@article {pmid41859031,
year = {2026},
author = {Motlak, M and Gill, C and Guzzardi, E and Barlow, S and Guilarte, G and Choudhary, S},
title = {Alcohol Use and Hidradenitis Suppurativa: An Unclear Relationship.},
journal = {Skin appendage disorders},
volume = {},
number = {},
pages = {},
pmid = {41859031},
issn = {2296-9195},
abstract = {BACKGROUND: Hidradenitis suppurativa (HS) may be linked to behavioral factors that exacerbate inflammation, gut microbiome, and healing.

SUMMARY: This review evaluates current evidence on the relationship between alcohol consumption and HS. Emerging studies show high incidences of alcohol and substance use disorders in HS patients. However, observational studies remain inconsistent: HS patients may experience higher alcohol-related burden, yet its association to disease progression and baseline severity remains unclear. Limitations of existing studies include self-reported exposures of alcohol, heterogeneous outcome measures, and potential confounding factors, such as stress.

KEY MESSAGES: Biologic plausibility remains, as alcohol can promote dysbiosis, inflammation, and oxidative stress that may influence disease activity and healing. This review highlights the need for larger, controlled trials that determine whether the reduction or elimination of alcohol may improve HS outcomes.},
}

@article {pmid41859075,
year = {2026},
author = {Chen, M and Zhang, J and Yang, H and Lei, L and Yang, L and Wang, S and Yu, H},
title = {JK5G postbiotics modulate gut microbiota and metabolome to alleviate cancer-related pain: a randomized controlled trial with multi-omics integration.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1764491},
pmid = {41859075},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Male ; Middle Aged ; Female ; *Probiotics/administration & dosage ; *Cancer Pain/metabolism/microbiology/therapy/etiology ; Quality of Life ; Double-Blind Method ; Adult ; Metabolomics/methods ; Aged ; Feces/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Cancer-related pain remains a critical clinical challenge, with existing opioid-based therapies often yielding inadequate relief and significant side effects. This study investigates the therapeutic potential of JK5G postbiotics-a formulation of inactivated Lactobacillus strains and metabolites-in modulating the gut-microbiome-immune axis to alleviate pain in cancer patients.

METHODS: This study employs a randomized, double-blind, placebo-controlled trial design involving 149 participants divided into two groups: a control group receiving patient-controlled subcutaneous analgesia (PCSA) plus placebo, and an experimental group receiving PCSA plus JK5G postbiotics. The primary outcomes were changes in gut microbiota composition assessed by 16S rRNA gene sequencing, and quality of life (QoL). The secondary outcomes included fecal metabolomics, adverse effects (AEs), blood inflammatory cytokines, and lymphocyte subsets. This study was registered at www.chictr.org.cn(ChiCTR2500108811).

RESULTS: JK5G supplementation significantly improved pain scores, QoL, and cognitive and social functioning compared to controls. Microbiome analysis revealed enrichment of beneficial taxa such as Akkermansia muciniphila and Bifidobacterium, alongside suppression of pathogenic Escherichia-Shigella. Machine learning identified five core microbial biomarkers (Akkermansia muciniphila, Bifidobacterium, Escherichia-Shigella, Blautia, Streptococcus), with SHAP analysis highlighting Akkermansia muciniphila and Bifidobacterium as top contributors. Metabolomic profiling demonstrated upregulation of 236 metabolites, including kynurenic acid and butyric acid, with tryptophan and butyrate metabolism emerging as key altered pathways. Immune profiling showed elevated CD3[+]CD4[+] T cells and reduced TNF-α levels, while MIMOSA2 analysis linked microbial taxa to metabolic shifts, such as correlations between Ruminococcus torques and butyric acid.

CONCLUSION: These findings suggest that JK5G may contribute to the amelioration of cancer-related pain by reshaping gut microbiota, modulating host metabolism, and enhancing immune responses. This study highlights the potential of JK5G postbiotics as an adjunct therapy, supporting the need for further validation in larger cohorts and mechanistic investigations to advance its clinical translation.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/showproj.html?proj=285304, identifier ChiCTR2500108811.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Metabolome/drug effects
Male
Middle Aged
Female
*Probiotics/administration & dosage
*Cancer Pain/metabolism/microbiology/therapy/etiology
Quality of Life
Double-Blind Method
Adult
Metabolomics/methods
Aged
Feces/microbiology
Multiomics

@article {pmid41859112,
year = {2026},
author = {Chen, H and Lou, G and Meng, F and Zhang, Y and Kuang, H and Yang, D},
title = {Critical role of reproductive tract microbiota and derived metabolites in inflammation, tumor immunity, and tumorigenesis of gynecological cancers: a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1734792},
pmid = {41859112},
issn = {1664-3224},
mesh = {Humans ; Female ; *Genital Neoplasms, Female/metabolism/immunology/microbiology/therapy/etiology ; Animals ; *Microbiota/immunology ; *Carcinogenesis/immunology ; Inflammation/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; *Genitalia, Female/microbiology/immunology ; },
abstract = {Gynecological malignancies, including ovarian, cervical, and endometrial cancers, present significant clinical challenges due to the epidemiological complexity and limitations in current therapeutic strategies. Emerging evidence highlights the critical role of the microbiome and its metabolites in modulating tumor initiation, progression, and treatment responses. This review explores the intricate mechanisms through which gut and reproductive tract microbiota influence gynecological cancers via immune regulation, metabolic reprogramming, and epigenetic modifications. Key microbial metabolites, such as short-chain fatty acids, bile acids, and estrogen-metabolizing intermediates, serve as molecular bridges in host-microbe communication, impacting chemotherapy resistance and immunotherapy efficacy. Furthermore, we discuss the translational potential of microbiome-targeted interventions, including probiotics, fecal microbiota transplantation, and precision microbial therapies, as innovative approaches for diagnosis, prognosis, and treatment. Understanding the microbiota-reproductive axis offers novel insights into overcoming therapeutic resistance and improving patient outcomes in gynecologic oncology.},
}

Humans
Female
*Genital Neoplasms, Female/metabolism/immunology/microbiology/therapy/etiology
Animals
*Microbiota/immunology
*Carcinogenesis/immunology
Inflammation/immunology/metabolism/microbiology
*Gastrointestinal Microbiome/immunology
*Genitalia, Female/microbiology/immunology

@article {pmid41859191,
year = {2026},
author = {Su, Y and Xia, Y},
title = {Gut microbiota dysbiosis and depression: Bidirectional interactions, mediating pathways, and microecological therapeutics.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101372},
pmid = {41859191},
issn = {2665-9271},
abstract = {The microbiota-gut-brain axis (MGBA) is increasingly recognized as a key target for ameliorating major depressive disorder (MDD). This review systematically synthesizes evidence on the bidirectional relationship between gut microbiota dysbiosis and MDD, and delineates the core mechanisms-such as neuroinflammation, neurotransmitter metabolism, and hypothalamic-pituitary-adrenal (HPA) axis dysregulation-through which this axis influences depressive pathogenesis. Further, the intestinal microbiota characteristics related to MDD, the main regulatory pathways, and the potential efficacy of microbiome-targeted intervention measures-including psychobiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary strategies-were sorted out. In the clinical assessment and drug research of depression, the assessment tools are mainly divided into two categories: clinician-rated and self-reported. These two types are often used together to provide multi-dimensional evidence of therapeutic efficacy. Evidence suggests that stress-related intestinal permeability may initiate gut dysbiosis, which in turn can impair barrier function, promote neuroinflammation, disrupt neurotransmitter synthesis, and overactivate the HPA axis, potentially exacerbating depressive symptoms. Interventions targeting the gut microbiota may help reshape microbial communities, increase short-chain fatty acids (SCFAs) and 5-Hydroxytryptamine (5-HT), and dampen inflammatory and stress responses, thereby offering a promising, non-pharmacological avenue for alleviating MDD. This review not only offers a theoretical foundation for microbiota-based therapeutics in MDD but also highlights pathways toward developing safe, effective non-pharmacological strategies for depression management.},
}

@article {pmid41859194,
year = {2026},
author = {Armah, J and Alzahid, S and Pei, Q and Cousin, L and Fanfan, D and Heldermon, C and Lyon, D},
title = {Associations among physical activity, diet, non-lifestyle characteristics and the gut microbiome of cancer patients: A scoping review and network analysis.},
journal = {Oncoscience},
volume = {13},
number = {},
pages = {85-103},
pmid = {41859194},
issn = {2331-4737},
abstract = {Lifestyle factors, such as physical activity and dietary modifications can beneficially modulate the gut microbiome of cancer patients, however their effects are often shaped by non-modifiable variables. This review and network analysis aims to synthesize current evidence on how both lifestyle and non-lifestyle factors affect the gut microbiome in cancer patients. A systematic search was conducted on Scopus, CINAHL, PubMed and Web of Science to produce 51 eligible studies for this review. A chi-square test of independence indicated that the distribution of gut bacteria function categories was significantly associated with the category of influencing factor (Χ[2] = 390.87, p = 0.032). Across studies, high physical activity and healthy diets were associated with increased abundances of saccharolytic/short-chain fatty acids and lactic acid-producing bacteria, alongside decreased abundances of pathogenic or opportunistic bacteria. However, these associations may also be influenced by non-lifestyle characteristics such as chemotherapy, age, and cancer type or stage which could mask the benefits of lifestyle interventions. This study highlights the limited but growing evidence linking physical activity, diet and the gut microbiome in cancer populations. Progress in this field will require larger, more integrative designs that account for non-lifestyle confounders and apply advanced analytical approaches to capture complex interactions.},
}

@article {pmid41859443,
year = {2026},
author = {Whitaker, BK and Gdanetz, K and Vaughan, MM and McCormick, S and Becker, T},
title = {Wheat mycobiome dynamics driven by interseasonal crop-crop transfer and Fusarium head blight.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1778987},
pmid = {41859443},
issn = {1664-302X},
abstract = {INTRODUCTION: Fusarium head blight (FHB) is a devastating disease of wheat that causes mycotoxin contamination in grains. Diseases like FHB have traditionally been managed with integrated strategies; but this has led to a proliferation of fungicide-resistant pathogens and soil erosion while full disease control has remained elusive. Leveraging the microbiome for more sustainable management is an alternative, however, translation of promising strategies is hampered by our limited understanding of crop microbiome differences across plant development and tissue types.

METHODS: We characterized fungal communities using amplicon sequencing across five developmental timepoints in wheat leaves and wheat heads, as well as in maize debris from the previous growing season. Samples were collected from two locations in Illinois, USA. We assessed how tissue type, site, developmental stage, and wheat variety contributed to mycobiome composition. Source-sink relationships among debris, leaves, and heads were evaluated, and taxa associated with high and low FHB conditions were identified. Network analyses were used to determine the roles of key fungal taxa in wheat head and maize debris microbiomes.

RESULTS: Mycobiome composition varied strongly by tissue type, though site and developmental timepoint were also important contributors. Host variety conditionally explained mycobiome variation in wheat heads, but not in leaves or debris. We also identified debris as a major fungal source to leaves early in development, but not later-and found that leaves were never a large inoculum source to head mycobiomes at either developmental stage tested. Taxa enriched under high FHB conditions in wheat heads belonged to the Ascomycota (Cladosporium, Pseudopithomyces), while taxa enriched under low FHB conditions primarily belonged to the Basidiomycota (Filobasidium, Sporobolomyces, Tilletiopsis, Entyloma). Fusarium spp. were important nodes in wheat head and maize debris microbiome networks.

DISCUSSION: This work shows that fungal movement from crop to crop across seasons, and between plant tissues within a season, shape phyllosphere microbiome dynamics and can indicate potential disease outcomes in the FHB pathosystem. As microbiome-based disease management develops alongside rapid growth in the biologicals industry and increased recognition of microbial roles in agriculture, this work highlights several promising directions. These include identifying basidiomycetous yeasts associated with low FHB, pinpointing taxa correlated with Fusarium in wheat heads and maize debris, and demonstrating that applying biocontrols to wheat leaves is unlikely to affect pathogen spread to heads. Future research should focus on controlled tests of microbe-microbe interactions and their impacts on plant immunity, disease suppression, and yield.},
}

@article {pmid41859445,
year = {2026},
author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W},
title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783810},
pmid = {41859445},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.},
}

@article {pmid41859446,
year = {2026},
author = {Bai, L and Wang, Z and Wang, H and Ma, B},
title = {Comprehensive evaluation of environment adaptability in wild and captive lenok (Brachymystax lenok): from the perspective of antioxidant capacity, immune response and gut microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1764670},
pmid = {41859446},
issn = {1664-302X},
abstract = {INTRODUCTION: The intestinal microbiota is considered an adaptive trait closely associated with reintroduction success and may contribute to the ecological fitness of B. lenok.

METHODS: In this study, intestinal morphology, digestive enzyme activity, immune parameters, and gut microbiota composition were compared between wild and farmed B. lenok to elucidate differences in intestinal and hepatic health under distinct aquatic environments.

RESULTS: Histological analysis showed that villi in the hindgut of wild individuals were longer and denser than those of farmed ones. Although the intestinal structure of farmed B. lenok remained intact, their villus morphology and density differed significantly from those of the wild group. Compared with the farmed group, wild B. lenok showed higher hepatic immune/antioxidant activity (elevated alkaline phosphatase (AKP), acid phosphatase (ACP), lysozyme (LYZ), and catalase (CAT), as well as glutathione (GSH) content) and up-regulated liver immune-related genes (c3, foxo1, igM, il-10, lyz, etc.), while farmed fish displayed higher intestinal stress markers (CAT, malondialdehyde (MDA) and a pro-inflammatory signature (il-6, il-1β upregulated). Microbiota profiling revealed higher abundance of Firmicutes and Bacteroidetes but a trend of decreasing Proteobacteria in the wild group.

DISCUSSION: Collectively, these findings demonstrate significant differences in intestinal morphology, digestive function, and microbial community composition between wild and farmed B. lenok. This study provides new insights for improving post-stocking adaptability in reintroduction programs and proposes novel conservation strategies for biodiversity restoration.},
}

@article {pmid41859449,
year = {2026},
author = {Han, Y and Huang, H and Zhang, Z and Li, X and Li, T and Zong, S},
title = {Microbiome and metabolome dynamics in phloem and rhizosphere of Pinus tabuliformis against Dendroctonus valens infestation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1754801},
pmid = {41859449},
issn = {1664-302X},
abstract = {Microbial communities play essential roles in mediating plant defenses against insect pests. However, how host-associated microbiota and metabolites jointly respond to bark beetle infestation remains largely unexplored. Here, we integrated microbiome and metabolome profiling to elucidate how Pinus tabuliformis regulates its phloem and rhizosphere responses under varying levels of Dendroctonus valens infestation. Both bacterial and fungal diversity, as well as the relative abundance of dominant taxa such as Erwinia and Pseudoxanthomonas, shifted significantly with infestation intensity. Concurrently, key plant defense metabolites-including terpenoids, jasmonates, and polyphenols-were markedly elevated. Pathway enrichment analysis indicated that the phloem was characterized by enhanced phenylpropanoid and flavonoid biosynthesis, whereas the rhizosphere soil accumulated terpenoids and polyketides, implicating both compartments in resistance modulation. In the phloem, differential bacterial and fungal taxa displayed distinct positive and negative correlations with phenylpropanoid intermediates and downstream derivatives, while in the rhizosphere, bacteria from Bacillota and fungi such as Candida and Ogataea were strongly linked to diterpenoids, sesquiterpenoids, flavonoids, and indole derivatives. These findings demonstrate that P. tabuliformis mounts a compartment-specific, microbiome-associated metabolic response to D. valens infestation, providing new insights into the ecological roles of symbiotic microbiota in plant defense and offering a mechanistic foundation for microbe-based pest management strategies.},
}

@article {pmid41859450,
year = {2026},
author = {Jia, J and Chen, L and Liu, Q and Wang, K and Zhao, K and Ren, X and Gao, X and An, J},
title = {Correction: Enhancement of soil microbial community stability by earthworms and collembolans in soil from abandoned coal mine land.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1803716},
doi = {10.3389/fmicb.2026.1803716},
pmid = {41859450},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1636784.].},
}

@article {pmid41859452,
year = {2026},
author = {Jia, C and Zhu, W and Yuan, Y and Xie, Q},
title = {How gut microbiota contribute to neuropsychiatric disorders: evidence from neuroimaging studies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1760096},
pmid = {41859452},
issn = {1664-302X},
abstract = {The interaction between the gut microbiota and central nervous system (CNS) diseases has emerged as a major focus in neuroscience and microbiome research. Accumulating evidence shows that gut microbiota influence the pathogenesis of neurodevelopmental, neurodegenerative, autoimmune, and psychiatric conditions via the microbiota-gut-brain axis. However, the underlying mechanisms are complex and not yet fully elucidated. Advances in multimodal magnetic resonance imaging, positron emission tomography, and diffusion tensor imaging, now enable in vivo visualization of associations between gut microbial alterations and abnormalities in brain structure and function, providing new perspectives for understanding the role of gut microbiota in CNS pathology. This review systematically reviews neuroimaging-based research linking gut microbiota to neurological diseases (e.g., Alzheimer's disease, multiple sclerosis, traumatic brain injury), and psychiatric disorders (e.g., schizophrenia, and autism spectrum disorder). It highlights the mediating roles of microbial metabolites, immune-inflammatory responses, and neuroimmune pathways, and discusses future directions integrating multi-omics data with neuroimaging technologies, as well as their potential clinical applications. What distinguishes this review from its predecessors in the same field is its explicit neuroimaging-driven framework rather than general mechanistic discussion.},
}

@article {pmid41859467,
year = {2026},
author = {Szydłowicz, M and Zajączkowska, Ż and Chabowski, M and Nowicki, M and Łukianowski, B and Gajdzis, P and Kváč, M and Calderón, EJ and Le Gal, S and Kicia, M},
title = {Multi-site screening for Pneumocystis jirovecii in lung cancer: possible tumour tissue colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1755638},
pmid = {41859467},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/complications/pathology ; *Pneumocystis carinii/isolation & purification/genetics ; Male ; Female ; Middle Aged ; Aged ; Genotype ; Aged, 80 and over ; *Pneumonia, Pneumocystis/microbiology/diagnosis ; DNA, Fungal/genetics ; Lung/microbiology ; Adult ; *Pneumocystis Infections/microbiology/diagnosis ; Polymerase Chain Reaction ; },
abstract = {OBJECTIVES: Recent studies suggest that various tumour types can be colonized by different microorganisms, but data on unusual opportunistic fungus - Pneumocystis jirovecii - remain scarce. Lung cancer patients are considered one of the risk groups for its infection. Since P. jirovecii tends to distribute focally within the lungs, this study aimed to determine whether it can be detected in lung tumour tissue.

METHODS: Fragments of neoplastic tissue (NPL), normal adjacent tissue (NAT) and respiratory secretions (RS) were collected from 70 patients with histologically confirmed primary lung cancer. DNA was extracted and analysed by nested-PCR targeting the mtLSU rRNA and CYB loci, followed by genotyping.

RESULTS: Pneumocystis jirovecii was detected in fourteen samples derived from 8/70 individuals (11.4%): two NPL, six NAT and six RS. In two patients, Pneumocystis was detected in all three specimen types; both were diagnosed with the same histological malignancy grade (G3, P=0.036). The genotype distribution varied across sample types in most cases.

CONCLUSIONS: The ability of Pneumocystis to colonize NPL may be linked to the stage of tumour advancement, suggesting that local tumour-related factors could influence its colonization. These findings support further investigation of the lung microbiome in the context of tumour-associated microenvironments and their potential utility as complementary biomarkers in lung cancer.},
}

Humans
*Lung Neoplasms/microbiology/complications/pathology
*Pneumocystis carinii/isolation & purification/genetics
Male
Female
Middle Aged
Aged
Genotype
Aged, 80 and over
*Pneumonia, Pneumocystis/microbiology/diagnosis
DNA, Fungal/genetics
Lung/microbiology
Adult
*Pneumocystis Infections/microbiology/diagnosis
Polymerase Chain Reaction

@article {pmid41859469,
year = {2026},
author = {Zafeiropoulou, K and Hageman, IL and Mu, T and Davids, M and Li Yim, AYF and Joustra, VW and Hakvoort, TBM and Satsangi, J and Chronas, K and Koelink, PJ and Wildenberg, ME and van den Wijngaard, RM and D'Haens, GR and de Jonge, WJ},
title = {Colonic biopsy-associated microbial signatures are predictive of response to anti-TNFα biological therapy in Crohn's disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1741002},
pmid = {41859469},
issn = {2235-2988},
mesh = {Humans ; *Crohn Disease/drug therapy/microbiology/pathology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/pathology ; Biopsy ; Middle Aged ; *Tumor Necrosis Factor-alpha/antagonists & inhibitors ; Treatment Outcome ; Adalimumab/therapeutic use ; Antibodies, Monoclonal, Humanized/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Infliximab/therapeutic use ; Ustekinumab/therapeutic use ; Intestinal Mucosa/microbiology/pathology ; Biological Therapy ; },
abstract = {INTRODUCTION: Crohn's disease (CD) is commonly treated with biologic therapies, including anti-TNFα agents, vedolizumab (VDZ), and ustekinumab (USTE), yet only a subset of patients respond to these treatments. This study aimed to evaluate the potential of the gut microbiome to predict treatment response.

METHODS: Adult CD patients initiating anti-TNFα (infliximab or adalimumab), VDZ or USTE were enrolled. Pre-treatment ileal and/or colonic biopsies were collected endoscopically. Treatment response after 26-52 weeks was defined by ≥50% reduction in the simple endoscopic score for CD and either a corticosteroid-free clinical response (≥3-point HBI decrease or remission [HBI ≤4] without systemic steroids) or a biochemical response (≥50% or ≤5 mg/L CRP reduction and ≥50% or ≤250 μg/g faecal calprotectin reduction) versus baseline. Mucosal microbiota was profiled by 16S rRNA gene sequencing of biopsies. Machine learning models predicting treatment response were trained using ASV-level count data. The impact of heat-killed bacteria on anti-TNFα-induced CD14[+]CD206[+] macrophages was tested in mixed lymphocyte reactions (MLRs).

RESULTS: A total of 125 patients were included: 39 on anti-TNFα, 47 on VDZ, and 39 on USTE. Clinical features were similar between responders and non-responders, aside from sex (USTE-colon) and CRP (USTE-ileum). No major microbial differences were observed in VDZ, USTE ileal or colon samples. However, in colonic biopsies, anti-TNFα responders had significantly higher pre-treatment α-diversity, and 3.9% of β-diversity variation associated with response. Among six models, the anti-TNFα colonic model performed significantly better than random (AUC = 0.90) to predict response. Mediterraneibacter gnavus ASVs associated with non-response, whereas Blautia ASVs associated with response, to anti-TNFα. When tested in MLRs, pretreatment with M. gnavus and B. luti led to a reduction in macrophage polarization, with a significantly stronger effect observed for M. gnavus compared with B. luti.

DISCUSSION: Taken together, this study demonstrates that the colonic mucosal microbiome prior to anti-TNFα treatment can distinguish responders from non-responders in CD, supporting its potential as a predictive biomarker.},
}

Humans
*Crohn Disease/drug therapy/microbiology/pathology
Male
Female
Adult
*Gastrointestinal Microbiome/drug effects
*Colon/microbiology/pathology
Biopsy
Middle Aged
*Tumor Necrosis Factor-alpha/antagonists & inhibitors
Treatment Outcome
Adalimumab/therapeutic use
Antibodies, Monoclonal, Humanized/therapeutic use
RNA, Ribosomal, 16S/genetics
Infliximab/therapeutic use
Ustekinumab/therapeutic use
Intestinal Mucosa/microbiology/pathology
Biological Therapy

@article {pmid41859568,
year = {2025},
author = {Adnan, D and Engen, PA and Villanueva, M and Raeisi, S and Ramirez, V and Naqib, A and Green, SJ and Bishehsari, F and Barnes, LL and Keshavarzian, A and Dhana, K and Voigt, RM},
title = {Oral microbiome brain axis and cognitive performance in older adults.},
journal = {NPJ dementia},
volume = {1},
number = {},
pages = {},
pmid = {41859568},
issn = {3005-1940},
support = {R01 AG052583/AG/NIA NIH HHS/United States ; R01 AG056653/AG/NIA NIH HHS/United States ; },
abstract = {The human oral microbiota is a community of microorganisms that reside in the oral cavity, including lingual, buccal, and saliva, each niche with a distinct microbial composition. Alterations in oral microbiota have been associated with an increased risk of Alzheimer's disease (AD). This study used data from 143 older adults in the MIND trial to evaluate the association between oral microbiome and cognitive function. Oral niche-specific differences (saliva, buccal, and lingual), as well as the microbiome composition differences (α and β diversity), were associated with cognitive function. A lower abundance of Gemella and a higher abundance of anaerobic pro-inflammatory bacteria (e.g., Parvimonas, Treponema, Dialister) were linked to a lower Cognitive Z Score. Porphyromonas, previously linked to AD, was not associated with cognition. The outcomes suggest that oral microbiota may be a biomarker for cognitive function. Further research is required to assess whether oral microbiota-directed strategies can positively impact cognitive decline.},
}

@article {pmid41859724,
year = {2025},
author = {Fei, Y and Lei, Z and Wang, Y and Joshua, M and Guo, L and Li, L},
title = {Overview of multi-omics approaches for pulmonary sarcoidosis.},
journal = {EC pulmonology and respiratory medicine},
volume = {14},
number = {1},
pages = {},
pmid = {41859724},
support = {R21 ES036375/ES/NIEHS NIH HHS/United States ; },
abstract = {PURPOSE: Here, we review recent findings in the transcriptome, proteome, metabolomics, and microbiome of pulmonary sarcoidosis and highlight differentially expressed genes, specific pathways, mechanisms, microorganisms, metabolites, and targeted therapeutics in the field.

RECENT FINDINGS: The transcriptome and proteome of pulmonary sarcoidosis have been widely studied in recent years. Many differentially expressed genes and signaling pathways have been identified. Several proteins have been identified as potential molecular markers of pulmonary sarcoidosis. The microorganisms and metabolites of patients with sarcoidosis also have certain specificity. We compared pulmonary sarcoidosis with other diseases, such as idiopathic pulmonary fibrosis, tuberculosis, and chronic beryllium disease, and found some differential diagnoses. Based on the identified pathways and mechanisms, targeted therapeutic strategies have been proposed.

SUMMARY: Many differentially expressed genes have been identified, including CBX8, CCL5, CXCL9, CXCL11, GBP1, GBP5, LINC01278, MMP12, PSMB9, STAT1, and TLE3, as well as the related enriched pathways, such as the IFN-γ, IL-1, IL-17, MHC, T-cell receptor, TNF, Th1, and Th2 signaling pathways. Proteins such as ABCG1, Apo A-I, CXCR5, MMP12, PD-1, PPARγ, and vitamin D-binding protein, together with the Fc galactosylation status of IgG4, are potential molecular markers for pulmonary sarcoidosis. Many specific microorganisms and metabolites in patients with sarcoidosis have also been found. Targeted drugs such as infliximab, nintedanib and rituximab have been proposed according to the discovered pathways and mechanisms.},
}

@article {pmid41859763,
year = {2026},
author = {Qin, YF and Zhang, WR and Wang, L and Wang, YF and Lin, D and Cai, TG and Li, HZ and Huang, QS and Rillig, MC and Zhu, D},
title = {Extracellular vesicles drive stress-induced antibiotic resistance spread in soil.},
journal = {Environmental science and ecotechnology},
volume = {30},
number = {},
pages = {100681},
pmid = {41859763},
issn = {2666-4984},
abstract = {Antimicrobial resistance threatens millions of lives annually, yet its acceleration by non-antibiotic pollutants remains poorly understood. Artificial sweeteners, now ubiquitous in soils and waters, are known individually to promote conjugative transfer of resistance genes, but real environments contain complex mixtures whose collective impact is unknown. Extracellular vesicles (EVs) released by stressed bacteria serve as protected, long-range vectors for antibiotic resistance genes (ARGs), yet whether sweetener diversity modulates this pathway has never been tested. Here we show that increasing artificial-sweetener diversity dramatically enriches ARGs, virulence factors and mobile genetic elements inside soil-derived Evs, driving compositional shifts in 30.5% of EV-associated genera while leaving the bulk microbiome largely undisturbed. EVs originate from a small, fast-growing Pseudomonadota subset that upregulates vesicle-biogenesis genes in response to oxidative and membrane stress; these vesicles selectively package chromosomal resistance traits and transfer phenotypic resistance to recipient Escherichia coli. This stress-induced decoupling reveals EVs as rapid, hidden mediators of resistome mobilization that community-level surveys miss. By demonstrating that pollutant diversity itself drives resistance dissemination through nanoscale vectors, our findings establish EVs as a critical new indicator within the One Health framework and call for revised environmental risk models that account for chemical complexity rather than single-compound exposures.},
}

@article {pmid41859944,
year = {2026},
author = {Jiang, M and Gomez, A and Seelig, DM and Gallaher, DD},
title = {Prune (dried plum) consumption does not reduce colonic tumor formation but drives beneficial changes in the gut microbiome of rats.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03398e},
pmid = {41859944},
issn = {2042-650X},
abstract = {Previous research has highlighted the potential benefits of prune consumption, including a changed gut microbiome composition and a reduction in colon cancer risk factors. This study investigated whether prune consumption reduced colon tumor development and led to positive changes in the large intestinal microbiome in a chemically induced colon cancer model in rats. Male Wistar rats were fed one of three diets: 5% (by energy) prune, 10% prune, or a prune-free control. Rats were fed the diets for 32 weeks. Rats received weekly injections of 1,2-dimethylhydrazine for 15 weeks to induce colon tumorigenesis. Colonic tumor number or size did not differ among the diet groups. However, there was a trend toward fewer small intestinal tumors in the 10% prune diet group (p < 0.1). Groups fed prune had heavier cecum tissue, indicating greater large intestinal fermentation. The prune diets increased taxonomic richness and altered bacterial species composition. Specifically, prune consumption was associated with increased abundance of Methanosphaera genus and taxa from the Lachnospiraceae family, such as Blautia and Coprococcus. Prune diets also increased total cecal SCFA amount, notably butyrate. However, 24 hour fecal excretion of p-cresol, indole, and total bile acids did not differ significantly among the groups. While prune consumption did not show a significant reduction in colonic tumor formation, potential benefits were noted in a trend towards reducing small intestine tumors, increasing large intestinal fermentation and SCFA production, and increasing microbial richness, suggesting prune consumption may provide other health benefits.},
}

@article {pmid41859980,
year = {2026},
author = {Akebota, N and Ma, RF and Yang, HQ and Li, YD and He, K and Liu, HY and Tang, KY and Zhu, Y},
title = {Behavioral smearing and physiological secretions drive divergent microbiome assembly during breeding in the crested ibis.},
journal = {Zoological research},
volume = {47},
number = {2},
pages = {361-373},
doi = {10.24272/j.issn.2095-8137.2025.407},
pmid = {41859980},
issn = {2095-8137},
mesh = {Animals ; *Microbiota/physiology ; *Birds/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Feathers/microbiology ; Seasons ; Reproduction/physiology ; Bacteria/classification/genetics ; },
abstract = {Host-microbiota interactions represent a key axis in animal adaptation, especially in species displaying pronounced seasonal variation in behavior and physiology. In avian species, behavioral processes associated with reproduction may influence symbiotic microbial communities, yet the underlying mechanisms remain poorly resolved. The endangered crested ibis (Nipponia nippon) exhibits a distinctive seasonal transition in plumage coloration, shifting from white in the non-breeding period to gray during breeding, a change linked to smearing behavior and deposition of black secretions from the neck region. In the present study, 16S rRNA sequencing across three body sites was performed to profile body surface microbiomes during breeding (gray-feather) and non-breeding (white-feather) stages. Breeding individuals exhibited lower microbial diversity, consistent with an influence of black neck secretions on microbiome structure. Microbial communities were differentiated more strongly by season than by body site, and microbial similarity among body sites increased during breeding, supporting redistribution of microbes through smearing behavior. Community assembly also showed clear season- and site-specific variation. Neck feathers exhibited a 36.5% better fit to the neutral model, indicating a stronger contribution of stochastic assembly, likely associated with microbial dispersal during smearing of black secretions. In contrast, neck skin showed a 36.3% lower neutrality and 11.87% more host-selected variants, indicating stronger deterministic selection associated with breeding-related secretions. These findings support a dual regulatory framework during breeding, in which behavioral smearing promotes microbial dispersal while physiological secretion strengthens host filtering. Such coordinated regulation likely drives seasonal microbiome variation and contributes to seasonal adaptation. Overall, this work provides novel insight into the integration of behavior and physiology in shaping host-microbiota interactions during critical life stages and establishes a microbiome-based perspective for crested ibis conservation.},
}

Animals
*Microbiota/physiology
*Birds/physiology/microbiology
RNA, Ribosomal, 16S/genetics
Feathers/microbiology
Seasons
Reproduction/physiology
Bacteria/classification/genetics

@article {pmid41859990,
year = {2026},
author = {Szczepanik, K and Kierończyk, B and Szymkowiak, P and Taciak, M and Barszcz, M and Tuśnio, A and Gawin, K and Dobrowolski, P and Świątkiewicz, M},
title = {Effects of Hermetia illucens larvae full-fat meal and astaxanthin on the microbiome and histomorphology of the large intestine in piglets.},
journal = {Polish journal of veterinary sciences},
volume = {29},
number = {1},
pages = {17-29},
doi = {10.24425/pjvs.2026.158497},
pmid = {41859990},
issn = {2300-2557},
mesh = {Animals ; Swine/microbiology/anatomy & histology ; *Animal Feed/analysis ; Larva ; *Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; Xanthophylls/pharmacology/administration & dosage ; *Intestine, Large/anatomy & histology/microbiology/drug effects ; Animal Nutritional Physiological Phenomena ; *Diptera ; },
abstract = {This study evaluated the effects of Hermetia illucens (HI) larvae full-fat meal and astaxanthin (AST) on large intestine histomorphometry, microbiota activity, and composition in pigs. Forty-eight pigs (8.7 kg) were divided into six groups: control (0HI), 2.5% HI (2.5HI), 5% HI (5HI), 2.5% HI + AST (2.5HI+AST), 5% HI + AST (5HI+AST), and AST alone (AST). The experiment lasted from 35 to 70 days of age. HI meal increased mucosal thickness (p<0.01), crypt depth (p<0.05), and width (p<0.05). Goblet cell counts increased in the 2.5HI (p<0.05), while enterocyte numbers decrease in the AST group (p<0.01). Dietary HI meal reduced concentrations of total short-chain fatty acids (SCFA), including butyrate (p<0.05), whereas AST increased acetic acid levels in multiple intestinal regions (p<0.05). Both additives modified microbial populations: AST increased total bacterial counts (p<0.001), while 2.5% HI meal reduced the abundance of the Bacteroides-Prevotella cluster (p<0.001). Significant interactions were detected for Lactobacillus/Enterococcus spp. and Enterobacteriaceae (p<0.001). HI meal decreased p-cresol concentrations in the middle colon (p<0.05), whereas AST reduced phenol in the distal colon (p<0.05) and indole in the middle colon (p<0.05). AST increased ammonia levels in the proximal colon (p=0.001). These findings suggest that HI meal and AST modulate intestinal fermentation, exhibit anti-inflammatory effects, and regulate microbial populations, potentially reducing harmful metabolites and odor emissions. Their dietary combination may have positive implications for intestinal health.},
}

Animals
Swine/microbiology/anatomy & histology
*Animal Feed/analysis
Larva
*Gastrointestinal Microbiome/drug effects
Diet/veterinary
Xanthophylls/pharmacology/administration & dosage
*Intestine, Large/anatomy & histology/microbiology/drug effects
Animal Nutritional Physiological Phenomena
*Diptera

@article {pmid41860010,
year = {2026},
author = {Medenica, S and Prelević, V and Zanković, N and Maggio, V and Rizzo, M},
title = {Cardiorenometabolic medicine as a new subspecialty in the light of novel pharmaceuticals with dual or triple benefits.},
journal = {Expert opinion on drug safety},
volume = {},
number = {},
pages = {},
doi = {10.1080/14740338.2026.2648248},
pmid = {41860010},
issn = {1744-764X},
abstract = {INTRODUCTION: There is a lack of clinical models which include comprehensive and holistic care of patients with cardiorenometabolic diseases and isolated care of those patients usually leads to poor clinical outcomes. Cardiometabolic diseases, encompassing conditions like type 2 diabetes, obesity, and atherosclerotic cardiovascular disease, represent a major global health burden. Their frequent coexistence due to shared mechanisms necessitates an integrated care approach, reflecting a critical paradigm shift. Therefore, necessity for a new integrated clinical model which include all those specialties should be the focus of a new, modern interdisciplinary approach.

AREAS COVERED: This review synthesizes mechanistic insights, safety data, and emerging interventions for cardiorenometabolic disease management. It examines cornerstone therapies like SGLT2 inhibitors and GLP-1 receptor agonists, highlighting their profound cardiovascular, renal, and metabolic benefits. Newer dual/triple incretin therapies are also discussed for their potential in weight loss and cardioprotection. Safety considerations, including genitourinary infections and gastrointestinal intolerance, are addressed. Additionally, emerging research on gut microbiota - derived metabolites and sleep optimization as modifiable risk pathways is explored. The literature search included papers published as of July 2025, identified using PubMed.

EXPERT OPINION: We advocate a holistic, risk-adapted approach integrating pharmacologic, behavioral, and metabolic dimensions to optimize patient outcomes and truly transform cardiometabolic care.},
}

@article {pmid41860216,
year = {2026},
author = {Chatman, CC and Olson, EG and Ricke, SC and Majumder, EL-W},
title = {Exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0246925},
doi = {10.1128/aem.02469-25},
pmid = {41860216},
issn = {1098-5336},
abstract = {UNLABELLED: The exposome encompasses all lifetime environmental exposures affecting health. Its complexity and high data dimensionality make it challenging to link specific exposure combinations to adverse health outcomes. Establishing relevant exposome criteria is key to addressing current knowledge gaps. This study evaluated contaminant levels in Wisconsin groundwater and their effects on host health. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards: nitrate, atrazine, and imidacloprid, and the emerging contaminant, microplastics. In this study, broilers were exposed to a low-dose chemical mixture (35,000 ppb nitrate + 1.7 ppb atrazine + 0.58 ppb imidacloprid) and high-dose chemical mixture (100,000 ppb nitrate + 3,000 ppb atrazine + 3,000 ppb imidacloprid) or polyethylene microplastics (PE MPs) for 49 days. Both contaminant types significantly altered the cecal microbiomes as determined by the enrichment of the genera Fournierella and Ruminococcus and an unclassified Coriobacteriaceae genus. Untargeted metabolomics revealed distinct but convergent patterns of metabolic reprogramming across exposures. Chemical mixtures modulated pathways linked to xenobiotic metabolism, pyruvate and thiamine metabolism, and other cofactor-dependent processes, consistent with a shift from oxidative, biosynthetically intensive metabolism toward glycolysis, fermentation, and detoxification. In contrast, PE fibers selectively suppressed oxidative and cofactor/vitamin pathways while perturbing bile acid, sphingolipid, and aromatic compound metabolism, indicating a simplified, maintenance-oriented energy state. Despite these pronounced metabolomic shifts, histopathology revealed no overt intestinal or systemic lesions in any treatment group, highlighting altered microbial activity despite the absence of gross pathological lesions and supporting a silent dysbiosis phenotype.

IMPORTANCE: Environmental contaminants in groundwater are increasingly common, yet their combined effects on animal health remain poorly understood. The current study shows that even low-level exposure to agricultural chemical mixtures and microplastics can alter the gut microbial metabolism in broiler chickens without intestinal damage. These subclinical shifts, characterized by altered energy pathways, cofactor scarcity, and microbial restructuring, highlight a form of silent dysbiosis. Our findings emphasize the need to integrate microbiome- metabolic endpoints into environmental risk assessments to predict earlier, more meaningful, functionally relevant impacts.},
}

@article {pmid41860224,
year = {2026},
author = {Bintarti, AF and Sulesky-Grieb, A and Colovas, J and Marolleau, B and Boureau, T and Simonin, M and Barret, M and Shade, A},
title = {Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0301925},
doi = {10.1128/spectrum.03019-25},
pmid = {41860224},
issn = {2165-0497},
abstract = {Drought is a critical risk for staple crops like common bean (Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither a strong response of the Red Hawk microbiomes to drought nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity, while its root had no legacy effect observed. This study demonstrates that below-ground plant microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries are useful to inform generalities and build theory toward prediction on microbiome responses to global change.IMPORTANCEDrought remains an important challenge in crop agriculture because of climate change, and plant microbiome management has potential to support plant resilience to drought. Here, we investigated the impact of drought and drought legacy across two generations on the root and rhizosphere microbiomes of the drought-susceptible legume common bean, a key staple food crop with production widely distributed across the Americas, Africa, Europe, and Asia, and which is of critical importance for food security in many of its production regions. Despite host plant decline with drought, the effects of drought on the microbiomes were either not observed, inconsistent, or weak, suggesting overall microbiome resistance and limited drought legacy. This work provides insights into how the stability of the below-ground plant microbiome can be driven by stress resistance, offering a different perspective on how the microbiome could be managed to support crops facing drought.},
}

@article {pmid41860424,
year = {2026},
author = {Guo, Y and Liu, W and Qiu, K and Si, H and Zhang, Y and Huang, Y and Yang, Y and Xie, Y},
title = {Linking Bacterial Diversity to Rhizosphere Ecological Stoichiometry and Nutrient Availability in a Clonal Desert Plant.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag076},
pmid = {41860424},
issn = {1365-2672},
abstract = {AIMS: This study aimed to examine the relationships between rhizosphere (RS) microorganisms of the desert pioneer plant Psammochloa villosa and soil nutrient availability, with the goal of clarifying microbial mechanisms supporting its persistence in desertified regions and identifying potential targets for microbiome-based management.

METHODS AND RESULTS: Using absolute quantification of 16S rRNA gene and ITS sequencing, microbial communities in the RS of P. villosa were compared with those in bulk soil (BS). The results showed that the rhizosphere of P. villosa had significantly lower total phosphorus (TP) but higher carbon-to-phosphorus (C/P) and nitrogen-to-phosphorus (N/P) ratios than BS, while the available nitrogen-to-available phosphorus ratio (AN/AP) was 4-5 times higher than N/P. This pattern suggests that the RS experiences stronger phosphorus limitation than BS. A lower fungi-to-bacteria (F/B) ratio in the RS relative to BS was positively associated with TP and negatively associated with soil C/P and N/P ratios, indicating a bacterial-dominated community under phosphorus-limited conditions. Structural equation modeling further indicated that rhizobacterial diversity strongly promoted the acquisition of available nutrients by significantly affecting soil organic carbon (SOC), TP, and stoichiometric balance.

CONCLUSIONS: These results indicate that bacterial diversity is tightly linked to the regulation of ecological stoichiometry and nutrient availability under P-limited conditions in the rhizosphere of P. villosa.},
}

@article {pmid41860558,
year = {2026},
author = {Bloom, P and Khanna, S},
title = {Fecal microbiota transplantation in chronic liver disease: Current and future state of the art.},
journal = {Hepatology communications},
volume = {10},
number = {4},
pages = {},
pmid = {41860558},
issn = {2471-254X},
mesh = {*Fecal Microbiota Transplantation/methods/trends/adverse effects ; Humans ; Gastrointestinal Microbiome ; *Liver Diseases/therapy ; Chronic Disease ; },
abstract = {Chronic liver diseases are associated with changes in gut microbiome composition and function. Early data suggest that fecal microbiota transplantation (FMT) may treat several chronic liver diseases, especially cirrhosis, hepatic encephalopathy, and alcohol-associated liver disease. Well-powered and multisite studies are needed to better understand which indications and subpopulations hold promise for FMT. At present, there is variability in the screening, processing, and administration of FMT. Some of this variability is inherent to the nature of FMT, but some of the variability could be standardized to optimize safety and efficacy. Ultimately, we may find that narrowed and donor-independent microbiome therapeutics are superior tools to provide a consistently effective result in chronic liver disease. Regulation of FMT for chronic liver disease indications in the United States will continue to require the rigid regulatory framework of other drugs, requiring an Investigational New Drug (IND) application.},
}

*Fecal Microbiota Transplantation/methods/trends/adverse effects
Humans
Gastrointestinal Microbiome
*Liver Diseases/therapy
Chronic Disease

@article {pmid41860619,
year = {2026},
author = {Fu, X and Chen, Y and Wang, Y and Chen, B and Chen, M and Lyu, J and Sun, H and Wang, Z and Xu, J and Li, GL and Ren, D},
title = {Microbiota in Chronic Suppurative Otitis media: association with Postoperative Tympanic membrane outcomes.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41860619},
issn = {1432-0614},
mesh = {Humans ; *Otitis Media, Suppurative/microbiology/surgery ; *Microbiota ; Female ; Male ; Chronic Disease ; Middle Aged ; Adult ; *Tympanic Membrane/microbiology/surgery ; Pseudomonas aeruginosa/isolation & purification/genetics ; Biomarkers ; Bacteria/classification/genetics/isolation & purification ; Aged ; Tympanic Membrane Perforation/microbiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Chronic suppurative otitis media (CSOM) is a prevalent condition with global health implications due to its impact on hearing and quality of life. Conventional treatments often fail because of bacterial biofilms and antimicrobial resistance. Effective treatment of CSOM depends on the precise determination of the middle ear microbiota; however, current microbial detection methods do not meet this need. Postoperative reperforation may compromise surgical outcomes. If the risk of perforation can be predicted immediately after surgery, sensitive antibiotics could be administered proactively for early intervention to optimize treatment efficacy. This study introduces 2b-RAD sequencing for the microbiome (2b-RAD-M), a novel technology designed to provide a comprehensive profile of the CSOM microbiota and identify diagnostic biomarkers that predict postoperative outcomes. We analyzed ear swabs from patients with postoperative perforation (PO), nonperforation (NPO), and otosclerosis (CON) using microbial diversity, relative abundance, and composition analyses. Bacillus_A_bombysepticus and Pseudomonas aeruginosa were identified as potential biomarkers, with Bacillus_A_bombysepticus demonstrating superior diagnostic accuracy (area under curve (AUC) = 0.92) compared to P. aeruginosa (AUC = 0.25). Functional predictions revealed that biological activities related to gene regulation, substance metabolism, and DNA repair were more prominent in the PO group. This study offers new insights into CSOM pathogenesis and progression, proposing Bacillus_A_bombysepticus as a novel biomarker for predicting postoperative outcomes that can indicate an increased risk of tympanic membrane reperforation for the first time. KEY POINTS: 2b-RAD-M technology enables comprehensive CSOM microbiota profiling and biomarker identification. Bacillus_A_bombysepticus (AUC = 0.92) outperforms Pseudomonas aeruginosa in diagnostic accuracy. Bacillus_A_bombysepticus predicts postoperative tympanic membrane reperforation via functional activity analysis.},
}

Humans
*Otitis Media, Suppurative/microbiology/surgery
*Microbiota
Female
Male
Chronic Disease
Middle Aged
Adult
*Tympanic Membrane/microbiology/surgery
Pseudomonas aeruginosa/isolation & purification/genetics
Biomarkers
Bacteria/classification/genetics/isolation & purification
Aged
Tympanic Membrane Perforation/microbiology
Anti-Bacterial Agents/therapeutic use

@article {pmid41860655,
year = {2026},
author = {Gu, Z and Song, C and Kang, X and Liu, T and Du, M and Wang, X and Zhao, H and Liu, J and Zhang, Y},
title = {Highly diverse and anaerobe-dominated vaginal microbiota in women living with HIV: a cross-sectional study.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41860655},
issn = {1439-0973},
support = {DTKF202303//Beijing Key Laboratory of Emerging Infectious Diseases Support/ ; ZYLX202126//Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support/ ; },
abstract = {INTRODUCTION: Although highly active antiretroviral therapy (HAART) suppresses HIV viral load and extends life, rising non-AIDS-defining events (NADEs) underscore the importance of long-term health, including reproductive tract health in women living with HIV (WLWH). This study compared vaginal microbiota in WLWH versus women without HIV infection (WLWNH) to inform reproductive health assessment and intervention.

METHODS: Vaginal swabs from 76 WLWH and 74 WLWNH (Beijing Ditan Hospital, Sept-Oct 2022) underwent 16S rRNA gene sequencing. We used hierarchical clustering to categorize community state types (CSTs I-V) and Adonis for inter-group differences. Pearson correlation assessed relationships between CD4 + T cells and differential bacteria, while Spearman correlation evaluated microbial co-occurrence network interactions (visualized via Gephi0.10.1). Neutral community modeling evaluated assembly processes.

RESULTS: WLWH exhibited higher vaginal microbial diversity. Compared to WLWNH, Gardnerella vaginalis showed higher relative abundance in WLWH CST III (P = 0.001). Additionally, urogenital pathogens Aerococcus christensenii and Ureaplasma urealyticum were significantly enriched in WLWH CST III (P = 0.028, P = 0.033; AUC = 0.704, 0.721, respectively) and CST IV (P = 0.024, P = 0.031; AUC = 0.657, 0.646, respectively). In CST III, CD4 + T cell counts correlated positively with Aerococcus christensenii (r = 0.49, P = 0.044). Neutral community modeling demonstrated that microbiota assembly in WLWH was primarily shaped by stochastic processes (R[2] = 0.37 vs 0.219) with significantly restricted microbial dispersal (Nm = 9 vs14).

CONCLUSIONS: WLWH exhibit a distinct, highly diverse vaginal dysbiosis enriched with anaerobic and urogenital pathogenic bacteria. This post-HIV infection dysbiosis may predispose women to subsequent genital infections; future longitudinal research comparing pre- and post-infection microbiome dynamics will be crucial for optimizing gynecological management.},
}

@article {pmid41860665,
year = {2026},
author = {Abedi, A and Moghaddam, MM and Kachuei, R and Fooladi, AAI},
title = {Exploring the role of metabolic disorders and gut microbiome in immune checkpoint regulation in cancer: PI3K/AKT/mTOR focus.},
journal = {Journal of physiology and biochemistry},
volume = {82},
number = {1},
pages = {},
pmid = {41860665},
issn = {1877-8755},
}

@article {pmid41860729,
year = {2026},
author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Ledesma-Hernandez, G and Cuezva, S and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V},
title = {Habitat Specialization and Airborne Dispersal Shape the Microbiome of a Gypsum Karst Cave.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02745-y},
pmid = {41860729},
issn = {1432-184X},
}

@article {pmid41861238,
year = {2026},
author = {Yao, ML and Dai, Y and Zhang, W},
title = {Natural Products from the Oral Microbiome.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-050248},
pmid = {41861238},
issn = {1545-4509},
abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.},
}

@article {pmid41861247,
year = {2026},
author = {Allen, WJ and Williams, S and Collinson, I},
title = {The Great Escape: Protein Trafficking from the Bacterial Cytosol to the Outer Membrane.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-011856},
pmid = {41861247},
issn = {1545-4509},
abstract = {To protect their delicate, carefully curated contents from the world, bacteria encase themselves within a protective envelope made up of sugars, lipids, and proteins. Cell envelopes give bacteria their characteristic shapes, provide rigidity and mechanical stability, and form a selective antechamber-granting access only to a desirable subset of environmental substances. Yet this protective layer is a double-edged sword: Its effectiveness at keeping things out also makes it difficult for things to leave, including the proteins required to interface with the outside world and form the envelope itself. Bacteria have solved this problem by constructing an array of proteinaceous nanomachines that expend energy to selectively shuttle proteins and other building blocks to their intended destinations. Here, we present an overview of our current understanding of how these transporters work, focusing on the major, conserved machines that ferry proteins across the cell envelope throughout the domain Bacteria. The emphasis is on recent discoveries and open questions, with the hope that answering these will provide new avenues to help combat the rising threat of antimicrobial resistance and the rapidly expanding list of diseases linked to human microbiome composition.},
}

@article {pmid41861743,
year = {2026},
author = {Addazii, D and Pinheiro, ACAS and Nissen, L and Tappi, S and Bordoni, A and Rocculi, P and Gianotti, A},
title = {Bridging the gap of gut microbiome effects of new food additives in food risk assessment: MICODE gut model to test new chitosan from seafood waste.},
journal = {Food chemistry},
volume = {512},
number = {},
pages = {148927},
doi = {10.1016/j.foodchem.2026.148927},
pmid = {41861743},
issn = {1873-7072},
abstract = {EFSA and FAO outlined guidelines to address data and methodological gaps in assessing the impact of food compounds on gut microbiota (GM) and human health, emphasizing the need for in vitro GM models and standardized biomarkers to integrate GM data into food safety risk assessments. Food texturizers are widespread in processed foods enhancing texture and stability, yet their effects on GM remain unclear. This study investigates three additives: a chitosan from seafood waste (CHIW), a chitosan standard (CHIC), and hydroxypropyl methylcellulose (HPMC), using fructo-oligosaccharides (FOS) as a prebiotic control. A standardized in vitro gastrointestinal model simulating digestion and colonic fermentation, combined with qPCR and GC-MS, assessed their influence on microbial composition and metabolic output, under the hypothesis that distinct carbohydrate polymers differently affect GM. CHIC and CHIW, derived from crustacean waste, promoted beneficial bacteria (Clostridium group IV, Bifidobacteriaceae) and boosted SCFAs production, including butyrate and propionate, with CHIW showing stronger prebiotic effects. HPMC was associated with reduced abundance of Lactobacillaceae and harmful metabolites. These findings support our hypothesis, demonstrate the responsiveness of in vitro GM models to dietary polymers, and reinforce the potential of GM-based screening in food safety assessment, suggesting native chitosan as a promising alternative to synthetic additives.},
}

@article {pmid41861747,
year = {2026},
author = {Fennessy, A and Slattery, L and Shelley, O and Reyes, LF and Martin-Loeches, I},
title = {Infectious complications of burns in the intensive care unit.},
journal = {Journal of critical care},
volume = {94},
number = {},
pages = {155519},
doi = {10.1016/j.jcrc.2026.155519},
pmid = {41861747},
issn = {1557-8615},
abstract = {BACKGROUND: Severe burn injury is associated with profound physiological derangement and remains a major cause of infection-related morbidity and mortality worldwide. Disruption of the skin barrier sustained immune dysregulation, prolonged intensive care unit (ICU) exposure, and extensive use of invasive devices create a uniquely infection-prone host environment. Infectious complications, particularly those caused by multidrug-resistant organisms (MDROs), continue to account for a substantial proportion of deaths in critically ill burn patients despite advances in surgical and critical care management.

OBJECTIVES: This narrative review aims to provide a comprehensive, clinically focused overview of infectious complications in critically ill burn patients, integrating current evidence on epidemiology, pathophysiology, microbial dynamics, diagnostic strategies, and contemporary management approaches relevant to daily ICU practice.

SOURCES OF EVIDENCE: A narrative synthesis of the published literature was performed, including international guidelines, observational studies, randomised trials, systematic reviews, and translational research focusing on burn-related infections, antimicrobial resistance, diagnostics, and emerging therapies.

CONTENT: The review examines the multifactorial pathophysiology underlying infection susceptibility following major burns, including loss of the cutaneous barrier, hyperinflammatory responses followed by immune paralysis, and burn-induced hypermetabolism. Dynamic patterns of microbial colonisation, biofilm formation, microbiome disruption, and the global rise of MDROs are explored. Diagnostic challenges in distinguishing colonisation from invasive infection are discussed, alongside traditional and advanced diagnostic modalities such as quantitative tissue cultures, biomarkers, multiplex molecular assays, and next-generation sequencing. Contemporary management strategies are reviewed, emphasising early surgical source control, pharmacokinetically optimised antimicrobial therapy, antimicrobial stewardship, and rigorous infection prevention and control practices. Emerging adjunctive therapies, including bacteriophage therapy, nanotechnology-based antimicrobials, microbiome-directed interventions, and immunomodulatory approaches, are also highlighted.

IMPLICATIONS: Effective infection management in burn patients requires an integrated, multidisciplinary approach that combines rapid diagnosis, early surgical intervention, tailored antimicrobial therapy, and robust infection prevention strategies. Advances in molecular diagnostics, precision medicine, and microbiome science hold promise for improving outcomes and mitigating the growing burden of antimicrobial resistance in burn ICUs.

CONCLUSIONS: Infectious complications remain a leading determinant of outcome following severe burn injury. Optimising infection care through early recognition, precise diagnostics, coordinated surgical and antimicrobial strategies, and emerging precision-based interventions is essential to reduce infection-related morbidity and mortality in this vulnerable patient population.},
}

@article {pmid41861866,
year = {2026},
author = {Kalimuthu, S and Leung, YY and Neelakantan, P},
title = {Oral mucositis in cancer therapy: A review of the clinical landscape and the emerging role of microbiome-host interactions.},
journal = {Critical reviews in oncology/hematology},
volume = {222},
number = {},
pages = {105282},
doi = {10.1016/j.critrevonc.2026.105282},
pmid = {41861866},
issn = {1879-0461},
abstract = {Oral mucositis (OM) is a debilitating toxicity of chemotherapy and radiotherapy that compromises nutrition, quality of life, treatment adherence, and overall cancer outcomes. Despite its clinical impact, therapeutic options remain limited, and our descriptive analysis of the clinical trial landscape reveals about 93.75% attrition rate from clinical success to regulatory approval, highlighting the limitations of single-pathway strategies that target epithelial injury alone. Emerging evidence implicates oral microbiome as an active contributor to OM initiation, inflammatory amplification, and delayed healing, interacting dynamically with host immune responses to shape disease trajectory. These insights support a shift toward multi-targeted therapeutic frameworks that concurrently address epithelial protection, host-immune modulation, and microbial dysbiosis. This approach is increasingly reflected in the growing pipeline shift toward multifunctional compounds and microbiome-based approaches. This suggests that successful OM management will require the integrated antimicrobial and anti-inflammatory approaches, potentially guided by patient-specific microbiome profiling.},
}

@article {pmid41861946,
year = {2026},
author = {Wang, ST and Li, L and Yang, Q and Zhang, GF},
title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.},
journal = {Environmental research},
volume = {299},
number = {},
pages = {124314},
doi = {10.1016/j.envres.2026.124314},
pmid = {41861946},
issn = {1096-0953},
abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.},
}

@article {pmid41862052,
year = {2026},
author = {Gunasekaran Rajalakshmi, S and K, RB and Viswanathan, P},
title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.},
journal = {Life sciences},
volume = {393},
number = {},
pages = {124336},
doi = {10.1016/j.lfs.2026.124336},
pmid = {41862052},
issn = {1879-0631},
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.

METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.

KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p < 0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.

SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.},
}

@article {pmid41862063,
year = {2026},
author = {Reytor-González, C and Frias-Toral, E and Annunziata, G and Simancas-Racines, D and Barrea, L},
title = {Obesity-Focused Dietary Interventions in Breast Cancer Care: A Comprehensive Review of Medical Nutrition Therapy Approaches and Efficacy in Prevention and Treatment.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2026.03.002},
pmid = {41862063},
issn = {1096-3650},
abstract = {Obesity is associated with an increased risk of developing breast cancer, particularly in postmenopausal women, through mechanisms such as excessive estrogen production, insulin resistance, and chronic low-grade inflammation, all of which promote tumor initiation and progression. Alterations in the gut microbiota, frequently observed in obesity, further exacerbate this risk by influencing estrogen metabolism, modulating immune responses, and promoting systemic inflammation, thereby creating a microenvironment conducive to breast cancer growth. Medical nutrition therapy plays a crucial role in managing these interrelated conditions, with dietary interventions such as the Mediterranean diet, ketogenic diet, and intermittent fasting showing potential to reduce weight, improve metabolic health, modulate the gut microbiome, and positively influence inflammatory and hormonal signaling. While short-term outcomes are promising, long-term studies are required to confirm their effects on breast cancer survival and recurrence. Personalized nutrition-accounting for genetic, epigenetic, and microbiome profiles-is emerging as a highly effective approach to enhance therapeutic outcomes. Integrating targeted nutritional strategies into breast cancer treatment protocols is essential to improve prognosis, optimize therapy responses, and enhance patients' quality of life. This narrative review examines the role of nutritional therapies in the prevention and management of obesity and breast cancer, emphasizing their impact on tumor biology, treatment efficacy, and patient health.},
}

@article {pmid41862100,
year = {2026},
author = {Cordeiro, J and Macela, C and Kleiner, R and Vaskovich-Koubi, D and Moura, LIF and Satchi-Fainaro, R and Florindo, HF},
title = {Harnessing the power of microbiome, nanotechnology, and immunity against cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114839},
doi = {10.1016/j.jconrel.2026.114839},
pmid = {41862100},
issn = {1873-4995},
abstract = {The human microbiome has emerged as a key player in health and disease, including cancer, which remains one of the leading causes of mortality worldwide. Although advances in understanding the tumor immune microenvironment and the development of immunotherapies have transformed cancer treatment, clinical efficacy remains limited by suboptimal response rates and severe side effects. Recent integrative research in cancer biology, immune-oncology, and cancer microbiome research, enabled by omics technologies and advanced bioinformatics, has begun to reveal intricate links between the microbiome, cancer progression, and immune modulation. These findings underscore the microbiome's pivotal role in shaping both therapeutic efficacy and resistance mechanisms. Currently, nanotechnology, propelled into mainstream success through the development of COVID-19 mRNA vaccines, is offering new tools for precision oncology. Nanomaterials are now being explored not only for targeted drug delivery but also for monitoring and modulating the microbiome, with significant potential for biomarker discovery and personalized medicine. In this article, we explore the role of the microbiota in tumorigenesis and cancer therapy, with a particular focus on its crosstalk with the immune system. We highlight emerging microbiota-targeted therapeutic strategies and discuss how nanotechnology-based systems are being designed to modulate the microbiome-immune-cancer axis. Finally, we discuss future directions in leveraging the convergence of microbiome science, nanotechnology, and immunotherapy to advance cancer treatment.},
}

@article {pmid41862195,
year = {2026},
author = {Raithel, M and Zlatou, V and Kremenevski, I and Hagel, AF and Konturek, P},
title = {[Endogenous Alcohol Production in the Human Micro- and Mycobiome: Auto-Brewery Syndrome].},
journal = {Zeitschrift fur Gastroenterologie},
volume = {64},
number = {3},
pages = {270-276},
doi = {10.1055/a-2772-7942},
pmid = {41862195},
issn = {1439-7803},
mesh = {Humans ; *Ethanol/metabolism ; *Dysbiosis/diagnosis ; *Gastrointestinal Microbiome/physiology ; *Mycobiome/physiology ; Syndrome ; Dietary Carbohydrates/adverse effects/metabolism ; },
abstract = {Pathological changes in the human microbiome and mycobiome can lead to endogenous production of toxic metabolites, including alcohol. Auto-brewery syndrome (ABS) is characterized by endogenous alcohol formation after high-carbohydrate intake in cases of dysbiosis or underlying disease.Cases described since 1948 were analyzed up to May 2025 via selective literature review regarding symptoms, pathophysiology, diagnostics, and therapy. Syndromes not clearly attributable to endogenous alcohol (e.g., autointoxication, intestinal fermentation syndrome) were excluded.Around 30 cases show variable clinical features with neuropsychiatric, gastrointestinal, and hepatological symptoms, sometimes causing emergencies or accidents. Alcohol is produced by microbial or mycotic overgrowth (e.g., E. coli, Klebsiella, Saccharomyces, Candida) following carbohydrate intake. Diagnosis requires detailed personal and external history, exclusion of other causes, and, if needed, monitored carbohydrate challenge with alcohol measurement. Treatment focuses on carbohydrate reduction, antibiotics or antifungals, and management of underlying conditions.ABS is rare but causes endogenous alcohol-related symptoms that must be considered in medical and legal evaluation of unexplained symptoms or incidents.},
}

Humans
*Ethanol/metabolism
*Dysbiosis/diagnosis
*Gastrointestinal Microbiome/physiology
*Mycobiome/physiology
Syndrome
Dietary Carbohydrates/adverse effects/metabolism

@article {pmid41862269,
year = {2026},
author = {Wakamatsu, N and Yoshioka, Y and Habu, M and Ariyoshi, W and Yamasaki, R},
title = {Surfactin selectively suppresses acidogenicity in Streptococcus sobrinus without inhibiting growth or biofilm formation.},
journal = {Journal of oral biosciences},
volume = {68},
number = {2},
pages = {100756},
doi = {10.1016/j.job.2026.100756},
pmid = {41862269},
issn = {1880-3865},
mesh = {*Biofilms/drug effects/growth & development ; *Peptides, Cyclic/pharmacology ; *Lipopeptides/pharmacology ; Lactic Acid/metabolism ; Hydrogen-Ion Concentration ; Dental Caries/prevention & control/microbiology ; Humans ; *Streptococcus/drug effects/growth & development/metabolism ; },
abstract = {OBJECTIVES: Dental caries are caused by organic acids produced by cariogenic bacteria through carbohydrate metabolism. Suppression of acid production without disrupting the oral microbiome is a promising preventive strategy against dental caries. Surfactin, a naturally derived biosurfactant, has several biological activities. However, its effects on acid production by cariogenic bacteria remain unclear. In this study, the effects of surfactin on lactate production, growth, biofilm formation, and metabolic activity of Streptococcus sobrinus, were investigated.

METHODS: In vitro assays were performed to distinguish surfactin-mediated suppression of acidogenic metabolism from its effects on bacterial growth or biofilm formation, combined with molecular and enzymatic analyses to explore the underlying regulatory mechanisms.

RESULTS: Surfactin significantly reduced lactate production in planktonic and biofilm-associated S. sobrinus, and it delayed environmental pH reduction in the presence of sucrose. Notably, these effects were observed without inhibition of bacterial growth or biofilm formation. There were no significant changes in the expression of lactate production-related genes, and lactate dehydrogenase activity was not inhibited by surfactin. In contrast, in the MTT assay, there was a transient reduction in metabolic activity, accompanied by delayed initiation of growth.

CONCLUSION: These findings indicate that surfactin selectively attenuates acidogenicity in S. sobrinus, without markedly affecting bacterial viability or biofilm architecture, which is consistent with an anti-virulence mode of action. Although further validation in more complex oral environments and comprehensive safety assessments are required, this study provides fundamental evidence supporting the potential of naturally derived biosurfactants as a basis for future preventive strategies for caries.},
}

*Biofilms/drug effects/growth & development
*Peptides, Cyclic/pharmacology
*Lipopeptides/pharmacology
Lactic Acid/metabolism
Hydrogen-Ion Concentration
Dental Caries/prevention & control/microbiology
Humans
*Streptococcus/drug effects/growth & development/metabolism

@article {pmid41862311,
year = {2026},
author = {Berry, AA},
title = {Gut check: converging evidence links microbiome to malaria risk.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.03.004},
pmid = {41862311},
issn = {1471-5007},
abstract = {Beyond genetics and immunity, the gut microbiome may be an underappreciated determinant of malaria parasite burden. Gustin et al. demonstrated that pre-infection microbiome composition predicts the level of Plasmodium parasitemia in both rhesus macaques and human volunteers, with convergent evidence pointing to Bifidobacterium as a potentially protective genus.},
}

@article {pmid41862401,
year = {2026},
author = {Mutalik, VK and Inman, JL and Chang, H and Arkin, A and Mao, JH},
title = {Phage therapy in oncology: opportunities for cancer prevention and treatment.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2026.02.001},
pmid = {41862401},
issn = {1471-499X},
abstract = {Bacteriophages (phages) are emerging as programmable biological therapeutics in oncology, extending beyond their traditional antimicrobial applications. This review proposes a phage-microbiome-immune-oncology axis that links microbial dynamics, immune modulation, and engineered phages to guide precision cancer prevention and therapy. Phages can eliminate cancer-associated bacteria, remodel the tumor microenvironment, enhance antitumor immunity, and deliver targeted therapeutic payloads. However, several critical challenges must be addressed to realize this therapeutic potential, particularly host immune responses that limit repeat dosing, inefficient tumor penetration, and the need for rigorous clinical validation. By examining phage-host-tumor interactions through robust model systems and highlighting translational opportunities, this review establishes phage therapy as a promising frontier in precision oncology that warrants accelerated clinical development.},
}

@article {pmid41862452,
year = {2026},
author = {Du, Z and Li, M and Lin, K and Xing, B and Ou, Y and Lin, Z and Song, W and Chen, J and Li, J and Li, J and Xiao, M},
title = {High-resolution phage-host assignment through key proteins using large language models.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70613-x},
pmid = {41862452},
issn = {2041-1723},
abstract = {Viral sequences in diverse environments remain largely uncharacterized, impeding our comprehension of their genetic makeup, biological interactions, and potential applications. This underscores an urgent need for innovative analytical methods. Here, we present the VirHost Hunter framework, which employs phage tails and lysins, bypassing the requirement for full genomes, for efficient and high-resolution host assignment. By harnessing Protein Language Models and Vision Transformers, VirHost Hunter captures protein functional homology despite sequence dissimilarity, significantly boosting prediction accuracy. In the scenario of disease-associated gut bacteria, the calibrated VirHost Hunter surpasses existing methods, doubling phage host assignments, expanding taxonomic reach, and revealing previously uncharacterized phages targeting gut bacteria, including Akkermansia and Prevotella. Therefore, we establish a gut phage lysin database, enabling the synthesis of a lysin that effectively and specifically targets an obesity-promoting bacterium. VirHost Hunter's precision and scalability mark a significant leap forward in virome research and present a promising avenue for microbiome therapies.},
}

@article {pmid41862473,
year = {2026},
author = {Daniels, M and Wijayagunasekera, D and Berry, D},
title = {Widespread effects of catecholamines on growth of human gut bacteria.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00948-2},
pmid = {41862473},
issn = {2055-5008},
support = {Grant-DOI 10.55776/ESP558//Austrian Science Fund/ ; },
abstract = {The interactions between hosts and their microbiomes are driven in part by chemical communication, which influences immune responses, metabolism, and microbial community structure. Neuroendocrine signals are central to this bidirectional communication, forming the basis of microbial endocrinology. Although host-derived hormones, including catecholamines, are known to affect microbial physiology, much of the existing literature focuses on a limited number of model organisms or complex in vivo systems, where disentangling direct microbial responses from host-mediated effects is challenging. As a result, systematic comparative analyses of direct bacterial responses under controlled conditions remain scarce. Here, we performed a systematic in vitro screen under anaerobic conditions to assess catecholamine effects on the growth dynamics of phylogenetically diverse human gut bacteria. Catecholamines altered multiple growth parameters in a species-specific manner, with effects detectable at nanogram concentrations. Multivariate analyses, including principal component analysis and non-metric multidimensional scaling, revealed lineage-associated response patterns across taxa. Although derived from monoculture experiments, these intrinsic responses provide a comparative framework for understanding how direct hormone-microbe interactions may contribute to microbiome dynamics under host stress. Overall, this study provides a quantitative cross-species dataset to inform future systems-level investigations in microbial endocrinology.},
}

@article {pmid41862558,
year = {2026},
author = {Soriano-Lerma, A and Soriano-Suárez, JS and Garcia-Rodriguez, M and Alferez, MJ and Soriano, M and Salcedo, JAG and Lopez-Aliaga, I},
title = {Molecular study of the small intestine dysbiosis derived from iron deficiency anaemia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44373-z},
pmid = {41862558},
issn = {2045-2322},
support = {Contratos PUENTE//Universidad de Granada/ ; [P_FORT_CENTROS_2023/09][AS1] , [P_FORT_GRUPOS_2023/102]//Universidad de Almería/ ; PID2020-120481RB-100/AEI/10.13039/50110001103//Ministerio de Ciencia e Innovación/ ; PI21/00497//Instituto de Salud Carlos III/ ; },
}

@article {pmid41862676,
year = {2026},
author = {Shim, SY and Lee, J and Linh, LTY and Kim, SR and Choi, HS and Lee, MG and Hwang, SG},
title = {Effects of short-term application of organic manure on the growth of forage maize (Zea mays L. cv. Kwangpyeongok) and soil bacterial communities.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45179-9},
pmid = {41862676},
issn = {2045-2322},
abstract = {While chemical fertilizers (CF) ensure rapid crop growth, relying exclusively on them can disrupt natural nutrient cycling and lead to environmental concerns such as nutrient imbalance. In contrast, organic amendments offer a sustainable alternative by promoting resource circulation; however, their efficacy is often variable and difficult to control, depending on complex interactions among application rates, plant types, and field conditions. Therefore, gaining comprehensive insights into their optimal use is essential to maximize agricultural benefits. This study evaluated the effects of composted Hanwoo manure (HM) applied at standard (HM_1x) and quadruple (HM_4x) rates on forage maize growth and soil microbial communities compared with CF and no treatment (NT). Growth parameters indicated that plant length was highest in the CF (219.33 cm) and HM_4 × (217.30 cm) groups, followed by HM_1 × (176.78 cm) and NT (172.02 cm). Soil analysis indicated that organic matter (OM) and available phosphorus (P2O5) were significantly higher in HM-treated soils than in NT. Microbiological analysis revealed distinct shifts in community composition linked to these chemical changes. In HM-treated soils, the relative abundance of Proteobacteria and Candidatus Saccharibacteria, known for their roles in OM decomposition and nutrient cycling, significantly increased. Conversely, the CF group showed a higher prevalence of Saprospiraceae, a phosphorus-removing bacterium, which is consistent with the observed reduction in available phosphorus in both soil and plant tissues in the CF treatment. Collectively, this study demonstrates that applying sufficient amounts of composted HM, where appropriate, can result in crop growth comparable to that of CF. Notably, we observed that such growth performance coincided with specific patterns in soil microbial communities related to nutrient availability. By highlighting these co-occurring trends, our research offers valuable insights into the biological dynamics of compost application for sustainable agriculture.},
}

@article {pmid41862790,
year = {2026},
author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H},
title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04966-0},
pmid = {41862790},
issn = {1471-2180},
support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; },
}

@article {pmid41863277,
year = {2026},
author = {Ely Arman, NI and Makpol, S},
title = {The Link between Gut Microbiome, Amyloid-Beta Deposition, Brain Inflammation, and Alzheimer's Disease: A Review of Current Literature.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X416900251207210728},
pmid = {41863277},
issn = {1875-6190},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by amyloid-beta (Aβ) plaques, neurofibrillary tangles, and cognitive decline. AD has gained increasing global attention. As the aging population continues to grow, the economic burden on individuals, families, and healthcare systems rises, emphasizing the urgent need for early detection and natural therapeutic approaches to address these challenges. The gut microbiota regulates essential physiological functions, including digestion, nutrient absorption, and inflammatory signaling. Dysbiosis, or changes in gut microbiome composition, is marked by the overgrowth of pathogenic bacteria and depletion of beneficial species. Gut dysbiosis is also linked to pathological features of AD, such as increased Aβ deposition, compromised intestinal and blood-brain barrier integrity, and neuroinflammation through the brain-gut microbiome axis (BGMA). However, the connection between the gut microbiome and AD pathological hallmarks remains unclear. This narrative review aims to explore current research on the relationship between gut dysbiosis and the pathological features of AD, with the goal of highlighting the role of the gut system in brain function and AD pathogenesis. Vitamin E, due to its antioxidative and anti-inflammatory properties, may serve as a promising natural option for modulating the gut microbiome while potentially delaying AD progression and promoting a balanced microbial composition.},
}

@article {pmid41863409,
year = {2026},
author = {Kaur, S and Bhandari, N and Mahajan, S and Mehta, D and Chauhan, S and Kumar, V and Rohilla, M and Mehta, S and Dhankhar, S},
title = {Molecular Pathways of Microbiota-derived Neuromodulation: An Integrative View.},
journal = {Current neurovascular research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672026427392260131184931},
pmid = {41863409},
issn = {1875-5739},
abstract = {INTRODUCTION: The gut microbiota, also called "the forgotten organ", is a complex and dynamic ecosystem of microorganisms that is fundamental to human physiology, neurobiology, and disease. This review examines the intricate relationships between the gut microbiota and the nervous system via the microbiota-gut-brain (MGB) axis. It discusses their endocrine, immunological, and neural pathways.

METHODS: A thorough literature search was performed across databases including PubMed, Scopus, Web of Science, and Google Scholar, using keywords such as "gut microbiota," "microbiota- gut-brain axis," "neuromodulation," "serotonin," "dopamine," "GABA," "norepinephrine," "prebiotics," "probiotics," and "faecal microbiota transplantation"..

RESULTS: This article explains how the gut microbiota impacts significant body's chemical messengers such as serotonin, dopamine, GABA, and norepinephrine. These are essential for brain functioning. All of these diseases have evidence linking inflammation of the gut and the brain. Furthermore, gut dysbiosis has been responsible for some of the most serious disorders of mankind through pandemics and plagues.

DISCUSSION: Moreover, prebiotics, probiotics, faecal microbiota transplantation (FMT), synbiotics, diet, and bioactive substances such as curcumin and flavonoids are new treatment approaches. These strategies help bring back a normal balance of gut microbes for mental and neurological health. Even though preclinical studies have shown promise, bringing it to humans is not simple. Issues like the strain, the individual, and sustained use make it a substantial challenge.

CONCLUSION: Future directions of work should combine and focus human-based research efforts with precise and personalized microbiome modulation, allowing us to leverage the gut-brain axis therapeutically.},
}

@article {pmid41863708,
year = {2026},
author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H},
title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41863708},
issn = {2509-2723},
abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.},
}

@article {pmid41863784,
year = {2026},
author = {Giannakogeorgou, A and van den Ende, T and Verhaar, BJH and de Clercq, N and van Laarhoven, HWM and Nieuwdorp, M},
title = {Targeting the gut microbiota as treatment for obesity and cancer cachexia.},
journal = {Expert opinion on emerging drugs},
volume = {},
number = {},
pages = {},
doi = {10.1080/14728214.2026.2650180},
pmid = {41863784},
issn = {1744-7623},
abstract = {INTRODUCTION: Obesity and cancer cachexia represent two seemingly contrasting yet interrelated ends of the metabolic disorder spectrum, both characterized by disrupted energy homeostasis, inflammation and neuroendocrine dysfunction, and associated with increased morbidity and mortality. Existing treatments often fail to address the complex underlying pathophysiological mechanisms. Emerging research highlights the role of the gut microbiome in the pathophysiology of both conditions and how it can serve as a novel therapeutic target.

AREAS COVERED: This review explores shared and distinct pathways linking obesity and cancer cachexia. Key systems discussed include the gut-brain axis as well as skeletal muscle and adipose tissue metabolism. We discuss how the gut microbiota influences these processes through (diet-derived) gut microbial metabolites that affect specific signaling pathways. The review evaluates the efficacy and limitations of current anti-obesity and cachexia therapies and summarizes clinical and preclinical interventions targeting the gut microbiome, including pre-, pro-, postbiotics and fecal microbiota transplantation.

EXPERT OPINION: The gut microbiota holds potential as a therapeutic target in metabolic diseases, offering opportunities for precision medicine based on microbial and metabolic profiles. While early microbiota-based therapies show promise, further investigation into mechanistic pathways and novel engineered microbiota is essential to develop effective treatments for obesity and cachexia.},
}

@article {pmid41864264,
year = {2026},
author = {Merrick, B and Mullish, BH and Goldenberg, SD and Khanna, S and Ahuja, V and Hvas, CL and Makharia, GK and Williams, HRT},
title = {A global evaluation of the use of faecal microbiota transplant (FMT).},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108574},
doi = {10.1016/j.ijid.2026.108574},
pmid = {41864264},
issn = {1878-3511},
abstract = {BACKGROUND: Faecal microbiota transplant (FMT) is an effective therapy for recurrent Clostridioides difficile infection (CDI); its use is increasingly being investigated for other indications. Although regional surveys and national registries have provided insight into local practices, a comprehensive global overview of FMT access, implementation and governance is lacking.

METHODS: A survey regarding key aspects related to FMT use was disseminated electronically to members of the World Gastroenterology Organisation, European FMT Network, and International Society of Infectious Diseases. Responses were analysed both descriptively and using appropriate statistical methods.

FINDINGS: 80 responses were obtained from 55 countries. FMT was available in significantly more Tier 1/2, than Tier 3/4, nations (24/28 vs 8/27; p<0.001). In countries lacking access to FMT reasons included: lack of expertise/infrastructure; financial constraints; regulatory uncertainty; and perceived lack of clinical need. Most countries using FMT employed both upper and lower gastrointestinal administration routes; 18/32 (56%) used capsulised FMT. Almost all countries with access to FMT used it to treat CDI, albeit with different thresholds for the number of CDI episodes prior to use. There were many non-CDI indications for FMT in current use. Payment for stool donation was reported by 10 countries.

INTERPRETATION: This is the first global overview of FMT availability and governance, highlighting substantial international inequities and considerable heterogeneity in regulation, clinical use, donor screening, and cost. Standardisation of practice and targeted support for lower income countries is needed to ensure equitable access and to promote safe, high-quality delivery as FMT and microbiome-based therapeutics continue to evolve.},
}

@article {pmid41864269,
year = {2026},
author = {Melchiorri, S and Besutti, VM and Castagliuolo, I},
title = {Blastocystis spp. in Fecal Microbiota Transplantation: Evidence, Policy, and the Screening Paradox.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108548},
doi = {10.1016/j.ijid.2026.108548},
pmid = {41864269},
issn = {1878-3511},
abstract = {OBJECTIVES: Fecal microbiota transplantation (FMT) is an established treatment for recurrent Clostridioides difficile infection (rCDI). However, the detection of Blastocystis spp. in potential donors remains controversial and often leads to donor exclusion, despite uncertain pathogenicity. This review aims to critically evaluate the available evidence on Blastocystis spp. transmission through FMT, its clinical impact, and the implications of current donor screening strategies.

METHODS: A narrative review of the literature was performed using PubMed, Embase, and Web of Science. Studies reporting Blastocystis spp. detection in FMT donors or recipients, transmission events, clinical outcomes, diagnostic methods, and microbiome associations were included and analyzed.

RESULTS: Across published reports, 34 FMT recipients were exposed to Blastocystis spp.-positive donor material. Transmission was limited to common subtypes (ST1-ST3), was transient, and was not associated with adverse clinical outcomes or reduced efficacy of FMT for rCDI. No cases of symptomatic infection were reported. Frozen stool preparations appeared to abolish parasite viability. Molecular screening methods markedly increased detection rates compared with microscopy, frequently identifying low-burden colonization of uncertain clinical relevance. Available data suggest that Blastocystis spp. carriage may coexist with a healthy microbiome and does not negatively impact FMT outcomes.

CONCLUSIONS: Current evidence indicates that Blastocystis spp. transmission through FMT in immunocompetent adults is clinically benign. Routine donor exclusion based solely on Blastocystis spp. detection may therefore be overly restrictive. A risk-based approach incorporating parasite burden, subtype, host factors, and processing methods may better balance patient safety with donor availability, supporting more sustainable FMT programs.},
}

@article {pmid41864480,
year = {2026},
author = {Rauf, M and Naveed, A and Asghar, MU},
title = {Post-acute sequelae of COVID-19: A disorder of impaired innate immune resolution - A narrative review.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {285},
number = {},
pages = {110701},
doi = {10.1016/j.clim.2026.110701},
pmid = {41864480},
issn = {1521-7035},
abstract = {Post-acute sequelae of COVID-19 (PASC) affect millions of people worldwide and are increasingly recognized as a disorder of failed innate immune resolution rather than a persistent viral infection. Emerging evidence shows that residual SARS-CoV-2 antigens, host-derived alarmins, reactivated latent viruses, and mucosal microbiome-derived products from oral-nasopharyngeal and gut reservoirs sustain the chronic activation of pattern-recognition receptors, inflammasomes, and complement pathways. In parallel, deficits in specialized pro-resolving mediators, impaired efferocytosis, and persistent tissue injury prevent physiological termination of inflammation. These unresolved cues drive long-lasting epigenetic and metabolic reprogramming of hematopoietic stem cells and myeloid lineages, creating maladaptive trained immunity states characterized by hyper-responsiveness or exhaustion of these cells. Thromboinflammatory processes, including aberrant NETosis and sustained interface signalingling, further reinforce self-perpetuating inflammatory circuits. Together, these pathways give rise to reproducible molecular endotypes, including thromboinflammatory, interferon-driven, and neuroinflammatory phenotypes, which explain clinical heterogeneity. Framing PASC as a disorder of impaired immune resolution within a mucosal microbial viral context provides a unifying mechanistic scaffold for biomarker identification and host-directed therapies. This review proposes that restoring active resolution programs, rebalancing metabolic-epigenetic networks, and dismantling pathogenic innate feedback loops are promising strategies for reversing the chronic immune imprint of PASC.},
}

@article {pmid41864590,
year = {2026},
author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , },
title = {Response to the "Letter to the Editor: ''Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism''.".},
journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jrn.2026.02.010},
pmid = {41864590},
issn = {1532-8503},
}

@article {pmid41864593,
year = {2026},
author = {Xu, K and Qian, Y and Zhao, C},
title = {Letter to the Editor Regarding "Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism".},
journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jrn.2026.01.010},
pmid = {41864593},
issn = {1532-8503},
}

@article {pmid41857652,
year = {2026},
author = {Russell, A and Gore, R and Wood, JL and Robert, KA},
title = {Characterising the gut microbiome of six Australian marsupials reveals captivity constrains microbiome.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00545-w},
pmid = {41857652},
issn = {2524-4671},
abstract = {BACKGROUND: The gut microbiome is an ecosystem of microbes that live within the host's digestive tract and are a vital component of host health. An increasing number of studies are investigating microbiome differences in wild and captive-managed populations to assist in species conservation and improve captive welfare. The gut microbiota of Australian marsupials has not been extensively studied but has long been recognised as having an important functional role in the digestive physiology and health of those in care. We used 16S rRNA gene sequencing to characterise and compare the faecal bacterial communities of six species of Australian marsupials from captive or wild origins over a large temporal and spatial scale.

RESULTS: We found the microbiome of captive marsupials had reduced microbial richness and diversity in two species, the brushtail possum and the Eastern grey kangaroo. Captivity was associated with gut microbiome compositional differences for half of the species tested. These compositional changes were accompanied by less pronounced seasonal variability in captivity.

CONCLUSIONS: This study provides valuable baseline data and demonstrates that captivity significantly alters the gut microbiota, suppressing its natural seasonal variability. These findings enhance our understanding of the gut microbiome in Australian marsupials. Future research should focus on determining the functional importance of these microbial communities and develop strategies to address any microbiome deficiencies in managed populations. Such efforts could ultimately improve the success of captive rearing and reintroduction programs.},
}

@article {pmid41857729,
year = {2026},
author = {Li, P and Guo, S and Zhang, Y and Hu, H and Cheng, T and Xu, B and Zeng, K and Huang, T and Dong, Z and BenHuo, and Lin, J and Wen, H and Sun, B},
title = {Multimodal deep learning for inflammatory bowel disease: a new frontier in cellular and molecular biomarker discovery to clinical translation.},
journal = {Journal of biological engineering},
volume = {20},
number = {1},
pages = {},
pmid = {41857729},
issn = {1754-1611},
abstract = {Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is a chronic, relapsing condition with heterogeneous clinical phenotypes and variable therapeutic outcomes. Deep learning (DL), combined with high-throughput sequencing and multi-omics, has advanced precision management by enabling integration of genomic, transcriptomic, microbiome, metabolomic, imaging, and clinical data. DL applications include molecular biomarker discovery, automated endoscopic and histopathological image analysis, patient stratification, disease monitoring, and prediction of therapeutic response, such as anti-TNF-α efficacy. Convolutional neural networks (CNNs) demonstrate exceptional performance in image interpretation and automated scoring. Challenges for clinical translation include limited multi-center datasets, inconsistent annotations, low interpretability, and privacy concerns. Addressing these issues through interpretable, efficient, and privacy-preserving DL frameworks, along with temporally resolved cross-institutional datasets, will facilitate real-time monitoring and personalized care, reshaping IBD diagnosis, treatment, and long-term management.},
}

@article {pmid41857737,
year = {2026},
author = {Lei, C and Wu, J and Fu, Z and Jin, R and Hu, B and Xu, K and Cheng, C and Shi, T and Gong, D and Huang, C and Qin, J},
title = {The microbiome of host saliva, gastric fluid, and gastric mucosa as accurate diagnostic tools for gastric cancer detection.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07953-1},
pmid = {41857737},
issn = {1479-5876},
}

@article {pmid41857777,
year = {2026},
author = {Xu, T and Qiu, X and Hang, Q and Qi, X and Mei, H and Guo, J and Zheng, Y and Ji, M and Xu, Q and Wu, B},
title = {Oral microbiome and Frailty: Insights from NHANES 2009-2012 and Mendelian Randomization Analysis.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glag079},
pmid = {41857777},
issn = {1758-535X},
abstract = {BACKGROUND: Frailty is associated with increased risks of disability, hospitalization, and mortality. Emerging evidence suggests that the oral microbiome may influence frailty development, but population-based evidence is limited and causal relationships remain unclear. This study explored the link between oral bacteria and frailty, using genetic analysis to investigate causality.

METHODS: We analyzed data from 2,696 adults aged ≥50 years in NHANES 2009-2012. Oral microbiome diversity was assessed using 16S rRNA gene sequencing. Frailty was measured using a 36-item Frailty Index. Survey-weighted linear regression and restricted cubic spline models examined associations between four α-diversity indices and frailty. β-diversity was quantified using Bray-Curtis dissimilarities and compared by frailty status using PERMANOVA. Bidirectional two-sample Mendelian randomization (MR) using GWAS data assessed causal relationships between taxa and frailty.

RESULTS: Lower α-diversity across all four indices were associated with higher frailty scores (P < 0.050). β-diversity differed by frailty (P = 0.001). MR analyses indicated that in saliva, Campylobacter_A, Saccharimonadaceae, and TM7x were protective, whereas Gemella was associated with increased frailty risk. In tongue samples, Saccharimonadaceae was a risk factor, while Fusobacterium, TM7x, and Solobacterium showed protective effects.

CONCLUSIONS: Oral microbiome diversity is inversely associated with frailty in U.S. adults, and MR analyses identify specific oral taxa potentially involved in frailty development. These findings provide population-level evidence and genetic support for the oral microbiome as a potential modifiable target to promote healthy aging.},
}

@article {pmid41857807,
year = {2026},
author = {Heidari, H and Vincent, M and Lawrence, DA},
title = {Integrating exposomics and multi-omics with dysbiosis biomarkers for clinical and environmental connections implicated in neuropathology. Cause and cure cluses.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfag034},
pmid = {41857807},
issn = {1096-0929},
abstract = {Multi-omic investigations into environmental effects on health and disease are aided by inclusion of microbial microbiomes with assessment of mirobes producing metabolites that differentially modulate host organ functions. The gut microbiome is key because many environmental toxicants enter the body orally and may disrupt gut microbes that help digest food, as well as the microbiome-gut-brain axis, which produces regulatory metabolites with systemic effects. Environmental stressors may differentially alter brain development and function, even among identical twins, in that over time, there may be divergence due to epigenetic effects from the environment, including microbes within the microbiome. The diversity of microbiomes is presented as playing a key role in the influence of organs on each other, health, and the development of disorders. The gut microbes and their metabolites may cause mitochondria to produce less ATP and more reactive oxygen species (ROS). The metabolites produced by microbes during the digestion of foods can nourish or harm a person's cellular and molecular functions and vary depending on each person's exposome. The detrimental effects of environmental stressors are discussed, focusing on how altered levels of neuropeptides, neurotransmitters, and the inflammatory/anti-inflammatory balance affect health and disorders. During ATP production, dysfunctional mitochondria may produce more ROS, which can lead to inflammation and oxidative stress, causing cell damage and disrupting products needed for neuronal development, connections, and functions. The balance between inflammatory/anti-inflammatory biomarkers and metabolites and between oxidants/antioxidants is discussed in relation to some clinical connections; for example, the proportions of CD4 and CD8 T cells in HIV patients and the ROS-to-glutathione ratio in inflammatory bowel disease and septic patients. These imbalances are reviewed regarding brain development and functions leading to anxiety, depression, and dementia. The integration of multi-omics, dysbiosis, and mitochondrial dysfunction with a person's clinical evaluation is discussed to inform the formulation of prevention measures and therapeutic interventions regarding environmental effects on the microbiome-gut-brain axis and physical and mental health.},
}

@article {pmid41857857,
year = {2026},
author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G},
title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e115290},
doi = {10.1136/bmjopen-2025-115290},
pmid = {41857857},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; },
abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.

METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

Humans
*Gastrointestinal Microbiome/immunology
Adult
Young Adult
*Brassica
Quality of Life
*Fermented Foods
Adolescent
Randomized Controlled Trials as Topic
*Conjunctivitis, Allergic/immunology/diet therapy
*Rhinitis, Allergic/immunology/diet therapy
Female
Male
Biomarkers

@article {pmid41858059,
year = {2026},
author = {Zeng, J and Wang, R and Gu, Z and Li, J and Huang, M and Shen, Q and Wang, M and Guo, S},
title = {Nitrate-constructed fungal communities and rhizosphere metabolites confer resistance to Fusarium wilt in cucumber.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71110},
pmid = {41858059},
issn = {1469-8137},
support = {32402674//National Natural Science Foundation of China/ ; 42577134//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Provincial Special Project for Carbon Peak Carbon Neutrality Science and Technology Innovation/ ; },
abstract = {Nitrogen fertilization regimes are a critical determinant of soilborne disease outcomes in intensive agriculture, yet the mechanisms through which different nitrogen forms exert their influence remain poorly understood. Our study investigates how nitrate and ammonium nutrition differentially modulate the severity of Fusarium wilt in cucumber by altering the rhizosphere microbiome and metabolome. We utilized a split-root system to study the effects of nitrate and ammonium on disease progression, integrating ITS amplicon sequencing and gas chromatography mass spectrometry metabolomics. Nitrate nutrition promoted the recruitment of beneficial fungal taxa and the accumulation of antifungal metabolites, which collectively suppressed pathogen growth and enhanced plant health. By contrast, ammonium supply created a rhizosphere environment conducive to pathogen growth by selectively enriching pathogenic fungi and driving metabolic reprogramming, which ultimately heightened plant susceptibility. Split-root experiments revealed that local nitrate application stimulated resveratrol accumulation and enriched Funneliformis in the rhizosphere. In vitro inhibition assays showed that resveratrol directly suppressed Fusarium mycelial growth, and pot experiments demonstrated that exogenous resveratrol application and inoculation with Funneliformis both enhanced plant performance. Our findings reveal how nitrogen forms regulate plant-microbe-metabolite interactions to determine soilborne disease outcomes, providing a foundation for nutrition-based management strategies that can reduce fungicide reliance through natural suppression.},
}

@article {pmid41858079,
year = {2026},
author = {Mbong Ngwese, M and Loum, S and Berg, L and Tyakht, AV and Youngblut, ND and Adegnika, AA and Kremsner, P and Ley, RE and Marsh, JW},
title = {Genomic and phenotypic characterization of a human gut Methanobrevibacter intestini strain G0370_i3 isolated in Gabon.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/17460913.2026.2645510},
pmid = {41858079},
issn = {1746-0921},
abstract = {AIMS: Methanogens are methane-producing archaea that are present in the human gut. Yet, their adaptation to diverse human lifestyles remains poorly understood. Here, we report the isolation of Methanobrevibacter intestini G0370_i3 from the stool of a healthy adult from Southern Gabon, Africa, where inhabitants maintain traditional subsistence lifestyles with diets distinct from industrialized populations.

MATERIALS AND METHODS: M. intestini was enriched from human stool, phenotypically characterized, and sequenced.

RESULTS: G0370_i3 growth relied on the presence of H2 and CO2 and could also grow on formate, in contrast to reports for the type strain. The genome encoded pathways for amino acid biosynthesis, cofactor metabolism, and secondary metabolite production. We identified 23 mobile genetic elements and five defense systems, indicating horizontal gene transfer and antiviral defense. No prophage regions were detected.The genome also encoded uridine diphosphate (UDP)-sugar metabolism pathways, indicating capacity for energy storage and cell wall adaptability. Genes encoding adhesin-like proteins suggest capabilities for host interaction. Phenotypically, G0370_i3 is a coccobacillus, grows optimally at 37°C, and tolerates antibiotics, salt, and oxygen stress.

CONCLUSIONS: These findings highlight the stress resilience and selective metabolic capabilities of M. intestini and underscore the importance of representing African populations in microbiome research.},
}

@article {pmid41858134,
year = {2026},
author = {Odendaal, J and Fishwick, K and Correia, GDS and Lee, YS and Makwana, K and Black, N and Southcombe, J and Thornton, J and Larsen, K and Hussain, Q and Hawkes, A and Kandiyil, A and Muter, J and Brighton, PJ and Vrljicak, P and Lucas, E and Granne, I and Bouliotis, G and Bennett, PR and Brosens, J and MacIntyre, DA and Quenby, S},
title = {CD138 expression in the endometrium associates with endometrial timing and inflammatory status but not microbiota composition.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deag032},
pmid = {41858134},
issn = {1460-2350},
support = {//Efficacy and Mechanism Evaluation (EME) Programme/ ; 17/60/22//National Institute for Health and Care Research and Medical Research Council partnership/ ; //Tommy's National Centre for Miscarriage Research, and the Imperial National Institute for Health and Care Research Biomedical Research Centre Pregnancy and Prematurity/ ; //Genesis Research Trust/ ; },
abstract = {STUDY QUESTION: What is the relationship between constitutive CD138 expression in the endometrium and the reproductive tract microbiota composition?

SUMMARY ANSWER: The presence of CD138+ cells in endometrial stroma is cycle-dependent and associated with impaired luteal phase endometrial timing but not altered vaginal or endometrial microbial composition.

WHAT IS KNOWN ALREADY: CD138-diagnosed chronic endometritis (CE) is associated with adverse reproductive outcomes including recurrent pregnancy loss (RPL) in uncontrolled studies. However, CD138 is constitutively expressed in the endometrium, potentially confounding the reported associations between CE, adverse endometrial function, and early pregnancy loss.

STUDY DESIGN, SIZE, DURATION: Translational cohort study of a subset of 103 samples derived from 737 women embedded within the CERM trial, a double-blinded, randomized interventional trial evaluating the impact of pre-pregnancy antibiotic treatment for CE in RPL patients.

Women aged ≥18 to <42 years, with a history of two or more first-trimester consecutive miscarriages were recruited from specialist RPL clinics. Endometrial biopsies, vaginal, ectocervical, and endometrial swabs were obtained 10 ± 4 days following a positive home ovulation test. Additional samples, including proliferative endometrium, were obtained from the Tommy's National Reproductive Health Biobank. Endometrial biopsies were processed for CD138 expression analysis and immunohistochemistry (IHC), histological dating based on Noyes' criteria, and molecular timing analysis. Metataxonomic profiling of microbiota was performed by sequencing of bacterial 16S ribosomal RNA genes alongside cytokine analysis.

IHC revealed three patterns of CD138 immunoreactivity: predominantly membranous punctate staining, predominantly diffuse staining, and a mixed pattern. CD138 is constitutively expressed on the basolateral membrane of glandular epithelial cells and a subset of non-immune stromal cells. Stromal expression was very high (>200 CD138-positive stromal cells/10 mm2) in 26 out of 27 proliferative endometrial samples. While CD138 immunoreactivity in the stroma declines markedly following ovulation (Mann-Whitney U-test; P < 0.005), gene expression analysis demonstrated a reduction in SDC1 expression encoding CD138/syndecan-1, across the menstrual cycle. When compared to CD138-negative samples, conspicuous diffuse staining in the stromal compartment was associated with significantly earlier endometrial histological dating (P < 0.01) and lower molecular timing ratios (P < 0.01). Poor correlation between CD138 and immunoreactivity was demonstrated. Sequencing of paired vaginal and ectocervical swabs and endometrial Tao brush samples collected from 114 patients demonstrated tightly interconnected microbial composition throughout the reproductive tract. No significant difference in vaginal, ectocervical, or endometrial community state type with CD138 expression was demonstrated. Analysis of supernatants of vaginal and ectocervical swabs and Tao Brush revealed an inverse correlation between the severity of stromal CD138 immunoreactivity in endometrial stroma and secreted levels of IL-10, TNF-α, and VEGF (q < 0.05).

LARGE SCALE DATA: Microbial and Metataxonomic raw data are available in the European Nucleotide Archive (Projects PRJEB83331 and PRJEB83332).

This study relied on patient-reported ovulation-based timing. This was, however, associated with the provision of validated ovulation tests. In addition, the study is limited by lack of collection of data on the underlying fertility-related co-morbidities due to exclusion of known contributory co-morbidities at the point of recruitment.

This study challenges the purported relationship between CD138+ CE and the pathophysiology of CE-associated RPL. The findings indicate endometrial CD138 levels are non-immune and non-bacterial driven and are associated with endometrial immaturity. CD138-based CE testing and treatment should not be performed outside of a research context.

Funding was provided by the Efficacy and Mechanism Evaluation (EME) Programme a National Institute for Health and Care Research and Medical Research Council partnership (17/60/22). Further funding was from Tommy's National Centre for Miscarriage Research, and the Imperial National Institute for Health and Care Research Biomedical Research Centre Pregnancy and Prematurity Theme. G.D.S.C. is supported by the Genesis Research Trust. All authors report no direct conflict of interest.

TRIAL REGISTRATION NUMBER: ISRCTN23947730.},
}

@article {pmid41858163,
year = {2026},
author = {Li, N and Wang, J and Qiu, G and Han, Z and Zhang, C and Yu, H},
title = {Synergistic Utilization of KOH-Modified Biochar and Nitrogen-Fixing Bacteria for Recovering Tetracycline-Contaminated Agricultural Soil and Promoting Crop Growth.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c16832},
pmid = {41858163},
issn = {1520-5118},
abstract = {Tetracycline (TC) contamination in agricultural soils poses a serious threat to crop production and ecosystem health. However, sustainable remediation strategies capable of both efficiently degrading antibiotics and simultaneously restoring impaired nitrogen cycling functions remain lacking. This work developed a synergistic system combining KOH-modified biochar (KOB) with two TC-resistant nitrogen-fixing bacteria (TCNFB): Chryseobacterium lathyri Cbl and C. elymi Cbe. Cbl showed superior TC degradation (47.3%) and nitrogenase activity (0.08 mmol of C2H4 g[-1] min[-1]). In pot experiments, the KOB-Cbl composite increased soybean biomass by 45.21% through rhizosphere microbiome restructuring, enhanced community stability, upregulation of nifD/H/K genes, suppressed denitrification, and elevated phytohormone levels. KOB's high surface area and pyridinic nitrogen enriched Chryseobacterium, enabling colocalized TC degradation and nitrogen fixation. This work reveals an agricultural soil remediation strategy based on synergistic interactions between functional materials and microorganisms, providing an effective pathway for concurrently addressing antibiotic pollution and enhancing crop growth.},
}

@article {pmid41858365,
year = {2026},
author = {Lommer, C and Schroeder, L and Amato, C and Dhakal, K and Kotian, C and Quiroga, D and Paskett, ED and Fu, MR and McAlearney, AS and Collins, S and King, TA and McLaughlin, SA and Myers, SP},
title = {Pharmacotherapy agents in prevention and treatment of breast cancer-related lymphedema: a systematic scoping review.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1751628},
pmid = {41858365},
issn = {2234-943X},
abstract = {BACKGROUND: Breast cancer-related lymphedema (BCRL) is a common and life-long adverse event affecting ~20% of breast cancer survivors. As existing non-pharmacologic management is burdensome, expensive, and variably effective, this systematic scoping review aims to identify pharmacologic and herbal agents for prevention and treatment for BCRL.

METHODS: PubMED, Embase, Web of Science Core collection, and the Cumulative Index to Nursing and Allied Health Literature were searched for studies published in English between 1993 and 2025 that investigated the preventative or therapeutic effect of pharmacologic or herbal agents on BCRL among adult stage I-III breast cancer patients. Studies describing interventions with systemically absorbed anti-inflammatories, anti-thrombotics, anti-coagulants, and blood product components were included. Systematic reviews, protocols for ongoing clinical trials, preclinical and non-human studies, editorials, and studies not exclusive to BCRL were excluded. Three reviewers screened and extracted data between June and August 2025. The primary outcomes of interest were reduction in BCRL incidence or severity.

RESULTS: Of the 217 articles screened, 37 were included in the final review. After full text review, 13 were excluded for repetitive data, non-English language, or irrelevant outcomes. The 24 studies included in the analysis investigated anti-diabetic, herbal, anti-inflammatory, anti-hypertensive, immunomodulatory, and microbiome modifying agents, and venoactive flavinoid derivates. Three studies explored the role of pharmacologic/herbal agents in BCRL prevention. While thiazolidinediones, anti-hypertensives, and non-steroidal anti-inflammatory drugs (NSAIDs) had no effect on BCRL incidence, glucagon-like peptide-1 receptor agonists (GLP-1 RA) were associated with BCRL prevention. In the 21 studies that assessed the effect of pharmacologic/herbal agents in BCRL treatment, NSAIDs/steroids, anti-hypertensives, microbiome/synbiotic supplements, and doxycycline showed no benefit and data for flavonoid-derived venoactive agents and herbal products were inconsistent. Immune-modulating therapies were associated with improved BCRL signs/symptoms in three studies.

CONCLUSION: This systematic scoping review found limited evidence suggesting that GLP-1 RAs may reduce the risk of BCRL and that immunomodulatory agents may improve signs/symptoms of BCRL. Rigorous prospective trials using standardized limb volume/edema, quality-of-life (QoL), and symptom measures and longer follow-up are needed to inform clinical practice aimed at preventing and treating BCRL.

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD420251055134.},
}

@article {pmid41858617,
year = {2026},
author = {Chen, N and Zhao, S and Yin, Z and Khan, S and Guo, J and Zhao, M},
title = {The potential of Protaetia brevitarsis as a functional food that enhances immune function and gut microbiota in mice.},
journal = {iScience},
volume = {29},
number = {4},
pages = {114939},
pmid = {41858617},
issn = {2589-0042},
abstract = {The issues of global hunger, malnutrition, and the increasing prevalence of diseases present considerable challenges to public health, emphasizing the urgent need for functional foods possessing immune-enhancing attributes. This study investigated the effects of Protaetia brevitarsis (Lewis) (PB), an edible insect, on immune modulation and gut microbiota composition in ICR mice. 160 male mice in four groups were treated with diets with different PB additions (0, 5%, 10%, and 20%). The results demonstrated that PB improved the cellular immune response of T cells (p ≤ 0.05), phagocytosis activity of macrophages (p ≤ 0.05), and humoral immunity in terms of elevated levels of serum hemolysin, IgG, and TNF-α (p ≤ 0.05), compared to the CK (100% basal diet) group. The gut microbial dynamics among treatments showed an increased microbiota diversity and abundance of beneficial bacteria, including Muribaculaceae and Muribaculum at genus level and Bacteroidota at phylum level with the increased PB (p ≤ 0.05). In conclusion, PB can enhance the immune function and gut microbiota, highlighting its potential as a functional food.},
}

@article {pmid41858644,
year = {2026},
author = {Khorshidi Asl, Z and Jafari, F and Rezazadeh, F and Kamyabi, H},
title = {Burning Mouth Syndrome and the Oral Microbiome: Unveiling Potential Links.},
journal = {Biomedicine hub},
volume = {11},
number = {1},
pages = {23-37},
pmid = {41858644},
issn = {2296-6870},
abstract = {BACKGROUND: Burning mouth syndrome (BMS) is a chronic neuropathic orofacial pain condition that remains challenging to manage due to its unclear etiology and limited treatment options. While multiple systemic factors have been proposed, emerging evidence suggests that oral microbial dysbiosis may contribute to neuroinflammatory and pain-related mechanisms. However, the role of the oral microbiota in BMS remains insufficiently understood.

SUMMARY: This review examines current evidence regarding the potential association between oral microbiota and BMS, with emphasis on hormonal regulation, immune function, and micronutrient balance. A comprehensive literature search identified studies reporting systemic alterations in patients with BMS. Available evidence suggests that BMS may be associated with changes in sex hormones, thyroid hormones, and neuroendocrine stress responses, potentially influenced by oral microbial composition. Alterations in immune mediators, particularly interleukin-6, and micronutrient imbalances such as vitamin B12 deficiency have also been reported in a subset of patients. These interconnected pathways may contribute to peripheral and central neuropathic pain mechanisms underlying BMS symptoms.

KEY MESSAGES: (i) Oral microbiota may interact with hormonal, immune, and micronutrient pathways relevant to BMS. (ii) The relationship between oral dysbiosis and BMS appears complex and potentially bidirectional. (iii) Further clinical and mechanistic studies are needed to clarify these interactions and inform targeted therapies.},
}

@article {pmid41858664,
year = {2026},
author = {Han, C and Luo, W and Peng, G and Tan, D and Liu, R and Cao, Y},
title = {Metarhizium anisopliae reshapes the citrus rhizosphere microbiome to enhance fruit quality via nutrient cycling.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1784405},
pmid = {41858664},
issn = {1664-462X},
abstract = {The rhizosphere microbiome is a critical regulator of nutrient acquisition and plant growth in citrus. Here, we evaluated the effects of the entomopathogenic fungus Metarhizium anisopliae CQMa421 on soil nutrient status, rhizosphere bacterial community structure, and fruit quality in citrus using soil physicochemical assays, plant physiological measurements, and 16S rRNA amplicon high-throughput sequencing. CQMa421 application markedly reshaped soil properties, increasing available potassium by 128.50% and organic matter by 75.05%. In addition, total nitrogen, alkali-hydrolyzable nitrogen, and available phosphorus increased by 112.68%, 155.30%, 305.74% respectively, while soil pH decreased by 0.4 units. CQMa421 treatment significantly increased leaf total nitrogen content and elevated fruit vitamin C by 12.00%. Microbial community profiling showed an enrichment of putatively beneficial taxa, including Proteobacteria and Firmicutes, in treated soils. Functional prediction suggested enhanced nutrient cycling potential, with increased representation of genes associated with carbohydrate metabolism and inorganic ion transport. Collectively, these results indicate that M. anisopliae CQMa421 acts as a plant growth-promoting fungus by enhancing soil nutrient availability and restructuring the rhizosphere microbiome, thereby improving the overall nutrient status of the soil and enhancing citrus fruit quality.},
}

@article {pmid41858670,
year = {2026},
author = {Mattei, V and Sergeant, K and Saracchi, M and Bulgari, D and Kunova, A and Pizzatti, C and Cortesi, P and Renaut, J and Pasquali, M},
title = {Differential modulation of tomato root exudates by Streptomyces strains underlies contrasting control of Fusarium oxysporum f. sp. lycopersici.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1759226},
pmid = {41858670},
issn = {1664-462X},
abstract = {INTRODUCTION: Rhizosphere microbiome is affected and modulated by the complex mixtures of bioactive molecules that are released by plant roots. In this work, two promising plant growth-promoting strains of Streptomyces spp. (DEF17 and DEF19) were evaluated for their capacity to modulate tomato roots and exudates metabolic profile and influence Fusarium oxysporum f. sp. lycopersici (Fol).

METHODS: Dual culture assays, chemotropism assays, and in planta pathogenesis assays were performed to evaluate the capability of the strains to inhibit Fol growth, repel Fol conidia, and induce plant defense mechanisms both in vitro and in vivo. Finally, untargeted LC-MS/MS analysis was performed to understand which metabolites are produced and released by tomato roots after plant-bacteria interaction occurs.

RESULTS: This study indicates that herbal formulas that could regulate the composition and proportion of gut microbiota have a positive effect in three stages (perioperative, postoperative, and advanced) of GC and CRC. They could promote the recovery of postoperative gastrointestinal function, increase tumor response, improve performance status, and reduce the incidence of adverse events. Herbal formulas exerted anti-cancer efficacy through multiple mechanisms and pathways; among them, the regulation of gut microbiota has not been paid enough attention. To further support the conclusion and better understand the role of gut microbiota in the treatment of GC and CRC, more rigorously designed, large-scale, and multicenter RCTs that focus on herbal formulas and gut microbiota are needed in the future.

DISCUSSION: Together, these results indicated that tomato plant protection against Fol is consistent with DEF17 through exudate-mediated modulation, highlighting a gap between in vitro antagonism and in planta efficacy.},
}

@article {pmid41858674,
year = {2026},
author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z},
title = {Microbiome and plant relationship: a symbiosis against phytopathogens.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1722279},
pmid = {41858674},
issn = {1664-462X},
abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.},
}

@article {pmid41858792,
year = {2026},
author = {Raber, J and Sharpton, TJ},
title = {Diet, gut microbiome, and cognition in neurodegeneration: a review and methodological framework.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1771904},
pmid = {41858792},
issn = {1663-4365},
abstract = {The gut microbiome influences brain function through the gut-brain axis via synthesis of neurotransmitters, production of metabolites affecting epithelial barrier integrity and immune modulation and signaling through the vagus nerve. In humans, microbiome diversity reflects healthy aging and predicts survival, while dysbiosis is increasingly implicated in neurodegenerative conditions including Alzheimer's disease, Parkinson's disease, multiple sclerosis, and ALS. Fecal transplant studies in germ-free mice demonstrate that microbiome alterations are sufficient to induce cognitive and neuropathological phenotypes, supporting causality in preclinical models. Genetic risk factors and environmental exposures affect both neurodegeneration risk and microbiome composition. In this review, we synthesize evidence from human cohorts and preclinical models on the gut-brain axis in cognitive health and disease. We then present a methodological framework for diet-microbiome-cognition research, addressing causal inference through mediation analysis, supervised approaches for deriving diet scores, validation strategies, and individual heterogeneity. This framework can guide development of microbiome-targeted dietary interventions to improve cognitive outcomes.},
}

@article {pmid41858899,
year = {2026},
author = {Kumar, M and Singh, S and Ojha, R and Kriti, M and Park, G and Verma, V and Pal, N and Sharma, P and Shubham, S and Pandey, MK and Parasannanavar, DJ and Sarma, DK and Tiwari, RR and Nagpal, R},
title = {Gut microbiome disparities reflect type 2 diabetes progression and medication status.},
journal = {iScience},
volume = {29},
number = {3},
pages = {115156},
pmid = {41858899},
issn = {2589-0042},
abstract = {Type 2 diabetes mellitus (T2D) prevalence is rapidly increasing in India, yet microbiome signatures linked to disease progression and oral antidiabetic therapy remain underexplored. We performed full-length 16S rRNA sequencing of fecal samples from prediabetics (PDs), untreated newly diagnosed T2D (UKT2D), and clinically diagnosed T2D patients (KT2D), alongside biochemical, anthropometric, and medication data. Despite comparable glycemic control and insulin resistance between UKT2D and KT2D groups, gut microbial diversity was significantly reduced in KT2D, coinciding with antidiabetic drug use, primarily metformin. Lactobacillus abundance increased with disease progression, while Clostridium_sensu_stricto_1 was associated with glucose homeostasis and insulin sensitivity. β diversity differed only between controls and PD, with no other pairwise differences. Collectively, these results indicate that T2D progression and oral antidiabetic medications remodel the gut microbiome in this south Asian cohort and highlight the need to reassess antidiabetic treatment efficacy using larger longitudinal studies.},
}

@article {pmid41856961,
year = {2026},
author = {Narimatsu, Y and Pleguezuelos-Manzano, C and Hornikx, D and Goerdeler, F and Jaroentomeechai, T and Flores, K and Narimatsu, S and Boot, C and Hansen, L and Durbesson, F and Vincentelli, R and Comstock, L and Clevers, H and Taleb, V and Corzana, F and Henrissat, B and Clausen, H and Hurtado-Guerrero, R and Büll, C},
title = {Discovery of a secreted Bacteroides fragilis mucinase that cleaves mucins with bis-T O-glycans through a carbohydrate binding module-dependent mechanism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644983},
pmid = {41856961},
issn = {1949-0984},
mesh = {*Bacteroides fragilis/enzymology/genetics/metabolism ; *Mucins/metabolism/chemistry ; *Polysaccharides/metabolism/chemistry ; Humans ; *Bacterial Proteins/metabolism/genetics/chemistry ; Substrate Specificity ; Glycoside Hydrolases/metabolism/genetics ; Gastrointestinal Microbiome ; Carbohydrate Binding Modules ; },
abstract = {Degradation of mucins at the host-microbial mucus interphase involves glycosidases that release monosaccharides from O-glycans and mucinases that cleave the mucin protein backbone. Mucinases recognize and cleave peptide bonds at specific sequence motifs with varying O-glycan structures required and/or permissible. Mucinases that digest mucins with intact O-glycans can potentially destroy the protective mucus, while mucinases that only digest mucins with partially degraded O-glycans may serve at a later stage of nutrient sourcing from mucins. Here, we discovered nine CBM-bearing M60-like mucinases across gut commensals and opportunists, including a conserved Bacteroides fragilis mucinase denoted HC11. We also investigated the previously described Bacteroides thetaiotaomicron mucinase BT4244, which together delineates two functional classes with distinct preferences: BT4244 for bis-Tn (GalNAcα1-O-Ser/Thr) and HC11 for bis-T (Galβ1-3GalNAcα1-O-Ser/Thr) O-glycans. Both mucinases harbor carbohydrate-binding modules (CBM32) that bind their cognate O-glycan motifs and are required - together with the catalytic domains - for efficient cleavage of extended mucin domains, which is consistent with cooperative engagement, but are not required for the cleavage of short glycopeptides. We show B. fragilis strains secrete HC11 and degrade mucins only after the removal of sialic acids. Together, these findings expand the mucinase repertoire by nine enzymes spanning commensals and opportunists, demonstrate that CBM32 domains are essential for efficient cleavage of extended mucin substrates likely by promoting multivalent engagement and substrate positioning, and nominateidentify CBM-catalytic cooperation as a mechanism and intervention point for controlling mucus turnover and barrier integrity.},
}

*Bacteroides fragilis/enzymology/genetics/metabolism
*Mucins/metabolism/chemistry
*Polysaccharides/metabolism/chemistry
Humans
*Bacterial Proteins/metabolism/genetics/chemistry
Substrate Specificity
Glycoside Hydrolases/metabolism/genetics
Gastrointestinal Microbiome
Carbohydrate Binding Modules

@article {pmid41857136,
year = {2026},
author = {Dutta, S and Khanh, NV and Lee, YH},
title = {Rhizosphere and endophytic bacterial communities of the endangered alpine modest primrose and their plant growth-promoting potential.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41389-3},
pmid = {41857136},
issn = {2045-2322},
abstract = {Plant microbiomes play critical roles in host growth and stress resilience, yet remain underexplored in alpine ecosystems. We investigated the rhizosphere and endophytic bacterial communities of an endangered alpine modest primrose (Primula modesta var. hannasanensis), which is endemic to the high-altitude regions of Korea. Using 16 S rRNA gene amplicon sequencing, we compared the bacterial communities in wild and cultivated populations. The rhizosphere microbiota exhibited greater diversity than the root endophytes, and cultivated plants harbored more diverse and compositionally distinct endophytic communities than wild plants, suggesting that cultivation influences the microbial structure. We isolated bacterial strains from these communities and identified Leifsonia lichenia JBCE310 and Chryseobacterium piperi JBCE316 as significantly enhancing seed germination and seedling growth of Primula malacoides and Arabidopsis thaliana. The co-inoculation yielded synergistic effects that were likely mediated by phytohormone production. These results highlight the functional potential of alpine plant-associated bacteria and provide potential microbial candidates for the conservation and ex situ propagation of endangered alpine flora.},
}

@article {pmid41857189,
year = {2026},
author = {Dalamaga, M and Rozani, S and Petropoulou, D},
title = {Why Is Colorectal Cancer Occurring Earlier? Metabolic Dysfunction, Underrecognized Carcinogens, and Emerging Controversies.},
journal = {Current obesity reports},
volume = {15},
number = {1},
pages = {},
pmid = {41857189},
issn = {2162-4968},
}

@article {pmid41857249,
year = {2026},
author = {Ríos Colombo, NS and Perez-Ibarreche, M and Lanka, P and Ross, RP and Hill, C},
title = {Establishing and analyzing the Simplified Human Intestinal Microbiota (SIHUMI) as a versatile in vitro gut microbiome model with qPCR-based strain-level tracking.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {41857249},
issn = {1750-2799},
support = {101027450//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101027450//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {A major challenge in microbiome research is the inherent complexity and inter-individual variability of the human gut microbiota. To address this, we have developed a detailed protocol for establishing and analyzing a Simplified Human Intestinal Microbiota (SIHUMI)-a defined, in vitro bacterial consortium composed of seven fully sequenced and anaerobically culturable human gut commensals. This model enables highly reproducible and controlled experiments, in which the individual growth of each member can be quantitatively tracked over time (up to 48 h) via species-specific qPCR. The protocol outlines optimized and standardized steps, including consortium setup, time-resolved sample collection, DNA extraction and qPCR analysis. It can be used to evaluate community dynamics in response to interventions such as nutrients, antimicrobials or other xenobiotics. The system is readily adaptable: additional strains can be incorporated, including pathogens (e.g., Clostridioides difficile), to transform it into an infectious disease model. In addition, we describe two optional rapid methods for assessing interspecies interactions and provide an open-source web app for generating interaction network plots. This enables exploration of ecological mechanisms and potential off-target effects. The entire workflow-from setup to data acquisition-can be completed within 1 week. This qPCR-based protocol offers a validated and accessible platform for gut microbiome research, providing a standardized, strain-level and time-resolved alternative to 16S- or fluorescence-based workflows and enabling quantitative, scalable analysis of defined microbial communities.},
}

@article {pmid41857413,
year = {2026},
author = {Yang, L and Peery, RC and Zhou, S and Chen, X and Farmer, LM and Gutierrez, F and Fowler, S and Zhang, L and Salamat, JM and Riggins, K and Shi, J and Shen, L},
title = {Weaning drives microbiome-mediated epigenetic regulation to shape immune memory in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41857413},
issn = {2058-5276},
support = {6-FY18-135//March of Dimes Foundation (March of Dimes)/ ; R21HD101035//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD100914//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01CA233472//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {During weaning, the transition to solid food diversifies the gut microbiome, triggering a programmed immune response critical for long-lasting mucosal immunity. Previous work showed that the gut microbiome mediates epigenetic development in intestinal stem cells (ISCs) during suckling, but what happens during weaning is unclear. Here, genome-wide profiling revealed that weaning-driven microbiome changes shape the DNA methylome and transcriptome of murine ISCs in an IFNγ-dependent manner. Specifically, we observe demethylation of enhancer elements essential for MHC class II genes, which results in a transcriptional memory that persists through differentiation into adulthood. IFNγ blockade, or low-dose penicillin to target Gram-positive bacteria, in early life impaired microbiome-mediated epigenetic control and mucosal immunity, and exacerbated colitis. Murine organoids primed with IFNγ showed rapid, amplified transcriptional responses upon secondary stimulations. These findings reveal that early-life events alter the gut microbiome and these changes reprogramme ISC epigenetic memory to shape mucosal immunity.},
}

@article {pmid41857429,
year = {2026},
author = {Xiao, S and Wang, M and Martin, TG and Scott, B and Fang, X and Liu, X and Yang, Y and Fu, S and Truong, SD and Gugel, JF and Maas, GL and Mullen, MP and Hill, JH and Li, VL and Markhard, AL and Zhao, M and Qi, W and Reghupaty, SC and Zhao, M and Spaas, J and Wei, W and Moholdt, T and Hawley, JA and Voldstedlund, CT and Richter, EA and Chen, X and Svensson, KJ and Bernstein, D and Leinwand, LA and Xu, Y and Long, JZ},
title = {Python metabolomics uncovers a conserved postprandial metabolite and gut-brain feeding pathway.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41857429},
issn = {2522-5812},
support = {R01DK124265//U.S. Department of Health Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes Digestive Kidney Diseases)/ ; K99DK141966//U.S. Department of Health Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes Digestive Kidney Diseases)/ ; },
abstract = {Most mammals consume small and frequent meals. By contrast, pythons are ambush predators that exhibit extreme feeding and fasting patterns and provide a unique model for uncovering molecular mediators of the postprandial response[1-3]. Using untargeted metabolomics, we show that circulating levels of the metabolite para-tyramine-O-sulphate (pTOS) are increased more than 1,000-fold in pythons after a single meal. In pythons, pTOS production occurs in a microbiome-dependent manner via sequential decarboxylation and sulphation of dietary tyrosine. In both pythons and mice, pTOS administration activates a neural population in the ventromedial hypothalamus (VMH). In mice, these VMH neurons are required for the anorexigenic effects of pTOS. Chronic administration of pTOS to diet-induced obese male mice suppresses food intake and body weight. pTOS is also present in human blood, where its levels are increased after a meal. Together, these data uncover a conserved postprandial anorexigenic metabolite that links nutrient intake to energy balance.},
}

@article {pmid41853378,
year = {2023},
author = {Zimmermann, P},
title = {Exploring the microbial landscape of the nasopharynx in children: a systematic review of studies using next generation sequencing.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1231271},
pmid = {41853378},
issn = {2813-4338},
abstract = {INTRODUCTION: The nasopharynx harbours a diverse and dynamic microbial community, which plays an important role in maintaining the health and homeostasis of the respiratory tract, as well as in immune system development. Understanding factors that influence the composition of the nasopharyngeal microbiome in children and its association with diseases is of particular importance, as children are at a heightened risk for respiratory infections and other adverse health outcomes.

OBJECTIVES: This review systematically summarises studies which investigated the nasopharyngeal microbiome in children, including its dynamics, stability over time, and the influence of intrinsic and extrinsic factors on its composition.

METHODS: MEDLINE was searched using the OVID interface. Original studies which investigated the nasopharyngeal microbiome using next generation sequencing in children were summarised.

RESULTS: The search identified 736 studies, of which 77 were included. The studies show that the nasopharyngeal microbiome in children is dynamic and influenced by many external factors. A high abundance of Haemophilus, Moraxella, and Streptococcus and a low abundance of Corynebacterium and Dolosigranlum are associated with adverse health outcomes such as respiratory tract infections, wheezing and asthma exacerbations. Factors which have been identified as risk factors for these adverse health outcomes, such as being born by Caesarean section, not being breast-fed, having siblings, day-care attendance, and antibiotic exposure have been shown to be associated with the aforementioned features in the nasopharyngeal microbiome.

CONCLUSION: The association between specific nasopharyngeal microbial profiles and adverse health outcomes highlights the potential of the nasopharyngeal microbiome as a marker for identifying children at risk for disease and even more importantly, as an avenue for targeted interventions and preventive strategies.},
}

@article {pmid41853380,
year = {2023},
author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN},
title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1067019},
pmid = {41853380},
issn = {2813-4338},
abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.},
}

@article {pmid41853381,
year = {2023},
author = {Li, L and Yan, Y and Wang, X and Hou, Y and Ding, L and Wang, Z and Song, Q and Ding, W and Zhang, X},
title = {Allicin modulates the intestinal microbiota to attenuate blood glucose and systemic inflammation in type 2 diabetic rats.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1102694},
pmid = {41853381},
issn = {2813-4338},
abstract = {INTRODUCTION: Allicin is a wide spectrum prebiotic for human health, but whether it can attenuate blood in diabetes patients is rarely reported. In this study, we built a rat model and investigated the effect of allicin on diabetes mellitus type 2 (T2DM). We found that allicin could effectively reduce blood glucose levels, regulate intestinal microbiota, reduce lipid and body weight accumulation, and systemic inflammation in T2DM rats.

METHODS: The rat model of type 2 diabetes was made by streptozotocin, and different doses of allicin were given orally by gavage. The intestinal contents of diabetes rats were sequenced and analyzed by 16S technology, and the clinical indicators of rats were detected for joint analysis.

RESULTS: Allicin can improve the intestinal flora of type 2 diabetes rats, enrich beneficial metabolites, reduce blood glucose, improve blood lipids, reduce systemic inflammation, and improve type 2 diabetes.

DISCUSSION: Intestinal microbiome analysis showed that allicin gavage significantly regulated the structure and main components of the intestinal microbiota in T2DM rats. Allicin increased the abundance of probiotic microbes, such as Lactobacillus, Clostridium and Akkermansia, while it reduced pathogenic microbes, such as Enterobacter, Erysipelatoclostridium and Colidextribacter. Allicin gavage increased the abundance of intestinal short-chain fatty acids, such as acetic acid and propionic acid. Correlation analysis showed that the increased gut microbes by allicin gavage were significantly associated with health physiological parameters but negatively related to serum inflammatory factors such as interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-a), and hypersensitive C-reactive protein (hs-CRP). In addition, our study also suggests that allicin may have prebiotic effects on chronic liver injury. This study shows that allicin can regulate various clinical symptoms of T2DM and is a potential therapeutic drug for T2DM.},
}

@article {pmid41853384,
year = {2023},
author = {Walusimbi, B and Lawson, MAE and Nassuuna, J and Kateete, DP and Webb, EL and Grencis, RK and Elliott, AM},
title = {The effects of helminth infections on the human gut microbiome: a systematic review and meta-analysis.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1174034},
pmid = {41853384},
issn = {2813-4338},
abstract = {UNLABELLED: The gut microbiome is important in shaping human health. One key factor that has been proposed to affect the gut microbiome is helminth infection. Unravelling the association and/or interaction between helminth infections and the gut microbiome may reveal new insights into the mechanisms through which parasitic worms impact the prognosis of infections and diseases. While considerable work has gone into reviewing data on the effect of helminth infection on gut microbiome in animal studies, less attention has been given to this area of research in human studies. This study set out to address this through an exhaustive systematic review of literature. Articles were identified through EMBASE, MEDLINE, Web of Science and Science Direct following a registered protocol (PROSPERO). After assessing methodological quality (ICROMS) and publication bias, a random effects meta-analysis was performed to investigate the overall effect that intestinal parasites can have on the human gut microbiome using alpha- and beta-diversity metrics and adjusting for age, sex and antihelminthic treatment taken by individuals. A total of 19 out of 3466 articles were included in the final meta-analysis. Our results show that helminth infection increases the host bacterial diversity, as well as microbial richness. This work further contributes to the understanding of how the gut microbiome structure changes depends on whether one is infected with helminths or not. It also lays the foundation for future research aimed at establishing how these interactions could explain the disparity in phenotypes such as infection, disease and vaccine responses reported in different regions worldwide.

https://www.crd.york.ac.uk/prospero/, identifier CRD42020192182.},
}

@article {pmid41853385,
year = {2023},
author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P},
title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1147082},
pmid = {41853385},
issn = {2813-4338},
abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.

OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).

METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.

RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.

CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.},
}

@article {pmid41853386,
year = {2023},
author = {Goemann, HM and Ulrich, DEM and Peyton, BM and Gallegos-Graves, V and Mueller, RC},
title = {Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1310790},
pmid = {41853386},
issn = {2813-4338},
abstract = {Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.},
}

@article {pmid41853387,
year = {2023},
author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC},
title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1199766},
pmid = {41853387},
issn = {2813-4338},
abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.},
}

@article {pmid41853500,
year = {2024},
author = {Wang, G and Menon, S and Wilsack, L and Rehak, R and Lou, L and Turbide, C and Auger, J and Tremblay, A and Mathieu, O and Binda, S and Tompkins, TA and Bruehlmann, S and Andrews, CN},
title = {Spatially and temporally precise microbiome profiling in the small intestine using the SIMBA capsule with X-ray tracking.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1321624},
pmid = {41853500},
issn = {2813-4338},
abstract = {INTRODUCTION: Few minimally invasive options for sampling the small intestinal (SI) luminal fluid exist to study the SI microbiota in health and disease. To address the lack of tools and methods to study GI regions that are difficult to access, Nimble Science developed a fully autonomous and passive sampling method, the Small Intestine MicroBiome Aspiration (SIMBA™) capsule, for convenient, high-quality, and reliable sampling to study the diet-microbiota interactions in the SI.

METHODS: The sealing efficacy and microbial DNA preservation capacity of the SIMBA capsules was first validated through in vitro simulation assays. Then, a clinical study was conducted with 20 healthy participants to validate the in vivo use of SIMBA capsules to reliably capture samples for SI microbiome analysis before and after an intervention (NCT04489329). Briefly, participants ingested the capsules at baseline and 7 days later, with a probiotic capsule containing a blend of L. rhamnosus R0011 and B. longum R0175. Following baseline SIMBA capsule ingestion, multiple low-dosage x-ray scans were performed to track the sampling location. Fecal samples corresponding with the baseline and intervention capsule were analyzed for comparison.

RESULTS: The SIMBA capsules' performance in vitro demonstrated the potential for contamination-free sampling with preservation of the microbial communities. Within the clinical study, the capsules performed safely and reliably for collection of SI content. X-ray tracking confirmed that 97.2% of the capsules completed sample collection in the SI regions before reaching the colon. Importantly, our data showed that the capsules sampled in the right area of the intestines and that baseline SIMBA microbiome profile is significantly different from fecal microbiome profile. SIMBA successfully detected a concurrent probiotic intervention in the small intestine, which was not detectable using stool samples.

DISCUSSIONS: The high accuracy of sampling location and sealing efficacy of the SIMBA capsules makes them potentially useful research tools in clinical trials for studying diet-microbiota interactions in health and disease, and perhaps eventually for the clinical diagnosis of GI tract conditions affecting the SI such as SIBO.},
}

@article {pmid41853502,
year = {2024},
author = {Tarrant, I and Finlay, BB},
title = {The potential of live biotherapeutic products in allergic disease: current findings and future directions.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1418633},
pmid = {41853502},
issn = {2813-4338},
abstract = {With the global prevalence of allergic disease continuing to rise at an alarming rate, the need for effective and safe therapeutics is paramount. Given the critical role of the early-life microbiota on immune development, emerging research suggests the potential use of live biotherapeutic products (LBP) for the prevention and treatment of childhood allergy. However, findings are limited and inconsistent. Therefore, the present review critically evaluates the current animal and human data on the therapeutic value of LBPs in allergy, the underlying immunological mechanisms by which LBPs may mediate allergy susceptibility, limitations of the current research that need to be addressed, and future research directions. Accordingly, LBPs may protect against allergic disease through several immunological and physiological mechanisms during early-life, including regulation of Th1/Th2 balance, SCFA-induced activation of GPR41/43 and HDAC inhibition, and maturation of epithelial barrier integrity. Taken together, current findings indicate powerful immunomodulatory properties of LBPs on allergic immune response, with LBPs offering exciting potential as a novel therapeutic tool for childhood allergy. However, the efficacy of LBPs in allergy is complex and influenced by many population and methodological factors, resulting in varied therapeutic benefits. While research thus far has focused on traditional probiotic strains, greater investigation into microbial consortiums selected from the microbiota of non-allergic infants may provide greater promise as a therapeutic tool for allergic disease. Further investigation, particularly into long-term efficacy, strain-specific effects, optimal supplementation regimes, and use of multi-strain consortiums, is necessary before findings can be translated into clinical applications to tackle childhood allergic disease.},
}

@article {pmid41853503,
year = {2024},
author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T},
title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1451735},
pmid = {41853503},
issn = {2813-4338},
abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.},
}

@article {pmid41853505,
year = {2024},
author = {Rusling, MR and DeMar, JC and Chakraborty, N and Hoke, AV and Miller, SA and Rosenberger, JG and Batuure, AB and Wilder, DM and Sajja, VS and Long, JB and Hammamieh, R and Gautam, A},
title = {The effect of dietary omega-6 fatty acid enrichment in rodent models of military-relevant acute traumatic psychological stress and traumatic brain injury.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1430340},
pmid = {41853505},
issn = {2813-4338},
abstract = {INTRODUCTION: Sequelae from traumatic brain injuries (TBIs) and post-traumatic stress disorder (PTSD) are major career-limiting factors for combat soldiers. Overlap between TBI and PTSD symptoms alongside other common comorbidities complicate the diagnosis and treatment. Systems-level and high-throughput approaches are key in understanding the underlying biomolecular mechanisms and differentiating these conditions.

METHODS: The present study identifies dietary factors and proposes mechanisms behind psychological stress and TBI, using established preclinical animal models and a multi-omics approach. Here, we used microbiome characterizations of rats exposed to simulations of blast-induced TBI and underwater trauma (UWT)-induced psychological stress. We further studied the effect of dietary omega-6 versus omega-3 polyunsaturated fatty acid (n-6, n-3 PUFA) enrichment on the insult responses. The use of excess n-6 PUFA was chosen due to its high prevalence in the Western diet and pro-inflammatory nature. Prior to TBI or UWT, animals were maintained for 6 weeks and continued thereafter on either a standard diet or two customized chows imbalanced and diminished in omega-3 content. Corresponding shams were carried out for all groups. Fecal bacterial microbiome populations were assessed using 16S rRNA gene sequencing.

RESULTS: Physiologic outcome modeling identified that dietary status affected post-TBI lactate dehydrogenase (LDH) and triglyceride levels, with n-3 PUFA having a large attenuating influence. The UWT model showed similar trends, with diet significantly altering LDH, terminal corticosterone (14 days post-exposure), and a fear behavior susceptibility. Fecal microbiome alpha diversity was significantly reduced by high levels of n-3 PUFA. Likewise, beta diversity of the microbiome was significantly affected by both diet and time but not exposure to TBI or UWT. Compositionally, temporal effects on the microbiome were more likely to be observed with the diets. The most affected features fell within the Proteobacteria phyla, in which n-3 PUFA enrichment significantly reduced Alphaproteobacteria in the TBI model and increased Gammaproteobacteria in the UWT group.

DISCUSSION: All these observations can influence the vulnerability or resilience of the warfighter to blast-induced TBI and acute psychological stress. The microbiome mechanisms facilitate and provide a knowledge-driven unbiased panel of signatures to discriminate between the two insults and is an essential tool for designing precise care management.},
}

@article {pmid41853506,
year = {2024},
author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S},
title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1484878},
doi = {10.3389/frmbi.2024.1484878},
pmid = {41853506},
issn = {2813-4338},
abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].},
}

@article {pmid41853507,
year = {2024},
author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S},
title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1359580},
pmid = {41853507},
issn = {2813-4338},
abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.},
}

@article {pmid41853509,
year = {2024},
author = {Fu, X and Shama, A and Norbäck, D and Chen, Q and Xia, Y and Zhang, X and Sun, Y},
title = {Exploring the role of indoor microbiome and environmental characteristics in rhinitis symptoms among university students.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1277177},
pmid = {41853509},
issn = {2813-4338},
abstract = {INTRODUCTION: Rhinitis is one of the most prevalent chronic respiratory diseases worldwide. There is emerging evidence suggesting that the indoor microbiome may contribute the onset and exacerbation of rhinitis symptoms, but comprehensive studies on this topic remain scarce.

METHODS: In this study, we assessed the microbiome assemblage of settled air dust collected in Petri dishes in 86 dormitory rooms of Shanxi University, China using 16s rRNA sequencing. A self-administered questionnaire, including questions about rhinitis symptoms and personal information, was completed by 357 students residing in these dormitories. Logistic and linear regression model was applied to examine the associations between environmental characteristics, indoor microbiome, and rhinitis.

RESULTS: The most abundant genera in the dormitories were Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%). Taxa richness in the class of Actinobacteria and Fusobacteriia was negatively/protectively associated with rhinitis (p<0.05). Six bacterial genera, including those from Actinobacteria (Actinomyces), Fusobacteriia (Fusobacterium), and Bacteroidetes (Prevotella and Capnocytophaga), were negatively/protectively associated with rhinitis. Conversely, seven genera, predominantly from Alphaproteobacteria and Betaproteobacteria (Sphingomonas, Caulobacter, uncharacterized Caulobacteraceae and Comamonadaceae), were positively associated with rhinitis. Living in higher floor level and higher indoor PM2.5 concentrations were associated with a higher abundance of taxa potentially protective against rhinitis and a lower abundance of taxa potentially increasing the risk of rhinitis (P<0.01). However, having curtain indoor and higher indoor CO2 concentrations were associated with a lower abundance of taxa potentially protective against rhinitis and a higher abundance of taxa potentially increasing the risk of rhinitis (P<0.01).

DISCUSSION: This study enhances our understanding of the complex interactions between environmental characteristics, indoor microbiomes, and rhinitis, shedding light on potential strategies to manipulate indoor microbiome for disease prevention and control.},
}

@article {pmid41853510,
year = {2024},
author = {Kim, H and Lee, K and Lee, JY and Kwon, BE and Kim, HJ and Park, H and Kim, T and Kwak, JG and Choi, JE and Hong, KH and Chun, J and Shin, C},
title = {Distinct Cutibacterium acnes subspecies defendens strains classified by multi-omics dissection alleviate inflammatory skin lesions of a rosacea-like mouse model.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1362408},
pmid = {41853510},
issn = {2813-4338},
abstract = {INTRODUCTION: Cutibacterium acnes (C. acnes) resides in various organs such as the skin, prostate, eye, nose, stomach, and intestine, indicating the possibility of extensive crosstalk between this bacterium and the human body. C. acnes strains are classified into three subspecies based on phylogenetics and distinguishable phenotypes. Among them, C. acnes subsp. defendens strains are characterized by anti-inflammatory features, raising expectations for their potential as future microbiome therapeutics. However, the heterogeneity of C. acnes subsp. defendens and its corresponding immunological functions have not been clearly addressed.

METHODS: The genetic diversity of the strains was assessed using single- and multi-locus sequence typing. Their immune-modulatory functions were evaluated in vitro using 2D and 3D assays with immune and epithelial cells. The anti-inflammatory effects were further confirmed in vivo using a rosacea-like mouse model. Comparative genomic and transcriptomic analyses were conducted to uncover mechanisms underlying the immunosuppressive activity of the strains.

RESULTS: We demonstrated that the newly isolated C. acnes subsp. defendens strains, exhibiting phenotypic heterogeneity, are distinctly clustered using single- and multi-locus sequence typing methods. These strains showed strong immune-regulatory functions in immune and epithelial cell-based 2D and 3D in vitro assays. Furthermore, their anti-inflammatory role was functionally confirmed in vivo using a rosacea-like mouse model, where they alleviated skin lesions characterized by hyperplasia and dermal inflammation. Comparative transcriptomics revealed that these strains may exert their immunosuppressive effects through the enhanced expression of acnecins and transcriptional variation in envelope stress regulators (specifically the two-component systems, CesSR homologs). Additionally, we propose that these C. acnes type II strains produce anti-inflammatory metabolites or peptides smaller than 3 kDa, which are associated with elevated pyrimidine and reduced L-arginine biosynthesis.

DISCUSSION: The newly isolated C. acnes subsp. defendens strains demonstrate significant anti-inflammatory properties both in vitro and in vivo, suggesting their potential as microbiome-based therapeutics. Their unique genomic and transcriptomic profiles, including the production of small bioactive compounds and specific transcriptomic patterns, underpin their immunosuppressive capabilities. These findings provide a foundation for developing novel treatments for inflammatory skin conditions, such as rosacea.},
}

@article {pmid41853511,
year = {2024},
author = {Pitell, S and Woo, C and Trump, E and Haig, SJ},
title = {Balancing water conservation and health: do water-saving showerheads impact the microbes we breathe in during showering?.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1416055},
pmid = {41853511},
issn = {2813-4338},
abstract = {Low-flow showerheads offer consumers economic and water-saving benefits, yet their use may inadvertently affect the microbial content of produced water and water-associated aerosols. This study aimed to compare the abundance and microbial composition of bacteria in shower water and associated respirable aerosols produced by various low flow rate (1, 1.5, and 1.8 gpm) showerheads. Our findings indicate that the lowest-flow showerhead produces water with lower total microbial and opportunistic bacterial pathogen densities compared to higher low flow rate counterparts. However, microbiome analysis revealed that 1.8 gpm flow rate showerheads exhibit reduced abundance of Gram-negative organisms and common biofilm-forming organisms, suggesting potentially lower pathogenicity compared to 1 and 1.5 gpm low-flow showerheads. Additionally, the number of respirable aerosols produced by showerheads as well as the partitioning of certain microorganisms from the water to aerosol phases was negatively correlated with flow rate, suggesting that there may be increasing exposure potential to pathogenic bioaerosols when using a 1gpm showerhead compared to a 1.8 gpm showerhead. However, the 1.5 gpm showerhead seemed to balance microbial partitioning, aerosol generation, and water conservation. Moreover, the microbial composition of aerosols produced from shower water was more influenced by the age of the showerhead than the flow rate, highlighting the significance of biofilm formation on the microbial community. Overall, our findings underscore the importance of evaluating the microbial risk associated with low-flow showerheads using multiple metrics in both water and aerosols, and dynamically assessing this over time, to ensure accurate future risk assessment.},
}

@article {pmid41853512,
year = {2024},
author = {Beilig, S and Pannekens, M and Voskuhl, L and Meckenstock, RU},
title = {Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1324967},
pmid = {41853512},
issn = {2813-4338},
abstract = {Oil reservoirs represent extreme environments where anaerobic degradation profoundly influences oil composition and quality. Despite the common observation of biodegraded oil, the microbial degradation rates remain largely unknown. To address this knowledge gap, we conducted microcosm incubations with light oil as carbon source, original formation water and sulfate as electron acceptor, closely mimicking in situ conditions to assess oil degradation rates. Samples were taken from a newly drilled oil well to exclude contamination with injection water and allochthonous microorganisms. At the end of the incubations, microbial community analyses with 16S rRNA gene amplicon sequencing revealed the most prominent phyla as Desulfobacterota, Thermotogota, Bacteroidota, Bacillota (formerly Firmicutes), and Synergistota, collectively accounting for up to 44% of relative abundance. Ion chromatography and reverse stable isotope labeling were used to monitor sulfate reduction and CO2 evolution respectively. We calculated an average degradation rate of 0.35 mmol CO2 per year corresponding to 15.2 mmol CO2/mol CH2(oil) per year. This resembles to approximately 200 years to degrade one gram of oil under the applied, presumably ideal conditions. Factoring in the available oil-water-contact (OWC) zone within the incubations yielded a degradation rate of 120 g CH2 m[-2] OWC per year, closely aligning with the modeled degradation rates typically observed in oil reservoirs. Moreover, our study highlighted the utility of the reverse stable isotope labeling (RSIL) approach for measuring complex substrate degradation at minute rates.},
}

@article {pmid41853514,
year = {2024},
author = {Asumang, P and Ntumi, R and Dwomoh, F},
title = {Unveiling microbial dynamics: a review of health and immune enhancement in school settings.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1488702},
pmid = {41853514},
issn = {2813-4338},
abstract = {This review focuses on the role of microorganisms in promoting health and immune function within school environments. Microbes, including bacteria, viruses, fungi, and other microorganisms, constitute the human microbiome and play a crucial role in various bodily functions and immune system development. The complex interactions between microorganisms and the immune system in schools, where children spend a significant amount of time, are not fully understood. While schools have traditionally emphasized hygiene practices to prevent the spread of infectious diseases, recent research has highlighted the potential consequences of reduced microbial exposure during early life. The "hygiene hypothesis" suggests that limited exposure to microbes in infancy may increase the risk of allergies, asthma, and autoimmune diseases in adulthood. This paper explores the microbial diversity found in schools, the benefits of exposure to different microorganisms, and the implications of hygiene practices on immune system development. It also examines current research on microbial intervention strategies and their potential to influence overall health in schools. Understanding the role of microbes in school environments has implications for public health policies and educational practices, aiming to create healthier and more conducive learning environments for the younger generation. By comprehensively exploring this topic, this review contributes to a broader understanding of the significance of microbes in promoting health and immune function in school settings and its relevance to future health research.},
}

@article {pmid41853515,
year = {2024},
author = {, and Barberio, D},
title = {Navigating regulatory and analytical challenges in live biotherapeutic product development and manufacturing.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1441290},
pmid = {41853515},
issn = {2813-4338},
abstract = {The recent FDA approvals of Rebyota™ and Vowst™ represent landmark milestones within the burgeoning field of live microbiota-based products. Future microbiota-based treatment approaches also hold significant promise for treating patients with a myriad of diseases and disorders, yet substantial hurdles hinder their development and utilization. Foremost, existing regulatory frameworks governing live biotherapeutic product (LBP) manufacturing development have notable gaps, requiring comprehensive expansion and refinement. Along with regulatory challenges, hurdles remain in the optimization and validation of analytical methodologies essential for characterizing LBPs, including for microbial identification, potency, and bioburden. To address these challenges, Microbiome Therapeutics Innovation Group (MTIG) spearheaded collaborative efforts, engaging industry leaders and the FDA in discussions aimed at catalyzing improvements in LBP analytics and refining the current regulatory landscape. Extrapolating on feedback from these discussions, this review highlights challenges and identifies critical gaps. Specific recommendations for future regulatory guidance are proposed, as are recommendations for interactions that developers can take now with regulatory agencies to support the development of maturing guidance. Key analytical factors to consider in LBP development are reviewed, highlighting strengths and weaknesses of various methodologies. Collaboration among regulatory and government agencies, industry, and academia, facilitated by coalitions like MTIG, will be instrumental in ushering the microbiota-based therapeutics field into the next phase of approvals and advancements, ultimately benefiting patients.},
}

@article {pmid41853517,
year = {2024},
author = {Dalman, MR and Simison, WB and Nielsen, D and Bhatta, S and Ramahi, N and Yee, C and Thapaliya, D and Kadariya, J and Cheatham, S and Olson, H and Smith, TC},
title = {Staphylococcus aureus carriage is associated with microbiome composition in the nares and oropharynx, not the hand, of monozygotic twins.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1457940},
pmid = {41853517},
issn = {2813-4338},
abstract = {BACKGROUND: Staphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic-resistant strains causing 11,000 deaths yearly and ~2% of the population nasally colonized with methicillin-resistant S. aureus, a search for predictive markers and associative relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with multi-site microbiome analyses to characterize the impacts of S. aureus on composition.

RESULTS: We recruited 147 monozygotic twin pairs and characterized three sites, i.e., the nares, oropharynx, and hand microbiomes, using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. The prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. The detection of S. aureus was statistically correlated with differences in microbiome composition across sites, as indicated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins' nares that were S. aureus culture-positive concordant, whereas twins that were culture-negative concordant had the most similarity in the oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively.

CONCLUSIONS: This improved understanding of S. aureus colonization in nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome is influenced by host genetics and S. aureus carriage.},
}

@article {pmid41853520,
year = {2024},
author = {Fu, X and Norbäck, D and Sun, Y},
title = {Editorial: Environmental microbiomes, metabolites, and respiratory diseases.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1388525},
doi = {10.3389/frmbi.2024.1388525},
pmid = {41853520},
issn = {2813-4338},
}