn = {1534-6242},
support = {HL109946, HL134569/GF/NIH HHS/United States ; HL166203, HL165688/GF/NIH HHS/United States ; },
abstract = {PURPOSE OF REVIEW: Abdominal aortic aneurysm (AAA) is a progressive and often fatal vascular disease for which effective pharmacological therapies are lacking. This review synthesizes recent mechanistic advances in AAA pathogenesis and evaluates their translational significance for therapeutic development.

RECENT FINDINGS: Single-cell and spatial transcriptomic findings have delineated marked cellular heterogeneity within aneurysmal tissue, revealing dynamic interactions among vascular and immune cell populations. Vascular smooth muscle cell phenotypic modulation and programmed cell death compromise aortic wall integrity, while endothelial dysfunction promotes leukocyte recruitment and mediates early vascular responses. Infiltrating macrophages, neutrophils, and adaptive immune cells orchestrate chronic inflammation and extracellular matrix degeneration, whereas eosinophils and regulatory T cells exert context-dependent protective effects. Local factors, including intraluminal thrombus and perivascular adipose tissue, as well as systemic modulators such as dyslipidemia, gut microbiota, and sex hormones, further shape disease initiation and progression. These mechanistic insights have identified novel therapeutic targets, including inhibitors of regulated cell death, immunomodulatory agents, lipid-lowering interventions, and microbiome-directed strategies, and potential biomarkers for earlier diagnosis and improved risk stratification.

SUMMARY: Emerging mechanistic insights have highlighted the complex interplay among vascular cells, immune cells, the local microenvironment, and systemic modulators in the pathogenesis of AAA. Integrating mechanistic insights with translational research will be crucial in developing targeted interventions that pave the way for effective AAA therapies.

GRAPHICAL ABSTRACT: [Image: see text]},
}

@article {pmid41615200,
year = {2026},
author = {Yang, J and Qin, X and Zhang, D and Dong, C},
title = {Microbial landscape: composition and health associations of environmental microbiome in key functional spaces of premium elderly care facilities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183725},
doi = {10.1128/spectrum.01837-25},
pmid = {41615200},
issn = {2165-0497},
abstract = {The environmental microbiome in elderly care facilities plays a crucial role in the health of aging populations with immunosenescence; however, its composition and health associations remain underexplored. This study characterizes the microbial ecology of premium elderly care facilities, focusing on key functional spaces, environmental drivers, and implications for resident health. We conducted 16S rRNA gene sequencing (V3-V4 regions) on 320 surface and air samples from six functional spaces (dining areas, medical facilities, bedrooms, bathrooms, recreational rooms, and corridors) across four premium elderly care facilities. Environmental parameters (temperature, humidity, CO2, and occupancy) were measured concurrently. Bioinformatics analysis (QIIME 2, DADA2, and Silva database) and statistical modeling (permutational multivariate analysis of variance, distance-based redundancy analysis, and PICRUSt2) were employed to assess microbial diversity, taxonomic composition, functional potential, and environmental correlations. Using 16S rRNA gene sequencing across four facilities in different geographic regions, we identified significant spatial heterogeneity in microbial diversity and composition, with dining areas and recreational rooms exhibiting higher richness (Shannon index: 6.07 ± 0.37) and human-associated taxa (e.g., Firmicutes), while medical facilities and bathrooms harbored lower diversity but elevated opportunistic pathogens (Pseudomonas and Klebsiella). Environmental parameters-particularly relative humidity (explaining 13.8% of community variation) and occupancy-strongly influenced the microbial structure. A core microbiome dominated by Proteobacteria, Firmicutes, and Actinobacteria was conserved across facilities, while functional predictions revealed space-specific traits, including predicted enrichment of antibiotic resistance genes in medical facilities (ARG Shannon diversity: 4.87 ± 0.42) and carbohydrate metabolism pathways in dining areas. Negative correlations between beneficial (Lactobacillus) and pathogenic taxa (Staphylococcus aureus) were consistent with potential ecological strategies for microbial balance, although validation with absolute quantification is needed. This study highlights the need for space-specific microbial management in elderly care environments, emphasizing humidity control, ventilation, and targeted hygiene to mitigate pathogen risks while preserving beneficial communities. Our findings suggest the potential value of ecologically informed stewardship over pathogen-centric approaches. Future research should integrate multi-omics and longitudinal health data to optimize microbiome-resident health interactions.IMPORTANCEAs people age, their immune systems weaken, making the elderly especially vulnerable to germs in their surroundings. This study reveals that the types and amounts of bacteria living on surfaces and in the air within premium elderly care facilities differ significantly depending on the room's purpose-such as dining areas, medical rooms, or bathrooms. We found that humidity and how many people use a space strongly influence these bacterial communities. Crucially, areas like medical rooms had more bacteria linked to infections and antibiotic resistance, while social spaces hosted more diverse and potentially beneficial bacteria. This shows that a "one-size-fits-all" cleaning approach is not ideal. Instead, tailoring hygiene practices and environmental controls (like managing humidity) to specific spaces could better protect residents' health by reducing harmful germs while supporting helpful ones, offering a smarter way to manage these critical living environments for our aging population.},
}

@article {pmid41615149,
year = {2026},
author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y},
title = {Gut microbiome signatures associated with depression and obesity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0126325},
doi = {10.1128/msystems.01263-25},
pmid = {41615149},
issn = {2379-5077},
abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.

IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.},
}

@article {pmid41615148,
year = {2026},
author = {Khan, MQN and Xiang, W-Q and Wei, Y-l and Ren, M-X},
title = {Microbial assembly among plant parts of a tropical tree in different habitats and seasons.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183525},
doi = {10.1128/spectrum.01835-25},
pmid = {41615148},
issn = {2165-0497},
abstract = {Microorganisms are exhibited in every environment, but their role in the ecosystem and host association remains to be understood. Microbiome research highlights environmental filtering as a factor shaping microbial communities in terrestrial ecosystems. We analyzed bacterial and fungal communities in flowers, leaves, branches, trunks, roots, and soil of wild and rice field-grown Bombax ceiba under different seasons using the recent advanced techniques of 16S rRNA and ITS rRNA amplicon pyrosequencing, respectively. Our findings revealed variation in microbial communities across different plant parts and heights (flower, leaf, branch, trunk, roots, and soil). NMDS and hierarchical clustering (Bray-Curtis dis) analysis revealed that bacterial and fungal communities related to endophytic (within plant tissue) and epiphytic (external plant surfaces) niches of above and below-ground parts significantly differed due to seasonal variation in rice and wild habitats. Moreover, seasonal variation significantly affected the number of shared OTUs and bacterial and fungal taxa across all plant parts in both habitats. The spring season significantly influenced microbial diversity, assembly, and correlation networks in plant parts, with the most potent effects in the rice field compared to the wild habitat of Bombax ceiba, influencing flowering and boosting Firmicutes abundance. Wild habitats possessed higher functional diversity than rice-grown fields in spring and autumn across all plant parts, indicating their strong relation with different environments. The outcomes of the present study revealed that seasonal changes across various habitats dynamically shape the plant microbiome, suggesting distinct ecological roles (e.g., nutrient cycling, pathogen suppression, and stress tolerance) for bacterial and fungal communities in various niches.IMPORTANCEThis study shows that seasonal variation and habitat type (wild vs rice field) significantly influence the diversity, composition, and assembly of bacterial and fungal communities in different plant parts of Bombax ceiba. By analyzing both endophytic and epiphytic niches across above- and below-ground compartments, it reveals the spatial complexity of plant microbiomes. Wild habitats support greater stability to microbiome and their functions as compared with rice fields, particularly in spring, indicating that land-use practices affect microbiome structure and function. The study gives the details on how the compositions of microbiomes associated with plants change with season, which can impart insight into sustainable crop-management strategies, as well as conservation measures.},
}

@article {pmid41615027,
year = {2026},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Rodríguez, CAD and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag012},
pmid = {41615027},
issn = {1751-7370},
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}

@article {pmid41615012,
year = {2026},
author = {Bazzar, B and Reshadfar, E and Namdar, P and Pourbagher, D and Lafmejani, RB and Soleimanzadeh, A},
title = {The Relationship Between Seminal Microbiome and Male Reproductive Wellness: A Systematic Review†.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioag003},
pmid = {41615012},
issn = {1529-7268},
abstract = {The seminal microbiome, which is composed of different types of bacteria in semen and seminal plasma, has a significant impact on male reproductive health by changing the quality of semen and fertility. Previously regarded as sterile, the male reproductive tract contains microbes originating from the gastrointestinal tract, reproductive organs, and external sources such as sexual partners. Dysbiosis alters sperm parameters, triggers inflammation and oxidative stress, and is associated with conditions such as infertility, HPV infection, prostatitis, prostate cancer, and azoospermia. This systematic review adhered to the PRISMA 2020 guidelines (with 2025 extensions for reproducibility) and examined studies from PubMed, Scopus, and Science Direct (2015-2025, with prior context), concentrating on human, in vitro, and rodent models. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes are among the most important phyla. Beneficial genera, such as Lactobacillus, improve sperm motility, concentration, and DNA integrity, whereas dysbiotic taxa, such as Prevotella, Pseudomonas, and Ureaplasma, are associated with declines. Sexual activity facilitates bidirectional microbial transfer, modifying diversity and fostering the dysbiosis. Inflammatory cytokines, reactive oxygen species, and metabolic disruptions are all involved in this process. Changes that are specific to a disease, such as higher levels of Fusobacterium in HPV-positive samples, worsen the situation. This review highlights how the microbiome alters sperm function and causes infertility. Standardized methods and long-term studies are needed to prove causality. Probiotics and other therapeutic interventions show promise in restoring balance and boosting fertility.},
}

@article {pmid41614969,
year = {2026},
author = {Williamson, E and Hill, K and Eisenhofer, R and Hogendoorn, K},
title = {Experimental evidence for the absence of a functional gut microbiome in the solitary bee Megachile tosticauda.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag012},
pmid = {41614969},
issn = {1574-6968},
abstract = {The eusocial honey bee is a model for insect microbiome research, with socially transmitted gut communities that play key roles in health and development. In contrast, solitary bees lack social transmission pathways and often have an environmentally acquired microbiome, which may or may not be functionally important. Using 16S rRNA gene metabarcoding, previous work has described the bacterial communities in the solitary resin bee Megachile tosticauda larval pollen provisions, brood, and adult bees, but their functional significance has yet to be studied. Here, we investigate the importance of live bacteria for larval development and survival with an antibiotic-feeding experiment, and test whether bacteria are present in adult guts using scanning electron microscopy. Removing live bacteria in the food and gut of feeding larvae had no significant effect on survival or growth. Microscopy revealed no bacterial colonisation of the adult gut, and the dominant taxon detected in larval pollen could not be cultured under targeted conditions. These results suggest an absence of a beneficial gut microbiome in M. tosticauda. Based on our findings, we propose that some bacteria detected by DNA-based methods in M. tosticauda may represent relic DNA, surface-associated or transient bacteria. Our findings highlight fundamental differences in the bacterial associations between social and solitary bees.},
}

@article {pmid41614864,
year = {2025},
author = {Li, J and Wang, F and Liu, D and Yang, W and Sun, H and Gao, M and Chen, D and Xu, H},
title = {Transcriptomic Profiling of Cutibacterium acnes IA1-Infected Keratinocytes Reveal Hub Genes and CLR Pathway in Acne Pathogenesis.},
journal = {Current issues in molecular biology},
volume = {48},
number = {1},
pages = {},
pmid = {41614864},
issn = {1467-3045},
abstract = {Acne vulgaris is a prevalent chronic inflammatory skin disorder affecting over 85% of adolescents. Emerging evidence indicates that Cutibacterium acnes phylotype IA1 contributes to acne initiation and progression, yet its precise mechanisms in epidermal keratinocytes remain unclear. This study investigated C. acnes IA1's effects on keratinocyte behavior using an in vitro HaCaT cell model. Cells were co-cultured with live C. acnes IA1 (CICC 10864) for 24 h. Transcriptomic profiling identified 769 differentially expressed genes (DEGs; adjusted p < 0.05, |log2FC| > 1), including 392 upregulated and 377 downregulated. The protein-protein interaction network analysis via Cytoscape revealed key hub genes (HNRNPA2B1, HNRNPM, RBM39). Enrichment analyses (GO, KEGG, Reactome, DO) highlighted significant involvement of the C-type lectin receptor (CLR) signaling pathway. Validation experiments showed cellular morphological changes, altered structure, and markedly elevated interleukin-6 (IL-6; p < 0.01), underscoring its role in inflammation. These findings suggest C. acnes IA1 drives acne pathogenesis by regulating hub genes that influence sebaceous gland inflammation, immune activity, and keratinocyte proliferation, positioning them as potential biomarkers for microbiome-targeted therapies. Limitations include the in vitro model's lack of in vivo skin microenvironment complexity and use of only one representative IA1 strain.},
}

@article {pmid41614786,
year = {2025},
author = {Baek, J and Cho, S and Lee, G and Ki, H and Kim, SY and Choi, GM and Kim, JH and Kim, JW and Park, CM and Kim, SY and Choi, BM and Choi, YG},
title = {Modulation of Moisturizing and Barrier Related Molecular Markers by Extracellular Vesicles Derived from Leuconostoc mesenteroides DB-21 Isolated from Camellia japonica Flower.},
journal = {Current issues in molecular biology},
volume = {47},
number = {12},
pages = {},
pmid = {41614786},
issn = {1467-3045},
support = {RS-2023-KH140908//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {Among the microorganisms present in the microbiome of Camellia japonica flowers, extracellular vesicles (EVs) derived from Leuconostoc mesenteroides were isolated to investigate their modulatory effects on moisturizing and barrier-related molecular markers. To identify the function of major proteins in L. mesenteroides DB-21-derived extracellular vesicles (LEVs), Gene Ontology (GO) analysis was performed, revealing ATP binding, ribosomal structural proteins, and metal ion binding as predominant molecular-function categories. These proteomic characteristics provide a molecular context that supports the interpretation of the moisturizing and barrier-related responses observed in this study. To further verify new findings, we performed functional evaluations using in vitro and 3D skin models. LEVs increased the mRNA expression level of HAS3, which encodes hyaluronic acid synthase. In addition, the expression levels of filaggrin and involucrin, key proteins involved in skin barrier formation, increased, and these markers were determined a concentration-dependent increase in a 3D artificial skin model. Also, we confirmed that the expression levels of filaggrin and involucrin, which were reduced by UVB damage, were restored when LEVs were applied. In conclusion, LEVs are effective in enhancing various molecular markers related to the skin barrier function, and these results reveal that they hold promise as next-generation microbiome-based functional ingredients.},
}

@article {pmid41614733,
year = {2025},
author = {Kim, D and Kim, WJ and Woo, HM and Jeong, H},
title = {PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.},
journal = {Current issues in molecular biology},
volume = {47},
number = {12},
pages = {},
pmid = {41614733},
issn = {1467-3045},
support = {ncheon National University Research Grant in 2023. 284//Incheon National University/ ; },
abstract = {16S rRNA amplicon sequencing has been an effective method for profiling microbial taxonomy in microbiome research, as it offers lower per-sample costs and higher sample throughput than shotgun metagenomics. Although 16S rRNA sequencing offers clear advantages over shotgun sequencing, it depends on precise trimming of low-quality bases at the 3' ends of reads. Given the widespread use of 16S rRNA amplicon sequencing, there is an increasing demand for analysis tools that can identify errors in the 3' region of reads and remove erroneous bases. While various algorithms for predicting trim locations are widely employed, most are command-line standalone tools, which pose challenges for users with limited computational background or resources. Furthermore, in the absence of biological or experimental priors such as amplicon size, trim position predictions may be unreliable. Here, we introduce PixelCut, a fully automated trim-position prediction framework that requires no hyperparameters or prior biological information for accurate prediction. Unlike most available algorithms that operate on raw FASTQ data, PixelCut analyzes the per-base quality report generated by FastQC to infer trimming positions. Based on the recommended quality score threshold from the quality report, PixelCut inspects the quality scores across bases and automatically determines the recommended trim position using character recognition techniques based on computer vision. We have also developed a user-friendly web application to make the method accessible to those without programming expertise, while offering a command-line version for advanced users. Through comprehensive computer simulations, we show that PixelCut produces taxonomic profiling results that are consistent with those from popular trim-location prediction algorithms.},
}

@article {pmid41614677,
year = {2026},
author = {Pettersson, M and La Sala, G and Gunnarsson, A and Vildhede, A and Sparklin, B and Holm, B and Petrović, D and Lasky, G and Turick, S and Szydlowska, M and Gopalakrishnan, V and Bake, T and Petersen, J and Brånalt, J and Westerlund, K and Taillefer, M and Henricsson, M and Ek, M and Warrener, P and Roth, R and Cohen, T and Sjögren, T and Fahlander, U and Jurva, U and Morias, Y and Liddle, J},
title = {Discovery of a Highly Potent and Selective Small-Molecule Inhibitor of In Vivo Anaerobic Choline Metabolism by Human Gut Bacteria.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c01451},
pmid = {41614677},
issn = {1520-4804},
abstract = {Trimethylamine (TMA) Lyase is an enzyme expressed in human gut bacteria that plays a pivotal role in the formation of trimethylamine oxide (TMAO), a metabolite implicated in the development of heart failure. Here, we describe a strategy to design covalent inhibitors targeting the active site thiyl radical involved in the catalytic cycle of the enzyme under anaerobic conditions. This strategy led to the discovery of 7, a previously unreported highly potent and selective inhibitor of TMA Lyase. When dosed orally to rats, 7 shows a significant reduction of circulating TMAO levels and, importantly, demonstrates inhibition of TMAO generated from a human microbiome when profiled in a human fecal mouse transplant model.},
}