@article {pmid41647966,
year = {2025},
author = {Twhigg, L and Ng, HM and Glyn, T and Wall, C and Purcell, R},
title = {Fibre, microbes and radiotherapy: unravelling the gut's impact on radiotherapy in cancer.},
journal = {ESMO gastrointestinal oncology},
volume = {9},
number = {},
pages = {100174},
pmid = {41647966},
issn = {2949-8198},
abstract = {The gut microbiome plays an integral role in many physiological functions, including immunity, metabolism, maintenance of membrane integrity and protection against pathogenic bacteria. Conversely, adverse changes in the gut microbiome-termed dysbiosis-have been linked to many diseases, including cancer. Dysbiosis can result from a range of endogenous and exogenous factors. Diet is one of the most important modulators of the gut microbiome; the indirect benefits of modulating the microbiome through diet interventions are beginning to be used in many disease settings. Beneficial microbes (commensals) can modulate the local and systemic immune environment through the production of metabolites, such as short-chain fatty acids (SCFAs). Commensal bacteria ferment dietary fibre to produce SCFAs, and increasing dietary fibre intake has been shown to both increase SCFA production in the colon and affect immune responses. Recent studies have shown that dietary fibre can increase tumour responses to immunotherapy and chemotherapy, but data on the effect of increased fibre and changes in the microbiome on radiotherapy are limited. In this article, we review the current evidence regarding dietary fibre interventions and modulation of the gut microbiome in improving outcomes in patients receiving pelvic radiotherapy.},
}

@article {pmid41647440,
year = {2026},
author = {Xu, H and Yu, J and Xia, L and Lei, X and Zhou, L and Lin, P and Su, S and Li, Y and Chen, C},
title = {Antibiotic exposure impairs the efficacy of first-line chemoimmunotherapy in non-small cell lung cancer through the regulation of gut microbiome and bile acid metabolism.},
journal = {Precision clinical medicine},
volume = {9},
number = {1},
pages = {pbag001},
pmid = {41647440},
issn = {2516-1571},
abstract = {OBJECTIVE: Previous antibiotic therapy is acknowledged to potentially reduce the efficacy of single-agent immune checkpoint inhibitors. Nevertheless, the impact of antibiotics on the results for patients undergoing chemoimmunotherapy remains unclear. This research investigated the influence of antibiotic treatment on the effectiveness of chemoimmunotherapy in advanced non-small cell lung cancer (NSCLC).

METHODS: We recorded the characteristics of patients with advanced NSCLC and assessed potential associations between the use of antibiotics and the efficacy of chemoimmunotherapy. A mouse model using Lewis lung carcinoma (LLC) cell lines was developed to assess the effects of antibiotics on the gut microbiome and metabolites. Fecal samples were analyzed using 16S rRNA gene sequencing and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) methods. Mouse fecal and serum samples and 16 human stool samples were used to validate the identified differentially metabolites. Deoxycholic acid (DCA) was further applied to a LLC mouse model.

RESULTS: This study included 387 NSCLC patients, among whom 86 patients had used antibiotics within the 30 days before the first cycle of chemoimmunotherapy (ATB group), and 301 patients had not used antibiotics (non-ATB group). Notable discrepancies were observed in overall survival and progression-free survival between the two groups, with overall survival recorded at 18.4 months versus 32.0 months, and progression-free survival at 7.6 months versus 13.0 months, in the ATB and non-ATB groups respectively. At the phylum level, the relative abundances of Proteobacteria, Cyanobacteria, and Deinococcus were increased in the ATB mice, while Firmicutes, Bacteroidetes, and Verrucomicrobia were decreased. We detected significant differences in DCA levels in the fecal and serum samples from mice as well as in the fecal sample from humans between the ATB and non-ATB groups. The respective proportions of CD4+ and CD8+ cells were greater in the non-ATB group than in the ATB group, whereas the proportion of Ki67-positive cells was greater in the ATB group. DCA was applied to LLC mice, and DCA along with chemoimmunotherapy effectively inhibited tumor growth in a LLC mouse model. The expression of programmed cell death ligand 1 increased in the DCA group.

CONCLUSIONS: Antibiotic exposure is associated with decreased efficacy of chemoimmunotherapy in patients with NSCLC via dysregulation of the gut microbiome and DCA metabolism.},
}

@article {pmid41647262,
year = {2025},
author = {Wang, Y and Chen, H and Chen, Y and Lu, Y and Wei, B and Wu, Z and Gao, H and Feng, L and Xie, F and Li, Q and Lin, W and Sun, X and Lin, H and Dong, B and Sun, P},
title = {Age-specific vaginal microecological dysbiosis associated with HPV infection: a large-scale cross-sectional study with targeted functional sequencing validation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1722367},
pmid = {41647262},
issn = {2235-2988},
mesh = {Female ; Humans ; Middle Aged ; *Papillomavirus Infections/microbiology/complications/virology ; Adult ; Cross-Sectional Studies ; *Vagina/microbiology/virology ; *Dysbiosis/microbiology ; Young Adult ; Adolescent ; Age Factors ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Papillomaviridae/genetics/classification ; Aged ; Bacteria/classification/genetics/isolation & purification ; Risk Factors ; Genotype ; },
abstract = {PURPOSE: The vaginal microecological parameters as a critical immune barrier, yet their age-dependent interaction with Human papillomavirus (HPV) infection remains poorly understood. To characterize age-dependent vaginal microbiota composition and function across the female lifespan, and to evaluate the selective impact of HPV infection on microecological stability and infectious risk.

METHODS: A total of 23,672 women were stratified into four age groups (18-34, 35-44, 45-55, and >55 years). Vaginal microecology was evaluated using Gram-staining, pH, hydrogen peroxide (H2O2), leukocyte esterase, and sialidase assays. HPV genotyping was performed in 2,116 women. Statistical analysis employed univariate screening, LASSO regression for variable selection, and multivariate logistic regression to identify independent microecological risk factors, with Benjamini-Hochberg false discovery rate (FDR) correction applied across all tests. A targeted subset (n = 88) underwent 16S rRNA sequencing with differential taxa analysis using LEfSe and Random Forest, as well as BugBase phenotype prediction and COG/KEGG pathway analysis, to validate age-specific HPV-microbiome interactions.

RESULTS: Normal flora prevalence declined linearly with age (78.7% vs. 48.8% postmenopause, q<0.001), while microbial diversity peaked during perimenopause. HPV infection was selectively associated with increased bacterial vaginosis (BV) (41.58% vs. 36.46%, q=0.032) and sialidase activity (28.14% vs. 21.69%, q=0.002), but decreased vulvovaginal candidiasis (VVC, 10.57% vs. 15.66%, q=0.003). Functional analyses revealed HPV-driven anaerobic enrichment (Gardnerella, Atopobium) and profound metabolic reprogramming specifically in women aged 35-44 years, marked by upregulation of lipopolysaccharide biosynthesis (fold change [FC] = 37.3, q = 0.028), arachidonic acid metabolism (FC = 33.3, q = 0.038), and NOD-like receptor signaling (FC = 62.1, q < 0.001), with concurrent apoptosis suppression (FC = 0.35, q = 0.046). Age-stratified risk modeling identified loss of H2O2-producing Lactobacilli as the strongest HPV risk factor in younger women (18-34 years, adjusted odds ratio [aOR] = 0.59), whereas BV and sialidase dominated in midlife (35-44 years, aOR = 1.64); no significant risk factors emerged postmenopause.

CONCLUSION: HPV infection selectively remodels vaginal microbiota composition and metabolic function in an age-dependent manner, with midlife women (35-44 years) representing a critical window for microbiota-based HPV prevention strategies.},
}

Female
Humans
Middle Aged
*Papillomavirus Infections/microbiology/complications/virology
Adult
Cross-Sectional Studies
*Vagina/microbiology/virology
*Dysbiosis/microbiology
Young Adult
Adolescent
Age Factors
RNA, Ribosomal, 16S/genetics
*Microbiota
Papillomaviridae/genetics/classification
Aged
Bacteria/classification/genetics/isolation & purification
Risk Factors
Genotype

@article {pmid41647191,
year = {2025},
author = {Yamasaki, A and Tomita, K},
title = {Editorial: Exploring the interconnection: obesity's role in asthma development and management.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1759789},
doi = {10.3389/falgy.2025.1759789},
pmid = {41647191},
issn = {2673-6101},
}

@article {pmid41647190,
year = {2025},
author = {Rank, MA and Barroso, DL and Conn, KA and Pecak, M and Scandura, M and Hirsch, AH and Gu, H and Whisner, CM and Shearer, H and Johnson, D and Argel, N and Bauer, CS and Williams, SN and Wright, BL and Woodward, J and Cope, EK},
title = {A randomized, double-blind, placebo-controlled trial of soluble corn fiber supplementation for children with asthma.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1707834},
pmid = {41647190},
issn = {2673-6101},
abstract = {INTRODUCTION: Asthma is a multifactorial disease influenced by genetic and environmental factors, including diet. The gut microbiome contributes to airway inflammation via the gut-lung axis, partly through production of short chain fatty acids (SCFAs) from bacterial fermentation of dietary fiber. We hypothesized that dietary fiber supplementation could modulate the gut microbiome and increase SCFAs in children with asthma.

METHODS: This is a double-blind, placebo-controlled trial of children who were randomized to consume 12 g of soluble corn fiber (SCF) as a supplement to their usual daily diet (50% the recommended daily fiber intake) or placebo for 4-6 weeks (clinicaltrials.gov NCT03673618). Dietary surveys, asthma symptom questionnaires, fecal, blood and nasal samples were collected before and after the intervention period to quantify fiber intake, asthma control, nasal and gut microbiome, and serum short chain fatty acids (SCFAs).

RESULTS: Of the 20 children enrolled, 15 completed the intervention with an average adherence rate of 83%. SCFA concentrations and gut microbiome changes varied by individual and treatment group. No significant differences in gut or nasal alpha or beta diversity were observed between groups post-intervention. However, differential abundance analysis showed a trend toward increased Bifidobacterium in the SCF group compared to placebo (ANCOM-BC p = 0.0004, FDR q = 0.073).

DISCUSSION: Supplementation of 50% of recommended daily fiber intake had minimal impact on asthma symptoms, the microbiome, or SCFA levels. Future studies should consider higher fiber doses, different fiber types, or targeting individuals with low baseline fiber intake to account for observed variability in microbiome and SCFA responses.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT03673618, identifier NCT03673618.},
}

@article {pmid41646975,
year = {2025},
author = {Wang, H and Zhou, C},
title = {Advances in the pathogenesis of rosacea.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1705588},
pmid = {41646975},
issn = {1664-3224},
mesh = {Humans ; *Rosacea/etiology/metabolism/immunology/pathology/genetics ; Animals ; *Skin/immunology/metabolism/pathology/microbiology ; Signal Transduction ; Immunity, Innate ; Dysbiosis ; Gastrointestinal Microbiome/immunology ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Toll-Like Receptor 2/metabolism ; Cathelicidins/metabolism ; },
abstract = {Rosacea is a chronic inflammatory cutaneous disorder predominantly affecting the centrofacial region, whose pathogenesis is complex and not yet fully understood. In this review we summarized the latest significant advances in the pathogenesis of rosacea in recent years. In genomic studies, the application of bioinformatics techniques such as whole-genome sequencing has identified novel susceptibility genes and linked multiple pathogenic mechanisms. Neurovascular dysfunction resulting from abnormal neuropeptides expression and dysregulated amino acid metabolism constitutes an important pathogenic factor in rosacea. The TLR2/LL-37/mTORC1 signaling axis, as a core regulatory pathway in innate immunity has been elucidated in detail. In addition, the dysbiosis of skin and gut microbiota, together with the impairment of skin barrier function, is also closely associated with the onset and progression of this disease. The deeper understanding of the pathogenesis of rosacea will benefit the development of new drugs and promote individualized diagnosis and treatment.},
}

Humans
*Rosacea/etiology/metabolism/immunology/pathology/genetics
Animals
*Skin/immunology/metabolism/pathology/microbiology
Signal Transduction
Immunity, Innate
Dysbiosis
Gastrointestinal Microbiome/immunology
Mechanistic Target of Rapamycin Complex 1/metabolism
Toll-Like Receptor 2/metabolism
Cathelicidins/metabolism

@article {pmid41646872,
year = {2026},
author = {Song, X and Zhai, Y and Zhang, M and Guo, J and Guo, B and Zhang, C and Jin, J and Wang, W and Xu, Y and Zhu, B and Li, X},
title = {Stochasticity Prevails but Differs: Tissue-Specific Assembly of Gut Microbiomes Across Seasons in an Amphibian Model.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73041},
pmid = {41646872},
issn = {2045-7758},
abstract = {Gut microbiota generally undergoes dynamic remodeling in concert with multifaceted self-regulation of amphibian hosts during key life stages, such as metamorphosis and hibernation. However, the spatiotemporal dynamics of amphibian gut microbiomes across the lifecycle remain poorly understood. In this study, we applied 16S rRNA gene amplicon sequencing to characterize the gut microbiomes of cultivated Black-spotted frog (Pelophylax nigromaculatus) across seasons. The gut microbiomes exhibited tissue-specific succession, and structural discrepancies between gut regions fluctuated temporally. Both small- and large-intestine microbiomes showed temporal decay patterns in abundance-unweighted intercommunity indices, but not in abundance-weighted indices. Compared with large-intestine microbiomes, small-intestine microbiomes were more randomized yet more centralized in terms of amplicon sequence variants, particularly within Proteobacteria (especially Pseudomonas). The alpha diversity of small-intestine microbiomes was comparatively lower, and their taxonomic composition was more stable over time. We further elucidated the assembly mechanisms of gut microbiomes by systematically analyzing dominant driving factors, ecological processes, phylogenetic traits, source-sink relationships, and co-occurrence networks. Stochastic processes played a dominant role in gut microbiome assembly, while deterministic processes (e.g., habitat filtering and microbial interaction) contributed more strongly to large gut microbiomes than to small gut microbiomes. Overall, this study provides insights into the ecological dynamics and assembly mechanisms of amphibian gut microbiomes across the lifecycle and may inform targeted microbiome modification for amphibian breeding and conservation.},
}

@article {pmid41646795,
year = {2026},
author = {Bivens, E and Atiq, O and Evans, T and Bimali, M and Brown, G and Crane, J and Darwish, N and Faulkner, JL and Govindarajan, R and Johnson, A and Kurilung, A and Lazarenko, O and Lu, YC and Marsh, K and Moreno, M and Nookaew, I and Robeson, M and Sunde, J and Ussery, D and Vural, E and Wilman, M and Nakagawa, M},
title = {A Randomized Double-Blind Placebo-Controlled Phase I/II Clinical Trial of a Human Papillomavirus Therapeutic Vaccine, PepCan, for Reducing Head and Neck Cancer Recurrence.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.09.26343801},
pmid = {41646795},
abstract = {OBJECTIVES: Head and neck cancer (HNC) has a high recurrence rate. Safety and effectiveness of PepCan in reducing recurrence for HNC patients were assessed.

METHODS AND ANALYSIS: PepCan consists of four human papillomavirus 16 (HPV 16) E6 peptides and a Candida skin testing reagent (Candin®, Nielsen Biosciences) as a vaccine adjuvant. Since Candida was known to have a general immune stimulating effects, patients were recruited regardless of their HPV status. Men and women with HNC who had no evidence of disease after standard surgery, chemotherapy, and/or radiation treatments were enrolled. They were randomized at 3:1 to PepCan versus placebo. Seven intradermal injections of PepCan or placebo (saline) were given every 3 weeks (first 4 injections) or 3 months (last 3 injections). They were followed with two visits 6 months apart. Safety was assessed using Common Terminology Criteria for Adverse Events version 5, and efficacy was assessed based on not having recurrence within 2 years. In addition, immune responses were examined using enzyme-linked immunospot assay for HPV 16 E6 response, fluorescent-activated cell sorter analysis for peripheral immune cells, and T cell repertoire analysis. Peripheral cytokines and gut and oral microbiome were also analyzed.

RESULTS: Seventeen patients were enrolled. The most common adverse events were grades 1 and 2 injection site reactions, and they occurred more frequently in the PepCan group (p <0.0001). Two patients had allergic reactions (grade 2 and grade 3), at the 6th vaccination, which were considered to be a dose-limiting toxicity (DLT). No serious adverse events were reported. In the intention-to-treat analysis (ITT), 45% (5/11) had non-recurrence in the PepCan group while 80% (4/5) had non-recurrence in the placebo group. For the per-protocol (PP) analysis, non-recurrence was 56% (5/9) for PepCan and 80% (4/5) for placebo. These differences were not statistically significant. Those who received PepCan and experienced non-recurrence had higher new T cell immune responses to HPV 16 E6 (p =0.05 for ITT and p =0.02 for PP). Pre-vaccination T helper type 1 cells were higher in the PepCan non-recurrence group compared to the PepCan recurrence group (p =0.01 for ITT and PP).

CONCLUSIONS: PepCan is safe although DLT can occur after multiple injections of PepCan. PepCan does not seem to be effective in reducing recurrence; however, the results are inconclusive given the small patient numbers. What is already known on this topic Head and neck cancer (HNC) has a high recurrence rate after reaching no evidence of disease status after standard therapies including chemotherapy, radiation, immunotherapy and survey. However, no intervention is available to reduce recurrence. What this study adds A therapeutic human papillomavirus vaccine called PepCan was tested in a clinical trial and has been shown to be safe. How this study might affect research, practice or policy If a sufficiently powered study demonstrates efficacy in reducing recurrence rate, then how HNC patients are treated after achieving the no evidence of disease status will change.},
}

@article {pmid41646784,
year = {2026},
author = {Ng, J and Trannguyen, J and Wilkinson, R and Conrad, F and Fehrenbach, S and Ebersole, B and Ghosh, D and Apewokin, S},
title = {Conditioning chemotherapy exposure is associated with epigenetic modifications in Clostridioides difficile isolates from stem cell transplant recipients.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.12.25342741},
pmid = {41646784},
abstract = {Clostridioides difficile is a highly methylated organism within the gut microbiome that is responsible for Clostridioides difficile infection (CDI), a common disease that is mediated by toxins production from the bacterium. C. difficile infection is ten times more common in chemotherapy patients than the average patient, but the reasons for this disparity are unclear. Conditioning chemotherapy (CC), an integral part of cancer treatments, has the ability to induce methylation changes in many cell types. We posit that CC induces methylation changes within C. difficile that may promote toxin production and consequently CDI. To test our hypothesis, we sought to identify the epigenetic changes, particularly methylation changes, within C. difficile isolates before and after chemotherapy and within isolates that express toxin and isolates that do not. After stool sampling, we isolated C. difficile by culture then sequenced and created a hybrid assembly of each isolate using nanopore long read sequencing and Illumina short read sequencing. Bioinformatics tools such as Dorado and Samtools were used to basecall and determine methylation states, while Unicycler was used for genome assembly. Methylartist was then used for data visualization. Genome-wide methylation profiling revealed distinct epigenetic signatures in Clostridioides difficile associated with toxin expression and chemotherapy exposure. Whole-genome 6mA analysis demonstrated significant differences between toxin-positive and toxin-negative isolates, with prominent methylation changes in tcdA and tcdE , while selected sporulation genes were unmethylated in toxin-negative strains. Chemotherapy was associated with a significant shift in global 6mA methylation patterns. Targeted 5mC analysis of the pathogenicity locus revealed reduced methylation around tcdB and across multiple toxin genes following chemotherapy, whereas sporulation genes remained unaffected. These findings indicate chemotherapy-associated epigenetic remodeling of toxin-associated loci in C. difficile .},
}

@article {pmid41646535,
year = {2026},
author = {Okeah, IR and Afzal, UM and Ali, FR},
title = {Impact of environmental pollution on acne: a systematic review.},
journal = {Skin health and disease},
volume = {6},
number = {1},
pages = {12-19},
pmid = {41646535},
issn = {2690-442X},
abstract = {In an increasingly urbanized world, environmental pollution is recognized for its adverse effects on both systemic and skin health. While its role in conditions such as atopic dermatitis and psoriasis is well documented, its impact on acne vulgaris remains less clear. This review aims to evaluate existing literature examining the association between environmental pollutants - such as particulate matter (PM2.5, PM10), nitrogen oxides (NO2, NOx) and traffic-related emissions - and the development, severity or exacerbation of acne. A systematic search of peer-reviewed English-language studies published between 2010 and 2025 was conducted using PubMed. Search terms included 'air pollution', 'particulate matter', 'PM2.5', 'PM10', 'NO2', 'NOx', 'environmental pollution', 'traffic pollution', 'acne' and 'acne vulgaris'. Studies were included if they investigated the relationship between environmental pollutants and acne in human populations. Of the 27 studies identified, 17 met inclusion criteria. Systematic reviews were also incorporated to provide broader context. Several studies demonstrated significant associations between pollutant exposure and acne exacerbation. A time-series study in China involving 71 625 outpatient visits found that each 10 μg m[-3] increase in SO2 and NO2 correlated with 1.02% and 2.13% increases in acne-related visits, respectively. Other studies appear to show pollutants being associated with increased sebum production and reduction of antioxidants. Proposed mechanisms include oxidative stress, microbiome disruption and follicular hyperkeratinization. However, study heterogeneity, lack of diversity and limited control for confounders limit generalizability. Longitudinal research is needed to clarify pollution's role in acne and inform targeted prevention strategies.},
}

@article {pmid41646429,
year = {2026},
author = {Doren, VV and Smith, S and Grimsley-Ackerley, C and Keith, J and Arthur, R and Claussen, H and Murray, P and Tangpricha, V and Hu, Y and Su, C and He, M and Kelley, C},
title = {The Biosocial Microbiome: Gender Identity, Geography, and Mucosal Microbial Phenotypes.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8368158/v1},
pmid = {41646429},
issn = {2693-5015},
abstract = {Background Transgender women (TGW) experience unique hormonal contexts and high HIV incidence, yet the mucosal microbiome among TGW remains understudied. Sex hormones and geography may shape microbial composition, but the relative contributions of gender identity, feminizing hormone therapy (FHT), and location to mucosal microbial phenotypes among key populations such as TGW are unknown. Methods We conducted a multi-site study of cisgender men who have sex with men (MSM) and TGW using FHT, both without HIV, in Atlanta, Georgia, USA (n = 58; 25 TGW, 33 MSM) and Bangkok, Thailand (n = 147; 97 TGW, 50 MSM), using cross-sectional sampling (n = 205). We also conducted longitudinal sampling in TGW (n = 21) pre/post FHT initiation. Rectal mucosal swabs were collected from all participants with optional neovaginal sampling in TGW. Microbiota composition was analyzed using 16S rRNA sequencing, and associations with gender identity, geography, and serum estradiol and testosterone concentrations were assessed using linear decomposition modeling (LDM)(1) and BOUTH analysis(2). Results Rectal microbiota differed significantly by both gender identity and geography via LDM and BOUTH analyses. TGW exhibited enrichment of estrogen-metabolizing taxa across sites, while MSM showed Prevotellaceae enrichment in Atlanta but not Bangkok. Alpha diversity varied by location but not gender identity. Neovaginal microbiota differed markedly from rectal composition, showing enrichment of skin- and gut-associated taxa (e.g., Prevotella, Peptostreptococcus, Porphyromonas) and anaerobic taxa associated with HIV seroconversion. Longitudinal analysis revealed no significant rectal microbiota shifts after short-term FHT initiation, possibly reflecting subtherapeutic hormone exposure. Conclusions These findings underscore the need to consider gender identity as a complex biosocial phenotype in HIV prevention and highlight the potential role of mucosal microbiota in shaping HIV vulnerability in TGW.},
}

@article {pmid41646428,
year = {2026},
author = {Lima, RD and Bauer, OR and Pauer, H and Hajiarbabi, K and Moreira, DA and Parente, TE and Ferreira, RBR},
title = {Cutibacterium acnes inhibits Staphylococcus lugdunensis biofilm formation through inhibition of autolysis and purine biosynthesis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8408722/v1},
pmid = {41646428},
issn = {2693-5015},
abstract = {Cutibacterium acnes is a predominant member of the human skin microbiome that plays a pivotal role in maintaining homeostasis and protecting the host against pathogen colonization. Staphylococcus lugdunensis , while also a resident of the skin microbiota, is an opportunistic pathogen capable of causing severe infections, associated with its ability to form biofilms. Building on our previous observation that C. acnes secretes molecules capable of inhibiting S. lugdunensis biofilm formation without inhibiting planktonic growth, we investigated the underlying molecular mechanisms of this phenomenon and its impact on pathogenicity. Here, we demonstrate that cell-free supernatants from various C. acnes strains exhibit dose-dependent antibiofilm activity targeting the initial stages of S. lugdunensis biofilm development. Additionally, extracellular molecules from C. acnes cultures significantly reduced the ability of S. lugdunensis to adhere to and invade human epithelial cells (A549) and to adhere to keratinocytes (HaCaT). Transcriptomic analysis revealed that C. acnes -derived molecules significantly repressed the expression of genes involved in purine biosynthesis in S. lugdunensis , while inducing the expression of the negative regulators of autolysis, lrgA and lrgB . Functional assays confirmed that C. acnes -derived molecules inhibit autolysis and extracellular DNA (eDNA) release by S. lugdunensis . Crucially, the addition of exogenous guanine suppressed the effect of C. acnes molecules on both biofilm formation and lrgA gene expression. Collectively, our data indicate that C. acnes molecules inhibit S. lugdunensis biofilm formation by depleting the intracellular guanine pool, which leads to repression of autolysis, thereby reducing the release of eDNA essential for biofilm structural integrity. These findings underscore the potential of exploiting interspecies microbiome interactions to better understand their role in pathogen exclusion.},
}

@article {pmid41646408,
year = {2026},
author = {Bosquet, JG and Osazuwa-Peters, O and Wagner, VM and Polio, A and Hoyd, R and Tarhini, AA and Cosgrove, CM and Huang, MS and Corr, BR and Leiser, AL and Salhia, B and Darcy, K and Dood, RL and Dockery, LE and Cavnar, MJ and Landrum, L and Chambers, L and Tan, AC and Jin, N and Rounbehler, RJ and Churchman, ML and Spakowicz, D},
title = {Intrinsic tumor factors and extrinsic environmental and social exposures contribute to endometrial cancer recurrence patterns.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8682460/v1},
pmid = {41646408},
issn = {2693-5015},
abstract = {Purpose In a previous study, we trained, validated and tested models of endometrial cancer (EC) recurrence integrating clinical, genomic and pathological data from the Oncology Research Information Exchange Network (ORIEN). Preliminary studies also have demonstrated that bacterial communities may influence the risk of EC recurrence by altering the local environment within the upper female genital tract. The objective of this study was to evaluate whether extrinsic and environmental factors, including tumor-associated bacterial communities, tumor immune contexture and air pollution alongside clinical, pathologic and genomic features are associated with EC recurrence across clinically relevant risk groups. Patients and Methods: We performed a retrospective, multi-institution, case-control study with data from the ORIEN network EC dataset. Data was stratified into low-risk, FIGO grade 1 and 2, stage I (N = 329), high-risk, or FIGO grade 3 or stages II-IV (N = 324), and non-endometrioid histology (N = 239) groups. RNA and DNA were extracted from tumor specimens and processed to obtain the necessary genomic/metagenomic data. Genus level microbiome data were extracted and curated) from RNA sequencing using Kraken2 , Bracken and exotic software packages. Risk of EC recurrence was evaluated by integrating microbiome and environmental data alongside existing clinical, pathological and genomic data using topic modelling with latent dirichlet allocation (LDA). Prediction models of EC recurrence were created using machine and deep learning analytics (ML and DL) with MATLAB apps and TensorFlow . Finally, performance of both topic and prediction models were externally validated in an independent EC dataset from TCGA. Results The resulting models, analyzed with topic modelling, demonstrated the complexity of factors involved in recurrence of disease for EC. The components of the resulting topic models, and specifically the microbiome, changed when environmental factors, like air pollutants, were introduced in the model. In the low-risk EC group, microbes that were quite abundant in models before introducing environmental factors, were scarcely seen afterwards, like genera Thermothielavioides , Theileria , Rhizoctonia . Bacillus was the genus with higher per-topic probability within all risk groups, especially for low-risk EC (28%). Ozone (O 3) was a resulting component of all risk groups' models. BMI was the sole informative clinical variable after data integration, and only present in the low-risk group. Resulting models from the high-risk and non-endometrioid groups included differential gene expressions: MMP13, S100A7, SMOC1, ACACA and ADD2, DLX5, SLCO2B1, NWD1 respectively. CNVs also were present in both low-risk and non-endometrioid groups, but their per-topic probabilities were low. The same was true for the immune contexture data. The components of the resulting topic models were used to train, validate and test prediction models of EC recurrence by risk groups. Performances of these models were excellent (@ 0.9). Despite some missing microbiome data in TCGA from resulting topic models, prediction models trained in the ORIEN set, had similar performances in TCGA testing set, with overlapping AUC 95% CIs. Conclusion Both extrinsic factors (tumor-associated bacterial communities, tumor immune contexture and air pollution) and intrinsic factors predict EC recurrence. The complexity of tumor and host factors influencing cancer relapses underscore the need for more individualized prediction models of disease outcomes.},
}

@article {pmid41646275,
year = {2025},
author = {Naddaf, R and Shmilovich, H and Carasso, S and Keshet-David, R and Herren, R and Gefen, T and Goshen-Lago, T and Zwang, Y and Livyatan, I and Shental, N and Haberfeld, O and Straussman, R and Markar, SR and Nilsson, M and Kashtan, H and Ben-Aharon, I and Geva-Zatorsky, N},
title = {Esophageal microbiome correlates with post-esophagectomy anastomotic leak in cancer patients.},
journal = {ESMO gastrointestinal oncology},
volume = {8},
number = {},
pages = {100172},
pmid = {41646275},
issn = {2949-8198},
abstract = {BACKGROUND: Despite continuous improvement in long-term survival after esophagectomy, potential serious post-operative complications, such as anastomotic leaks (ALs), still occur. Several risk factors for ALs have been proposed, including environmental factors. Our main objective was to examine the correlation of esophageal tumor microbiome composition and functional profile with ALs. Additionally, we analyzed the microbiome of esophageal tumors and their potential correlation with clinical features of the patients.

MATERIALS AND METHODS: Surgical specimens of esophageal tumors and adjacent normal tissues were collected from consecutive patients who underwent an esophagectomy. Formalin-fixed paraffin-embedded (FFPE) tissue samples were processed using 16S ribosomal DNA multiple fragments amplicon sequencing to characterize bacterial microbiome composition. The tumor and normal tissue microbiome and bacterial functional profile were analyzed based on the clinical outcome of ALs.

RESULTS: Out of 60 patients who met the inclusion criteria, 52 (86.7%) patients had both normal adjacent tissue (NAT) and tumor (T) FFPE samples included with sufficient bacterial DNA extracted for analysis. A total of 28% of participants had esophageal ALs. Proportion tests [P < 0.05, false discovery rate (FDR) < 0.25] revealed operational taxonomic units (OTUs) significantly present in T samples as opposed to NAT samples, as well as significantly present OTUs in patients with AL as opposed to patients without AL complication.

CONCLUSIONS: In this study, we provide a profile of the understudied esophageal microbiome and its connection to ALs. Our results can provide potential clues on how to avoid ALs by considering a patient's personal microbiome when providing perioperative care.},
}

@article {pmid41646110,
year = {2024},
author = {Kennedy, J and Iyer, K and Grinspan, A and Lai, J},
title = {Safe and successful fecal microbiota transplantation for recurrent Clostridioides difficile infection in a child with an intestinal transplant.},
journal = {Intestinal Failure (New York, N.Y.)},
volume = {4},
number = {},
pages = {100046},
pmid = {41646110},
issn = {2950-4562},
abstract = {Fecal microbiota transplantation (FMT) treats patients with recurrent Clostridioides difficile infections (CDI) by restoring the colonic flora with a balanced microbiome. There are currently no reports of safe and successful FMT in pediatric patients with history of intestinal transplant on immunosuppression. Our case report describes a 6-year-old boy with a multi-visceral transplant (including: stomach, small bowel, colon, liver, pancreas, and en-bloc bilateral kidneys) who had recurrent CDI episodes treated with antibiotics (including prolonged tapers). After multiple recurrences, he had a FMT via colonoscopy. The fecal preparation was inserted in the transplanted cecum without complication. The patient did well without any adverse events or need for hospitalization and the FMT was a success, as he had no recurrent symptoms in the 3 months following FMT.},
}

@article {pmid41645949,
year = {2025},
author = {Narang, H and Ahuja, V},
title = {'Mining' the Gut: The Microbiome 'Lassonde curve'.},
journal = {The National medical journal of India},
volume = {38},
number = {5},
pages = {257-263},
doi = {10.25259/NMJI_1737_2025},
pmid = {41645949},
issn = {2583-150X},
}

@article {pmid41645895,
year = {2026},
author = {Krishna, M and Boyer, JL},
title = {Ileal Bile Acid Transporter Inhibitors in Cholestasis: Potential for More Than Just Paediatrics?.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {3},
pages = {e70524},
doi = {10.1111/liv.70524},
pmid = {41645895},
issn = {1478-3231},
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Cholestasis/drug therapy ; *Ileum/metabolism/drug effects ; Organic Anion Transporters, Sodium-Dependent/antagonists & inhibitors ; Pruritus/drug therapy/etiology ; Enterohepatic Circulation/drug effects ; Carrier Proteins ; Membrane Glycoproteins ; Methylamines ; Thiazepines ; },
abstract = {Ileal bile acid transporter inhibitors (IBATi) are a new, attractive therapeutic mechanism to alter the enterohepatic circulation through depletion of the bile acid pool by blocking bile acid reuptake in the ileum leading to improvements in pruritus and liver function in cholestatic liver diseases. These drugs may also have an impact on immunity, the gut microbiome, and motility. IBATi are approved in Japan for the treatment of idiopathic chronic constipation. There are two IBATi, maralixibat and odevixibat, that have been extensively investigated in clinical trials and are FDA approved for cholestatic pruritus in progressive familial intrahepatic cholestasis and Alagille syndrome. Clinical trials exploring IBATi in other cholestatic conditions, such as biliary atresia, primary biliary cholangitis, and primary sclerosing cholangitis, are currently ongoing. In this review, we will outline the emerging data regarding the physiology and mechanism of action for the IBATi class, an overview of clinical trials that led to the approval of maralixibat and odevixibat, ongoing clinical trials in adult cholestatic liver diseases, and the future of this drug class in systemic apical sodium bile acid transporter inhibitors.},
}

Humans
*Bile Acids and Salts/metabolism
*Cholestasis/drug therapy
*Ileum/metabolism/drug effects
Organic Anion Transporters, Sodium-Dependent/antagonists & inhibitors
Pruritus/drug therapy/etiology
Enterohepatic Circulation/drug effects
Carrier Proteins
Membrane Glycoproteins
Methylamines
Thiazepines

@article {pmid41645696,
year = {2026},
author = {Peng, J and Yan, Q and Hassan, MU and Imran, M and Haider, FU and Liang, J and Wang, X and Ali, S},
title = {Metarhizium anisopliaeMitigates the Phytotoxicity of Lead and Nanoplastics on Rice by Modifying Physiological, Transcriptomic, Metabolomic Activities, and Soil Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e21570},
doi = {10.1002/advs.202521570},
pmid = {41645696},
issn = {2198-3844},
support = {YNDG202402YY02//Yunnan Daguan Laboratory/ ; 2023530000241004//Key Science and Technology Projects of YNTC/ ; 2024CXTD11//Modern Agricultural Technology Industry System of Shandong province/ ; },
abstract = {Polyethylene nanoplastics (NP) and lead (Pb) increasingly co-occur in agriculture, where their effects exacerbate phytotoxic impacts. We tested whether the endophytic entomopathogenic fungus, Metarhizium anisopliae, can mitigate individual or combined stress of NP and Pb in rice by examining fungus-soil-plant mechanisms using physiological assays, transcriptomics, metabolomics, and rhizosphere microbiome profiling. Rice seedlings were grown under eight treatments (individual or combined stress of Pb and NP, with or without M. anisopliae). Individual and combined Pb and NP stress reduced seedling growth, chlorophyll content, and hormonal levels, while increasing oxidative damage. Pb and NP interactions showed synergistic toxicity, causing severe growth suppression and lipid peroxidation, and repressing photosynthesis and hormone-related pathways. M anisopliae inoculation alleviated these effects and enhanced rice growth by reducing Pb uptake and translocation, restoring antioxidant and hormonal balance, and up-regulating pathways including flavonoid biosynthesis, ABC transporters, and hormone signaling. Pb measurements showed fungal inoculation restricted Pb uptake as a protective mechanism. M. anisopliae reshaped the soil bacterial community, enriching taxa associated with plant growth promotion and contaminant tolerance. These findings identify M. anisopliae seed inoculation as a strategy to mitigate Pb and NP phytotoxicity in rice by integrating contaminant uptake control with plant and rhizosphere reprogramming.},
}

@article {pmid41645639,
year = {2026},
author = {Toppila-Salmi, S and Reitsma, S and Hox, V and Gane, S and Gevaert, P and Maza-Solano, J and Helevä, A and Sulku, I and Santala, K and Kangasniemi, I and Klimek, L and Chaker, A and Karavelia, A and Rudenko, M and Pfaar, O and Van Gerven, L and Ariana, S and Schiappoli, M and Lundberg, M and Hagemann, J and Eguíluz-Gracia, I and Moreira, A},
title = {Comorbid Chronic Rhinosinusitis and Asthma: Shared Risk Factors and Treatment Implications-An EAACI Task Force Report.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70237},
pmid = {41645639},
issn = {1398-9995},
support = {40211//European Academy of Allergy and Clinical Immunology (EAACI) under the EAACI (project Prevalence and predictive factors for comorbid CRS and asthma/ ; //Foundation of the Finnish Anti-Tuberculosis Association/ ; //Tampereen Tuberkuloosisäätiö/ ; //Allergy Research Foundation/ ; //State funding for university-level health research/ ; },
abstract = {Chronic rhinosinusitis (CRS) and asthma are prevalent conditions that often coexist. These diseases share common inflammatory mechanisms, such as T-helper cell 2 (T2)-high inflammation, driven by interleukin (IL)-4, IL-5, and IL-13 cytokines. The frequent comorbidity between CRS, especially CRS with nasal polyps (CRSwNP), and asthma exacerbates disease severity, impairs quality of life, and complicates treatment. Patients with NSAID-exacerbated respiratory disease (N-ERD) represent a severe phenotype of this disease, characterized by the coexistence of CRSwNP, asthma, and NSAID hypersensitivity, which poses unique therapeutic challenges. This EAACI Task Force explores the shared risk factors, including genetic predispositions, epithelial barrier dysfunction, microbiome dysbiosis, underlying CRS, and asthma. It also evaluates current therapeutic strategies such as biologics, aspirin therapy after desensitization (ATAD), and endoscopic sinus surgery (ESS). Biologics have shown their effectiveness and safety in the treatment of asthma and CRS. Dupilumab, mepolizumab, depemokimab, and omalizumab have emerged as transformative therapies, particularly for patients with severe type 2 inflammation. Tezepelulumab is effective for both T2-high and T2-low asthma and CRSwNP. Itepekimab has shown its effect in asthma and is under investigation for CRSwNP. Omalizumab is effective in allergic asthma and CRSwNP. ATAD provides an additional disease-modifying approach for N-ERD, though patient adherence and tolerability remain critical challenges. ESS significantly improves asthma control, reduces medication use, and enhances sinonasal outcomes, particularly in severe asthma cases; however, these patients often need recurring surgeries. Despite these advances, treatment outcomes vary based on individual phenotypes and endotypes, underscoring the need for personalized approaches. The report highlights gaps in the literature, such as the lack of head-to-head trials comparing biologics, ATAD, and surgery. Future research should focus on refining treatment algorithms, identifying biomarkers for treatment selection, and assessing long-term outcomes to optimize care for patients with CRS, asthma, and N-ERD.},
}

@article {pmid41645608,
year = {2026},
author = {Bohn, B and Tilves, C and Tanaka, T and Ferrucci, L and Chia, CW and Spira, A and Mueller, NT},
title = {Initiation of Proton Pump Inhibitors is Associated with Gut Microbiome Diversity and Composition: a new-user target trial emulation within the Baltimore Longitudinal Study of Aging.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwag026},
pmid = {41645608},
issn = {1476-6256},
}

@article {pmid41645592,
year = {2026},
author = {Sindelar, M and Kocurkova, A and Simek, M and Roudnicky, P and Ambrozova, G and Kubala, L and Turkova, K},
title = {Revisiting Hyaluronan Catabolism in Bacteroides: Pathway Conservation, Overlooked Proteins, and Predictive Accuracy.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70227},
doi = {10.1002/mbo3.70227},
pmid = {41645592},
issn = {2045-8827},
support = {//Czech Academy of Sciences/ ; 25-16326S//Czech Science Foundation/ ; LX22NPO5104//Next Generation EU/ ; LM2023042//MEYS CR/ ; 90254//MEYS CR/ ; CZ.02.01.01/00/23_015/0008175//European Regional Development Fund-Project/ ; },
mesh = {*Hyaluronic Acid/metabolism ; *Bacteroides/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; Proteomics ; *Metabolic Networks and Pathways/genetics ; Gastrointestinal Microbiome ; },
abstract = {The ability of gut microbes to degrade host- and diet-derived glycans is central to microbiome ecology and host interactions, yet predicting these functions in silico remains challenging. Hyaluronan (HA), a glycosaminoglycan (GAG) abundant in host tissues and dietary supplements, is depolymerized by specialized polysaccharide utilization loci (PULs) in Bacteroides. Here, we combined comparative protein analysis, functional assays, and quantitative proteomics to evaluate the reliability of sequence-based predictions of HA utilization. Clustering of more than 3900 PL8 and GH88 protein sequences from 54 Bacteroides species did not distinguish known HA degraders from nondegraders, underscoring the limited predictive power of these enzymes alone. Experimental validation in Bacteroides acidifaciens DSM 111135 and Bacteroides thetaiotaomicron DSM 2079 confirmed HA degradation, as HA-derived fragments were identified by liquid chromatography-mass spectrometry. Proteomic profiling revealed coordinated induction of both canonical GAG-specific PULs-encoded proteins and noncanonical accessory proteins (BT4410/BT4411) in response to HA in both species. Incorporating such noncanonical components into comparative frameworks may improve prediction of glycan utilization potential and help link microbial genomic content to ecological function in the gut.},
}

*Hyaluronic Acid/metabolism
*Bacteroides/metabolism/genetics
*Bacterial Proteins/metabolism/genetics
Proteomics
*Metabolic Networks and Pathways/genetics
Gastrointestinal Microbiome

@article {pmid41645591,
year = {2026},
author = {Han, SJ and Wei, JL and Xu, QQ and Wei, XH and Shang, H},
title = {Association of Butyrate Supplementation with Cardiovascular Disease:A Narrative Review.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {3},
pages = {e70374},
doi = {10.1002/mnfr.70374},
pmid = {41645591},
issn = {1613-4133},
support = {82574739//National Natural Science Foundation of China/ ; 2024-JYB-JBZD-046//The Fundamental Research Funds for the Central Universities/ ; 2025M773867//China Postdoctoral Science Foundation/ ; },
mesh = {Humans ; *Cardiovascular Diseases/prevention & control ; *Butyrates/pharmacology/administration & dosage ; *Dietary Supplements ; Gastrointestinal Microbiome/drug effects ; Animals ; },
abstract = {Cardiovascular diseases (CVDs) have long been a significant source of the global disease burden and a leading cause of death and disability. In recent years, the precise microbiome modulation of the gut has made remarkable progress as a new strategy for treating CVDs, especially its production of short-chain fatty acids, the primary way the gut flora affects the organism. Butyrate, one of the critical metabolites of short-chain fatty acids, butyrate uniquely restores intestinal barrier function, suppresses systemic inflammation, promotes immune tolerance, and regulates energy metabolism while antagonizing the pro-atherogenic metabolite trimethylamine-N-oxide (TMAO) via the gut-heart axis. Preclinical studies consistently show that butyrate supplementation mitigates heart failure (HF), atherosclerosis, myocardial infarction, hypertrophic cardiomyopathy, hypertension, and cancer-related cardiac injury, and concurrently ameliorates metabolic syndrome, dyslipidaemia, and hyperglycaemia. However, clinical translation is currently hampered by a lack of large-scale human randomized controlled trials (RCTs) and an insufficient understanding of human dose-response relationships. This review synthesizes knowledge on butyrate's cardiovascular actions, details the underlying mechanisms, and highlights critical evidence gaps to inform future translational research.},
}

Humans
*Cardiovascular Diseases/prevention & control
*Butyrates/pharmacology/administration & dosage
*Dietary Supplements
Gastrointestinal Microbiome/drug effects
Animals

@article {pmid41645327,
year = {2026},
author = {Zubair, A and Alkahtani, AM and Shahani, MY and Afghan, N},
title = {Gut microbiome-based strategies for HIV prevention and therapy, current challenges and future prospects.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {11},
pmid = {41645327},
issn = {1757-4749},
abstract = {The gut microbiome has become a primary controller of host immunity as well as the pathogenesis of human immunodeficiency virus (HIV) infection. Commensal microbes in healthy persons keep the intestinal and other body barriers intact and regulate mucosal and systemic immune responses and generate metabolites, including short-chain fatty acids and indole derivatives that suppress inflammation and stimulate epithelial healing. These functions are impaired by HIV infection via depletion of gut CD4 + T cells, damage caused to epithelium, microbial translocation, and microbiota disruption. In this review article, we summarize recent studies suggesting that a balanced microbiome can mitigate HIV susceptibility and progression by preserving mucosal defenses, limiting systemic immune activation, and generating antiviral compounds. Other interventions, including probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation (FMT), have been trialed with mixed outcomes in most cases, showing small but significant changes in the gut microbial composition and/or inflammatory markers. Current evidence highlights the potential of microbiome-targeted strategies to support HIV management; however, substantial gaps remain. Future research should focus on defining protective microbial signatures, developing next-generation live biotherapeutics, exploring metabolite-based therapies, and conducting large, mechanistically driven clinical trials. Harnessing the microbiome's protective functions could offer novel approaches to reducing HIV transmission, mitigating inflammation, and improving immune reconstitution in infected individuals.},
}

@article {pmid41645314,
year = {2026},
author = {Lu, R and Zhang, Z and Cai, J and Zhao, G and Shen, W and Yang, Y and Jiang, Z and Hu, H},
title = {Veillonella, Neisseria, Prevotella, and Lachnoanaerobaculum enrichment in salivary microbiome predicts gallstone disease.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03869-0},
pmid = {41645314},
issn = {2047-783X},
support = {81770625, 81770626//National Natural Science Foundation of China/ ; },
abstract = {INTRODUCTION: Gallstone disease (GSD) is a common hepatobiliary disorder influenced by bile composition, biliary drainage, and gallbladder motility. Emerging evidence suggests that oral microbiota may contribute to GSD development, but its role remains unclear. This study explores salivary microbiome alterations in GSD patients and their potential clinical relevance.

METHODS: This study enrolled 58 GSD patients and 10 age-matched healthy controls. Salivary microbiome profiles were characterized using high-resolution 16S rRNA amplicon sequencing. All participants underwent comprehensive clinical evaluations including physical examinations, oral health assessments, anthropometric measurements, and fasting venous blood sampling for serum biochemical analysis. A multi-dimensional approach was applied to investigate host-microbiome interactions and their potential role in GSD pathogenesis.

RESULTS: Comparative analysis revealed significant microbial divergence between GSD patients and healthy controls, characterized by increased α-diversity indices and distinct β-diversity clustering. The linear discriminant analysis effect size (LEfSe) analysis identified 65 differentially abundant taxonomic features across multiple phylogenetic levels, including 7 phyla, 9 classes, 11 orders, 16 families, and 22 genera, representing 550 operational taxonomic units (OTUs). Notably, Veillonella, Neisseria, Prevotella, and Lachnoanaerobaculum were markedly enriched in the GSD cohort. The developed eXtreme Gradient Boosting (XGBoost) diagnostic model demonstrated exceptional discriminatory capacity, achieving a mean AUC of 0.994 under rigorous fivefold cross-validation. Redundancy analysis (RDA) and Spearman correlation analysis showed strong associations between microbial community structure and key biochemical markers, including chenodeoxycholic acid (CDCA) and alkaline phosphatase (ALP). Functional prediction using PICRUSt2 indicated substantial metabolic pathway alterations in GSD patients, particularly enhanced activity in energy production, amino acid metabolism, and secondary metabolite biosynthesis.

CONCLUSIONS: Salivary microbiome dysbiosis in GSD patients demonstrated significant associations with disrupted bile acid homeostasis, suggesting a potential role of the oral microbiota in modulating lithogenic processes. The markedly altered microbial signatures may contribute to GSD pathogenesis, while the XGBoost-based diagnostic model shows considerable promise as a noninvasive tool for GSD detection.},
}

@article {pmid41645302,
year = {2026},
author = {Barrett, DE and Heintzman, LJ and Davidson, GR and Jackson, CR and Moore, MT},
title = {Barking up the right tree: ecological insights into the microbiome of bald cypress tree bark.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00862-2},
pmid = {41645302},
issn = {2524-6372},
abstract = {BACKGROUND: Trees and their associated microbes provide numerous ecosystem services including carbon sequestration, nutrient cycling and phytoremediation. Tree bark represents a large and seasonably stable habitat for microbial communities. However, the tree bark microbiome remains largely understudied, particularly for wetland tree species. In the Lower Mississippi River Basin, bald cypress (Taxodium distichum) are the predominant tree species in many wetlands, including lakes and streams connected to large agroecosystems dominated by row-crop agriculture. These water bodies are often managed for irrigation and drainage needs and are subject to agrochemical runoff from adjacent fields. Thus, we sought to understand how hydrology affects the bald cypress bark microbiome.

RESULTS: We collected 278 bark samples over six months from 18 trees located in three different lakes. Using 16S rRNA gene sequencing, we found that the bald cypress tree bark microbiome was largely consistent between trees within a lake as well as between different lakes, with a core microbiome that includes bacterial taxa that were present in over 95% of samples collected. Hydrology had a significant influence on microbiome structure, with different sections of bark having distinct bacterial communities depending on if the bark was submerged, just above the water, or dry. Water quality was significantly correlated with alpha diversity of wet bark, which was more diverse than dry bark and had higher relative abundances of bacteria that may be providing relevant ecosystem services such as denitrification, methane oxidation, and pollutant degradation.

CONCLUSIONS: Wetlands are important for nutrient cycling and water quality regulation. Our study provides insights into microbial dynamics of these ecosystems and how hydrology can impact the microbial communities present, which in turn may be impacting water quality. This work is the first to the describe the bark microbiome of a wetland tree species and lays the groundwork for future studies assessing the functional role of the microbiome in wetland ecosystem services.},
}

@article {pmid41645294,
year = {2026},
author = {Zhang, ZY and Wei, GF and Hou, LY and Zhang, GZ and Li, XD and Li, M and Meng, L and Wu, GY and Xu, J and Zhou, YX and Sun, C and Dong, LL},
title = {Effects of developmental stage-driven fungal community shifts on biomass and metabolite accumulation in Gastrodia elata.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00860-4},
pmid = {41645294},
issn = {2524-6372},
support = {CI2023E001TS03-04-01//grants from the Scientific and technological innovation project of China Academy of Chinese Medical Science/ ; 2024SF-ZDCYL-03-10//Shaanxi Province Key R&D Plan/ ; HJSYF2024(31)//Nuclear Technology R&D Program/ ; },
abstract = {BACKGROUND: Fungal communities play crucial roles in plant development and metabolite accumulation, especially in fully mycoheterotrophic medicinal plants like Gastrodia elata. While the importance of fungal symbiosis in G. elata is recognized, how fungal community dynamics evolve across its entire growth cycle and how they influence biomass and bioactive compound accumulation remain largely unclear.

RESULTS: High-throughput sequencing combined with multi-omics analyses revealed that developmental progression significantly shapes fungal diversity and composition, thereby influencing biomass and metabolite accumulation in G. elata. These effects are mediated by stage-specific selective recruitment and dynamic remodeling of fungal communities in both rhizome and rhizosphere compartments. Structural equation modeling indicated that developmental stage, fungal α-diversity, and community structure exert both direct and indirect effects on biomass and the accumulation of bioactive compounds. High-resolution association network analyses further identified key functional fungal groups, particularly wood and soil saprotrophs, as major contributors to seed stem biomass regulation. Notably, the symbiotic fungus Armillaria showed the strongest positive correlation with gastrodin accumulation, while wood saprotrophs and plant pathogens also significantly influenced its levels.

CONCLUSIONS: This study systematically elucidates the dynamic changes in fungal communities across different developmental stages of G. elata and their effects on biomass and bioactive metabolite accumulation. Our findings highlight the central role of microbe-plant-metabolite interactions in regulating biomass and bioactive metabolite production, offering valuable insight for optimizing the cultivation and quality of medicinal plants through microbiome-targeted strategies.},
}

@article {pmid41645277,
year = {2026},
author = {Ramírez, GA and Bar-Shalom, R and Perez, T and Epchtien, RE and Furlan, A and Romeo, R and Gavagnin, M and Garber, AI and Lalzar, M and Steindler, L},
title = {Diel transcriptional dynamics of a marine sponge and its microbiome in a natural environment.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {12},
pmid = {41645277},
issn = {2524-4671},
support = {GBMF9352//Gordon and Betty Moore Foundation/ ; 933/23//Israel Science Foundation/ ; },
}

@article {pmid41645116,
year = {2026},
author = {Wang, X and Long, T and Shen, L and Hu, Y and Zou, Y and Wang, Z and Yang, K and Dai, F and Song, L},
title = {Periodontal disease-associated oral and gut microbiome changes in female rheumatoid arthritis patients.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-07831-8},
pmid = {41645116},
issn = {1472-6831},
support = {no. 82460196//the National Natural Science Foundation of China/ ; no. 20252BCG330024//the Key R&D Program of Jiangxi Province, China/ ; no. jxsq2023201045//the Double Thousand Talents Project of Jiangxi Province/ ; no. G/Y3034//the High-level and High-skilled Leading Talent Training Project of Jiangxi Province/ ; },
}

@article {pmid41645099,
year = {2026},
author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z},
title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04800-7},
pmid = {41645099},
issn = {1471-2180},
support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.

RESULTS: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.

CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.},
}

@article {pmid41645047,
year = {2026},
author = {Thalib, HI and Fatima, N and Fakruddin, FH and Ali, HH and Khan, S and Zubair, MTM and Pereira, M and Sayed Hassan, FE},
title = {Modulating the Gut Microbiome as a Therapeutic Approach in Multiple Sclerosis: Implications for Gut-Brain Interactions and Immune Pathways: A Narrative Review.},
journal = {Brain and behavior},
volume = {16},
number = {2},
pages = {e71254},
doi = {10.1002/brb3.71254},
pmid = {41645047},
issn = {2162-3279},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Multiple Sclerosis/immunology/microbiology/therapy/metabolism ; Animals ; *Dysbiosis/immunology ; *Brain-Gut Axis ; Probiotics ; Brain/immunology ; },
abstract = {PURPOSE: Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system characterized by progressive disability. Emerging evidence has implicated gut microbiome dysbiosis, characterized by decreased short-chain fatty acids (SCFAs)-producing taxa and increased pro-inflammatory species, in disturbed immune signaling, T-helper17/T-regulatory cells imbalance, disturbed tryptophan metabolism, and disrupted integrity of the blood-brain barrier. In this review, we summarize the mechanistic and therapeutic insights from studies that have explored the gut microbiome in MS.

METHOD: We performed a literature search in PubMed, Scopus, Web of Science, and ClinicalTrials.gov from database inception to January 2025; only English-language articles were included, comprising human MS cohorts and preclinical experimental autoimmune encephalomyelitis models. Of these, approximately 95 human and preclinical studies fulfilled the inclusion criteria. Evidence synthesis was narrative, without meta-analysis.

FINDING: There has been a consistent depletion of beneficial genera such as Faecalibacterium and Roseburia, expansion of Akkermansia muciniphila, and reduction in microbial metabolites such as butyrate, propionate, and neuroactive indole derivatives in MS patients across studies. These changes promote intestinal permeability, exaggerated pro-inflammatory cytokine responses, and microglial activation. The therapeutic approach of restoring microbial balance includes therapies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and dietary interventions. Early trials have shown modest improvements in relapse rates, fatigue, immune profiles, and microbiome composition. Results across randomized studies are heterogeneous, with no significant clinical benefit in several. Pilot trials report modest reductions in relapse rate (RR ≈ 0.85) and fatigue (Cohen's d ≈ 0.3), but several double‑blind RCTs showed no significant benefit (p  >  0.05) in up to 40% of participants, highlighting variable effect sizes.

CONCLUSION: Interventions aimed at the microbiome are promising as adjunct approaches to the treatment of MS, acting principally through the restoration of SCFAs, immune modulation, and strengthening of the gut-brain axis. Larger, longer-term randomized trials are required to confirm clinical efficacy, define responder phenotypes, and inform personalized microbiome-based therapies.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
*Multiple Sclerosis/immunology/microbiology/therapy/metabolism
Animals
*Dysbiosis/immunology
*Brain-Gut Axis
Probiotics
Brain/immunology

@article {pmid41645037,
year = {2026},
author = {Zhao, G and Mosby-Tourtellot, CA and Rosero, J and Schultz, AC and Khan, E and Elamrani, O and Ferraro, MJ and Kima, PE and Jones, MK},
title = {Induction of DNA-mediated immune responses by bacterial extracellular vesicles results in control of murine norovirus infection.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2624171},
doi = {10.1080/19490976.2026.2624171},
pmid = {41645037},
issn = {1949-0984},
mesh = {Animals ; *Extracellular Vesicles/immunology ; *Norovirus/immunology/physiology ; Mice ; *Caliciviridae Infections/immunology/virology ; Toll-Like Receptor 9/genetics/immunology ; Mice, Inbred C57BL ; Membrane Proteins/genetics/immunology ; Virus Replication ; Interferon-beta/immunology ; *Bacteria/immunology/genetics ; Interferon Type I/immunology ; Gastrointestinal Microbiome ; Mice, Knockout ; STING Protein ; },
abstract = {Commensal bacteria have been a centerpiece for understanding interkingdom impacts on viral replication. Multiple groups have investigated the roles commensal bacteria played in regulating enteric virus infection and it has been found that the mechanisms through which this regulation occurs varies between the viruses and bacteria explored. For noroviruses, commensal bacteria enhance or suppress viral infection in a region-dependent manner. Recently, it was found that the extracellular vesicles (EVs) produced by commensal bacteria can suppress norovirus infection. In this study, we used murine norovirus (MNV) to probe the immunological mechanisms induced by bacterial EVs. Global analysis of gene expression pointed to induction of cytosolic DNA pathways; thus, we evaluate the DNA content packaged within the bacterial EVs and DNA-sensing pathways that activate type I interferons (IFN), including STING and TLR9. Our results showed that loss of sting or tlr9, significantly decreased IFNβ production and recovered MNV replication in the presence of bEVs. Collectively, these data demonstrated bEVs of certain gram-negative bacteria can initiate antiviral DNA-mediated type I IFN production pathways and that these pathways are involved in the suppression of MNV replication. These findings expose novel mechanisms through which the native microbiota aids the host in controlling an enteric viral infection and offers a fresh perspective on interkingdom host‒microbiota interactions.},
}

Animals
*Extracellular Vesicles/immunology
*Norovirus/immunology/physiology
Mice
*Caliciviridae Infections/immunology/virology
Toll-Like Receptor 9/genetics/immunology
Mice, Inbred C57BL
Membrane Proteins/genetics/immunology
Virus Replication
Interferon-beta/immunology
*Bacteria/immunology/genetics
Interferon Type I/immunology
Gastrointestinal Microbiome
Mice, Knockout
STING Protein

@article {pmid41645021,
year = {2026},
author = {Lussac-Sorton, F and Narayana, JK and Wizla, N and Tatopoulos, A and Baravalle, M and Rotidis, L and Houdoin, V and Llerena, C and Reix, P and Sermet, I and Languepin, J and Charpentier, E and Lefranc, M and Alves Gomes, P and Bui, S and Beaufils, F and Berger, P and Chotirmall, SH and Delhaes, L and Enaud, R},
title = {Gut-lung microbial dynamics with lumacaftor/ivacaftor in children with cystic fibrosis: a prospective multicenter study.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41645021},
issn = {1530-0447},
abstract = {BACKGROUND: CFTR modulators such as lumacaftor/ivacaftor (LUM/IVA) may reshape microbiota-mycobiota composition in the lungs and gut. While the gut-lung axis is established in other settings, little is known about its role following modulator therapy, particularly in the 2-11 age group.

METHODS: In a prospective national multicentre study, 116 children with cystic fibrosis (2-11 years) starting LUM/IVA were followed for 12 months. Stool and sputum were collected at baseline, 3, 6 and 12 months. Bacterial and fungal communities were profiled by 16S rRNA and ITS2 sequencing; diversity, dysbiosis indices, faecal and sputum calprotectin, and gut-lung microbial networks were analysed.

RESULTS: LUM/IVA was associated with increased bacterial diversity and compositional shifts in gut and lung microbiota, alongside a significant reduction in faecal calprotectin. Airway mycobiota diversity remained stable. Two lung microbiome response profiles emerged: "responders" (greater bacterial diversity gain) and "non-responders" (minimal change). Baseline gut and lung composition predicted these profiles with 81% accuracy in a random-forest model. Inter-organ microbial interactions peaked at 3 months after initiation and then diverged between profiles, indicating distinct gut-lung axis remodelling.

CONCLUSION: LUM/IVA influences gut-lung microbiota-mycobiota dynamics, with heterogeneous responses between paediatric patients. Identifying factors predictive of response is a key future challenge.

IMPACT: In 116 children aged 2-11, lumacaftor/ivacaftor reshaped gut and lung microbiota and reduced fecal calprotectin over 12 months. First pediatric multicenter study integrating bacterial and fungal profiling of stool and sputum with gut-lung network analyses; identifies two distinct lung microbiome response profiles. Baseline gut and lung composition predicted the response profile with approximately 81% accuracy. Highlights a 3-month interaction peak and baseline profiling as practical markers to guide monitoring and microbiome-informed precision care.},
}

@article {pmid41644858,
year = {2026},
author = {Vaghela, P and Dave, B and Dabhade, A and Deshmukh, R and Prajapati, B and Alsaidan, OA and Patel, S and Mehta, A and Singh, A and Dudhat, K},
title = {Redrawing the gut map: evolving probiotic approaches to microbiota modulation in inflammatory bowel disease.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {3},
pages = {51},
pmid = {41644858},
issn = {1572-9699},
mesh = {*Probiotics/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Inflammatory Bowel Diseases/microbiology/therapy ; Dysbiosis/therapy ; },
abstract = {Inflammatory bowel disease (IBD), comprising Ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory disorder of the gastrointestinal tract (GIT) that occurs due to several factors, including, but not limited to, gut microbiota dysbiosis, immune dysregulation, and environmental factors. Despite significant advances in IBD pharmacotherapy, patients often experience treatment failures due to suboptimal treatment responses, frequent relapses, and are also susceptible to developing several adverse effects (AEs), highlighting the need for developing alternative therapies. A growing body of evidence necessitates the importance of maintaining gut microbiome homeostasis, which is commonly disrupted in IBD. Probiotics have emerged as promising adjunctive IBD therapies due to their capacity to modulate immune responses, restore gut microbial balance, and preserve mucosal barrier integrity. Multiple probiotic strains, including Escherichia coli (E. coli) Nissle 1917, Lacticaseibacillus rhamnosus GG, Bifidobacterium longum (B. longum), Saccharomyces cerevisiae var. boulardii (S. boulardii), and combination formulations, such as VSL#3 (Lactobacillus, Bifidobacterium, and Streptococcus thermophilus), have demonstrated superior efficacy in inducing and maintaining remission in comparison with placebo and comparable efficacy with conventional treatments, such as mesalazine. While the efficacy of probiotics has been demonstrated in UC through several clinical studies, evidence supporting their use in CD remains inconsistent, with studies yielding mixed or inconclusive results. This highlights the necessity for additional carefully designed, large-scale studies specifically targeting CD patients to better understand the therapeutic potential of probiotics in a broader context. Finally, emerging innovations in genetic engineering and clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) technology offer exciting prospects for the development of precision probiotics, which could possess both diagnostic and treatment benefits and further expand the clinical utility of probiotics in IBD treatment.},
}

*Probiotics/therapeutic use
Humans
*Gastrointestinal Microbiome/drug effects
*Inflammatory Bowel Diseases/microbiology/therapy
Dysbiosis/therapy

@article {pmid41644826,
year = {2026},
author = {Zhang, X and Zhang, W and Cheng, Y and Zhang, M and Xie, J and Yang, S and Yang, Y and Zhang, Z and Bai, W and Kong, W},
title = {Characterization of spatio-temporal variations in carposphere microbial diversity of olive in Longnan, China.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {76},
pmid = {41644826},
issn = {1573-0972},
support = {NWNU-LKZD2022-02//Key Scientific Research Project of Northwest Normal University/ ; 22YF7NA118//Key Research and Development Project of Gansu Province/ ; 24ZYQA039//Central Government Guides Local Science and Technology Development Funds/ ; },
mesh = {China ; *Bacteria/classification/genetics/isolation & purification ; *Olea/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fungi/classification/genetics/isolation & purification ; Biodiversity ; Phylogeny ; Spatio-Temporal Analysis ; High-Throughput Nucleotide Sequencing ; Fruit/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The fruit surface microbiome influences quality formation and disease occurrence, yet carposphere microbial diversity and functions remain poorly studied. This study employed 16S rRNA and ITS high-throughput sequencing technology to investigate the spatiotemporal variation patterns of the olive carposphere microbiome in Longnan City, Gansu Province, China, with respect to cultivars, maturity stages, and geographical locations. The results showed that the olive carposphere bacterial communities were dominated by Proteobacteria, and their abundance increased with fruit ripening. Methylobacterium-Methylorubrum showed significant enrichment at the mature stage, while Streptococcus served as a dominant genus across all geographical regions. For fungal communities, Ascomycota was the predominant phylum, while Nothophoma and Aureobasidium identified as the major genera. Diversity analyses revealed that both bacterial and fungal communities in the olive carposphere varied with cultivar, maturation stage, and geographical location. Among these factors, geographical location emerged as the most dominant driver, which implies that the environment and human activities play an important role in determining the carposphere microbiome. These findings enhance our understanding of the microbial diversity in olive carposphere, also provide valuable species information for the future use of microbial technology to modulate the fruit quality and prevent and control biological diseases.},
}

China
*Bacteria/classification/genetics/isolation & purification
*Olea/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Fungi/classification/genetics/isolation & purification
Biodiversity
Phylogeny
Spatio-Temporal Analysis
High-Throughput Nucleotide Sequencing
Fruit/microbiology
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid41644796,
year = {2026},
author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J},
title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41644796},
issn = {2058-5276},
support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.},
}

@article {pmid41644742,
year = {2026},
author = {Ziogas, DC and Theocharopoulos, C and Martinos, A and Lyrarakis, G and Stefanou, D and Anastasopoulou, A and Gogas, H},
title = {Toward Microbiome-Informed Melanoma Care: The Gut Microbiota in Melanoma Evolution, Immunotherapy Response and Immune-Related Toxicity.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {10},
pmid = {41644742},
issn = {1534-6269},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Melanoma/immunology/therapy/microbiology/pathology ; *Immunotherapy/adverse effects/methods ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; },
abstract = {PURPOSE OF REVIEW: The gut microbiome (GM) has emerged as a pivotal modulator of melanoma pathogenesis and progression through its influence on systemic inflammation, immune surveillance, and antitumor immunity. Inter-individual variability in GM composition may underlie differences in immune checkpoint inhibitor (ICI) responsiveness and the development of immune-related adverse events (irAEs). This review aims to synthesize current knowledge on the complex interplay between the GM, host immunity, and melanoma, emphasizing its relevance to disease development, therapeutic response, and toxicity.

RECENT FINDINGS: Both preclinical and clinical evidence have demonstrated that alterations in microbial diversity and composition can affect melanoma outcomes. Depletion or imbalance of specific microbial taxa has been linked to an increased risk of melanoma development or, conversely, to reduced tumor burden. In patients treated with ICIs, distinct taxonomic GM signatures have been correlated with therapeutic efficacy and the likelihood of developing irAEs. Emerging studies have also explored strategies to modulate the GM-including diet, antibiotics, probiotics, and fecal microbiota transplantation-to restore gut "eubiosis" and enhance antitumor immune responses. The intricate crosstalk between the gut microbiome, host immunity, and melanoma significantly influences disease biology and treatment outcomes. A deeper understanding of these interactions will be critical to the development of microbiome-informed, personalized approaches to melanoma management and immunotherapy optimization.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Melanoma/immunology/therapy/microbiology/pathology
*Immunotherapy/adverse effects/methods
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use

@article {pmid41644724,
year = {2026},
author = {Polidoro, EE and Stosiek, N and Laman, JD and Palmer, CA and Kriesel, JD},
title = {Spinal fluid antibody profile against bacteria demonstrates intrathecal antibody production in demyelinating diseases.},
journal = {Journal of molecular medicine (Berlin, Germany)},
volume = {104},
number = {1},
pages = {41},
pmid = {41644724},
issn = {1432-1440},
mesh = {Humans ; Female ; *Antibodies, Bacterial/cerebrospinal fluid/immunology ; Male ; Adult ; Middle Aged ; *Demyelinating Diseases/immunology/cerebrospinal fluid/microbiology ; Immunoglobulin G/cerebrospinal fluid/blood ; *Bacteria/immunology ; Multiple Sclerosis/immunology/cerebrospinal fluid ; Enzyme-Linked Immunosorbent Assay ; Aged ; *Antibody Formation ; Young Adult ; },
abstract = {This study follows work establishing multiple sclerosis (MS) microbial candidates from RNA sequencing of human brain samples. A subsequent study demonstrated anti-microbial immune responses in cerebrospinal fluid (CSF) of patients with demyelinating diseases (DD) and other neurologic diseases (OND). We aim to expand evidence for specific anti-microbial responses in CSF of patients with DD. CSF IgG ELISA assays were developed from 20 bacteria identified as MS microbial candidates. CSF responses from patients with DD (N = 16) and OND (N = 8) were determined using commercial CSF as positive and negative controls. CSF reactivity was expressed as ELISA Index (EI) values against each of the lysates. Antibody Index (AI) values were determined by comparing CSF reactivity and diluted serum samples with equivalent IgG concentrations. AI values > 1.5 were considered positive, 1.0-1.49 equivocal, and < 1.0 negative. Most samples from both groups displayed reactivity across all 20 lysates, with an overall rate of 87.8%. CSF EI values were highest against Haemophilus, Aggregatibacter, and Streptococcus, lowest against Veillonella, Fusobacterium, and Alistipes. Twenty-five percent of subjects with DD and 13% with OND had AI > 1.5 to at least one lysate. Clustering of AI values from four DD samples against Bacteroides and Lactobacillus was observed. This serological study shows reactivity against multiple bacteria in CSF from patients with primary DD including MS and OND. Elevated AI in four DD and one OND subject provides evidence for specific intrathecal antibody production in these patients. KEY MESSAGES: This study measured humoral immune responses in the cerebrospinal fluid (CSF) of human subjects with multiple sclerosis (MS) and other demyelinating diseases against 20 candidate bacteria previously identified by sequencing of diseased human brain tissue. The method described here involves diluting CSF to match the serum IgG concentrations, running an ELISA, and calculating an Antibody Index (AI). The methods described here are improved by directly measuring banked CSF and serum IgG concentrations in the laboratory. Several subjects with demyelinating diseases clustered strongly for responses against Bacteroides, Lactobacillus, Akkermansia, and Alistipes, found in the normal flora in the human gut and female genital tract.},
}

Humans
Female
*Antibodies, Bacterial/cerebrospinal fluid/immunology
Male
Adult
Middle Aged
*Demyelinating Diseases/immunology/cerebrospinal fluid/microbiology
Immunoglobulin G/cerebrospinal fluid/blood
*Bacteria/immunology
Multiple Sclerosis/immunology/cerebrospinal fluid
Enzyme-Linked Immunosorbent Assay
Aged
*Antibody Formation
Young Adult

@article {pmid41644412,
year = {2026},
author = {Nisley, MJ and Burrough, ER and Spencer, JD and Mendoza, OF and Krishnan, HB and Gabler, NK},
title = {Dietary soybean-derived trypsin inhibitor protein reduces nursery pig performance and may exacerbate F18 enterotoxigenic Escherichia coli disease.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag026},
pmid = {41644412},
issn = {1525-3163},
abstract = {Soybean-derived trypsin inhibitor proteins (TIU) impair amino acid bioavailability and increase exogenous and endogenous nitrogen flow to the hindgut, thereby attenuating pig growth performance. High protein diets potentiate proteolytic fermentation induced alterations to the gut microbiome, which may increase opportunistic enterotoxigenic Escherichia coli (ETEC) proliferation and exacerbate disease. We hypothesized that feeding high TIU diets to nursery pigs would reduce growth rates and exacerbate F18 ETEC disease. Two hundred and eighty-eight (5.42 ± 0.93 kg BW; Camborough 1050 × 337, [PIC, Hendersonville, TN]) newly weaned pigs were evenly allotted across two control rooms (CON) and two challenge rooms (ETEC). Pigs were allotted based on sex and α-(1,2) fucosyltransferase (FUT1) genotype, with both factors evenly distributed across all pens. Pens were randomly assigned to corn-soy diets consisting of 1.1, 2.4, or 4.2 TIU/mg, creating six treatments: CON1.1, CON2.4, CON4.2, ETEC1.1, ETEC2.4, and ETEC4.2 (8 pens/treatment). On day 10 (day post-infection [dpi] 0), pigs in the ETEC rooms were orally inoculated with 5 ml of 3.8 × 109 cfu/ml of an F18 ETEC culture. Pooled pen feces were assessed for dry matter (DM) on dpi 0, 3, 5, 7, 9, 11, 14, and 21. Pen growth performance, medical treatments, and mortality were assessed prior to infection (dpi -10 to 0) and post infection (dpi 0 to 28). On dpi 5 and 12, one pig/pen was sacrificed to assess ileal mucosal attachment of F18 ETEC via in situ hybridization. Pen was the experimental unit and data were analyzed for the interactive and main effects of diet and challenge. Increasing dietary TIU to 4.2 TIU/mg led to a 13-16% decrease in ADG compared to the 1.1 TIU/mg diets, regardless of the challenge (P = 0.014). A diet × challenge interaction was observed regarding mortality, with ETEC2.4 showing a 20.8% mortality rate compared to 0% in CON2.4 (P = 0.001). Similarly, 22.9% of ETEC2.4 pigs required antibiotic treatment compared with 0% of CON2.4 pigs (P = 0.001). Fecal DM from dpi 0-21 showed no interaction, but ETEC pens had lower fecal DM compared to CON pens from dpi 3-11 (P < 0.0001). On dpi 5, ileal F18 attachment was increased in ETEC versus CON pigs (3.7 × 10-3 vs 0.1 × 10-3 F18 copies/μm2, P < 0.0001). By dpi 12, ileal F18 attachment did not differ between challenge groups (P > 0.05), suggesting disease resolution. In conclusion, diets at or greater than 2.4 TIU/mg decreased pig growth and reduced livability in ETEC-infected nursery pigs.},
}

@article {pmid41644129,
year = {2026},
author = {Kreft, D and Hurka, S and Gurusinga, FF and Röthig, T and Vilcinskas, A and Tegtmeier, D},
title = {Towards Functional Fertilisers: Feed Composition Shapes Microbial Community Structure and Viability in Black Soldier Fly (Hermetia illucens) Frass.},
journal = {Environmental microbiology},
volume = {28},
number = {2},
pages = {e70249},
doi = {10.1111/1462-2920.70249},
pmid = {41644129},
issn = {1462-2920},
support = {FKZ 031B1274//German Federal Ministry of Research, Technology, and Space/ ; //Fraunhofer-Gesellschaft/ ; },
mesh = {Animals ; *Animal Feed/analysis/microbiology ; *Microbiota ; *Bacteria/classification/isolation & purification/genetics ; *Fertilizers/analysis/microbiology ; Larva/microbiology ; Fungi/isolation & purification/genetics/classification ; *Simuliidae/microbiology/growth & development ; *Diptera/microbiology ; Aquaculture ; },
abstract = {Black soldier fly larvae (BSFL) are increasingly valued as a sustainable protein source for aquaculture and can be reared on local industrial side streams, enhancing their environmental and economic benefits. The resulting frass-a byproduct of larval excreta and residual feed-shows promise as an organic fertiliser. In addition to its nutrient content, frass contains microbial communities that may enhance plant growth through phytohormone production, nitrogen fixation, and organic matter turnover. Yet, the roles of feed composition and thermal hygienisation in shaping these communities remain underexplored. This study examined the impact of five feed substrates, including industrial side streams and a control diet, on frass microbial composition, and assessed responses to thermal treatment. Feed nutrients were characterised, and microbial communities profiled using amplicon sequencing. Viable populations were quantified via culture-based methods, with bacterial isolates taxonomically classified. Feed type was the dominant factor influencing frass microbiota, with distinct communities reflecting substrate nutritional profiles. High-fibre diets promoted fungal diversity and abundance, while high-protein feeds enriched specific bacterial taxa. Thermal hygienisation had a heterogeneous effect on viable counts but minimal impact on overall community structure. These findings support microbiome-informed feed design to tailor frass microbial profiles for enhanced biofertiliser function in sustainable agriculture.},
}

Animals
*Animal Feed/analysis/microbiology
*Microbiota
*Bacteria/classification/isolation & purification/genetics
*Fertilizers/analysis/microbiology
Larva/microbiology
Fungi/isolation & purification/genetics/classification
*Simuliidae/microbiology/growth & development
*Diptera/microbiology
Aquaculture

@article {pmid41644071,
year = {2026},
author = {Ndjeambong, YC and Velmurugan, S and Patidar, P and Chouhan, V and Kundu, A and Balamurugan, A and Hussain, Z and Kumar, A},
title = {Rhizomicrobiome Diversity and Bioactive Bacterial Metabolomes of Cultivated and Wild Solanum Species Suppress Ralstonia pseudosolanacearum.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108354},
doi = {10.1016/j.micpath.2026.108354},
pmid = {41644071},
issn = {1096-1208},
abstract = {Bacterial wilt caused by Ralstonia pseudosolanacearum remains one of the most destructive diseases threatening eggplant production worldwide, as effective management options are limited, resistance in cultivated varieties is often unstable, and chemical control measures are largely ineffective and environmentally unsustainable. In this study, we profiled the rhizobacterial microbiomes of wilt-susceptible Solanum melongena and wilt-resistant S. torvum cultivated in contrasting soils from Cameroon and India representing non-endemic and endemic regions of bacterial wilt. A combined culture-dependent methodology together with 16S rRNA amplicon sequencing was used to elucidate the structure and functional attributes of the microbial communities. Soil origin was the principal factor influencing microbiome composition (PERMANOVA R[2] = 0.34, p = 0.001), followed by host genotype (R[2] = 0.21) and root niche (R[2] = 0.14). The wilt-resistant S. torvum consistently supported higher bacterial diversity and was enriched with core taxa, including Bacillus and Methanocella. Fourteen rhizobacterial isolates, mainly Bacillus spp., showed strong antagonistic activity against R. pseudosolanacearum. Metabolomic analyses using LC-QTOF-MS/MS and GC-MS indicated the production of lipopeptides and polyketides by Bacillus spp., while Pseudomonas plecoglossicida produced phenazine derivatives and indole-3-acetic acid. In greenhouse experiments, Bacillus cereus, B. velezensis, and Priestia megaterium significantly improved seed germination and seedling vigor at inoculum densities of 10[6]-10[7] CFU mL[-1]. Together, these results show that eggplant-associated rhizobacteria, particularly Bacillus spp. and P. plecoglossicida, contribute to bacterial wilt suppression and offer potential for sustainable disease management.},
}

@article {pmid41643678,
year = {2026},
author = {Wei, M and Yi, X and Lin, Z and Cai, J and Chen, S and Zhou, F and Cai, H and Lu, X and Tang, J and Shi, Y and Cui, L and Yang, L and Jing, X and Zeng, Y and Wu, R and Shu, T and Li, Y and Yang, F and He, Y and Zhao, Z and Yang, Y and Zhu, W and Jiang, Q and Zhang, W and Tan, X and Ma, Z and Fan, X and Ma, W and Li, S and Shu, W and Wei, H and Xiang, Z and Gilbert, JA and Gong, S and Wang, Z},
title = {Ketogenic diet alleviates septic lung injury via microbial gut-lung axis.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2026.01.005},
pmid = {41643678},
issn = {1932-7420},
abstract = {Sepsis is characterized by impaired immunity to infection, leading to multi-organ dysfunction, with the lung being the most vulnerable organ. Here, we show that ketogenic diet (KD) alleviates sepsis-induced lung injury through a microbial-gut-lung axis. KD alters the gut microbiota in mice and humans, enriching Limosilactobacillus reuteri and Lactiplantibacillus plantarum. Specific strains of these species produce a flavin-dependent monooxygenase (FMO) that converts oleic acid in KD into azelaic acid (AZA). During sepsis, AZA translocates to the lung, where it promotes neutrophil apoptosis and expands MerTK[+] alveolar macrophages (AMs) via PPAR-γ activation, enhancing efferocytosis and resolution of lung injury. In patients with sepsis, elevated AZA correlates with improved clinical outcomes, including survival rates, ventilation-free days (VFDs), and pulmonary function, along with increased MerTK[+] AMs and apoptotic neutrophils in patient lungs. These findings uncover a pathway of gut-lung crosstalk mediated by diet-microbiome interactions, highlighting the therapeutic potential of KD and microbiome modulation in sepsis.},
}

@article {pmid41643502,
year = {2026},
author = {Perrett, BM and Miliku, K and Moraes, TJ and Simons, E and Mandhane, P and Kebbe, M},
title = {Gut microbiota responses to complementary food sources differ by milk feeding type.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {58},
number = {},
pages = {106587},
doi = {10.1016/j.clnu.2026.106587},
pmid = {41643502},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Early-life nutrition shapes host-microbe interactions with lasting consequences for health. While dietary patterns are known to influence the infant gut microbiome, the impact of solid food source (homemade, commercial, or mixed) has not been examined. Our aims were to determine how solid food source at 6 months relates to infant gut microbiome diversity and composition at 1 year, and whether relationships differ by milk feeding type..

METHODS: We conducted a secondary analysis within the Canadian Healthy Infant Longitudinal Development (CHILD) cohort. Solid food source was assessed at 6 months, and stool samples at 1 year were profiled using 16S rRNA sequencing. Generalized linear models were used to assess alpha-diversity; permutational multivariate analysis of variance (PERMANOVA) was used to evaluate beta-diversity based on OTU-level Bray-Curtis dissimilarities; and Microbiome Multivariate Association with Linear Models 2 (MaAsLin2), using centered log-ratio normalization, was used to examine taxa-level associations, adjusting for relevant perinatal and dietary covariates. Effect modification by milk feeding type (human milk, formula, combination, or weaned) at 6 months and 1 year was examined. Benjamini-Hochberg correction was applied (p < 0.05; q < 0.25).

RESULTS: A total of 368 infants were included. At 6 months, most were mixed-fed (n = 154; 41.8 %), followed by homemade-fed (n = 143; 38.9 %) and commercially-fed (n = 71; 19.3 %). Solid food source explained only 0.53 % of gut microbiota variability. Differences were most pronounced in formula-fed infants: at 6 months, those given homemade or mixed foods showed higher abundances of Firmicutes, Turicibacteraceae, and Turicibacter compared with commercially fed infants. Within this group, mixed feeding was further linked to higher Eubacteriaceae and Lachnospiraceae (all q < 0.25). At 1 year, formula-fed infants who received homemade foods had higher microbial diversity (p = 0.028) but lower Shannon diversity (p = 0.041) than those receiving commercial foods, suggesting shifts in both community richness and evenness. No significant differences in gut microbiome diversity and composition were observed in the overall cohort or among infants receiving human milk or fully weaned (q > 0.25).

CONCLUSIONS: Solid food source is a previously under-investigated driver of infant microbiome variability, with effects contingent on milk feeding. Human milk may buffer against dietary choices, whereas formula-fed infants show heightened sensitivity to complementary food source, informing precision nutrition in early life.},
}

@article {pmid41643413,
year = {2026},
author = {Nunes, AT and de Almeida, DL and Faleiros, CA and Poleti, MD and de M Oliveira, EC and Moreira, FM and Gallo, SB and Fukumasu, H},
title = {Maternal chromium supplementation increases lamb weaning weight and modulates rumen microbiota.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {2},
pages = {101755},
doi = {10.1016/j.animal.2026.101755},
pmid = {41643413},
issn = {1751-732X},
abstract = {Maternal nutrition during gestation can program offspring development and may influence the establishment of the rumen microbiome, with implications for growth and rumen health. However, the effects of maternal chromium (Cr) supplementation on offspring rumen microbial communities and performance in sheep remain poorly characterised. This study investigated the effects of maternal Cr supplementation during late gestation and early lactation on the offspring microbiome and performance in lambs. Fifteen pregnant ewes were assigned to two treatments in a randomised design: no Cr supplementation and 1.5 mg chromium propionate per ewe/day. Male Dorper × Santa Inês lambs (n = 19) were weaned at 80 d. They were provided creep feeding from 20 d to weaning, and finished in individual feedlot pens until slaughter at 132 d. The rumen microbiota of the offspring at slaughter was characterised. Feed intake, BW, daily gain, feed efficiency, and carcass yield were measured. Maternal Cr supplementation increased the weaning weight of lambs (P = 0.048), although no differences were observed in the feed intake, daily gain, or carcass weight. While the overall microbial diversity was unchanged, Cr increased Flexilinea (P = 0.042), SP3-e08 (P = 0.040) and U29-B03 (P = 0.037), genera linked to fibre degradation and volatile fatty acid modulation. Conversely, Cr reduced Streptococcus (P = 0.029), potentially lowering lactic acid accumulation and ruminal acidosis risk, and Oribacterium (P = 0.025) and Pseudobutyrivibrio (P = 0.008), genera involved in glycolysis and cell wall biosynthesis. In conclusion, supplementation with 1.5 mg chromium propionate during late gestation and early lactation increased lamb weaning weight and modulated rumen microbial taxa, suggesting potential improvements in nutrient utilisation and rumen stability.},
}

@article {pmid41642554,
year = {2026},
author = {Vuong, TTB and Le, TTV and Le, LGH and Le, TN and Do, MD},
title = {Analysis of the Facial Skin Bacterial Community in Vietnamese Individuals with Sensitive Skin and Clinical Relevance.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {41642554},
issn = {2193-8210},
abstract = {INTRODUCTION: Sensitive skin (SS) is a common clinical condition characterized by exaggerated sensory responses such as burning, stinging, itching, and irritation to otherwise nonpathological stimuli, most frequently affecting the face. The underlying mechanisms remain incompletely understood, particularly with regard to the role of the skin microbiome.

METHODS: This study investigated the facial skin microbiota in Vietnamese adults with SS and examined its associations with clinical symptoms and skin physiological parameters. A total of 75 participants were enrolled, including 45 with SS and 30 with nonsensitive skin (NSS). Clinical assessment included evaluation of subjective symptoms, symptom regularity, time of symptom onset, trigger factors, and objective measurements of skin pH, sebum, hydration, transepidermal water loss (TEWL), erythema, and melanin index. Bacterial communities were profiled using 16S rRNA gene sequencing targeting the V3-V4 region.

RESULTS: Participants with SS exhibited significantly higher erythema and TEWL across all sex and age subgroups, as well as elevated skin pH in female and middle-aged participants (p < 0.05). Alpha and beta diversity metrics did not differ significantly between SS and NSS groups. However, differential abundance analysis using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) identified 53 bacterial genera with significant compositional differences, indicating subtle community restructuring. A total of 32 genera, including Peredibacter, Enterobacter, and Marmoricola, were enriched in SS, whereas Streptococcus, Escherichia-Shigella, and Weissella were depleted. Correlation and stratified analyses further revealed genus-level associations with skin physiological parameters, clinical symptoms, anatomical locations, symptom regularity, and time since symptom onset.

CONCLUSIONS: SS is associated with subtle but distinct alterations in facial skin microbiome composition, in parallel with measurable changes in skin physiological parameters related to barrier function and reactivity. The results indicate associations between microbial composition, skin physiological parameters, and clinical characteristics in the SS phenotype, and offer a population-specific microbiome reference for Vietnamese facial skin.},
}

@article {pmid41642539,
year = {2026},
author = {Shenthilvel, RK and Umashankar, TA and Uvarajan, D and Mathuraj, M and Ravikumar, M},
title = {"Unfolding Parkinson's Disease Through the Microbiome-Gut-Brain Axis".},
journal = {Journal of molecular neuroscience : MN},
volume = {76},
number = {1},
pages = {25},
pmid = {41642539},
issn = {1559-1166},
mesh = {Humans ; *Parkinson Disease/microbiology/therapy/metabolism ; *Gastrointestinal Microbiome ; Animals ; *Brain/metabolism ; *Brain-Gut Axis ; },
abstract = {Parkinson's disease (PD) is a progressive and multifactorial neurodegenerative disorder primarily caused by the loss of dopaminergic neurons in the substantia nigra. This neuronal loss leads to characteristic motor symptoms such as tremors, rigidity, and slowness of movement. Although PD has long been regarded as a disorder originating in the brain, recent findings suggest that the gut-brain axis, the intricate communication network between the gastrointestinal tract and the central nervous system also plays an important role in the development and progression of PD. Interestingly, early non-motor symptoms such as constipation and other bowel irregularities often appear several years before the onset of motor symptoms, indicating that changes in gut function may precede and even contribute to neurodegeneration. The gut microbiota influences neuronal signaling, immune activity, and metabolic balance through neuroactive molecules such as neurotransmitters, short-chain fatty acids (SCFAs), and cytokines. In PD, microbial imbalance, intestinal barrier dysfunction, and chronic inflammation are closely linked to the misfolding and accumulation of α-synuclein (α-syn), which can spread from the gut to the brain through the vagus nerve in a prion-like manner. Current therapeutic approaches are increasingly exploring ways to restore gut microbial balance using probiotics, prebiotics, dietary interventions, fecal microbiota transplantation (FMT), and SCFA supplementation. These strategies not only aim to relieve symptoms but may also have the potential to slow disease progression. This review discusses the mechanisms through which the gut-brain axis contributes to PD, summarizes key clinical and preclinical findings, and highlights emerging gut-targeted therapeutic approaches.},
}

Humans
*Parkinson Disease/microbiology/therapy/metabolism
*Gastrointestinal Microbiome
Animals
*Brain/metabolism
*Brain-Gut Axis

@article {pmid41642392,
year = {2026},
author = {Banerjee, A and Choudhury, A and Goswami, A},
title = {The gut-brain axis in arsenic-induced toxicity: mechanisms, consequences, and therapeutic perspectives.},
journal = {Metabolic brain disease},
volume = {41},
number = {1},
pages = {30},
pmid = {41642392},
issn = {1573-7365},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Animals ; *Brain/drug effects/metabolism ; *Arsenic/toxicity ; Dysbiosis/chemically induced ; *Arsenic Poisoning/metabolism ; *Brain-Gut Axis/drug effects/physiology ; Oxidative Stress/drug effects ; },
abstract = {Chronic ingestion of arsenic frequently occurring in contaminated groundwater poses a serious dual threat to neurological health. Environmental toxicants present in groundwater are highly correlated with onset of neuropathological effects through complex gut-brain axis interactions. The systematic review of literature aims evaluate the neurobehavioural consequences and molecular outcome of a groundwater contaminant, arsenic with microbiota alteration involving animal studies and epidemiological data. Arsenic disrupts the gut microbiota, diminishing beneficial bacteria and promoting harmful strains, which in turn compromise gut barrier integrity, trigger inflammation and oxidative stress, leading to alteration in critical metabolic pathways involved in neurotransmitter production and mitochondrial function. Animal studies have shown that chronic exposure intensifies these effects, causing more pronounced microbial dysbiosis alongside worsened cognitive and behavioural deficits. Mechanistically, arsenic impairs neural signaling by elevating reactive oxygen species, disrupting synaptic and mitochondrial dynamics, and inducing neuroinflammation after its accumulation in brain tissues, while gut-derived neuroactive compounds exacerbate neuroinflammation and neuronal damage irrespective of significant arsenic deposition in the brain. Therapeutic strategies that reinforce gut health, such as targeted probiotic and prebiotic supplementation have demonstrated the ability to restore microbiome balance, strengthen barrier function, reduce neuroinflammatory markers and improve behavioural outcomes in experimental models. These microbiota-focused interventions, when combined with conventional measures like chelation to remove toxic metals and the deployment of water treatment infrastructure in affected regions, suggest a powerful integrated approach. By addressing both the source of contamination and the downstream biological consequences, this multimodal strategy holds significant promise for mitigating arsenic-induced neurotoxicity and protecting at-risk populations in affected communities.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
Animals
*Brain/drug effects/metabolism
*Arsenic/toxicity
Dysbiosis/chemically induced
*Arsenic Poisoning/metabolism
*Brain-Gut Axis/drug effects/physiology
Oxidative Stress/drug effects

@article {pmid41642353,
year = {2026},
author = {Gholizadeh, P and Faghfuri, E},
title = {Reprogramming Gastric Cancer Therapy: A Microbiome-Guided Approach to Precision Oncology.},
journal = {Current microbiology},
volume = {83},
number = {3},
pages = {150},
pmid = {41642353},
issn = {1432-0991},
}

@article {pmid41642241,
year = {2026},
author = {Zheng, Y and Fang, X and Gao, J},
title = {Re-engineering insulin for oral delivery: structural modifications, advanced formulation strategies, and future directions.},
journal = {Drug delivery},
volume = {33},
number = {1},
pages = {2624192},
doi = {10.1080/10717544.2026.2624192},
pmid = {41642241},
issn = {1521-0464},
mesh = {Humans ; Administration, Oral ; *Insulin/administration & dosage/chemistry/pharmacokinetics ; *Hypoglycemic Agents/administration & dosage/chemistry/pharmacokinetics ; *Drug Delivery Systems/methods ; Animals ; Drug Carriers/chemistry ; Biological Availability ; Diabetes Mellitus/drug therapy ; },
abstract = {Oral insulin delivery represents a transformative approach to diabetes management, offering improved patient compliance and physiological insulin delivery patterns compared to subcutaneous injection. However, multiple gastrointestinal barriers, including enzymatic degradation, mucus entrapment, epithelial impermeability, and first-pass metabolism, have limited oral bioavailability to below 1% for unmodified insulin. This review comprehensively examines contemporary strategies to overcome these barriers. We analyze structural modifications of insulin, including PEGylation, lipidation, cyclization, and glycoengineering, which enhance stability while maintaining biological activity. The analysis extends to sophisticated formulation technologies incorporating nanocarriers (polymer-based, lipid-based, inorganic nanocarriers, and metal organic frameworks), biomimetic systems, and stimuli-responsive mechanisms for protection and delivery. A central focus is on absorption-enhancing strategies, which range from chemical permeation enhancers to precise biological mechanisms like receptor-mediated transcytosis and other active transport pathways. Emerging tools such as microbiome-based carriers and smart devices are also discussed. Despite significant progress in preclinical models, challenges remain in manufacturing scalability, inter-patient variability, long-term safety, and regulatory approval. Future directions emphasize hybrid delivery systems, digital health integration, and personalized formulations. Realizing clinically viable oral insulin requires continued multidisciplinary collaboration addressing biological, technological, and translational barriers to transform diabetes care.},
}

Humans
Administration, Oral
*Insulin/administration & dosage/chemistry/pharmacokinetics
*Hypoglycemic Agents/administration & dosage/chemistry/pharmacokinetics
*Drug Delivery Systems/methods
Animals
Drug Carriers/chemistry
Biological Availability
Diabetes Mellitus/drug therapy

@article {pmid41642221,
year = {2026},
author = {Pavan, RR and Sullivan, MB and Tisza, MJ},
title = {CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
doi = {10.1099/mgen.0.001632},
pmid = {41642221},
issn = {2057-5858},
mesh = {*Computational Biology/methods ; Genome, Viral ; *DNA Viruses/genetics/classification ; *DNA, Single-Stranded/genetics ; Phylogeny ; Metagenomics/methods ; *Molecular Sequence Annotation/methods ; *Software ; },
abstract = {ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.},
}

*Computational Biology/methods
Genome, Viral
*DNA Viruses/genetics/classification
*DNA, Single-Stranded/genetics
Phylogeny
Metagenomics/methods
*Molecular Sequence Annotation/methods
*Software

@article {pmid41642002,
year = {2026},
author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB},
title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0364525},
doi = {10.1128/mbio.03645-25},
pmid = {41642002},
issn = {2150-7511},
abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.},
}

@article {pmid41641857,
year = {2026},
author = {Marcinkowska, K and Wrzesińska-Krupa, B and Obrępalska-Stęplowska, A},
title = {Insights Into Sequences of Viral and Bacterial Origin in the Metatranscriptome of Centaurea cyanus L. Susceptible and Resistant to Acetolactate Synthase (ALS)-Inhibiting Herbicides.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70287},
pmid = {41641857},
issn = {1758-2229},
support = {2020/04/X/NZ9/01767//National Science Centre/ ; },
mesh = {*Herbicides/pharmacology ; *Acetolactate Synthase/antagonists & inhibitors ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Herbicide Resistance ; *Centaurea/microbiology/virology ; Arylsulfonates/pharmacology ; Transcriptome ; Poland ; Plant Weeds/virology/microbiology ; *Plant Viruses/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {Cornflower (Centaurea cyanus L.) is a widespread weed in cereal crops and is commonly controlled with sulfonylurea herbicides. In Poland, populations of cornflower resistant to acetolactate synthase inhibiting herbicides, such as tribenuron-methyl, have been increasingly reported. Both target-site and non-target-site resistance mechanisms may contribute to this phenomenon. Plant-associated microorganisms are known to play essential roles in alleviating abiotic stress. Moreover, weeds are considered reservoirs of plant pathogenic viruses. Since bacteria and viruses associated with cornflower have not been analysed to date, data mining was undertaken to identify viral and bacterial sequences in metatranscriptome datasets obtained from plant biotypes that are both susceptible and highly resistant to tribenuron-methyl. Using MEGAN6 and Kraken2, taxonomic classification revealed the presence of sequences of two double-stranded RNA viruses belonging to the family Partitiviridae, which have not been described before. For bacterial sequences, 19 genera were identified, including Bacillus, Mesorhizobium and Acinetobacter, some of which are associated with plant growth promotion or xenobiotic degradation. Although the presence of partitiviruses was unrelated to herbicide resistance status, some bacterial genera (e.g., Rothia) were more abundant in resistant than in susceptible plants. These results suggest that those bacterial genera present in weeds may be involved in counteracting ALS-inhibiting herbicides.},
}

*Herbicides/pharmacology
*Acetolactate Synthase/antagonists & inhibitors
*Bacteria/genetics/classification/isolation & purification/drug effects
*Herbicide Resistance
*Centaurea/microbiology/virology
Arylsulfonates/pharmacology
Transcriptome
Poland
Plant Weeds/virology/microbiology
*Plant Viruses/genetics/classification/isolation & purification
Phylogeny

@article {pmid41641785,
year = {2026},
author = {Ma, R and An, H and Feng, Y},
title = {Two-sample Mendelian randomization study of gut microbiota and inflammatory proteins: Predictive, preventive, and personalized treatment for migraine.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-01711},
pmid = {41641785},
issn = {1673-5374},
abstract = {The human gut microbiota is increasingly recognized as a significant factor in the pathogenesis of migraine, potentially via inflammatory pathways. Identifying specific human gut microbiota components associated with migraines, along with the investigation of particular inflammatory proteins, is essential for advancing primary prediction, targeted prevention, and personalized treatment strategies for migraines. We conducted a two-sample Mendelian randomization study using publicly available summary statistics from genome-wide association studies. Data for 473 human gut microbiota taxa were obtained from the Finnish national health survey conducted by the National Institute for Health and Welfare study (FINRISK, n = 5959 European participants). Genome-wide association study data (https://www.ebi.ac.uk/gwas/) for 91 circulating inflammatory proteins were obtained from 14,824 participants across 11 cohorts using the Olink Target 96 Inflammation panel. Migraine outcome data were obtained from the FinnGen R12 release, with cases defined using ICD-10 code G43. All genome-wide association study analyses were adjusted for sex, age, genotyping batch, and 10 genetic principal components to control population stratification (genomic inflation factors: 1.00-1.05). Inverse variance-weighted Mendelian randomization was the primary analysis method, with Mendelian randomization-Egger, weighted median, and mode-based methods as sensitivity analyses. Two-step Mendelian randomization mediation analysis quantified the proportion of the effects of human gut microbiota on migraine that are mediated through inflammatory proteins. Thirty-seven bacterial genera were found to be associated with migraine using the inverse variance-weighted method. Of these, 18 genera exhibited a negative association, while 19 genera demonstrated a positive association with migraine risk. Additionally, eight inflammatory proteins were found to increase the risk of migraine. Among human gut microbiota, four were observed to reduce inflammatory protein levels, whereas another four were associated with increased inflammatory protein levels. Additionally, five gut microbiota were identified to influence migraine through inflammatory proteins in both Mendelian randomization analyses. Specifically, Actinobacteria, Brachyspiraceae, CAG-269 sp001915995, and Paraglaciecola were found to affect migraine outcomes via inflammatory proteins, with mediation proportions of 12%, 19%, 15.5%, and 6.7%, respectively. Lawsonibacter sp002161175 was identified to influence migraine risk through Oncostatin-M and SLAM, with mediation proportions of 15.6% and 11.3%, respectively. Our study elucidated the role of specific human gut microbiota alterations in the pathogenesis of migraine and highlighted the mediating effects of inflammatory proteins. Targeting these particular human gut microbiota alterations offers a promising strategy for predictive, preventive, and personalized medicine in migraine management, resulting in substantial clinical advancements.},
}

@article {pmid41641698,
year = {2026},
author = {Aktary, Z and Sorg, K and Cucchiarini, A and Vesco, G and Noury, D and Zhang, R and Jourdain, T and Verga, D and Mahou, P and Olivier, N and Bohálová, N and Porubiaková, O and Brázda, V and Bouvier, M and Kwapisz, M and Clouet-d'Orval, B and Allers, T and Lestini, R and Mergny, JL and Guittat, L},
title = {Archaeal G-quadruplexes: a novel model for understanding unusual DNA/RNA structures across the tree of life.},
journal = {Nucleic acids research},
volume = {54},
number = {4},
pages = {},
pmid = {41641698},
issn = {1362-4962},
support = {ANR-20-CE12-0023//ANR/ ; ANR-11-EQPX-0029//ANR/ ; ANR-10-INBS-04//ANR/ ; ANR-22-CE12-0009-01//ANR/ ; },
mesh = {*G-Quadruplexes ; *DNA, Archaeal/chemistry/genetics ; *Haloferax volcanii/genetics ; *RNA, Archaeal/chemistry/genetics ; Thermococcus/genetics ; Genome, Archaeal ; Archaea/genetics ; Phylogeny ; Nucleic Acid Conformation ; },
abstract = {Archaea, a domain of microorganisms found in diverse environments, including the human microbiome, represent the closest known prokaryotic relatives of eukaryotes. This phylogenetic proximity positions them as a relevant model for investigating the evolutionary origins of nucleic acid secondary structures such as G-quadruplexes (G4s) which play regulatory roles in transcription and replication. Although G4s have been extensively studied in eukaryotes, their presence and function in archaea remain poorly characterized. In this study, a genome-wide analysis of the halophilic archaeon Haloferax volcanii identified over 5800 potential G4-forming sequences. Biophysical validation confirmed that many of these sequences adopt stable G4 conformations in vitro. Using G4-specific detection tools and super-resolution microscopy, G4 structures were visualized in vivo in both DNA and RNA across multiple growth phases. Comparable findings were observed in the thermophilic archaeon Thermococcus barophilus. Functional analysis using helicase-deficient H. volcanii strains further identified candidate enzymes involved in G4 resolution. These results establish H. volcanii as a tractable archaeal model for G4 biology.},
}

*G-Quadruplexes
*DNA, Archaeal/chemistry/genetics
*Haloferax volcanii/genetics
*RNA, Archaeal/chemistry/genetics
Thermococcus/genetics
Genome, Archaeal
Archaea/genetics
Phylogeny
Nucleic Acid Conformation

@article {pmid41641501,
year = {2026},
author = {Mei, S and Cao, Q and Huang, G and Chen, D and Kitts, DD and Chen, X},
title = {Polyphenol-Rich Coffee Leaf Extract Alleviates High-Fat Diet-Induced Intestinal Barrier Dysfunction through Modulation of Barrier Integrity, Enterohepatic Axis, and Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13455},
pmid = {41641501},
issn = {1520-5118},
abstract = {A polyphenol-rich extract (WEAC) from coffee leaf was previously shown to protect the epithelial barrier integrity. This study investigated the protective effects of WEAC in C57BL/6 mice fed a high-fat diet (HFD). WEAC supplementation (100-200 mg/kg·bw) reduced body weight and lowered TNF-α levels in serum, colon, liver, and brain in mice. WEAC improved mouse intestinal barrier integrity by upregulating the tight-junction protein and reducing intestinal d-lactic acid leakage. Liver histology revealed reduced lipid accumulation and ballooning degeneration, corresponding to decreased triglyceride, total cholesterol, and low-density lipoprotein cholesterol levels. The WEAC intervention also decreased total bile acid levels and altered short-chain fatty acid profiles and key phytochemical metabolism. Furthermore, WEAC reduced the Firmicutes/Bacteroidetes ratio, increased the Parabacteroides, unclassified_Muribaculaceae, and Akkermansia abundance, and lowered the Blautia levels. Additionally, WEAC showed no adverse effects in mice fed a normal diet. Overall, WEAC mitigated HFD-induced intestinal barrier damage and enterohepatic function, reduced systemic inflammation, and stabilized the gut microbiome.},
}

@article {pmid41641458,
year = {2025},
author = {Bai, H and Xu, Y and Qu, S and Li, B and Wang, X},
title = {The influence of the maternal microbiome on offspring neurodevelopment: a critical review of associations, controversies, and challenges.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1737795},
pmid = {41641458},
issn = {1662-4548},
abstract = {The role of the maternal microbiome in offspring neurodevelopment has become a prominent topic in neuroscience, yet its true causal status is under intense scrutiny. This critical review moves beyond conventional deconstructions of popular hypotheses in the field (e.g., "prenatal programming" "windows of opportunity") to challenge a more fundamental premise. We systematically argue that the currently observed associations along the "microbiota-gut-brain axis" may reflect complex confounding, with macroscopic social factors such as socioeconomic status (SES) being the true underlying drivers. The core thesis of this paper is that the maternal microbiome is, to a great extent, a "biological imprint" of the mother's living environment, diet, and stress levels-a highly sensitive "proxy" indicator acting as a biological mediator heavily shaped by the environment, rather than solely as an independent driver. By integrating evidence from social epidemiology, we contend that positioning the microbiome alongside factors like SES in a "flattened" network model is misleading. Instead, we propose a Hierarchical Causal Model where socioeconomic factors act as top-level "master regulators," systematically shaping all downstream biological processes, including the microbiome. Through a critical analysis of interventions such as Fecal Microbiota Transplantation (FMT) and vaginal seeding, this review further exposes the translational predicaments that arise from neglecting this hierarchical structure. Ultimately, this review advocates for a paradigm shift: from searching for a single "microbial panacea" to understanding the microbiome's true position within the socio-biological system, and proposes a conceptual framework for future research that is more aligned with real-world complexity and endowed with greater sociological imagination.},
}

@article {pmid41641369,
year = {2026},
author = {Wang, N and Luo, L and Yang, X},
title = {The gut-eye axis in age-related macular degeneration: from microbial dysbiosis to targeted intervention strategies.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10876},
pmid = {41641369},
issn = {1535-3699},
mesh = {Humans ; *Macular Degeneration/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/complications/therapy ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Animals ; Prebiotics ; },
abstract = {Age-related macular degeneration (AMD) represents a leading cause of irreversible blindness among the older persons. Characterized by a complex pathogenesis and multiple risk factors, AMD poses substantial challenges for treatment and has emerged as a significant public health concern. The gut microbiota constitutes a vast and dynamically evolving ecosystem, with a healthy microbial community playing an essential role in maintaining host homeostasis through its involvement in digestion and immune defense. However, alterations in microbial composition or function can compromise intestinal barrier integrity, trigger systemic inflammation, and contribute to disease pathogenesis. Evidence now underscores the influence of gut microbiota on the development and progression of AMD. This review examines the mechanisms by which gut microbes may contribute to AMD pathogenesis and evaluates the therapeutic potential of interventions targeting the gut microbiome-including dietary modifications, Pharmacological and Biological Agents, probiotics, prebiotics, and fecal microbiota transplantation-for AMD management.},
}

Humans
*Macular Degeneration/microbiology/therapy
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology/complications/therapy
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Animals
Prebiotics

@article {pmid41641367,
year = {2026},
author = {Chapman, JA and Frey, AM and Dueñas, ME and Palmer, JM and Masi, AC and Embleton, ND and Trost, M and Berrington, JE and Stewart, CJ},
title = {Optimising the induction of inflammation within preterm infant-derived intestinal epithelial organoids.},
journal = {Npj gut and liver},
volume = {3},
number = {1},
pages = {5},
pmid = {41641367},
issn = {3004-9806},
abstract = {Preterm infants born <32 weeks gestation have abnormal microbial colonisation and dysregulated inflammation within the gut. Preterm infant-derived intestinal organoids (PIOs) represent a valuable model for investigating gut microbiome-host interactions and inflammatory responses. We optimised an inflammation model in PIO monolayers incubated within an anaerobic co-culture system that recreates the physiological oxygen gradient of the intestinal epithelium. We trialled multiple stimuli, including live and heat-killed pathobiont consortia, lipopolysaccharide (LPS) and flagellin. We found that a combination of apical LPS and basolateral flagellin, incubated for 3 h, elicited the most robust response. This was characterised by enhanced pro-inflammatory cytokine secretion, the potential for chemokine-driven immune recruitment, TNFα and IL17C pathway signalling, shifts from NF-κB to AP-1-mediated responses, and signs of tissue remodelling. This provides a framework for appropriate study design to disentangle the impacts of microbiome-host interactions in health and disease using intestinal organoids.},
}

@article {pmid41641316,
year = {2026},
author = {Zhang, X and Wang, J and He, Y and Xiao, X and Fan, J and Ma, X},
title = {Mucosal-associated invariant T cells and the gut-kidney axis: a review.},
journal = {Clinical kidney journal},
volume = {19},
number = {2},
pages = {sfaf366},
pmid = {41641316},
issn = {2048-8505},
abstract = {Mucosal-associated invariant T (MAIT) cells are a distinct subset of innate-like lymphocytes that bridge microbial homeostasis and tissue immunity. These evolutionarily conserved cells are activated via the recognition of microbial metabolites presented by the MR1 molecule and establish stable residency in the kidney, where they profoundly influence local immune-metabolic processes. There is growing interest in the robust regulatory capacities of MAIT cells in renal physiology and pathology. This review systematically delineates their paradoxical roles in kidney diseases. Under specific conditions, they exert protective functions by suppressing inflammation and maintaining tissue homeostasis. Conversely, in distinct microenvironments, they adopt a pro-inflammatory phenotype, exacerbating pathological progression through the release of inflammatory cytokines and cytotoxic effector functions. The gut-kidney axis serves as a critical regulatory hub, wherein dysbiosis-derived signals can significantly amplify the renal impact of MAIT cells. Focusing on clinical translation, we provide an in-depth exploration of innovative strategies targeting MAIT cells, including adoptive cell therapy, receptor-targeting agents, and microbiome reconstruction. These approaches position MAIT cells as promising therapeutic targets for a new generation of immune-mediated kidney diseases.},
}

@article {pmid41641314,
year = {2026},
author = {Heneberg, P and Heneberg Šimčíková, D},
title = {Untangling amino acid metabolism in renal diseases: mechanisms, dysregulation, and critical gaps.},
journal = {Clinical kidney journal},
volume = {19},
number = {2},
pages = {sfaf380},
pmid = {41641314},
issn = {2048-8505},
abstract = {Amino acid metabolism is closely linked with kidney physiology and pathology. In acute kidney injury, chronic kidney disease, diabetic kidney disease, and autosomal dominant polycystic kidney disease, disturbances in the branched-chain amino acids, tryptophan, glutamine, taurine, and sulfur amino acids pathways are consistently observed. Specific metabolites such as D-serine, kynurenine intermediates, and branched-chain keto acids are associated with disease progression. Taurine and indoxyl sulfate have also been proposed as therapeutic targets. At the nephron level, transporters and enzymes controlling amino acid flux influence nitrogen balance, oxidative stress, fibrosis, inflammation, and tubular injury. In chronic kidney disease, impaired amino acid handling contributes to protein-energy wasting, altered muscle metabolism, and systemic complications. In autosomal dominant polycystic kidney disease, cyst fluid metabolomics has revealed alterations in tryptophan and polyamine metabolism. The use of nutritional interventions, microbiome modulation, and selective supplementation as therapeutic strategies is being explored, although clinical trial evidence remains limited. Several key issues remain unresolved, including the need for isotope tracer studies to define renal amino acid kinetics in humans, the rigorous validation of metabolite biomarkers across diverse populations, the integration of diet and microbiome-derived metabolites into mechanistic frameworks, and the systematic evaluation of sex-specific differences. Longitudinal studies are scarce, thus restricting predictive power and therapeutic translation. Further mechanistic clarification may support the development of biomarkers and targeted therapies.},
}

@article {pmid41641227,
year = {2026},
author = {Tajdari, M and Abolghasemi, S and Khanniri, E and Bayanati, M and Hakimimofrad, R and Mahboubi-Rabbani, M},
title = {A Comprehensive Review of Acne Treatments: Unpacking the Chemical Structures and Effective Bioactive Compounds.},
journal = {Health science reports},
volume = {9},
number = {2},
pages = {e71803},
pmid = {41641227},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Acne vulgaris is a frequent skin disorder, affecting a large part of the population worldwide, and strongly influencing not only the physical but also the mental aspects of health. The choice of therapy for acne vulgaris is a very difficult one because the multifactorial causality of the disease and interindividual variability in response to treatment should be considered. This article aims to provide a comprehensive review of the drugs used in the treatment of acn\e vulgaris, along with their chemical structure.

METHODS: A comprehensive search of relevant databases (PubMed, Google Scholar, Web of Science, and Scopus) was conducted using keywords such as "acne vulgaris", "chemical structure", "mode of action", and "structure-activity relationship". We reviewed articles published up to 2025. The authors reviewed articles that discussed the chemical structure and structure-activity relationships of drugs used in the treatment of acne vulgaris. In addition, articles on acne vulgaris pharmacotherapy were also reviewed.

RESULTS: In this review, all the current modalities for the management of acne vulgaris are presented and grouped according to their chemical nature, including topical applications and systemic administration. In this light, we go further into the mechanism of action of each treatment, its efficacy and safety, and possible side effects. New therapeutic agents targeting the skin microbiome, inflammation, and hormonal imbalance are also a focus. We finally propose one step for choosing an optimum therapy based on the subject's constitution, the severity of post-acne scarring, and associated comorbidities.

CONCLUSION: The present review would benefit general physicians in adapting their management to treat zits and pimples for the improvement of their patients, with particular importance given to the knowledge of the chemical structures of various drugs.},
}

@article {pmid41641220,
year = {2026},
author = {Huang, YY and Li, CY and Li, Y and Fang, H and Ke, XY},
title = {Characteristics and functions of the gut microbiome in monozygotic twins with autism spectrum disorders of varying severity.},
journal = {World journal of psychiatry},
volume = {16},
number = {2},
pages = {111012},
pmid = {41641220},
issn = {2220-3206},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by pronounced behavioral heterogeneity and individual variability. Growing evidence indicates a strong association between gut microbiota and ASD; however, differences in microbial functions across varying levels of ASD severity remain poorly understood. Monozygotic twins (MZs) provide an appropriate model for examining the influence of nonshared environmental factors in ASD.

AIM: To investigate the effects of the gut microbiome in MZs with ASD using 16S ribosomal RNA sequencing.

METHODS: Participants were recruited from the Chinese MZs with autism spectrum disorder (MZCo-ASD) cohort and stratified into mild MZCo-ASD and severe MZCo-ASD (MZCo-ASD-H) groups based on their Childhood Autism Rating Scale scores. Fecal samples were collected and analyzed using 16S ribosomal RNA sequencing.

RESULTS: Although overall microbial diversity did not differ significantly between the groups, gut microbiota composition was notably altered. At the genus level, Por phyromonas was significantly enriched in the MZCo-ASD-H group. Clusters of Orthologous Groups analysis revealed decreased expression of key genes in the MZCo-ASD-H group, including fructose-1,6-bisphosphatase, membrane-bound lytic murein transglycosylase, PasI (part of the RatAB toxin-antitoxin system), HmoA, and a glycoside hydrolase family 25 domain-containing protein. Kyoto Encyclopedia of Genes and Genomes Orthology analysis showed that msmF (K10118) and msmG (K10119), involved in oligosaccharide transport, were significantly downregulated in the MZCo-ASD-H group, suggesting a reduced microbial capacity for prebiotic carbohydrate utilization.

CONCLUSION: Despite similar overall diversity, children with severe ASD exhibited distinct gut microbiota structures and functional impairments. The enrichment of Porphyromonas, along with the reduced expression of genes involved in carbohydrate metabolism and stress responses in the high-severity group, suggests an association between gut microbial dysregulation and ASD severity. These findings provide new insights into microbiota-related mechanisms underlying ASD and highlight potential functional targets for intervention.},
}

@article {pmid41641127,
year = {2025},
author = {Rogalidou, M},
title = {Clostridioides difficile infection in pediatric inflammatory bowel disease: current understanding and clinical challenges.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1753289},
pmid = {41641127},
issn = {2296-2360},
abstract = {Clostridioides difficile infection (CDI) represents a significant and increasingly recognized complication in children with inflammatory bowel disease (IBD), contributing to prolonged hospitalization and risk of adverse outcomes. Children with IBD are particularly susceptible due to frequent antibiotic exposure, healthcare system contact, immunosuppressive therapy, and underlying gut dysbiosis, all of which promote colonization and toxin-mediated intestinal injury. Distinguishing CDI from an IBD flare is challenging, as gastrointestinal symptoms and systemic inflammation overlap, and asymptomatic toxigenic colonization is common. Management recommendations for pediatric IBD-associated CDI are largely extrapolated from adult studies, with prompt initiation of targeted antibiotics being critical. Immunosuppressive therapy is generally continued, with escalation considered if diarrhea persists despite CDI-directed therapy. Fecal microbiota transplantation (FMT) has emerged as a safe and promising option for recurrent CDI in children with IBD, although careful patient selection, donor choice, and timing remain crucial. Key challenges persist in differentiating true CDI from IBD flares, understanding the clinical impact of asymptomatic colonization, and optimizing microbiome-targeted interventions. Future research should prioritize biomarker-driven diagnosis, individualized therapeutic strategies, and longitudinal evaluation of microbiome-based treatments to improve outcomes in pediatric patients with concurrent CDI and IBD.},
}

@article {pmid41640962,
year = {2026},
author = {Goyal, MK and Chowdhary, R and Vohra, C and Patel, M and Kalra, S and Mehta, M and McNulty, R and Goyal, K and Vuthaluru, AR and Goyal, O},
title = {Current management strategies for sarcopenia and frailty in cirrhosis: Missing link in transplant candidacy.},
journal = {World journal of hepatology},
volume = {18},
number = {1},
pages = {115048},
pmid = {41640962},
issn = {1948-5182},
abstract = {Sarcopenia and frailty are pervasive, interrelated syndromes in cirrhosis that worsen morbidity, quality of life, transplantation waitlist outcomes, and post-transplant survival. This review synthesized contemporary evidence on definitions, epidemiology, mechanisms, diagnosis, prognostic impact, and management with an emphasis on implementable strategies in hepatology practice. Sarcopenia affects 40%-70% of patients with cirrhosis, and frailty affects 20%-50% of patients with cirrhosis with variations across populations and definitions. Mechanistic drivers include hyperammonemia, systemic inflammation, endocrine disturbances, malnutrition and accelerated starvation, gut-liver-muscle axis alterations, mammalian target of rapamycin inhibition, and inactivity. Diagnosis spans simple bedside tests such as handgrip strength, chair stands, gait speed, and the Liver Frailty Index as well as imaging modalities including computed tomography-based skeletal muscle index, dual energy X-ray absorptiometry, magnetic resonance imaging, and bioimpedance. Both sarcopenia and frailty independently predict hepatic decompensation, hospitalizations, waitlist dropout, and mortality, providing additive prognostic value beyond model for end-stage liver disease (MELD)/MELD-Na, and they are associated with longer intensive care unit and hospital stays and worse post-transplant outcomes. Management requires a multimodal approach: Optimization of cirrhosis complications and ammonia-lowering therapy; adequate nutrition with 1.2-1.5 g/kg/day protein and a late-evening snack; structured aerobic and resistance exercise programs; cautious use of testosterone in hypogonadal males; and emerging therapies such as beta-hydroxy-beta-methylbutyrate, vitamin D, L-carnitine, microbiome modulation, and myostatin inhibitors. Routine screening and multidisciplinary prehabilitation should be embedded in standard care pathways, and incorporation of sarcopenia and frailty metrics alongside MELD may refine risk stratification, enhance transplant allocation, and improve long-term outcomes.},
}

@article {pmid41640922,
year = {2026},
author = {Iturbe Cordero, AA and Jaramillo, AP and Vasquez, J},
title = {Perioperative Antimicrobial Prophylaxis for Invasive Dental Procedures: A Systematic Review and Random-Effects Meta-Analysis of Randomized and Placebo-Controlled Studies.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e100755},
pmid = {41640922},
issn = {2168-8184},
abstract = {Prophylactic antimicrobials are frequently administered before invasive dental procedures (including implant placement and extractions) to reduce early infectious complications and procedure-related bacteremia; however, clinical benefit remains debated and must be balanced against ecological disruption and antimicrobial resistance. Evidence from experimental work indicates that even a single prophylactic dose of amoxicillin may transiently perturb the oral microbiome and select resistant strains. A Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)-guided systematic review was conducted. PubMed, Embase, and Cochrane databases were searched. Screening identified 10 randomized placebo-controlled/comparator trials (486 records; 289 duplicates removed; 197 screened; 72 full texts reviewed) for qualitative synthesis and meta-analysis. Included studies evaluated perioperative prophylaxis (systemic antibiotics and/or local antiseptic prophylaxis) versus placebo or no prophylaxis in invasive dental procedures. Outcomes were harmonized across studies as early procedure-related infectious outcomes and/or bacteremia-related endpoints, with secondary assessment of postoperative morbidity indicators (e.g., pain/analgesic use where available). Meta-analysis was performed in Review Manager (RevMan) version 5.4 (2020; The Cochrane Collaboration, London, United Kingdom), using an inverse-variance random-effects model. Across all invasive dental procedures (~1,950 participants pooled), prophylaxis did not demonstrate a statistically significant overall reduction in the primary pooled endpoint (MD -0.12, 95%CI -0.31 to 0.07; random-effects; I[2] ≈ 99%). In the dental-surgery subgroup, the pooled effect similarly crossed the null (MD -0.17, 95%CI -0.45 to 0.11; I[2] ≈ 99%). Individual trials showed marked reductions in post-extraction bacteremia surrogates with chlorhexidine mouthwash prophylaxis and with intravenous amoxicillin-clavulanate in extraction settings, whereas in uncomplicated extractions among well-controlled type 2 diabetes, antibiotics did not reduce postoperative complications and were associated with greater analgesic consumption. Implant trials reported low event rates and did not consistently demonstrate clinically meaningful superiority of routine prophylaxis. Funnel plot inspection suggested possible small-study effects influenced by outliers, but interpretation was constrained by extreme between-study heterogeneity. In this pooled analysis of randomized and placebo-controlled studies spanning heterogeneous invasive dental procedures, routine prophylactic antimicrobial strategies did not yield a consistent overall benefit on early infectious/bacteremia-related outcomes, and secondary postoperative morbidity outcomes showed no clear improvement. In parallel, microbiological evidence indicates that single-dose prophylaxis can promote short-term ecological disturbance and selection of resistant oral flora. Future trials should standardize endpoints (distinguishing clinical infection/implant failure from surrogate bacteremia measures), stratify by baseline risk, and prioritize antimicrobial stewardship to identify the limited patient subsets most likely to benefit.},
}

@article {pmid41640815,
year = {2026},
author = {de Souza Alves, CC and de Castro, SBR and Brugiolo, ASS},
title = {Editorial: Novel therapeutic targets in autoimmune diseases: intestinal microbiota and adaptive immunity regulation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1779062},
doi = {10.3389/fimmu.2026.1779062},
pmid = {41640815},
issn = {1664-3224},
}

@article {pmid41640761,
year = {2025},
author = {Fosso, E and Gizzi, G and Tartaglia, M and Prigioniero, A and Ranauda, MA and Maisto, M and Labella-Ortega, M and Zuzolo, D and Guarino, C},
title = {Management affects the diversity and functions of root and leaf-associated microbiomes: implications for olive resilience.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1699667},
pmid = {41640761},
issn = {1664-462X},
abstract = {This study explores the impact of organic, conventional, and traditional agricultural management on the aboveground and belowground microbiomes of Olea europaea L. cv. Ortice, a cultivar widely cultivated in southern Italy's agricultural landscape. Through metabarcoding analyses (16S rRNA and ITS), we assessed the influence of farming approaches on the microbiome traits of the olive holobiont. Our findings demonstrate that agricultural management practices significantly shape microbiome composition both aboveground and belowground. The conventional management was associated with the highest number of microbial biomarkers aboveground, mainly belonging to Rhizobiaceae and Rhodocyclaceae families. Instead, Fusarium (family Nectriaceae) was the most abundant taxon under organic treatment. Regarding root-associated microbiome, organic management supported a greater number of microbial biomarkers, including the bacterial genera Actinophytocola and Streptomyces, both known for their roles in promoting plant health and protecting against pathogens. In traditional systems, biomarkers included taxa from the order Burkholderiales and the species Nocardioides islandensis. Functional analysis of the aboveground fungal community revealed a higher capacity for endophytic interactions in traditional management, predominantly involving known pathogenic species such as Alternaria alternata, Aureobasidium spp., and Cladosporium spp. Similarly, traditional management was associated with significant enrichment of phototrophic functions belowground, mainly attributed to the bacterium Rhodopseudomonas palustris. Conversely, the potential for endophytic interactions was significantly greater under conventional management and was primarily linked to fungi within the class Sordariomycetes. Management practices shape distinct microbial communities both aboveground and belowground of olive groves, potentially influencing the resilience of Mediterranean agroecosystems and underscoring the importance of sustainable strategies.},
}

@article {pmid41640760,
year = {2025},
author = {Zhang, C and Yang, L and Zhang, X and Zhao, Y and Tang, J and Cheng, Z and Cao, Y and Wu, S and Li, G and Yang, L and Wei, K},
title = {Regional climate variation structures the phyllosphere microbiome of flue-cured tobacco.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1733198},
pmid = {41640760},
issn = {1664-462X},
abstract = {INTRODUCTION: Climate change poses major challenges to agriculture, with phyllosphere microbiota playing a key but poorly understood role in plant adaptation.

METHODS: We examined structural and functional responses of the phyllosphere microbiome in flue-cured tobacco (Nicotiana tabacum L.) across climatic gradients, using multi-regional sampling, high-throughput sequencing (16S rRNA/ITS), and functional prediction (PICRUSt2).

RESULTS: Leaf starch, total sugar, and reducing sugar contents varied significantly (26.87-32.25%, 14.24-16.74%, and 9.96-11.26%, respectively). Bacterial communities were primarily shaped by precipitation (41.7% variance explained), whereas fungal communities were mainly driven by temperature (27.3%). Microbial networks showed climate-adaptive patterns: complex, cooperative networks (85.99% positive edges) in high-precipitation areas versus simplified, drought-tolerant networks (Nodes: 93, Edges: 1124) dominated by Sphingomonas (86.50%) and Methylobacterium (10.24%) in arid regions. Metabolic potential shifted along the gradient: Communities in low-precipitation areas were enriched with genes potentially encoding starch-degrading enzymes (e.g., α-amylase), while those in high-precipitation areas showed enhanced potential for sucrose synthesis (e.g., via sucrose synthase).

DISCUSSION: This study reveals the adaptive strategies of phyllosphere microbial communities in response to climate variations. Under low-rainfall conditions, community metabolism shifts toward starch degradation, which may aid host osmoregulation. In contrast, under humid conditions, dominant taxa such as Sphingomonas and Methylobacterium collaboratively enhance sucrose synthesis. This metabolic reprogramming aligns with structural changes in microbial networks: transitioning from complex, cooperative networks in humid regions to simplified, stress-tolerant networks in low-rainfall areas. Key metabolic functions are primarily contributed by low-abundance taxa, suggesting the vital role of the rare biosphere in maintaining functional redundancy. Based on these findings, we propose that microbial communities may enhance adaptability by retaining core metabolic functions, such as starch degradation, within rare taxa when facing drought or temperature fluctuations. This study provides a theoretical framework for improving crop climate resilience through microbiome management.},
}

@article {pmid41640612,
year = {2026},
author = {Liu, ZX and Liu, XY and Tan, WW and Zhang, WB and Zhang, YL and Zheng, L and Dai, YC},
title = {Characteristics of gut microbiota and metabolites in patients with ulcerative colitis with fatigue.},
journal = {World journal of gastroenterology},
volume = {32},
number = {3},
pages = {115264},
pmid = {41640612},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Colitis, Ulcerative/microbiology/complications/metabolism ; Male ; Female ; Adult ; Feces/microbiology ; Middle Aged ; *Fatigue/microbiology/etiology/metabolism ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Bacteria/isolation & purification/classification/genetics ; Quality of Life ; Young Adult ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic, non-specific inflammatory bowel disease. The gut microbiome undergoes significant changes in UC. Fatigue is a highly prevalent and debilitating extraintestinal symptom of UC, which negatively affects quality of life. However, its relationship with gut microbes and metabolites remains unclear.

AIM: To assess the gut microbiota and metabolomic characteristics of patients with UC with fatigue (HUCF).

METHODS: A total of 120 participants were recruited and divided into four groups (n = 30 per group) based on the diagnosis of UC and Fatigue Scale-14 scores: HUCF, UC without fatigue (HUCN), healthy with fatigue (HHF), and healthy without fatigue (HHN). Fresh stool samples were collected for 16S rRNA sequencing and untargeted metabolomic analysis.

RESULTS: Metabolomic analysis revealed significant differences among the four groups (principal component analysis/partial least squares discriminant analysis, P = 0.001), with differential expression of metabolites such as linoleoyl ethanolamide, arachidonoyl ethanolamide, glycocholic acid, and thromboxane (TX). Notably, TX was detected only in the HUCF group. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed alterations in eicosanoid, tryptophan, and tyrosine metabolism in the HUCF group. Microbial richness and diversity were significantly lower in the HUCF group than in the other three groups. The HUCF group showed enrichment of Hyphomicrobiales, Brucella, Eisenbergiella, Pediococcus, and Sellimonas. The HUCN group showed enrichment of Campylobacter-related taxa. The HHF group showed enrichment of Fusobacterium, Desulfovibrionaceae, and Bilophila. The HHN group showed enrichment of beneficial genera such as Adlercreutzia. Notably, Anaerococcus, a beneficial genus, was enriched in the HUCF group. Correlation analysis indicated that specific microbes (e.g., Faecalibacterium and Escherichia-Shigella) were associated with the severity of UC and fatigue.

CONCLUSION: Patients with HUCF exhibit a distinct gut microbial structure and metabolomic profile. The pro-inflammatory metabolite TX and the genus Anaerococcus are uniquely enriched in patients with HUCF, suggesting their potential roles in the development of HUCF. These findings provide novel insights and a theoretical basis for improving the clinical management of HUCF.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Colitis, Ulcerative/microbiology/complications/metabolism
Male
Female
Adult
Feces/microbiology
Middle Aged
*Fatigue/microbiology/etiology/metabolism
Metabolomics
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Bacteria/isolation & purification/classification/genetics
Quality of Life
Young Adult
Dysbiosis/microbiology

@article {pmid41640608,
year = {2026},
author = {Velikova, T and Ali, H and Batselova, H and Chervenkov, L and Miteva, D and Peruhova, M and Gulinac, M and Tomov, L and Mitova-Mineva, Y and Velev, V},
title = {Interplay between viral infections and gut microbiota dysbiosis: Mechanisms and therapeutic potential.},
journal = {World journal of gastroenterology},
volume = {32},
number = {3},
pages = {112437},
pmid = {41640608},
issn = {2219-2840},
mesh = {Humans ; *Dysbiosis/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; *COVID-19/immunology/microbiology/complications/therapy ; SARS-CoV-2 ; Prebiotics/administration & dosage ; *Virus Diseases/immunology/microbiology/therapy ; Animals ; },
abstract = {Viral infections, particularly those triggered by emerging pathogens like severe acute respiratory syndrome coronavirus 2, are increasingly recognized for their profound impact on the gut microbiota, causing dysbiosis, a condition characterized by an imbalance in microbial communities. Recent studies suggest that alterations in gut microbiota can influence disease progression, immune responses, and clinical outcomes. The bidirectional relationship between the gut microbiota and the host immune system is crucial in shaping responses to infection. Furthermore, dysbiosis has been linked to exacerbated inflammation, impaired mucosal barrier function, and altered drug metabolism, thereby complicating both disease pathogenesis and treatment efficacy. This review examines the interplay between viral infections and gut microbiota dysbiosis, with a focus on the underlying mechanisms and potential therapeutic strategies to modulate host immunity. We also evaluate the potential of microbiome-based interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, as therapeutic strategies for restoring microbial balance and mitigating the severity of infections. The paper underscores the need for further research to optimize microbiota-targeted therapies and integrate them into clinical practice, offering a comprehensive approach to managing dysbiosis in viral infectious diseases.},
}

Humans
*Dysbiosis/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Probiotics/therapeutic use
Fecal Microbiota Transplantation
*COVID-19/immunology/microbiology/complications/therapy
SARS-CoV-2
Prebiotics/administration & dosage
*Virus Diseases/immunology/microbiology/therapy
Animals

@article {pmid41640423,
year = {2026},
author = {Sola-Leyva, A and Pérez-Prieto, I and Canha-Gouveia, A and Salas-Espejo, E and Molina, NM and Vargas, E and Apostolov, A and Pathare, ADS and Vela-Moreno, S and Ruiz-Durán, S and Romero, B and Sánchez, R and Castilla-Alcalá, JA and Saare, M and Acharya, G and Salumets, A and Altmäe, S},
title = {Comprehensive 16S rRNA gene sequencing and meta-transcriptomic analyses of the female reproductive tract microbiota: two molecular profiles with different messages.},
journal = {Human reproduction open},
volume = {2026},
number = {1},
pages = {hoag001},
pmid = {41640423},
issn = {2399-3529},
abstract = {STUDY QUESTION: Does the analysis of endometrial microbes provide the same information when using DNA or RNA sequencing-based techniques?

SUMMARY ANSWER: DNA vs RNA-based microbial analysis techniques demonstrated significant microbial compositional differences and lack of transcriptionally active lactobacilli in the endometrium.

WHAT IS KNOWN ALREADY: Our understanding of the endometrial microbiome is primarily based on DNA-based 16S rRNA gene profiling, but DNA detection does not imply the presence of living microbes. While this method is cost-effective and widely used, it has notable limitations, including the underestimation of microbial diversity, abundance, and functionality, as well as limited species-level resolution. While the microbiome reflects DNA-based characterization, the microbiota more precisely captures metabolically active communities. In this context, meta-transcriptomic analysis, an RNA-based approach, addresses these shortcomings by capturing functional transcripts that are actively expressed in living microbes.

STUDY DESIGN SIZE DURATION: This cross-sectional study consisted of 49 reproductive-aged women (27-42 years old) who were receiving ART. By simultaneously analysing the microbial composition and gene expression within female reproductive tract samples, we sought to provide a more comprehensive understanding of the microbiota and functional potential of these samples.

Vaginal swabs, endometrial brushing, and endometrial biopsy samples were collected from 49 participants during the mid-secretory phase of their menstrual cycle, 6-9 days after the luteinizing hormone surge for parallel 16S rRNA gene sequencing and meta-transcriptome analyses. For DNA-based analysis, the 16S rRNA gene V4 region was sequenced. For RNA-based analysis, total RNA was extracted followed by ribosomal RNA depletion. Strand-specific total RNA sequencing libraries were prepared and sequenced. Taxonomy was assigned by using Kraken2 (v2.2.1), and Bracken (v2.7).

Our findings suggest that in low-microbial-biomass environments such as the endometrium, the correlation between 16S rRNA gene sequencing and meta-transcriptomics is relatively weak. This highlights the limitations of microbial analysis of low-microbial-biomass samples. Alternatively, microbial functions and genome activity may be tissue-specific and dependent on the host tissue environment. Moreover, RNA-based analysis provides higher resolution in detecting certain pathogens, even within the endometrium.

LARGE SCALE DATA: The data presented in the study are deposited in the NCBI SRA Database, accession number PRJNA1247240.

High levels of host RNA and the low abundance of microbial reads in the endometrium complicate microbial identification. Our findings indicate that RNA-seq enables precise profiling of the vaginal microbiome and, in cases of dysbiosis, reveals higher pathogen activity than DNA-based approaches. However, the limited sample size restricts the generalization of these conclusions.

Contrary to the general belief of the dominance of Lactobacillus in the human endometrium, our study suggests that the endometrial microenvironment may be harbouring DNA fragments and/or cells of lactobacilli originating from the lower reproductive tract. Our study results indicate a need to re-consider/re-analyse the endometrial microbiome in health and disease.

This work was supported by the projects Endo-Map PID2021-127280OB-I00, ROSY CNS2022-135999, and ENDORE SAF2017-87526-R funded by MICIU/AEI/10.13039/501100011033 and by FEDER, EU. This work was also supported by the Estonian Research Council grants (PSG1082 and PRG1076), Swedish Research Council grant no. 2024-02530 and Novo Nordisk Foundation grant no. NNF24OC0092384. Additionally, A.S.L. and I.P.P. acknowledge Becas Fundación Ramón Areces para Estudios Postdoctorales-Convocatorias XXXV and XXXVI, para Ampliación de Estudios en el Extranjero en Ciencias de la Vida y de la Materia. A.S. is supported by Horizon Europe (NESTOR, grant no. 101120075) and the Ministry of Education and Research Centres of Excellence grant TK214 name of CoE. All the authors declare no conflict of interest.},
}

@article {pmid41640411,
year = {2025},
author = {Fernández-Pastrana, VM and Mora, MR and González-Reguero, D and Probanza, A and Iglesias, DP and Gómez, PAJ},
title = {Use of PGPB in bio-fertilisation: preserving the soil microbiome and enhancing field production of alfalfa.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1735729},
pmid = {41640411},
issn = {1664-302X},
abstract = {Sustainable fodder production requires fertilisers that increase yield without compromising soil ecology. We tested whether a humic-rich biofertiliser derived from valorised horticultural waste (ORGAON® PK) could be enhanced with two genomically screened plant-growth-promoting bacteria (PGPB) in a field trial with Medicago sativa. The crude residue substantially increased biomass, and the addition of Bacillus sp. C1 or Pseudomonas sp. C2 further redirected these gains towards improved fibre digestibility or greater protein and energy content. Soil microbial diversity was maintained, although community composition shifted towards taxa involved in organic-matter degradation and nitrification. Both inoculants persisted without displacing dominant native genera, and biofertilised soils showed reduced susceptibility to β-lactam antibiotics. Overall, pairing OPK with targeted PGPB enhanced forage yield and quality while supporting microbiome resilience, highlighting a promising One-Health-aligned alternative to mineral fertilisers. Multi-season trials are now needed to validate broader applicability.},
}

@article {pmid41640410,
year = {2025},
author = {Wang, X and Cheng, Y and Huang, J and Xu, F and Jiang, J and Nalinratana, N and Jin, L and Xue, Y},
title = {Engineered probiotics for inflammatory bowel disease therapy: mechanisms, delivery strategies, and precision medicine.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1696524},
pmid = {41640410},
issn = {1664-302X},
abstract = {Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD), is a prevalent chronic gastrointestinal disorder. Conventional therapies are often limited by adverse effects and suboptimal long-term efficacy. Probiotics have emerged as promising therapeutic alternatives for IBD because of their ability to modulate the gut microbiota, reinforce intestinal barrier integrity, and regulate immune responses. However, their clinical translation is hampered by challenges within the harsh gastrointestinal milieu, including low viability, poor colonization, and insufficient target specificity. This review focuses on the engineering of probiotics designed to overcome these limitations for IBD management. We outline the therapeutic potential and mechanisms of action of probiotics in IBD, with a critical emphasis on discrepancies between preclinical and clinical observations. We subsequently discuss the drawbacks of conventional probiotic therapies, highlighting gaps between in vitro efficacy and in vivo performance. We then highlight cutting-edge engineering strategies, encompassing advanced encapsulation techniques, genetic engineering approaches, novel delivery systems, and molecular-targeting modifications, with quantitative comparisons of their advantages, limitations, and translational potential. The application of these engineered probiotics specifically in UC and CD treatment is explored, with detailed analyses of preclinical models and clinical trials. We also address personalized interventions tailored to individual gut microbiome profiles. Despite significant promise, critical challenges remain, including long-term safety, stability, and accurate prediction of therapeutic responses for engineered probiotics in IBD. Nevertheless, with ongoing advancements in gene editing, synthetic biology, and microbial safety engineering, engineered probiotics represent a promising direction in IBD therapy that will enable more precise, effective, and personalized treatment modalities, provided that safety, reproducibility, and regulatory compliance are prioritized.},
}

@article {pmid41640408,
year = {2025},
author = {Sun, G and Zou, Q and Wang, B},
title = {The interplay of carbon and nitrogen cycling driven by watershed microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1696238},
pmid = {41640408},
issn = {1664-302X},
abstract = {Microorganisms play central roles in regulating carbon and nitrogen cycling across watersheds, driving processes such as organic matter decomposition, primary production, nitrification, and denitrification. Rapid advances in high-throughput sequencing and environmental monitoring have enabled unprecedented insights into the taxonomic diversity and functional capacities of microbial communities under global change. In this review, we synthesize findings from studies published in recent years to evaluate how hydrological connectivity, redox gradients, temperature shifts, and nutrient loading shape microbial metabolism across rivers, lakes, wetlands, and coastal interfaces. We further summarize emerging evidence on how antibiotic resistance genes (ARGs) propagate through these ecosystems and influence microbial functions. The integration of multi-omics technologies including metagenomics, metatranscriptomics, combined with ecological and biogeochemical modeling provides new opportunities to quantify microbe-mediated carbon sequestration and nitrogen transformation. Finally, we discuss current knowledge gaps, including the limited understanding of ARG-driven community restructuring and the insufficient mechanistic resolution of microbe-environment interactions under future climate scenarios. This review highlights the need for cross-scale, data-integrated frameworks to better predict how microbial processes regulate watershed-level biogeochemical cycles in a rapidly changing world.},
}

@article {pmid41640388,
year = {2026},
author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J},
title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e72952},
pmid = {41640388},
issn = {2045-7758},
abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.},
}

@article {pmid41640304,
year = {2026},
author = {Hart, DW and Ng, AS and Gazińska, P and Goldin, R and Gopal, P and O'Dell, N and Zargar, A and Pytowski, L and Montazid, S and Bardella, C and East, JE and Tomlinson, IP and Koch, N and Bennett, NC and Irshad, S},
title = {Characterisation of bacteria-induced colitis and its modulation by probiotics in naked mole rats: a new mammalian model for acute inflammatory disease.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.70034},
pmid = {41640304},
issn = {1096-9896},
support = {DST-NRF (GUN 64756)//Department of Science and Technology-National Research Foundation/ ; //The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC)/ ; },
abstract = {Enteropathogenic bacteria are a major cause of morbidity and mortality globally. While mouse models have been indispensable in advancing our understanding of infectious enteric diseases, key differences in intestinal microbiota and immunobiology between mice and humans underscore the need for alternative mammalian models that better recapitulate human disease states. The naked mole rat (NMR), the longest-lived rodent and a model of healthy ageing, presents a unique opportunity. It possesses an exceptionally robust intestinal barrier, an abundance of goblet cells, a thicker mucin layer, and reduced gut permeability compared to mice. Additionally, the NMR gut microbiome exhibits compositional and functional features shared with human centenarians and traditional-lifestyle populations (e.g. Hadza hunter-gatherers), including an enrichment of health-associated taxa and metabolic pathways. Here, we leverage this model to show that systemic Citrobacter braakii infection is associated with colonic inflammation and epithelial injury that closely mimics human haemorrhagic colitis. Infected NMRs develop mucosal erosions, ulcerations, depletion of goblet cells, expansion of proliferative compartments, and active inflammation in the lamina propria. Without intervention, systemic inflammation associated with sepsis ensues and results in high mortality. Furthermore, we demonstrate the utility of this model for therapeutic testing by showing a strong effect of a probiotic cocktail comprising lactobacilli, bifidobacteria, streptococci, and enterococci. Treatment with this cocktail promoted mucosal healing, restored intestinal homeostasis, and exerted an anti-inflammatory effect. Taken together, we establish the NMR as a translatable model for investigating disease mechanisms in infectious colitis, including disruptions in mucosal barrier permeability, gut microbial ecology, and local and systemic immune regulation, as well as for testing functional probiotic strains as potential therapeutics. © 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.},
}

@article {pmid41639970,
year = {2026},
author = {Hey, JC and Saalfrank, J and Rasamoelina, T and Razafindrakoto, AR and Razafindralava, M and Rajaoniarivo, VG and Kutz, JM and Ratefiarisoa, S and Thye, T and Kislaya, I and Graspeuntner, S and Rakotomalala, Z and Randrianasolo, BS and Rakotomalala, RS and Marchese, V and Rakotozandrindrainy, R and Koecher-Andrianarimanana, D and Rausche, P and Remkes, A and May, J and Hoekstra, PT and van Dam, GJ and Corstjens, PLAM and Gheit, T and Rakotoarivelo, RA and Bang, C and Fusco, D},
title = {The vaginal microbiota of adult Malagasy women of reproductive age in the Marovoay district: first characterization and exploration of associations with human papillomavirus and Schistosoma haematobium infections.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag065},
pmid = {41639970},
issn = {1537-6613},
abstract = {BACKGROUND: The vaginal microbiome plays an important role for women's health. Changes in its composition have been associated with several sexually transmitted infections, including human papillomavirus (HPV) or parasitic infections such as Schistosoma haematobium (Sh). In Madagascar, gynaecological conditions such as chronic manifestations of Sh infections (female genital schistosomiasis, FGS), HPV infections, and cervical cancer are highly prevalent; however, data on the interplay between these conditions and the vaginal microbiota (VM) is still scarce. Additionally, the majority of data originates from the Global North, generating a biased understanding of "healthy" VM across different geographical and social contexts. The objective of our study was to characterize for the first time the VM of adult women of reproductive age in Madagascar and to describe the variability of the vaginal environment in presence of three conditions affecting the urogenital tract.

METHODS AND RESULTS: We characterized the VM of 443 participants, identifying the five community state types (CSTs I - V) with CST IV (57.1 %, diverse) and CST III (34.1 %, Lactobacillus iners-dominated) as the most prevalent. CSTs were associated with previous antibiotics usage, while variability in the alpha and beta diversity was associated with dietary behaviour and previous antibiotics usage. Differential abundance analysis showed variations among specific taxa in HPV- and FGS-positive participants.

CONCLUSION: With this first study of the VM in Madagascar we contribute to a broader understanding of vaginal health as well as narrowing the gap of VM research in sub-Saharan Africa by enriching microbiota databases.},
}

@article {pmid41639557,
year = {2026},
author = {Aran, K},
title = {What my cave stay taught me about sensors.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41639557},
issn = {1476-4687},
}

@article {pmid41639421,
year = {2026},
author = {Tashiro, H and Kuwahara, Y and Kurihara, Y and Konomi, Y and Takahashi, K},
title = {Distinct gut microbiome signatures associated with sedentary behavior improvement following rehabilitation in chronic obstructive pulmonary disease patients with higher functional exercise capacity.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38360-7},
pmid = {41639421},
issn = {2045-2322},
support = {20K17184, 23K15210//Japan Society for the Promotion of Science/ ; 22K11370, 25K14535//Japan Society for the Promotion of Science/ ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is associated with reduced functional exercise capacity and increased sedentary behavior, both of which worsen prognosis. Although rehabilitation is a standard intervention, its impact on physical activity and gut microbiota remains incompletely understood. The present study enrolled 37 stable COPD patients and based on 6-min walk distance (6MWD), patients were classified into higher and lower functional exercise capacity. Physical activity was monitored using a tri-axial accelerometer, and gut microbiome composition was analyzed via 16S rRNA sequencing before and after a 12-week, home-based, rehabilitation program. At baseline, the higher functional exercise capacity group had significantly greater lower limb muscle mass, phase angle, and time spent in moderate-to-vigorous activity than the lower functional exercise capacity group. Rehabilitation did not significantly improve 6MWD or muscle mass in either group. However, sedentary time decreased significantly in the higher functional exercise capacity group, whereas it increased in the lower group. Gut microbiome profiles differed between the two groups at baseline and showed distinct changes after rehabilitation. Notably, the family level for Enterococcaceae decreased post-intervention only in the higher functional exercise capacity group. In COPD patients with higher functional exercise capacity, distinct changes in the gut microbiota were observed among participants whose sedentary time decreased.},
}

@article {pmid41639396,
year = {2026},
author = {Weber, D and Tariq, M and Hazenberg, M and Poeck, H and Malard, F},
title = {Microbiome, GvHD, and immune reconstitution in allogeneic hematopoietic cell transplantation.},
journal = {Bone marrow transplantation},
volume = {},
number = {},
pages = {},
pmid = {41639396},
issn = {1476-5365},
abstract = {The gut microbiota has emerged as a critical factor influencing outcomes following allogeneic hematopoietic cell transplantation (alloHCT). Notably, disruptions to the intestinal microbiome-referred to as dysbiosis-have been strongly linked to the development of acute graft-versus-host disease (aGVHD). The gut microbiome interacts closely with the host immune system, influencing both immune reconstitution and alloHCT complications. As a result, microbiome-targeted strategies are being investigated to improve outcomes and include antibiotic stewardship, prebiotic and diet intervention, probiotics including fecal microbiota transfer (FMT) and postbiotics. These approaches are being investigated not only as a therapeutic intervention in particular for aGVHD, but also as preventive strategies.},
}

@article {pmid41639095,
year = {2026},
author = {Walusimbi, B and Lawson, MA and Bancroft, AJ and Nassuuna, J and Trivedi, DK and Taylor, G and Sanya, RE and Webb, EL and Kateete, DP and Grencis, RK and Elliott, AM},
title = {The gut microbiome and metabolome associate with Schistosoma mansoni infection and cardiovascular disease risk in Uganda.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68983-3},
pmid = {41639095},
issn = {2041-1723},
support = {R120442//Royal Society/ ; NIHR134531//DH | National Institute for Health Research (NIHR)/ ; Z10661/Z/18/Z//Wellcome Trust (Wellcome)/ ; 088785/Z/09/Z//Wellcome Trust (Wellcome)/ ; 095778/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Helminth infections are consistently associated with reduced cardiovascular disease (CVD) risk, yet the biological mechanisms underlying this relationship remain unclear. The gut microbiome and metabolome are key regulators of cardiometabolic health and may mediate infection-associated effects on host physiology. Here we show that Schistosoma mansoni infection associates with distinct gut microbial and metabolic profiles linked to CVD risk in people living in Uganda. In a cross-sectional study of 209 individuals living in communities with contrasting S. mansoni endemicity, we profile the gut microbiome using 16S rRNA gene sequencing and the faecal metabolome using liquid chromatography-mass spectrometry. S. mansoni infection associates with increased gut microbial diversity and distinct taxonomic signatures, including enrichment of taxa such as Treponema and depletion of Prevotella and Streptococcus. Several infection-associated microbial taxa statistically mediate the relationships between S. mansoni infection and cardiovascular disease risk. Faecal metabolomic profiling identifies infection-associated metabolites, and integrative analyses showed linked microbe-metabolite networks associated with cardiovascular risk.These findings identify gut microbiome and metabolome signatures associated with S. mansoni infection and cardiovascular disease risk in Uganda. Although causality cannot be inferred, this work provides insight into host-parasite-microbiome interactions and highlights microbial and metabolic pathways relevant to cardiometabolic health.},
}

@article {pmid41638512,
year = {2026},
author = {Yan, Q and Yuan, S and Mou, W and Liu, J and Yu, Z and Li, Y and Zhang, Z},
title = {The blood microbial community signatures in patients with acute ischemic stroke.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108322},
doi = {10.1016/j.micpath.2026.108322},
pmid = {41638512},
issn = {1096-1208},
abstract = {BACKGROUND: While systemic inflammation and metabolic dysregulation contribute to acute ischemic stroke (AIS)development, the function of the peripheral blood microbiome, which reflects systemic states, remains unclear. This study aimed to characterize these blood microbial signatures and define their clinical relevance in AIS.

METHODS: Blood microbiome profiles from 61 AIS patients and 54 controls were analyzed by 16S rRNA sequencing. Patients were stratified by baseline NIHSS scores and followed for 3-month outcomes to assess prognostic microbial signatures.

RESULTS: AIS patients exhibited a distinct blood microbiota profile compared to controls, characterized by reduced richness and significant structural changes. These alternations included a reduction of key commensal bacteria, such as Akkermansia, and an increase in opportunistic taxa like Meiothermus. Crucially, these microbial dysregulations were strongly correlated with host metabolic parameters, including blood glucose, homocysteine, and lipid levels. However, classification models based on the blood microbial signature failed to predict disease severity and 3-month neurological outcomes. In contrast, alterations in the blood microbiome demonstrated potential as an indicator of AIS severity (AUC = 0.733).

CONCLUSION: Our findings reveal that the blood microbiome in AIS is highly dysregulated, reflecting the host's systemic metabolic health. This strong association suggests circulating microbial signatures could play a role in stroke's pathophysiology, potentially influencing metabolic and inflammatory processes. As a result, analyzing these signatures could lead to the development of minimally invasive biomarkers for disease assessment and may also reveal novel therapeutic targets for managing systemic dysfunction in stroke patients.},
}

@article {pmid41638450,
year = {2026},
author = {Nogueira, LM and Meurer, EC and Pileggi, M},
title = {Modulation of Clostridioides difficile virulence by metabolites derived from probiotic consortia and genetically edited strains.},
journal = {Biotechnology advances},
volume = {88},
number = {},
pages = {108818},
doi = {10.1016/j.biotechadv.2026.108818},
pmid = {41638450},
issn = {1873-1899},
abstract = {Clostridioides difficile infection (CDI) continues to pose a significant clinical and biotechnological challenge, primarily driven by antimicrobial resistance and frequent recurrence. Emerging strategies are shifting the therapeutic focus from pathobiont eradication to virulence suppression, achieved by targeting the key metabolic and regulatory networks that underpin C. difficile pathogenicity in the gut. This review synthesizes multi-omic data demonstrating that a synergistic approach-restoring secondary bile acid metabolism (through the bai operon), boosting short-chain fatty acid (SCFA) production, and disrupting quorum-sensing systems (e.g., luxS, agr)-can collectively suppress toxin expression, biofilm formation, and spore germination. We further examine how synthetic biology and metabolic engineering are paving the way for next-generation solutions, including engineered probiotics, designer microbial consortia, and live biotherapeutic products endowed with programmable quorum quenching capabilities and optimized metabolic outputs. The integration of genomics, transcriptomics, proteomics, and metabolomics, with computational modeling, now enables the predictive design and industrially scalable production of these microbiome-based interventions. Together, these advances mark a pivotal transition from empirical probiotic use to the era of precision, mechanism-driven microbiome therapeutics designed to achieve durable control of CDI recurrence.},
}

@article {pmid41638261,
year = {2026},
author = {Bröker, BM and Bachert, C},
title = {Microbial influences on chronic rhinosinusitis.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.01.019},
pmid = {41638261},
issn = {1097-6825},
abstract = {The nasal microbiome is altered in chronic rhinosinusitis (CRS), characterized by increased bacterial density and higher relative abundance of Staphylococcus aureus compared to healthy adults. This review examines determinants of S. aureus nasal colonization, focusing on immune control and its evasion by the bacteria. CRS and asthma share pathomechanisms of chronic airway inflammation and often co-occur. In both conditions, many patients are sensitized to secreted factors of S. aureus - enterotoxins (SE) and serine protease-like proteins (Spls) - and produce specific IgE, which influences the disease course. Therefore, we propose to incorporate S. aureus-specific IgE measurements into the routine diagnostic evaluation of CRS and asthma.},
}

@article {pmid41533436,
year = {2026},
author = {Cox, IJ and Lauridsen, MM and Le Guennec, A and Fagan, A and Heitmann, GG and Lukose, T and Verna, EC and Bajaj, JS},
title = {Serum and Urinary Metabolomics Reflect the Early Stages of De Novo Metabolic Syndrome After Liver Transplant: A 2-Center Longitudinal Study.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000968},
pmid = {41533436},
issn = {2155-384X},
support = {R21TR003095/TR/NCATS NIH HHS/United States ; 1I01CX002472, 2I01CX001076//U.S. Department of Veterans Affairs/ ; },
abstract = {INTRODUCTION: Liver transplantation (LT) recipients are at high risk of developing de novo metabolic syndrome (MetS), which contributes to cardiovascular and cerebrovascular morbidity. This study investigated serum and urinary metabolic changes after LT to identify microbial and metabolic markers associated with MetS development.

METHODS: We conducted a prospective, 2-center longitudinal study with biospecimen collection pre-LT and at 6 months, 1 year, and 2-9 years post-LT. Nuclear magnetic resonance spectroscopy was used to characterize serum and urine metabolomic profiles from 73 to 44 patients, respectively. MetS was defined as body mass index >30 kg/m 2 plus at least 1 additional metabolic abnormality.

RESULTS: MetS prevalence increased from 11% pre-LT to 36% post-LT. Post-LT, serum metabolite profiles showed increased phosphocholines and lipid-CH 3 (low density lipoprotein), whereas urine profiles demonstrated higher levels of trimethylamine- N -oxide (TMAO) and phenylacetylglutamine. Patients who developed or had persistent MetS exhibited smaller increases in serum phosphocholines and lipid-CH 3 but greater elevations in urinary TMAO levels compared with patients who remained MetS-free.

DISCUSSION: LT is followed by distinct metabolic shifts reflecting changes in both hepatic lipid metabolism and gut-liver microbial cometabolism. Elevated urinary TMAO, together with reduced serum phosphocholine and lipid-CH 3 responses, characterize patients who develop post-LT MetS and may serve as early biomarkers of cardiometabolic risk in LT recipients.},
}

@article {pmid41647444,
year = {2025},
author = {Follestad, P and Filbin, P and Thompson, B and Dobner, P and Jaffe, A and Perlmutter, A and Zwickey, H},
title = {Gut-Mind Interactions in Psychedelic Healing: A Case Study Assessing the Effects of Huachuma and Ayahuasca on the Mind and Microbiome.},
journal = {Journal of restorative medicine},
volume = {15},
number = {},
pages = {63-79},
pmid = {41647444},
issn = {2330-2941},
abstract = {BACKGROUND: Psychedelic plant medicines such as Ayahuasca and Huachuma (San Pedro cactus) are gaining scientific attention for their potential to improve mental health. However, the interplay between these traditional medicines, the gut microbiome, and mental health outcomes remains underexplored.

OBJECTIVE: The main objectives of this study are to investigate the effects of Ayahuasca and Huachuma ceremonies on the gut microbiome, depression, and subjective connectedness in a single patient and to generate hypotheses for future studies.

CASE: A 35-year-old female with prior psychedelic experience participated in separate Ayahuasca and Huachuma ceremonies. Qualitative data were collected through patient interviews. Quantitative data included stool samples collected before and after each ceremony for microbiome analysis, as well as survey data using the Hamilton Depression Rating Scale (HAM-D) and Watts Connectedness Scale (WCS) administered pre- and post-ceremony.

RESULTS: Both ceremonies resulted in substantial reductions in depression scores (HAM-D decreased: Ayahuasca from 18 to 6; Huachuma from 12 to 2) and connectedness scores (WCS increased: Ayahuasca from 62.3% to 95.37%; Huachuma from 58.32% to 84.65%). Although Ayahuasca and Huachuma induced different gut microbial composition shifts, reductions in pro-inflammatory taxa, normalization of inflammation-linked bacterial species, and increases in beneficial butyrate-producing bacterial species were observed for both. These microbial shifts aligned with improved subjective mental health and reduced inflammation. Qualitative interviews revealed distinct archetypal experiences with each medicine, informing personalized therapeutic approaches.

CONCLUSION: This hypothesis-generating case study illustrates a potential link between psychedelic-induced microbiome changes and improvements in mental health which may contribute to reduced inflammation and sustained antidepressant effects via the microbiota-gut-brain axis.},
}

@article {pmid41638211,
year = {2026},
author = {Blackmer-Raynolds, L and Lipson, LD and Kozlov, A and Yang, A and Hill, EJ and Sampson, MM and Hamilton, AM and Fraccaroli, I and Kelly, SD and Chopra, P and Chang, J and Sloan, SA and Sampson, TR},
title = {Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101481},
doi = {10.1016/j.cels.2025.101481},
pmid = {41638211},
issn = {2405-4720},
abstract = {The native microbiome influences numerous host processes, including neurological function. However, its impacts on diverse brain cell types remain poorly understood. Here, we performed single-nucleus RNA sequencing on the hippocampus of wild-type, germ-free mice, revealing the microbiome-dependent transcriptional landscape across all major neural cell types. We found conserved impacts on key adaptive immune and neurodegenerative transcriptional pathways. Mono-colonization with select indigenous microbes identified organism-specific effects on brain myeloid cell transcriptional state. Escherichia coli colonization induced a distinct myeloid cell activation state, increased brain-resident CD8[+] T cells, and shaped amyloid phagocytic capacity, suggesting heightened disease susceptibility. Finally, E. coli-exposed 5xFAD mice displayed exacerbated cognitive decline and amyloid pathology, demonstrating the sufficiency of intestinal E. coli to worsen Alzheimer's disease-relevant outcomes. Together, these results emphasize the broad, species-specific, microbiome-dependent consequences on neural cell states and highlight the capacity of specific microbes to modulate disease susceptibility.},
}

@article {pmid41638193,
year = {2026},
author = {Costa, PCTD and Magnani, M and Martins, VJB and Moraes, RCS and Silva-Luis, CC and Rodrigues, JMA and Cabral, L and Noronha, MF and Vitalis, O and Chikh, K and Godet, M and Vidal, H and de Brito Alves, JL},
title = {Multicomponent intervention improves gut microbiome and cardiac autonomic function in childhood obesity.},
journal = {American journal of physiology. Heart and circulatory physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpheart.00769.2025},
pmid = {41638193},
issn = {1522-1539},
support = {41903.612.28794.22092020//Fundação de Apoio à Pesquisa do Estado da Paraíba (FAPESQ)/ ; 88881.711922/2022//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; },
abstract = {Childhood obesity is associated with gut microbiome dysbiosis, inflammation, and early cardiac autonomic dysfunction. Lifestyle interventions integrating physical activity and dietary modification represent a primary strategy to mitigate cardiometabolic risk during childhood. This longitudinal intervention study investigated cardiovascular, autonomic, inflammatory, metabolic, and gut microbiome-related outcomes before and after a 4-month program combining structured physical exercise with food and nutrition education in 51 children with obesity aged 7 to 10 years. The intervention promoted favorable dietary changes, including reduced intake of saturated fatty acids (SFA), sodium, and total energy. These modifications were accompanied by a reduction in body fat percentage and systemic inflammation, evidenced by lower circulating interleukin-17A (IL-17A) and tumor necrosis factor-alpha (TNF-α) levels. Improvements in biochemical profiles were observed, including increased albumin and high-density lipoprotein cholesterol (HDL-c), and reduced serum triglyceride and urea levels. Metabolomic analyses revealed beneficial shifts in circulating phosphatidylethanolamines, phosphatidylglycerols, choline, and branched-chain amino acids (BCAA). Cardiovascular assessments demonstrated significant reductions in systolic and diastolic blood pressure and improvements in heart rate variability, indicating enhanced cardiac autonomic modulation. Gut microbiota analyses showed no differences in alpha or beta diversity; however, Bray-Curtis volatility analyses identified significant within-subject compositional shifts. Exploratory multivariate analyses suggested potential associations between specific gut taxa (e.g., Ligilactobacillus, Streptococcus, Roseburia), circulating metabolites, and cardiovascular autonomic indices, supporting the existence of microbiota-metabolite-heart interactions. In summary, a 4-month multicomponent lifestyle intervention improved cardiovascular autonomic function, inflammatory status, and cardiometabolic profiles in children with obesity. These findings highlight the cardiovascular benefits of early lifestyle modification and support integrative approaches targeting autonomic and metabolic pathways in pediatric obesity.},
}

@article {pmid41638192,
year = {2026},
author = {Ding, N and Wu, H and Hua, Y and Hua, R and Li, B and Xie, Y and Xiong, Y and Bai, T and Shi, X and Shen, T and Liu, P and Liu, J and Yang, X and Xu, Y and Meng, Z and Lan, B and Zhou, J and Liu, B and Shyy, JY and Yuan, Z and Wu, Y and Li, T},
title = {Gut microbiota-derived isovaleric acid alleviates atrial fibrillation by suppressing GSDME-dependent pyroptosis.},
journal = {Cell metabolism},
volume = {38},
number = {2},
pages = {370-387.e10},
doi = {10.1016/j.cmet.2025.12.017},
pmid = {41638192},
issn = {1932-7420},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Pyroptosis/drug effects ; *Atrial Fibrillation/metabolism/microbiology/pathology ; *Pentanoic Acids/metabolism/pharmacology ; Mice ; Humans ; Mice, Inbred C57BL ; Myocytes, Cardiac/metabolism ; Male ; Ruminococcus/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Hemiterpenes ; },
abstract = {Atrial fibrillation (AF), a common and clinically significant cardiac rhythm disturbance, is associated with gut microbial dysbiosis. However, the precise role of the microbiota and associated metabolism in this condition remain unclear. Through integrated analysis of clinical cohorts and multiple animal models, we identified an intestinal symbiont, Ruminococcus gnavus (R. gnavus), which suppresses the occurrence of AF and atrial fibrosis by producing the leucine-derived branched-chain fatty acid isovaleric acid (IVA). R. gnavus colonization or exogenous IVA supplementation reduced AF susceptibility and improved fibrosis-driven atrial remodeling. Mechanistically, R. gnavus metabolizes dietary leucine into IVA through its unique enzyme 2-oxoisovalerate ferredoxin reductase γ-subunit (vorC). Microbiome-derived IVA activates G protein-coupled receptor 109A (GPR109A) on atrial cardiomyocytes, inhibiting interleukin (IL)-6/signal transducer and activator of transcription 3 (STAT3) signaling activation and blocking gasdermin E (GSDME)-mediated pyroptosis through a STAT3-GSDME feedforward circuit. These results reveal that the microbial metabolism of dietary leucine and the production of IVA play pivotal roles in preventing AF onset and progression.},
}

Animals
*Gastrointestinal Microbiome
*Pyroptosis/drug effects
*Atrial Fibrillation/metabolism/microbiology/pathology
*Pentanoic Acids/metabolism/pharmacology
Mice
Humans
Mice, Inbred C57BL
Myocytes, Cardiac/metabolism
Male
Ruminococcus/metabolism
Receptors, G-Protein-Coupled/metabolism
Hemiterpenes

@article {pmid41637999,
year = {2026},
author = {Horvath, A and Haller, R and Schmid-Zalaudek, K and Goswami, N and Wagner-Skacel, J and Habisch, H and Madl, T and Stadlbauer, V},
title = {The beneficial effect of a multispecies probiotic intervention on quality of sleep - a randomized, double-blinded, placebo-controlled study.},
journal = {Journal of psychiatric research},
volume = {195},
number = {},
pages = {244-256},
doi = {10.1016/j.jpsychires.2026.01.040},
pmid = {41637999},
issn = {1879-1379},
abstract = {STUDY OBJECTIVES: Sleep disorders are common and impair performance and health. The intestinal microbiome regulates human chronobiology. Microbiome modulation through probiotic intervention might therefore harbor the potential to treat sleep disorders. We tested this hypothesis in a randomized, double-blind, placebo-controlled study.

METHODS: We randomized 130 volunteers with self-reported impaired quality of sleep (PSQI>5) in a 1:1 ratio to a 28-day intervention with either a multispecies probiotic (OMNiBiOTiC® STRESS Repair) or a placebo. Participants completed validated questionnaires to estimate quality of sleep, quality of life and perceived stress, and collected stool samples for 16S rRNA sequencing before and after the intervention. Ninety-four participants finished the study and were included in the analysis.

RESULTS: Baseline characteristics were similar between the probiotic group (n = 50; 88.6 % female, 41.2 ± 10.6 years old) and the placebo group (n = 44; 88.0 % female, 40.1 ± 10.7 years old), including the initial PSQI score (10.1 ± 2.7 vs. 10.5 ± 2.6). The probiotic intervention led to an improved sleep efficiency and latency, and thereby improved quality of sleep beyond an observable placebo effect (6.8 ± 2.9 vs. 7.7 ± 3.1; p = 0.036, probiotic and placebo group, respectively). Probiotic bacteria were partially recovered in the microbiome, causing a slight shift in beta diversity in the probiotic group. The intervention did not influence quality of life or perceived stress.

CONCLUSIONS: In conclusion, this well-powered RCT shows that the intervention with a multispecies probiotic improved quality of sleep beyond the effect of a placebo intervention, and that the modulation of the microbiome may therefore be of clinical benefit in alleviating sleep disturbances.},
}

@article {pmid41637678,
year = {2026},
author = {Eriksen, E and Graff, P and Afanou, AK},
title = {Bacterial Communities as Modulators of Innate Immune Signalling: An In Vitro Perspective on Toll-Like Receptor Activation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70289},
doi = {10.1111/1758-2229.70289},
pmid = {41637678},
issn = {1758-2229},
support = {//National institute of occupational health, Oslo (STAMI)/ ; //IVAR-IKS/ ; //The federation of Norwegian Industries/ ; //Norwegian Union of Municipal and General Employees (NUMEG)/ ; },
mesh = {*Immunity, Innate ; *Bacteria/classification/genetics/isolation & purification/immunology ; *Toll-Like Receptors/immunology/genetics/metabolism ; Humans ; *Microbiota/immunology ; Signal Transduction ; Dust/analysis ; },
abstract = {Investigating the work-environmental microbiome is critical for assessing occupational risk associated with exposure to microorganisms. The present study examined the bacterial composition of inhalable dust from waste sorting plants and explored their potential to induce Toll-like receptors (TLR) in vitro, thereby providing insights into the immunomodulatory potential of complex microbial communities from occupational settings. These findings highlight how few dominant bacterial species shape the immune activation properties of the overall bacterial community, where less abundant taxa play a crucial role in immune modulation through TLR activation. The strong association between TLR activation and rare yet highly inductive bacterial taxa demonstrates their potential immunological significance, suggesting that even low-abundant microbes may have a disproportionate impact on immune responses and occupational health outcomes.},
}

*Immunity, Innate
*Bacteria/classification/genetics/isolation & purification/immunology
*Toll-Like Receptors/immunology/genetics/metabolism
Humans
*Microbiota/immunology
Signal Transduction
Dust/analysis

@article {pmid41637499,
year = {2026},
author = {Stief, P and Niggemann, J and Bligh, M and Buck-Wiese, H and Wünsch, U and Steinke, M and Hehemann, JH and Glud, RN},
title = {Hydrostatic pressure induces strong leakage of dissolved organic matter from "marine snow" particles.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaec5677},
pmid = {41637499},
issn = {2375-2548},
abstract = {Marine snow forms at the ocean surface, sinks to depth, and ultimately enables carbon sequestration in the seabed. Fast-sinking marine snow particles, such as diatom aggregates, encounter a rapid increase in hydrostatic pressure during their descent. Using incubations in rotating pressure tanks, we found that pressure levels corresponding to 2- to 6-kilometer water depth induce leakage of dissolved organic matter (DOM) from diatom aggregates equivalent to ~50% of their initial carbon contents. The leaked DOM proved to be diatom-derived and changed the amount and composition of DOM in the surrounding seawater substantially. Ultrahigh-resolution mass spectrometry, high protein-like fluorescence, and low carbon:nitrogen ratios classified the leaked DOM as labile. The bioavailability of leaked DOM was demonstrated by its rapid utilization by a pelagic microbial community, leaving mainly recalcitrant DOM behind. Pressure-induced DOM leakage likely weakens the gravitational "biological carbon pump" and supplies labile DOM to the pelagic microbiome of the deep ocean.},
}

@article {pmid41637186,
year = {2026},
author = {Xu, X and Sun, T and Qing, X and Liu, S and Yang, P and Dong, M and Liu, J and Ren, Y and Shen, Q and Scheu, S and Li, R and Kowalchuk, GA and Krashevska, V},
title = {Meloidogyne nematodes reprogram rhizosphere metabolism to suppress antagonistic microbiota and enable bacterial pathogen co-infection.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116949},
doi = {10.1016/j.celrep.2026.116949},
pmid = {41637186},
issn = {2211-1247},
abstract = {Root-knot nematodes cause substantial crop losses by compromising plant immunity and facilitating invasion by soil-borne bacterial pathogens, yet the mechanisms underlying nematode-facilitated co-infection remain poorly understood. Here, we quantify the global prevalence of nematode-pathogen co-infection and integrate multi-omic analyses across greenhouse and in vitro experiments. We show that nematode invasion activates plant defense gene expression but concurrently disrupts rhizosphere homeostasis, resulting in microbiome dysbiosis that overrides host resistance. Meloidogyne invasion induces pronounced metabolic reprogramming, characterized by depletion of tomatidine and accumulation of carbohydrate metabolites such as galactose. These shifts selectively suppress Streptomyces-dominated antagonistic microbiota while enriching Acidovorax, which exhibits nutritional synergy with Ralstonia. Using synthetic microbial community transplantation, we demonstrate a functional transition from pathogen-suppressive to pathogen-permissive bacteriomes following nematode invasion. Together, our findings reveal how nematodes and bacterial pathogens cooperatively subvert plant-microbe metabolic signaling to undermine rhizosphere immunity, highlighting actionable targets for microbiome-based disease control.},
}

@article {pmid41636526,
year = {2026},
author = {Dove, AS and Abdelsattar, AS and Abutaleb, NS and Seleem, MN},
title = {Identification of the cannabinoid receptor 1 antagonist, ibipinabant, as a potent inhibitor of Neisseria gonorrhoeae.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0123125},
doi = {10.1128/aac.01231-25},
pmid = {41636526},
issn = {1098-6596},
abstract = {Neisseria gonorrhoeae, the causative agent of the second-most prevalent sexually transmitted bacterial disease globally, has been classified as an urgent threat to public health and a high-priority pathogen. Concerningly, N. gonorrhoeae has developed resistance to nearly all FDA-approved drugs. Currently, no approved oral therapies exist, with parenteral administration of ceftriaxone as the only available FDA-approved treatment option for multidrug-resistant gonococcal infections. Yet, ceftriaxone-resistant isolates have now been identified globally, further highlighting the urgent need for the development of novel antibacterial agents. In a screen of 2,528 small molecules targeting G-protein-coupled receptors and related signaling pathways, ibipinabant, a potent cannabinoid receptor 1 antagonist, was identified as having the most potent anti-gonococcal activity. Ibipinabant demonstrated potent activity against a panel of 20 N. gonorrhoeae isolates, without inhibiting some representative Lactobacillus species of the vaginal microbiome. A time-kill assay revealed that ibipinabant is bactericidal, clearing the burden of N. gonorrhoeae (below the limit of detection) within 12 h. Ibipinabant was also able to clear the intracellular burden of N. gonorrhoeae inside human endocervical cells more effectively than the drug of choice, ceftriaxone. This drug was non-toxic against multiple cell lines and did not induce hemolysis of human red blood cells. Finally, in the in vivo mouse model of N. gonorrhoeae genital tract infection, ibipinabant showed a significant reduction (>95%) in the gonococcal burden after 2 days of treatment. Altogether, these results indicate that ibipinabant is a promising candidate for drug repurposing as a novel antimicrobial against multidrug-resistant N. gonorrhoeae.},
}

@article {pmid41636510,
year = {2026},
author = {Anne Hallowell, H and Malogan, J and Suez, J},
title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100225},
doi = {10.1128/msystems.01002-25},
pmid = {41636510},
issn = {2379-5077},
abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.},
}

@article {pmid41636504,
year = {2026},
author = {Mahooti, M and Safaei, F and Mousavian, Z and Samimiazad, A and Bakhtiyarizadeh, M and Emadi, A and Babae, L and Hassani, FS and Eskandari, A and Azman, EM and Zare, D},
title = {Potential of yeast probiotics as immunomodulators: a new frontier in cancer management.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/17460913.2026.2624283},
pmid = {41636504},
issn = {1746-0921},
abstract = {Probiotic yeasts have attracted attention for immunological and functional advantages. They alter inflammatory pathways through immune system induction activities, mitigating some cancer-related immune system pathways, and can be an option in treating inflammation-related diseases such as cancer. Current research has directed to survey mechanisms behind the anti-cancer effects of this genus. It has been demonstrated how probiotic yeasts can be used in managing cancer incidence alone or with other current cancer therapies. This could be possible through their potential in suppression of tumor progression by up-regulating apoptosis, activating immune cells, secreting cytokines, managing inflammation by gut microbiome improvement, and helping short-chain fatty acids production. Recent studies have focused on this genus due to its characteristics, ranging from their capacity to survive in the human gastrointestinal tract, resistance to antibiotics, and lack the ability to transfer genetic elements such as antibiotic resistance genes to pathogenic microorganisms. This review surveys anti-cancer potential of probiotic yeasts through their distinct effects, such as managing inflammation and modulating the immune system, and summarizes current studies of probiotic yeasts. The literature search was conducted from 2000 to 2025, with 2% of reviewed studies before 2000. The databases used were PubMed, Scopus, and Web of Science.},
}

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0226425},
doi = {10.1128/spectrum.02264-25},
pmid = {41636495},
issn = {2165-0497},
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

@article {pmid41636304,
year = {2026},
author = {Brown, LP and Marizzi, A and Borrego, CM and Gionchetta, G and Zhengzheng, Z and Carneiro, RB and Gago-Ferrero, P and Matamoros, V and Subirats, J},
title = {Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13541},
pmid = {41636304},
issn = {1520-5851},
abstract = {The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse-oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel antibiotic resistance families for monitoring. Reclaimed effluents exhibited lower AMR exposure levels than those typically reported for secondary effluents (<0.5 ARGs/cell), while mobile genetic element (MGE) abundances were comparable to secondary effluents (1-2 MGEs/cell). Effluent communities differed by WWTP configuration: membrane bioreactor combined with ultrafiltration favored nutrient-removal/oxidative-stress taxa and reduced transferable MGEs, whereas plants relying on physical separation (sand filtration or reverse osmosis) retained fecal-associated taxa and MGEs. Specific clinically relevant ARGs persisted after treatments, including aadA and aph(3'')-Ibs (resistance to aminoglycosides), ermB and mphA (resistance to macrolides), and blaOXA-129 (resistance to beta-lactams), which we identify as sentinel markers for monitoring reclaimed water and sludge. We advance a generalizable two-step framework, metagenomic discovery to identify sentinel markers, followed by targeted assays for streamlined surveillance, that provides the first operational blueprint for integrating AMR into water reuse management under the EU regulation.},
}

@article {pmid41636271,
year = {2026},
author = {Sung, HH and Chalamalasetty, N and Alzainal, A and Liu, H and Wang, L and Arikita, PC and Wei, ICX and Wang, HL and van den Bosch, MHJ and Caird, MS and van der Kraan, PM and Kozloff, KM and Davidson, EB},
title = {The Role of Wnt Signaling in Age-Related Alveolar Bone Loss and Regeneration.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70085},
pmid = {41636271},
issn = {1600-0765},
support = {5K08DE030116/DE/NIDCR NIH HHS/United States ; P30AR069620/NH/NIH HHS/United States ; R21AR075197/AR/NIAMS NIH HHS/United States ; },
abstract = {The periodontium is a uniquely dynamic tissue system requiring precise signaling for lifelong adaptation. The canonical Wnt/β-catenin pathway is a master regulator of bone homeostasis; however, its role in the specialized environment of the alveolar bone-marked by rapid turnover, complex mechanical forces, and exposure to the oral microbiome-remains incompletely understood, particularly in the context of aging. This review critically synthesizes evidence on Wnt signaling in alveolar bone remodeling, with a focus on age-related dysregulation, contrasting established paradigms from long bone biology with emerging oral-tissue-specific data. Wnt/β-catenin signaling is essential for periodontal homeostasis, orchestrating osteoblastogenesis and mechanotransduction. Its activity is compartment-specific within the periodontium and is potently suppressed in pathology. Key mechanisms of age-related decline include the upregulation of Wnt antagonists (e.g., sclerostin, DKK1), cellular senescence, altered FoxO-Wnt crosstalk under oxidative stress, and impaired mechanosensing. These changes converge to disrupt regenerative capacity, tipping the balance toward net alveolar bone loss. Therapeutically, sclerostin inhibition demonstrates robust preclinical efficacy in rescuing bone loss in models of periodontitis and estrogen deficiency. However, the potential cardiovascular risks of systemic Wnt activation suggest that redirecting efforts toward localized delivery strategies could be a promising alternative. Aging induces a multifaceted suppression of regenerative Wnt signaling in the periodontium. Modulating the Wnt pathway shows great potential for oral bone regeneration. However, significant challenges exist, especially in designing local delivery systems that are both safe and effective. Overcoming these hurdles is crucial for successful clinical applications. Future research must bridge the gap between skeletal biology and direct oral-specific investigations to enable targeted therapies that preserve periodontal health in an aging population.},
}

@article {pmid41636127,
year = {2026},
author = {Silva-Luis, CC and Trindade da Costa, PC and Baccin Martins, VJ and de Brito Alves, JL},
title = {The influence of ultra-processed foods on gut microbiome and inflammatory markers in schoolchildren from Northeastern Brazil.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70369},
pmid = {41636127},
issn = {1536-4801},
support = {#41903.612.28794.22092020//Paraíba State Research Foundation/ ; //CAPES/ ; },
abstract = {OBJECTIVE: This study investigated the relationship between the consumption of ultra-processed foods (UPF), dietary profile, and inflammation on the intestinal microbiome in children.

METHODS: A cross-sectional study was conducted using data from a community-based controlled trial involving 82 children aged 7-11 years enrolled in public schools in João Pessoa, Paraíba, Brazil. The gut microbiome was assessed by 16S rRNA gene sequencing. Dietary intake was assessed by a 24-h food recall and UPF intake was estimated using the NOVA system. Anthropometry, socio-economic variables, and cytokines (IL-2, IL-4, IL-6, IL-10, IL-17a, IFN-γ, and TNF-α) were also assessed.

RESULTS: Children in the third tertile (higher consumption of UPF) had a higher intake of calories from UPF (p < 0.01), trans-fatty acids (p = 0.01), thiamine (p = 0.02), while the intake of protein (p = 0.01), and copper (p = 0.04) was lower. Children in the third tertile had lower abundance of Ruminococcaceae (p = 0.04) and Barnesiellaceae (p = 0.02) and higher abundance of the Monoglobaceae and Erysipelotrichaceae (p = 0.04). Several bacterial genera showed significant correlations with inflammatory cytokines. Dorea and Subdoligranulum were associated with IL-17A and IL-10; Agathobacter with IL-6, IL-10, and IFN-γ; Faecalibacterium with IL-10, IFN-γ, and TNF-α; Fusicatenibacter and Bifidobacterium with IL-10; and Roseburia with TNF-α (all q < 0.05).

CONCLUSIONS: A high UPF intake was associated with a poorer-quality diet and changes in the composition of the gut microbiome, suggesting potential interactions between diet, microbial communities, and immune responses.},
}

@article {pmid41636025,
year = {2026},
author = {Shi, H and Shi, F and Wagle, R and Gonzalez-Gonzalez, MA and Mell, B and Oliver, B and Zhu, T and Joe, B and Durgan, DJ},
title = {Bacterial Extracellular Vesicles Mediate Microbiota-Host Communication to Regulate Blood Pressure in Male Rats.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYPERTENSIONAHA.125.25962},
pmid = {41636025},
issn = {1524-4563},
abstract = {BACKGROUND: Altered gut microbiota composition has been implicated in the development of hypertension. Evidence suggests bacterial products and metabolites can enter circulation, act on peripheral tissues, and modulate blood pressure (BP). We identified extracellular vesicles (EVs) of bacterial origin (bacterial extracellular vesicles [bEVs]) in the circulation of spontaneously hypertensive stroke-prone rats (SHRSP). We hypothesized that bEVs mediate communication between microbiota and the host, and that bEVs from SHRSP microbiota contain unique cargo that promotes hypertension.

METHODS: EVs were isolated from plasma and cecal content of SHRSP and Wistar-Kyoto (WKY) rats. Multiomics analysis, including 16S rRNA sequencing, small RNA sequencing, lipidomics, and proteomics were performed to assess the cargo of bEVs. BEVs from WKY and SHRSP were transplanted by oral gavage to WKY and SHRSP recipients, and the effects on BP and sympathetic activity were monitored. The potential role of bEVs on BP was also evaluated in Dahl S and obstructive sleep apnea models of hypertension.

RESULTS: Significant differences were observed in WKY and SHRSP bEV cargo, including small RNAs, proteins, and PAMPs (pathogen-associated molecular patterns). Transplantation of SHRSP bEVs to WKY rats increased renal sympathetic nerve activity and elevated BP. Moreover, we showed that bEVs influence BP regulation in Dahl S and obstructive sleep apnea-induced hypertension.

CONCLUSIONS: Our findings position bEVs as critical mediators of microbiota-host communication in BP regulation and demonstrate that bEVs from the altered SHRSP microbiota promote hypertension. Our findings shed new light on the role of bEVs in hypertension pathogenesis and offer new perspectives for diagnostics and therapeutic interventions.},
}