@article {pmid41710320,
year = {2026},
author = {Kerai, T and Woolhouse, M and Nyazema, NZ and Mutapi, F},
title = {A narrative review of heterogeneity in SARS-CoV-2 infection outcomes and vaccine efficacy: strategizing pandemic preparedness in Africa.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1761547},
pmid = {41710320},
issn = {2296-2565},
mesh = {Humans ; *COVID-19/epidemiology/prevention & control/immunology ; Africa/epidemiology ; *Vaccine Efficacy ; SARS-CoV-2 ; *COVID-19 Vaccines/immunology ; *Pandemics/prevention & control ; Pandemic Preparedness ; },
abstract = {Disease epidemiology during the COVID-19 pandemic differed greatly across the globe. In contrast to early pandemic predictions, Africa recorded the fewest SARS-CoV-2 related hospitalizations and deaths. Hypotheses proposed to explain this paradox include underreporting, age demographics, climate, national mitigation strategies, lifestyle factors, pre-existing cross-reactive protection, and host genetic determinants. This traditional, narrative review evaluates these hypotheses investigated in the published literature, and highlights knowledge gaps which limit our understanding and obscure validation of potential explanations. It also discusses how responses to vaccines, the primary intervention sought to control infectious disease outbreaks, may vary both within the African population and across other continents. Potential explanations in the literature include pre-existing immunity, poor nutrition, immune modulating co-infections, comorbidities, microbiome composition, genetic polymorphisms, and demographic factors. Previous studies have shown that pre-existing (infection-derived) immunity or cross-reactive immune responses can augment vaccine-elicited positive responses and can protect against reinfection in a way similar to immunization. Conversely, there are also studies showing that prior immunity interferes with the efficacy of new vaccines through mechanisms like original antigenic sin and immune imprinting. Thus, there is need for more immunology studies to understand the relative contribution of pre-existing cross-reactive immune responses to the epidemiology of new pathogens. These studies are particularly essential to understand the differences between pandemic preparedness and population vulnerability, as well as to inform vaccine development and vaccine effectiveness monitoring studies. SARS-CoV-2 serves as an important case study to understand heterogeneity between and within populations in immune responses to both the pathogen and to vaccination. This understanding is crucial in informing vaccine research and development aimed at supporting the 100-day mission for when the next pandemic threat emerges.},
}

Humans
*COVID-19/epidemiology/prevention & control/immunology
Africa/epidemiology
*Vaccine Efficacy
SARS-CoV-2
*COVID-19 Vaccines/immunology
*Pandemics/prevention & control
Pandemic Preparedness

@article {pmid41710234,
year = {2026},
author = {Kumar, P and Rani, S and Dahiya, P and Kaur, B and Kumar, P and Arora, K and Kumar, A and Dang, AS and Suneja, P},
title = {Indole-3-Acetic Acid Production and Molecular Insights into its Biosynthetic Pathway.},
journal = {Indian journal of microbiology},
volume = {66},
number = {1},
pages = {1-19},
pmid = {41710234},
issn = {0046-8991},
abstract = {UNLABELLED: IAA synthesis by endophytes plays an important role in establishing a successful relationship between bacteria and plants. There are multiple pathways of IAA biosynthesis, IPyA pathway being widespread among endophytes. A total of five bacterial endophytes, Pseudomonas lini PRN1, Bacillus sp. PHR5, Ochrobactrum sp. PHR6, Bacillus sp. AJhN4 and Pantoea agglomerans CPHN2, were used in the present study. Out of these, three isolates Bacillus sp. PHR5, Ochrobactrum sp. PHR6, and Bacillus sp. AJhN4 were screened and optimized for IAA production by varying physicochemical parameters using OFAT. The presence of IAA in crude extracts was confirmed by ultra-performance liquid chromatography (UPLC) using IAA as standard. The highest IAA producing isolate was further used for scale-up of IAA production. Maximum production of 947 µg/ml IAA was obtained with 10% inoculum size, pH 9, DO of 60 after 19 h at 30 °C using 2-L stirred tank bioreactor. The study was further carried out, to specifically decipher the IAA pathway in this isolates and to characterize the ipdC gene. The genomic analysis of ipdC gene sequence of P. agglomerans CPHN2 performed and specific primers designed after annotation and amplicons of size 1720 bp and 2500 bp were obtained respectively. It was also observed that the IPDC protein is coded by the negative or antisense strand of DNA. Homology modelling approach was employed to develop a structural model of the IPDC proteins by utilizing sequences from closely related organisms, as well as from P. agglomerans CPHN2 IPDC protein sequence. All IPDC protein models exhibited significantly higher binding energy with indole-3-pyruvate compared to pyruvate. Among these, the IPDC from P. agglomerans CPHN2 showed the maximum binding energy with indole-3-pyruvate relative to other IPDC proteins. In the present study, the identification of the Indole-3-pyruvate (IPyA) pathway and characterization of the ipdC gene in Pantoea agglomerans offers insights into optimizing the IAA production for sustainable agriculture. Understanding the enzymatic pathways also opens avenues for genetic engineering in microbial biotechnology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01535-3.},
}

@article {pmid41710230,
year = {2026},
author = {Sundaram, K and Vajravelu, LK},
title = {Tuberculosis Prognosis and Clinical Synergistic Activity with gut Microbiome.},
journal = {Indian journal of microbiology},
volume = {66},
number = {1},
pages = {84-94},
pmid = {41710230},
issn = {0046-8991},
abstract = {The association between tuberculosis and gut microbiota is notable clinical synergistic action. Tuberculosis is a highly contagious illness that poses a huge global risk. Mycobacterium tuberculosis, an acid-fast bacillus, is responsible for one of the top ten death associated lethal infection. The study of human commensal bacteria has a strong link to tuberculosis and its treatment. The gut microbiota is frequently altered with antimycobacterial drugs. Importantly, there was a significant association found between the gut microbiome and the brain via the gut-brain axis. This interaction is also thought to exist along the gut-liver and gut-lung axis, with possible connections to appropriate organs as well. Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, Verrucomicrobia, and Fusobacteria make up the majority of the microbiota in mammals' guts. Crucially, substantial data from human and animal studies shows that mycobacterial infection causes an imbalance in the gut microbiota, known as gut microbial dysbiosis. This dysbiosis is distinguished by variations in the abundance of certain microbes, particularly those that produce short-chain fatty acids (SCFAs), such as Bifidobacterium and Ruminococcus. The review examined various studies on the association between tuberculosis and gut microbiota in order to develop a clinical algorithm and potential immune regulation against tuberculosis employing crucial gut commensal bacteria.},
}

@article {pmid41710228,
year = {2026},
author = {Li, W and Wei, F and Liu, H and Lv, M and Zhao, D and Qin, X and Liu, X},
title = {Microbiome-Metabolomics Reveals the Bidirectional Associations Between Aging and Depression.},
journal = {Indian journal of microbiology},
volume = {66},
number = {1},
pages = {243-259},
pmid = {41710228},
issn = {0046-8991},
abstract = {UNLABELLED: Aging increases the susceptibility to depression, and depression accelerates the aging process of body. However, it is needed to be studied deeply that the connotations of the correlation between aging and depression. By integrally applying metabolome and microbiome techniques, the study aimed to explore underlying mechanisms of bidirectional associations between aging and depression. Aging rat model and depression rat model were carried out. Classical behaviors were measured to assess the impacts of aging and depression on rats. On top of this, potential changes in the organism are revealed to elucidate the bi-directional associations between aging and depression based on the 16S rRNA sequencing of gut flora and [1]H-NMR of gut metabolites, respectively. Depression weakened the ability of autonomous activities, spatial memory, and gastrointestinal functions of rats, which are also closely related to aging. Vice versa, aging also weakens the autonomous activities of rats, which frequently appears in depression. Secondly, valine, propionate, etc. are potential fecal metabolites that are commonly shared by aging and depression, and these metabolites are closely related to changes in gut microbiota composition. Lastly, both aging and depression decreased the ratio of Firmicutes to Bacteroidetes. Spearman's analysis found that a variety of metabolites, including proline, strongly correlated with Lactobacillus and Corynebacterium, suggesting that these bacterial species play a significant role in the metabolic changes observed in both aging and depression. Meanwhile, differential metabolites and gut microbiota were strongly associated with the number of rearings and gastrointestinal movement of rats, suggesting that potential associations between aging and depression remarkably occur at multiple levels. Exploring the bidirectional association of aging and depression from the perspectives of metabolome and microbiome will not only deepen our understanding of aging and depression, but also provide novel ideas for clinically treating the co-existence and co-occurrence of aging with depression.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01538-0.},
}

@article {pmid41710156,
year = {2026},
author = {Espinosa, P and Hinojosa-Figueroa, MS and Vallejo, P and Pérez, F and Burneo, G and Villarreal, C and Rodas, JA and Leon-Rojas, JE},
title = {Microbial dysbiosis as a diagnostic marker in psychiatric disorders: a systematic review of gut-brain axis disruptions.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1728473},
pmid = {41710156},
issn = {1662-4548},
abstract = {BACKGROUND/OBJECTIVES: Mental health disorders represent a major global health burden. Recent interest has surged in the microbiome-gut-brain axis, which may influence psychiatric pathophysiology. This systematic review evaluates alterations in intestinal microbiome (IM) composition between individuals with psychiatric disorders-such as schizophrenia, autism spectrum disorder (ASD), mood and eating disorders-and healthy controls, with a focus on diagnostic relevance.

METHODS: We conducted a systematic review across PubMed, Scopus, CENTRAL, and PsycINFO, following PRISMA 2020 guidelines. Studies were included if psychiatric diagnoses were made using DSM-V and intestinal dysbiosis was characterised at the phylum, family, and genus levels. Only observational and interventional studies were considered. Microbial alterations were extracted and analysed both qualitatively and quantitatively. Risk of bias was assessed using NIH Quality Assessment Tools.

RESULTS: A total of 80 studies involving 2,691 participants met the inclusion criteria. Across disorders, consistent disruptions were observed in Firmicutes, Bacteroidetes, and Actinobacteria phyla presented as the percentage of affected patients within each disorder. Autism spectrum disorder (ASD) was associated with decreased Firmicutes (↓ 4.79%) and Bacteroidetes (↓ 3.29%) and increased Bifidobacteriaceae (↑ 5.86%) and Eggerthellaceae (↑ 5.50%). Mood disorders, including major depressive disorder and bipolar disorder, showed increased Christensenellaceae (↑ 18.1%) and decreased Ruminococcaceae (↓ 2.0%). Schizophrenia was marked by elevations in Lachnospiraceae, Christensenellaceae, and Enterobacteriaceae (↑ 11-28%) and reductions in Akkermansia and Turicibacteraceae (↓ 9-28%). Anorexia nervosa and binge eating disorder displayed profound dysbiosis, including ↓ Lactobacillus (48.5%) and complete loss of Akkermansia (100%). ADHD showed a Firmicutes/Bacteroidetes imbalance (↑ 49.8%, ↓ 56.6%). These alterations suggest microbial signatures that are both disorder-specific and partially overlapping.

CONCLUSION: Our findings highlight reproducible patterns of gut microbial dysbiosis that may represent candidate microbial biomarkers and inform future diagnostic research. Microbiome profiling has potential as a non-invasive adjunct to psychiatric diagnosis, warranting further exploration. Future longitudinal and mechanistic studies using standardised methods are essential to validate these microbial signatures and their diagnostic utility.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42021254293, CRD42021254293.},
}

@article {pmid41710143,
year = {2026},
author = {Yu, X and Zhang, Y and Shi, LJ and Wang, H},
title = {Dual Role of the Endometrial Microbiome-Immune Axis: From Endometrial Homeostasis to Reproductive Disorders.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {559370},
pmid = {41710143},
issn = {1179-1411},
abstract = {The homeostasis of the uterine environment is crucial for reproductive health. Recent studies have revealed the complex interplay between the endometrial microbiome, immune system, and the endometrium. Under normal physiological conditions, the microbiome, primarily composed of Lactobacillus species, promotes a healthy reproductive environment by maintaining local immune homeostasis, inhibiting the growth of pathogenic microorganisms, and regulating the integrity of the endometrial barrier. However, dysbiosis can abnormally activate local immune responses, disrupting the immune tolerance mechanisms of the endometrium and thereby compromising pregnancy maintenance and overall reproductive health. This study uniquely highlights the role of the endometrial microbiome in modulating immune responses specifically within the uterine environment, a critical factor for reproductive success. Our findings also suggest novel therapeutic strategies targeting microbiome modulation and immune regulation, offering promising avenues for improving reproductive health outcomes. This review aims to explore the regulatory mechanisms of the microbiome-immune axis in both physiological and pathological conditions, with a particular focus on how these interactions specifically influence the uterine environment, while also considering the broader implications of microbiome-immune interactions throughout the entire body. We will analyze its potential role in reproductive health issues and discuss new therapeutic strategies based on microbiome and immune modulation.},
}

@article {pmid41710083,
year = {2026},
author = {Boracchini, R and Canova, C and Bendoni, S and Di Chiara, C and Giaquinto, C and Baraldi, E and Cantarutti, A},
title = {Recurrent wheezing as a mediator between early-life exposures and childhood asthma: a mediation analysis in an Italian primary care paediatric cohort.},
journal = {BMJ public health},
volume = {4},
number = {1},
pages = {e003442},
pmid = {41710083},
issn = {2753-4294},
abstract = {INTRODUCTION: Asthma represents a significant global public health concern, especially in children, due to its high prevalence and burden on the healthcare system. Early-life exposures, particularly to antibiotics and bronchiolitis, have been independently linked to an increased risk of wheezing and subsequent asthma. Despite extensive research on these risk factors, their interplay and combined impact throughout early childhood remains unclear. This study aims to clarify these relationships by investigating the mediating role of recurrent wheezing in the inception of childhood asthma.

METHODS: A retrospective birth-cohort study was conducted using data from the Italian Pedianet database, including children followed for at least 5 years. Exposure to antibiotics and bronchiolitis during the first year, episodes of wheezing between ages 1-4, and asthma diagnoses from age 5 onward were identified in outpatient records. Mediation analysis assessed the association between early-life exposures and asthma risk, with recurrent wheezing considered a potential mediator.

RESULTS: Among 121 255 children, 2.33% developed asthma after age 5. Our results support the hypothesis that early-life bronchiolitis and antibiotic use increase asthma risk through an indirect pathway mediated by recurrent wheezing, which accounts for the majority of the effect (up to 74%), and a direct pathway, independent of wheezing, which may reflect mechanisms such as immune dysregulation, airway remodelling or microbiome alterations. The strong mediated component underscores recurrent wheezing as a clinically relevant marker and key target for preventive strategies. Nonetheless, the presence of a residual direct effect suggests that interventions focusing exclusively on wheezing may not entirely eliminate asthma risk (up to 70%), even though they could substantially reduce it.

CONCLUSIONS: Our findings highlight the importance of preventing bronchiolitis and wheezing to reduce asthma incidence, supporting antibiotic stewardship and respiratory syncytial virus immunisation as public health interventions.},
}

@article {pmid41710035,
year = {2026},
author = {John, J and Ortiz, M and Ramond, P and Campbell, BJ},
title = {Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag021},
pmid = {41710035},
issn = {2730-6151},
abstract = {Functional redundancy (FRed) is expected to buffer ecosystems against change, yet it has rarely been characterized in natural systems. How changes in microbial metabolisms, activity, and FRed in ecosystems are influenced by temporal, spatial, and environmental patterns is especially unclear. Here, we analyzed paired metagenomic and metatranscriptomic datasets from surface water samples collected in the Chesapeake and Delaware Bays, USA. These adjacent estuaries experience similar climatic conditions but differ in nutrient availability, salinity, and other environmental factors. We reconstructed 345 high quality metagenome assembled genomes and assessed their metabolic flexibility, and the extent of gene encoded (potential) and expressed (realized) FRed as a function of environmental drivers, microbial lifestyle (free living vs. particle attached), and gene function. The microbiomes exhibited high metabolic flexibility, reflecting their potential, and in many cases, realized gene expression, to exploit diverse energy sources, ranging from organic carbon substrates to trace gases. Potential and expressed FRed varied across seasons, lifestyles, and gene functions, and was structured within each bay by environmental factors such as temperature, salinity, and concentrations of phosphate, silicate, and chlorophyll a. These findings highlight variability in community-level metabolism, and FRed across estuarine microbiomes, shaped by environmental conditions, seasonality, and lifestyle, and provide insights into how these communities may respond to future perturbations.},
}

@article {pmid41709968,
year = {2026},
author = {Chen, J and Pan, S and Huo, W and Wang, W and Tan, Z and Wu, Y and Kong, Y and Yin, C and Gan, K and Zhao, M and Gao, M and Xia, Q and Li, J and Lu, Y and Yang, R and Liu, Y},
title = {Fuzheng Jiedu Formula Ameliorates Acute Lung Injury by Modulating Gut Microbiota to Enhance Short-Chain Fatty Acid.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {556752},
pmid = {41709968},
issn = {1178-7031},
abstract = {AIM OF STUDY: The objective of this research is to clarify the mechanism by which FZJDF mitigates lipopolysaccharide (LPS)- ALI through the enhancement of short-chain fatty acids (SCFAs) production by Clostridium butyricum (C. butyricum), and the modulation of the gut microbiota-gut-lung axis.

MATERIALS AND METHODS: The mice were treated with FZJDF for 7 days and then treated with LPS. The therapeutic efficacy of FZJDF against LPS-induced ALI was evaluated through lung-to-weight ratio, Inflammatory factor, pathological changes. Additionally, the intestinal barrier function was evaluated by analyzing tight junction protein expression levels. 16S rRNA gene sequencing was employed to monitor alterations in the intestinal microbiome and pulmonary microbiota, while gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography (UPLC) were utilized to quantify the concentrations of SCFAs. Ultimately, the necessity of C. butyricum for FZJDF's therapeutic influence was confirmed through antibiotic-mediated gut microbiota depletion.

RESULTS: FZJDF significantly decreased lung-to-weight ratio and reducing inflammatory cell infiltration of neutrophils. Furthermore, it significantly elevated the expression levels of tight junction proteins. It is plausible that FZJDF may improve intestinal and lung microecological imbalance and stimulate the synthesis of SCFAs. Notably, we determine C. butyricum as the crucial bacterium for the role of FZJDF in gut barrier repair and suppression of lung inflammation in ALI mice. The use of antibiotics led to the repair of the intestinal barrier and a failure in SCFAs production, whereas C. butyricum colonization restores the therapeutic effect of FZJDF in ALI mice, further confirming that FZJDF attenuates ALI.

CONCLUSION: Our results imply that FZJDF could exert its palliative effect in ALI by regulating the intestinal microbiota to increase the production of SCFAs, which in turn inhibits neutrophil-mediated inflammatory responses. These findings support microbiota-targeted traditional medicine as a translational strategy for acute lung injury.},
}

@article {pmid41709953,
year = {2026},
author = {Chung, PH and Boursi, B and Baris, H and Leong, JY and Nickel, JC and Chisari, E and Parvizi, J and Tipton, CD and Ancira, J and Hochberg, A and Rifkin, J and Phillips, CD},
title = {Variations in Urinary Microbiota on a Short-Duration Space Mission to the International Space Station.},
journal = {JU open plus},
volume = {4},
number = {2},
pages = {e00017},
pmid = {41709953},
issn = {2771-554X},
abstract = {INTRODUCTION: Space travel exposes crew to substantial stressors, which may potentially alter their microbiome and be detrimental to their health and safety. We hypothesize that urinary microbiota is altered during a short-duration spaceflight to the International Space Station (ISS).

METHODS: Urine samples were collected from 4 male crew members. One crew member provided samples while on orbit on the ISS using a urine collection kit (UCK) designed for low-gravity environments. This crew member also provided paired mid-stream and UCK samples on Earth prelaunch and on return for direct comparison of collection methods. Three additional crew members provided mid-stream samples prelaunch and on return, and also for follow-up timepoints to serve as ex post facto control samples. Urine was stored at -80℃ and sent for 16s next-generation sequencing (MicroGenDX, Lubbock, TX).

RESULTS: Bacterial load (P = .52), species richness (P = .64), and differences in microbiota composition (P = .26) did not significantly vary by the collection method (mid-stream vs UCK). Significant differences in species richness, load, and microbial composition among preflight, orbital, and return mission samples were detected (P = .047, F = 1.8092, df = 2.9, R2 = 0.34076). Orbital microbial composition significantly differed from preflight (P = .03) and return (P = .03), whereas preflight and return samples did not differ (P > .05). Comparison with the limited follow-up ex post facto Earth-bound samples serving as controls showed no significant differences among preflight or return mission samples, but preflight (P = .04) and return (P = .05) did significantly differ compositionally from orbital samples. Continuous temporal effects on composition were evaluated through which bacterial load (P = .05) was statistically significant, peaking during the orbital period.

CONCLUSIONS: Results are consistent with an effect of space travel altering the urinary microbiota. Further studies are needed to confirm this result and to better understand whether such changes may be detrimental to the health and safety of space travelers and professional astronauts.},
}

@article {pmid41709889,
year = {2026},
author = {Salo, V and Remitz, A and Lauerma, A and Salava, A},
title = {Topical probiotic Lactobacillus lactis treatment in atopic dermatitis: a placebo-controlled pilot study on tolerability and efficacy.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1694229},
pmid = {41709889},
issn = {2296-858X},
abstract = {INTRODUCTION: Microbiome-targeted treatments have been investigated in atopic dermatitis (AD). We aimed to investigate the tolerability and efficacy of probiotic Lactobacillus lactis lysate cream in AD.

METHODS: A total of 13 patients with mild-to-moderate AD were treated with differently concentrated probiotic creams (3, 10, and 30%) for 4 weeks. The severity of AD [Eczema Area and Severity Index (EASI) and Investigator Global Assessment (IGA)], epidermal barrier function (TEWL), and the impact of AD [Dermatology Life Quality Index (DLQI), Patient-Oriented Eczema Measure (POEM), Atopic Dermatitis Control Tool (ADCT), and pruritus and sleep disturbance visual analog scale (VAS)] were measured at baseline (BL) and at 4 and 8 weeks. Comprehensive clinical patient data and laboratory values, including blood eosinophil count, total serum IgE levels, and specific IgEs to aeroallergens, were obtained.

RESULTS: Comparison of the treatment groups and longitudinal comparisons at various time points showed no significant differences regarding AD severity (EASI, p = 0.76, CI: 0.65-1.00), epidermal barrier dysfunction (TEWL, p = 0.37, CI: 0.19-0.73), or patient-reported subjective impact of AD (DLQI, p = 0.76, CI: 0.65-1.00; POEM, p = 0.76, CI: 0.35-0.88; ADCT, p = 0.72, CI: 0.65-1.00; pruritus VAS 0.67, CI: 0.55-1.00; sleep disturbance VAS, p = 1.00, CI: 0.79-1.00) between different probiotic lysate concentrations and placebo. The probiotic lysate cream was well-tolerated, and there were no significant adverse effects. The limitations of the study were the small patient cohort and group sizes. There was also a relatively short follow-up, and no evaluation of long-term effects was conducted.

DISCUSSION: In our patient cohort, topical probiotic L. lactis lysate cream showed good tolerability, but it did not show efficacy in the treatment of mild-to-moderate AD. Although topical probiotics have been reported to be effective in a limited number of studies, more placebo-controlled clinical studies are needed to explore their potential role in the treatment of AD.

CLINICAL TRIAL REGISTRATION: https://eudract.ema.europa.eu, Identifier EudraCT 2020-000514-15.},
}

@article {pmid41709871,
year = {2026},
author = {Fuller, DT and Mondal, S and Sur, S and Pal, N},
title = {Dirichlet Distribution Parameter Estimation With Applications in Microbiome Analyses.},
journal = {Statistics in medicine},
volume = {45},
number = {3-5},
pages = {e70454},
doi = {10.1002/sim.70454},
pmid = {41709871},
issn = {1097-0258},
mesh = {*Microbiota ; Humans ; Computer Simulation ; *Models, Statistical ; Likelihood Functions ; Sample Size ; },
abstract = {Microbiome analysis is the process of identifying the composition and function of a community of microorganisms in a particular location, which is essential in understanding human and environmental health. Properly quantifying microbial composition, however, remains challenging and relies on statistical modeling of either the raw taxonomic abundances or the relative abundances. Relative abundance measures are commonly preferred over the absolute abundances for microbiome analysis because absolute abundance values are dependent on the sequencing depth and sequencing method. Despite this, literature on modeling relative abundance by meaningful probability distribution, followed by subsequent statistical inferences, is limited. In this work, the Dirichlet distribution is proposed to model the relative abundances of taxa directly without the use of any further transformation (e.g., additive log-ratio transform, isometric log-ratio transform). In a comprehensive simulation study, we have compared biases and standard errors of two methods of moments estimators (MMEs) and the maximum likelihood estimator (MLE) of the Dirichlet distribution. comparison of these estimators is done over three cases of differing sample size and dimension: (i) Small dimension and small sample size; (ii) small dimension and large sample size; (iii) large dimension with both small and large sample sizes. As expected, the MLE shows the overall best performance because there is no loss of information since this estimator is based on the (minimal) sufficient statistics. We then explore the asymptotic properties of the MLE utilizing the Fisher information alongside our simulation results. We demonstrate the applicability of Dirichlet modeling methodology with four real world microbiome datasets and show how the estimated mean relative abundances obtained from the Dirichlet MLE (DMLE) differ from those obtained by a commonly used method, that is-Bayesian Dirichlet-multinomial estimator (BDME), which works with absolute abundances. For all the four datasets, the DMLE results are comparable to the BDME results while requiring much less computational time for both single uses and for large simulations.},
}

*Microbiota
Humans
Computer Simulation
*Models, Statistical
Likelihood Functions
Sample Size

@article {pmid41709346,
year = {2026},
author = {Araújo, M and Mendes-Frias, A and Silvestre, R},
title = {Sex differences in immune modulation: implications for infection, inflammation, and nutritional supplementation.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00857-1},
pmid = {41709346},
issn = {2042-6410},
support = {10.54499/2022.13772//Fundação para a Ciência e a Tecnologia/ ; 10.54499/2021.07836//Fundação para a Ciência e a Tecnologia/ ; 10.54499/LA/P/0050/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The immune system is central to maintaining homeostasis and orchestrating defense against infection and the regulation of inflammatory responses, yet its activity is far from uniform across individuals. Sex differences profoundly shape immune responses, with sex hormones driving distinct patterns of susceptibility to infectious diseases and inflammatory conditions. Nutrition further adds a powerful layer of modulation: vitamins, amino acids, and other bioactive compounds influence immune function and disease outcomes, often in a sex-dependent manner. The microbiome, whose composition is itself influenced by sex, is a critical regulator of both intestinal and systemic immune disorders, making it an attractive target for therapeutic intervention. In this review, we examine the dynamic interplay between sex, nutrition, and the immune system, emphasizing their combined impact on infection, inflammation, and immunomodulation. A deeper understanding of these interactions will be key to advancing personalized nutritional and therapeutic strategies designed to optimize immune health.},
}

@article {pmid41709287,
year = {2026},
author = {Toyoshi, E and Watanabe, M and Namai, F and Yamane, K and Kashima, T and Ikeda-Ohtsubo, W and Agista, AZ and Yoshida, A and Sakuma, T and Fukuda, I and Suzuki, K and Yoshioka, G and Imai, Y and Tsuchida, S and Nishiyama, E and Shinkai, H and Muneta, Y and Uenishi, H and Tobe, R and Shirakawa, H and Maekawa, M and Mano, N and Kitazawa, H and Nishiyama, K},
title = {Dynamics of tryptophan metabolites and microbial adaptations during corn by-product fermentation in the pig gut microbiome.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {32},
pmid = {41709287},
issn = {1674-9782},
support = {Grant-in-Aid for Challenging Research (Exploratory) (23K18072)//Japan Society for the Promotion of Science (JSPS)/ ; Grant-in-Aid for Scientific Research (B) (23K27051)//Japan Society for the Promotion of Science (JSPS)/ ; Development of Innovative Technology grant (JPJ007097)//Bio-oriented Technology Research Advancement Institution (BRAIN)/ ; },
abstract = {BACKGROUND: Food by-products, such as corn germ meal from starch processing, are increasingly used as sustainable feed supplements, reducing competition between food and feed and supporting the valorisation of food waste. However, their effects on gut microbial metabolism and host health remain unclear. This study aimed to determine how corn germ meal fermentation influences microbial community structure and metabolite production using an ex vivo pig faecal culture system.

RESULTS: Corn germ meal supplementation significantly altered the microbial composition, increasing diversity and enriching fibre-degrading Prevotellaceae, a key bacterial family involved in complex carbohydrate metabolism. Metabolomic analysis revealed marked increases in tryptophan-derived metabolites, including indoleacrylic acid, indolepropionic acid, and indolelactic acid, which act as ligands for the aryl hydrocarbon receptor and have anti-inflammatory properties. Prevotella-mediated catabolite repression reduced Escherichia coli-derived indole formation, redirecting microbial tryptophan metabolism toward the production of these bioactive compounds. Microbial and metabolic responses differed among farms, reflecting farm-specific microbiome structures.

CONCLUSIONS: Corn germ meal supplementation reshapes gut microbial communities, enhances metabolic activity, and promotes the generation of bioactive tryptophan metabolites with potential immunomodulatory effects. These findings highlight the value of corn by-products as dietary fibres that can drive beneficial microbial cross-feeding and influence host intestinal homeostasis. Although demonstrated in an ex vivo setting, this study provides a mechanistic basis and preclinical evidence for future in vivo studies, supporting the sustainable utilisation of food industry by-products to improve gut health and resource efficiency in livestock production.},
}

@article {pmid41709267,
year = {2026},
author = {Baquer, F and Grillon, A},
title = {Interaction between tick and host microbiotas: a four-step waltz.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07308-1},
pmid = {41709267},
issn = {1756-3305},
abstract = {Tick-borne diseases represent a growing public health concern worldwide, yet the microbial factors that govern pathogen transmission remain incompletely understood. Over the past decade, high-throughput metagenomics and functional studies have revealed that two distinct microbial communities-the vertebrate host's skin microbiota and the tick's own microbiome-act synergistically as key modulators of pathogen acquisition, persistence within the vector, and successful transmission to the vertebrate host. At the feeding site, the skin microbiota orchestrates local cutaneous immunity, influences inflammatory responses, and can either hinder or inadvertently facilitate dermal establishment of tick-borne pathogens such as Borrelia burgdorferi sensu lato (s.l.), Anaplasma phagocytophilum, Rickettsia species, Babesia spp., and tick-borne encephalitis virus. Tick feeding itself induces rapid and sometimes long-lasting dysbiosis of the skin microbial community, creating temporal windows of vulnerability for pathogen invasion. Concurrently, within the tick vector, a core set of endosymbiotic bacteria, including Rickettsia buchneri, Midichloria mitochondrii, Coxiella-like, and Francisella-like endosymbionts, engage in complex mutualistic, competitive, and facilitative interactions. These symbionts regulate vector competence through nutrient provisioning (especially B-vitamins), direct competition for niche space, and immune priming or suppression of the tick's innate immune system. Such interactions ultimately determine the maintenance, abundance, and transmissibility of tick-borne pathogens. By integrating these dual host-vector microbiome perspectives in a comprehensive review, we highlight emerging mechanistic insights into transmission ecology and biologically grounded targets for the prevention and control of tick-borne diseases, including anti-microbiota vaccines and paratransgenic and microbiome-based approaches.},
}

@article {pmid41709136,
year = {2026},
author = {Ferrary Américo, M and Vilela Rodrigues, T and Henry, C and Marques da Silva, W and Verano-Braga, T and Azevedo, V and Chatel, JM},
title = {Insights into the proteome of next-generation probiotic Faecalibacterium duncaniae A2-165 through label-free proteomics approach.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04814-1},
pmid = {41709136},
issn = {1471-2180},
}

@article {pmid41709019,
year = {2026},
author = {Marco, ML and Cunningham, M and Bischoff, SC and Clarke, G and Delzenne, N and Lewis, JD and Meisel, M and Merenstein, D and O'Toole, PW and Staudacher, HM and Szajewska, H and Wells, JM and Quigley, EMM},
title = {The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41709019},
issn = {1759-5053},
abstract = {The term 'gut health' is increasingly used as a catch-all phrase by many stakeholders, including scientists, health-care professionals, industry and the general public, to describe a wide range of health-related concepts. Despite its widespread use, particularly in relation to studies on diet, fermented foods, biotics and the gut microbiome, it remains unclear what the term gut health means. Therefore, an expert panel was convened by the International Scientific Association for Probiotics and Prebiotics to address the current state of scientific and clinical knowledge on the physiology, manifestation, application and measurement of the concept of gut health. The panel evaluated the term in the context of the central role of the gastrointestinal tract in health and overall well-being and proposed a definition of gut health as "a state of normal gastrointestinal function without active gastrointestinal disease and gut-related symptoms that affect quality of life". The definition was developed mindful of the functional, subjective and extrinsic domains that contribute to gut health. In this Consensus Statement, clinically relevant and accessible metrics to assess these domains are reviewed and a comprehensive approach to gut health is proposed that is relevant to clinical practice as well as to studies of dietary and biotic interventions.},
}

@article {pmid41708960,
year = {2026},
author = {Liu, SS and Ye, L and Li, XX and Dai, QQ and Gao, Y and Chen, GH and Fang, YS and Zhao, HC and Du, WD},
title = {Intratumoral microbiome evaluated progression and outcome of patients with HBV-associated hepatocellular carcinoma.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-04654-5},
pmid = {41708960},
issn = {2730-6011},
support = {2017zhyx37//Institute of Translational Medicine of Anhui Province/ ; },
}

@article {pmid41708693,
year = {2026},
author = {Gottschalk, EC and Chabanovska, O and Vasudevan, P and Barrantes, I and Kreikemeyer, B and Bergmann-Ewert, W and Engelmann, R and Müller-Hilke, B and Lang, H},
title = {Potential biomarkers for early periodontal inflammation: investigating CD5[+] B cells, salivary cytokines and oral microbiome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {7192},
pmid = {41708693},
issn = {2045-2322},
mesh = {Humans ; Male ; Biomarkers/metabolism ; Female ; *CD5 Antigens/metabolism ; Middle Aged ; *Saliva/metabolism ; Adult ; *B-Lymphocytes/metabolism/immunology ; *Cytokines/metabolism ; Cross-Sectional Studies ; *Microbiota ; *Periodontitis/metabolism/microbiology/diagnosis ; *Chronic Periodontitis/microbiology/metabolism ; Inflammation ; Gingivitis/microbiology ; },
abstract = {Periodontitis is a highly prevalent chronic inflammatory disease that causes progressive destruction of the tooth-supporting apparatus and is linked to multiple systemic disorders. Despite its high prevalence, early biomarkers capable of predicting individual susceptibility remain elusive. The multifactorial nature of the disease and the lack of a validated, specific indicators hinder reliable early diagnosis before irreversible tissue damage occurs. CD5[+] B cells, known for their autoreactive potential and role in bone resorption, have been previously found elevated in advanced periodontitis. Due to their association with tissue destruction, these cells may hold predictive value even at earlier stages. However, their systemic relevance in early periodontal inflammation is scarcely explored. This cross-sectional study examined differential subsets of circulating CD5[+] B cells as potential systemic biomarkers of early periodontal disease. Sixty patients were grouped as healthy, gingivitis and moderate chronic periodontitis. Multiple regression analysis revealed that besides age (p = 0.009), the double negative (CD27[-]IgD[-]) subset of CD5[+] memory B cells was related to periodontitis, while total CD5[+] B cell levels remained unchanged. To characterize the oral inflammatory milieu, salivary cytokines and the composition of the subgingival microbiome were analyzed. Salivary IL-8 levels and IL-17A detection rates were significantly elevated in periodontitis. Microbiome profiling further identified an exploratory correlation between Megasphaera and salivary IL-8 in gingivitis, which may represent an early-stage signal but requires validation in larger follow-up cohorts.},
}

Humans
Male
Biomarkers/metabolism
Female
*CD5 Antigens/metabolism
Middle Aged
*Saliva/metabolism
Adult
*B-Lymphocytes/metabolism/immunology
*Cytokines/metabolism
Cross-Sectional Studies
*Microbiota
*Periodontitis/metabolism/microbiology/diagnosis
*Chronic Periodontitis/microbiology/metabolism
Inflammation
Gingivitis/microbiology

@article {pmid41708595,
year = {2026},
author = {Moses, AB and Yeh, AC},
title = {The gut microbiome in graft-versus-host disease: mechanisms of immune modulation and therapeutic approaches.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2631224},
doi = {10.1080/19490976.2026.2631224},
pmid = {41708595},
issn = {1949-0984},
mesh = {*Graft vs Host Disease/immunology/therapy/microbiology ; Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Hematopoietic Stem Cell Transplantation/adverse effects ; Immunity, Innate ; T-Lymphocytes/immunology ; Gastrointestinal Tract/microbiology/immunology ; Adaptive Immunity ; Probiotics/administration & dosage ; },
abstract = {Graft-versus-host disease (GvHD) remains a major complication of allogeneic hematopoietic stem cell transplantation and occurs when T cells from the donor graft target recipient-derived antigen on host tissue. The involvement of the gastrointestinal (GI) tract drives morbidity and mortality-not coincidentally, the GI tract also harbors the most complex and abundant human microbial reservoir. In this review, we first revisit how the microbiota initiates, propagates, and protects against GvHD in the context of both innate and adaptive immunity. Historically, the impact of the microbiota on GvHD has been ascribed primarily to the activation of innate immunity, setting the stage for donor alloreactivity. Although established models of GvHD focus on donor-host genetic disparity as the principal driver of donor T-cell activation, commensal microbes in the GI tract, whose collective gene content exceeds that of the human genome by more than two orders of magnitude, constitutes an immense and poorly understood source of potential T-cell antigens. We next discuss the evolution of therapeutic approaches aimed at modifying the microbiota to improve GvHD outcomes, incorporating over 40 clinical studies spanning the last 40 years, from broad decontamination strategies to pre/probiotic approaches and targeted ecosystem replacement, including fecal microbiota transplantation.},
}

*Graft vs Host Disease/immunology/therapy/microbiology
Humans
*Gastrointestinal Microbiome/immunology
Animals
Hematopoietic Stem Cell Transplantation/adverse effects
Immunity, Innate
T-Lymphocytes/immunology
Gastrointestinal Tract/microbiology/immunology
Adaptive Immunity
Probiotics/administration & dosage

@article {pmid41708505,
year = {2026},
author = {Liu, F and Cheng, P and Li, L and Li, W and Tu, C and Shan, J and Xiao, W and Liu, J and Peng, Y and Zhu, Y},
title = {Phoxim sublethal effect induces vitellogenin mediated reproductive enhancement and alters microbial symbiosis across generations in Hylyphantes graminicola.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70627},
pmid = {41708505},
issn = {1526-4998},
support = {2023M731035//China Postdoctoral Science Foundation/ ; 2024AFB477//Natural Science Foundation of Hubei Province/ ; 32400360//National Natural Science Foundation of China/ ; 2025K009//the Opening Project of Hubei Key Laboratory of Resource Utilizition and Quality Control of Characteristic Crops/ ; },
abstract = {BACKGROUND: Phoxim, a widely used organophosphate insecticide, poses potential risks to non-target natural enemies. Hylyphantes graminicola is a dominant predatory spider in agroecosystems, yet the sublethal effects and transgenerational impacts remain poorly characterized. This study aimed to systematically evaluate the physiological, molecular, and microbial changes in H. graminicola induced by low lethal concentration of phoxim exposure across two successive generations.

RESULTS: Laboratory bioassays determined the LC30 of phoxim to be 9.442 mg/L. Exposure at this concentration significantly reduced female longevity but increased fecundity in both F0 and F1 generations, suggesting a potential hormetic effect. Transcriptomic analysis revealed that reproduction-related genes were significantly upregulated in the F0 generation, whereas detoxification genes were markedly expressed in the F1 generation. Functional validation through RNAi confirmed that vitellogenin (Vg) and cytochrome P450 (CYP2J1) are crucial in reproduction and detoxification, respectively. Furthermore, acetylcholinesterase (AChE) was also found to be involved in regulatory phoxim exposure. Moreover, microbiome profiling demonstrated substantial shifts across generations, including decreased Wolbachia and increased Candidatus_Cardinium abundance, which may be related to the observed increase in fecundity. The results showed that a low lethal concentration of phoxim exposure can trigger complex physiological and microbial changes across generations.

CONCLUSION: These findings underscore the necessity of optimizing insecticide application intervals within Integrated Pest Management (IPM) frameworks to preserve biological control provided by beneficial arthropods. © 2026 Society of Chemical Industry.},
}

@article {pmid41708473,
year = {2026},
author = {Liss, MA and White, JR and Doris, M and Lai, Z and Johnson-Pais, TL and Leach, RJ and Goros, M and Gelfond, J and Wickes, B},
title = {Gut Microbiome as a Lifestyle Risk Factor Associated with Prostate Cancer.},
journal = {European urology focus},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.euf.2026.01.001},
pmid = {41708473},
issn = {2405-4569},
abstract = {BACKGROUND AND OBJECTIVE: Most prostate cancer prevention strategies suggest lifestyle modifications, which lack personalization. Gut microbiome is increasingly recognized as an influencing factor in nongastrointestinal cancers, including prostate cancer. The use of gut microbiome as a lifestyle biomarker could help identify individuals with lifestyle more prone to prostate cancer and allow for modification. We aimed to develop a gut microbiome-based biomarker derived from patients undergoing prostate cancer screening.

METHODS: We assessed whether the future cancer risk can be evaluated based on a microbiome risk analysis. After extracting DNA, sequencing, and performing a bioinformatics analysis, we identified 39 unique microbial genera of importance. We utilized an artificial intelligence model to calculate their presence, abundance, and weighted significance, generating a microbiome score (Prostate Cancer Risk Insight using Microbiome UnderStanding [PRIMUS]) that ranges from 0 to 1.

KEY FINDINGS AND LIMITATIONS: Men with an increasing PRIMUS signature showed a sequential increase in prostate cancer risk. The prostate cancer risk persisted after a median follow-up of 4.5 yr. As a risk-assessment tool, the microbiome score compared favorably with prostate cancer risk calculators. Study limitations include the use of two patient groups to diversify the population for both a screening and a prebiopsy scenario; however, the cohorts used different collection methods, including stool, rectal swabs, and glove tip samples, but the same DNA isolation and sequencing. We relied on the longitudinal approach to help reduce these initial differences.

The gut microbiome may serve as a lifestyle risk factor for prostate cancer, but it is not intended to guide biopsy decisions. The implications of this study hinge on the potential for modifiability of the microbiome that could be tested in future clinical trials on prostate cancer risk reduction.},
}

@article {pmid41708401,
year = {2026},
author = {Feyera, T and Johannsen, JC and Langendijk, P and Vodolazska, D},
title = {Review: Colostrum production and intake- functional roles in piglet survival, future reproduction, and the challenge of genetic selection.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {101773},
doi = {10.1016/j.animal.2026.101773},
pmid = {41708401},
issn = {1751-732X},
abstract = {This review explores the vital role of colostrum in neonatal piglet survival, growth, and development, emphasising the physiological, nutritional, and immunological functions of colostrum. It highlights the challenges posed by genetic selection for larger litters, which often outpace the sow's capacity to produce and deliver adequate colostrum to each piglet. Drawing on extensive experimental data and recent literature, the review examines factors influencing colostrum production and intake, the impact of maternal nutrition on colostrum production, and the long-term effects of colostrum intake on piglet health and reproductive performance. It appears that dietary interventions during late gestation and the transition period have limited impact on a sow's ability to produce colostrum, although targeted nutritional strategies show promise in enhancing piglets' intake of colostrum and colostrum compositions such as fat, amino acids, and immunoglobulins. Future research should integrate genome, transcriptome, metabolome, and microbiome data to develop machine learning models that predict piglet performance based on early colostrum intake, thereby enabling timely interventions to improve their growth and survival during lactation.},
}

@article {pmid41707838,
year = {2026},
author = {Benagiano, G and Pluchino, N and Archer, D and Stanczyk, FZ},
title = {ESTROBOLOME: IS THERE A MISSING LINK?.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106967},
doi = {10.1016/j.jsbmb.2026.106967},
pmid = {41707838},
issn = {1879-1220},
abstract = {Estrogens play an important role throughout a woman's life; therefore, disrupting their physiological production will alter hormonal balance with consequences for estrogen-related conditions, such as endometriosis and adenomyosis. The gut microbiome (GM) plays a critical role in regulating systemic estrogen concentrations, since a number of microorganisms present in the GM possess the enzyme β-glucuronidase (β-GLC), a key factor in regulating host estrogen metabolism. Although most studies have focused on the conversion of estrogen glucuronides to active estrogens by β-GLC in gut bacteria, it is known that the GM also contains steroid sulfatases (STS), which are able to convert inactive sulfated estrogens to active ones. This is especially important because estrone (E1) sulfate (E1S) is quantitatively the most important estrogen in the human and can be readily converted to E1 and estradiol (E2). It has been shown that estrogen sulfates are present in bile and can therefore reach the intestines, raising the possibility of biologically active E1 and E2 formation in the intestine by bacterial enzyme transformation. Everything depends on the presence of sulfatases in the GM, and in this respect, STS have been found in a variety of microbial species. This means that sulfatases are poised to reactivate estrogens, which are then capable of undergoing enterohepatic recirculation and exerting systemic effects throughout the body. Given that estrogen sulfates represent the largest component of circulating estrogens that are secreted by the liver into the intestines via the bile, the role of gut microbial sulfatases may be superior to that of β-GLC.},
}

@article {pmid41707830,
year = {2026},
author = {Yuan, C and Zhao, Y and Huang, J and Fan, G and He, Z and Hu, X and Fu, Y and Lu, W},
title = {Integrated microbiome and metabolome unveiled the effect of carbonate buffer mixture alleviating subacute rumen acidosis - Mediated endometritis in dairy goats.},
journal = {Veterinary journal (London, England : 1997)},
volume = {316},
number = {},
pages = {106601},
doi = {10.1016/j.tvjl.2026.106601},
pmid = {41707830},
issn = {1532-2971},
abstract = {Subacute ruminal acidosis (SARA) is a prevalent metabolic disorder in ruminants, often associated with systemic inflammatory responses triggered by elevated levels of lipopolysaccharides (LPS). This study aimed to evaluate whether a carbonate buffer mixture (CBM) could alleviate SARA-induced endometritis in dairy goats by modulating the microbiota and metabolic profiles. A total of 30 healthy lactating dairy goats with similar body weight were selected for the experiment. Inflammatory markers were assessed in both uterine tissue and serum. The microbial communities in the rumen and uterus were characterized using 16S rRNA gene sequencing, while alterations in serum metabolites were analyzed via untargeted metabolomics. The results demonstrated that CBM supplementation effectively reversed SARA induced by a high-concentrate diet, reduced neutrophil infiltration, LPS levels, and inflammatory cytokine concentrations in the endometrium, and enhanced the expression of tight junction proteins in uterine tissue. Additionally, CBM mitigated SARA-induced dysbiosis of the uterine microbiota by restoring the relative abundance of key bacterial taxa, including Lachnospiraceae, Prevotella, and Ruminococcus, while also modulating rumen bacterial populations such as Stenotrophomonas, Aerococcus, and Acinetobacter. Metabolomic profiling revealed that SARA significantly increased serum concentrations of creatinine, L-methionine, and L-tyrosine, while decreasing levels of tryptamine, gabapentin, and sphinganine. These findings suggest that CBM may restore rumen pH and microbial balance in SARA-affected goats, thereby influencing systemic metabolite profiles, promoting uterine microbiota homeostasis, reducing endometrial injury, and ultimately alleviating endometritis. Collectively, this study highlights a potential link between the ruminal microenvironment and uterine health, and provides new insights into the therapeutic role of CBM in managing SARA-induced endometritis.},
}

@article {pmid41707761,
year = {2026},
author = {Maki, KA and Barb, JJ and Xu, S and Papneja, S and Alkhatib, J and Butera, G and Wallen, GR},
title = {From Alpha Diversity to Zeitgebers: Functional Implications and Potential Mechanisms Linking the Gut Microbiome to Sleep and Circadian Disruption (Part II).},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106609},
doi = {10.1016/j.neubiorev.2026.106609},
pmid = {41707761},
issn = {1873-7528},
abstract = {The bidirectional relationship between sleep physiology and the gut microbiome is mediated by overlapping neuroendocrine, immune, and metabolic pathways, though mechanistic evidence, particularly in humans, remains limited. This scoping review, the second in a two-part series, synthesizes preclinical and translational research examining not only gut microbial composition but also biomarkers reflecting host metabolic or functional responses to sleep and circadian disruption. We reviewed 74 preclinical rodent studies and 65 human studies that assessed sleep, gut microbiome outcomes, and at least one biomarker related to hormones, metabolites, neurotransmitters, or inflammation. Across studies, consistent links emerged between sleep and circadian disruption and changes in host homeostasis through microbiome-mediated mechanisms. These include activation of the hypothalamic-pituitary-adrenal axis, altered bile acid metabolism, inflammation-related microbial shifts, and disrupted tryptophan pathways. Together, these findings suggest that altered sleep influences metabolic and immune function via gut microbial signaling pathways. We highlight directions for future mechanistic research, particularly in translational models, to clarify causal pathways and support microbiome-informed strategies for mitigating the health consequences of sleep and circadian disruption.},
}

@article {pmid41707760,
year = {2026},
author = {Maki, KA and Barb, JJ and Alkhatib, J and Butera, G and Wallen, GR},
title = {From Alpha Diversity to Zeitgebers: Bacterial Gut Microbiome Associations with Sleep and Circadian Disruption (Part I).},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106578},
doi = {10.1016/j.neubiorev.2026.106578},
pmid = {41707760},
issn = {1873-7528},
abstract = {Sleep is a vital behavioral state influencing multiple body systems, including the gut-brain axis, which involves bidirectional communication between the brain and gastrointestinal system. This scoping review examines and provides a comprehensive overview of literature examining the relationship between sleep and the gut microbiome to identify literature gaps. Seventy-four pre-clinical rodent studies and 65 human translational studies reporting direct sleep and gut microbiome associations were synthesized. We found variable alpha diversity responses to sleep pathology, with decreased alpha diversity more consistent in longer sleep disruption periods. Preclinical studies showed variable phylum-level responses, while in humans, sleep disruption was linked to decreased Bacillota and circadian disruption to increased Bacillota. Unhealthy sleep patterns were commonly associated with reduced levels of beneficial genera such as Faecalibacterium and Lactobacillus, and increased Clostridium, though findings were not consistent across all studies. Recommendations are made to ensure rigorous, reproducible research in this field. The potential for gut microbiome modulation as a therapeutic target is highlighted, with suggested future research directions for preventing sleep disruption and pathology.},
}

@article {pmid41707756,
year = {2026},
author = {Lou, S and Li, W and Wang, G and Qian, H and Zhou, J},
title = {Microbiome-Gut-Liver Axis in Chronic Inflammation and Cancer Immunotherapy: Multi-omics Insights and a Translational Roadmap Toward Personalized Medicine.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105217},
doi = {10.1016/j.critrevonc.2026.105217},
pmid = {41707756},
issn = {1879-0461},
abstract = {Gut-liver axis is critical to integrate microbial, metabolic, and immune signaling networks to control hepatic homeostasis and carcinogenesis. Gut microbial balance disruption (dysbiosis) stimulates chronic inflammation, metabolic disorders, and transition from non-alcoholic fatty liver disease (NAFLD) to hepatocellular carcinoma (HCC). Latest evidence points to the gut and intratumoral microbiota's roles in shaping immune regulation and responsiveness to immunotherapy against cancer. This review encapsulates the latest evidence on the microbiome-gut-liver axis in chronic liver disease and cancer, highlighting multi-omics evidence, mechanisms of immune modulation, and translational avenues to microbiome-informed precision medicine in HCC. Comprehensive literature search on PubMed, Scopus, Web of Science, and Embase (until September 2025) focused on the gut-liver axis, microbiome, immune checkpoint inhibitors (ICIs), and multi-omics integration. Only mechanistically and translationally relevant peer-reviewed studies were included. Dysbiosis disrupts the permeability of the intestines and metabolism of bile acids and affects immune signaling to induce hepatic inflammation and fibrogenesis. Multi-omic studies identify key microbial metabolites, short-chain fatty acids, secondary bile acids, and tryptophan derivatives to govern the function of T-cell and responsiveness to checkpoint. Clinical research demonstrates that increased abundance of taxa like Akkermansia muciniphila, Bifidobacterium longum, and Faecalibacterium prausnitzii improves ICI efficacy but antibiotic exposure decreases therapeutic efficacy. Tumor-residing microbiomes further determine immune infiltration and risk of recurrence. Multi-omic and computational integration of gut and tumor microbiome data provides mechanistic insight to microbial-informed immunotherapy. Standardization, regulatory convergence, and ethical guidelines are critical to translate microbiome therapeutics, namely fecal microbiota transplantation, engineered probiotics, and metabolite-directed interventions to safe and individualized strategies to treat liver cancer.},
}

@article {pmid41707749,
year = {2026},
author = {Bantavi, V and Gloeck, L and Leven, P and Zafeiropoulou, K and Welting, O and Sengül, H and Efferz, P and Schneiker, B and McCulloch, TR and Wilhelm, C and Blaess, S and Fuss, A and Derikx, JPM and Sovran, B and de Jonge, WJ and Wehner, S and , },
title = {Tryptophan indole metabolites reduce anastomotic leakage through aryl hydrocarbon receptor-driven interleukin-22 production.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101756},
doi = {10.1016/j.jcmgh.2026.101756},
pmid = {41707749},
issn = {2352-345X},
abstract = {BACKGROUND: Colorectal cancer often requires surgical resection of the tumor and an anastomosis. Anastomotic leakage (AL) occurs in 2.8-30% of patients which increases postoperative morbidity and complications. The preoperative microbiome composition is implicated in AL. Recent studies have shown that microbial tryptophan (Trp) metabolism into aryl hydrocarbon receptor (AhR) indole-derivatives contributes to intestinal tissue healing. Here, we addressed the role of Trp and its metabolites in AL in a CRC patient cohort and a colon-anastomosis mouse model.

METHODS: Targeted quantitative metabolomics was performed in preoperative fecal samples from patients with CRC recruited in the REVEAL cohort (n = 388), including 19 AL cases. Anastomotic Healing (AH) was tested in a mouse model using wildtype, AhR[-/-], Villin[Cre]Ahr[fl/fl], and IL-22 drug-targeting to evaluate the role of AhR and IL-22 in AL.

RESULTS: Fifty-two of the 388 patients with available preoperative fecal samples were matched for AH/AL occurrence (AL, n = 19; AH, n = 33). Amongst Trp metabolites, indole-3-acetic acid was significantly reduced in AL compared to matched AH male patients. AhR[-/-] mice displayed more severe AL, reduced IL-22 expression, and a marked loss of IL-22-expressing type 3 ILCs compared to wildtype mice. Neutralizing IL-22 antibody augmented AL in wildtype mice, while IL-22Fc application ameliorated AL in AhR[-/-] mice. AhR agonism failed to rescue healing under IL-22 deficiency. Furthermore, low-Trp diet-fed wildtype mice exhibited reduced fecal concentration of AhR agonists and, AhR-agonist producing bacteria, and augmented AL. This phenotype was prevented by dietary supplementation with the AhR agonist indole-3-carbinol.

CONCLUSION: Stimulation of the AhR/IL-22 by synthetic agonists or dietary-derived Trp-metabolites can prevent AL.},
}

@article {pmid41707708,
year = {2026},
author = {Lyons, CE and Smith, AD and Schwartzman, G and Hickman, A and Grant-Kels, JM},
title = {Managing Skin Diseases that Flare During Pregnancy and in the Postpartum period: Part 1-Classification, Epidemiology & Pathogenesis.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2026.01.089},
pmid = {41707708},
issn = {1097-6787},
abstract = {Pregnancy induces immunologic, hormonal, vascular, neurogenic and skin barrier changes that may exacerbate inflammatory dermatoses as atopic dermatitis (AD), and psoriasis. Part I of this CME reviews pregnancy-induced shifts in immunity, hormones, vascular dynamics and barrier function that can change the course of common dermatoses, including AD, psoriasis, acne, melasma, hidradenitisi suppurativa, and other conditions. Additionally, in Part II we present updated safety and pharmacokinetic data that supports the judicious use of topical, systemic and procedural therapies (eg, phototherapy, biologics) through gestation and lactation, replacing reliance solely on FDA categories. We include practical treatment options to enhance the balancing of maternal disease control with fetal and neonatal safety.},
}

@article {pmid41707656,
year = {2026},
author = {Sarwal, R and Tarca, V and Dubin, CA and Kalavros, N and Bhatti, G and Bhattacharya, S and Butte, A and Romero, R and Stolovitzky, G and Oskotsky, TT and Tarca, AL and Sirota, M},
title = {Benchmarking large language models for predictive modeling in biomedical research with a focus on reproductive health.},
journal = {Cell reports. Medicine},
volume = {7},
number = {2},
pages = {102594},
doi = {10.1016/j.xcrm.2026.102594},
pmid = {41707656},
issn = {2666-3791},
mesh = {Humans ; Female ; *Biomedical Research/methods ; *Reproductive Health ; *Benchmarking ; Premature Birth/genetics ; Pregnancy ; Gestational Age ; DNA Methylation ; Large Language Models ; },
abstract = {Large language models (LLMs) are increasingly used for code generation and data analysis. This study assesses LLM performance across four predictive tasks from three DREAM challenges: gestational age regression from transcriptomics and DNA methylation and classification of preterm birth and early preterm birth from microbiome data. We prompt LLMs with task descriptions, data locations, and target outcomes and then run LLM-generated code to fit prediction models and determine accuracy on test sets. Among the eight LLMs tested, o3-mini-high, 4o, DeepseekR1, and Gemini 2.0 can complete at least one task. R code generation is more successful (14/16) than Python (7/16). OpenAI's o3-mini-high outperforms others, completing 7/8 tasks. Test set performance of the top LLM-generated models matches or exceeds the median-participating team for all four tasks and surpasses the top-performing team for one task (p = 0.02). These findings underscore the potential of LLMs to democratize predictive modeling in omics and increase research output.},
}

Humans
Female
*Biomedical Research/methods
*Reproductive Health
*Benchmarking
Premature Birth/genetics
Pregnancy
Gestational Age
DNA Methylation
Large Language Models

@article {pmid41707638,
year = {2026},
author = {Rakhshandeh, M and Khanjani, M},
title = {The First Report of Enterobacter Endosymbionts in the Dried Fruit Mite (Carpoglyphus lactis L.) (Acari, Acarida) Reared on Apricots in the Laboratory.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70294},
doi = {10.1111/1758-2229.70294},
pmid = {41707638},
issn = {1758-2229},
mesh = {Animals ; *Symbiosis ; *Enterobacter/isolation & purification/genetics/classification/physiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Acaridae/microbiology ; *Prunus armeniaca/parasitology ; DNA, Bacterial/genetics/chemistry ; },
abstract = {Carpoglyphus lactis (Linnaeus), a member of the family Carpoglyphidae, is recognised both as a common storage mite and a significant source of indoor allergens. Despite extensive studies on its biology and distribution, little is known about its associated microbiome. In this study, for the first time, we investigated the bacterial symbionts of C. lactis reared under sterile laboratory conditions on dried apricots. Following surface sterilisation, bacterial isolates were cultured and identified through biochemical tests and molecular analyses targeting the 16S rRNA and gapA genes. Phylogenetic analyses revealed that the isolated strains shared over 98% similarity with Enterobacter hormaechei and clustered specifically within the E. hormaechei subsp. xiangfangensis clade. These findings confirm the presence of Enterobacter species as endosymbionts in C. lactis for the first time. The symbiotic relationship may contribute to host stress tolerance, nutritional efficiency and modulation of allergenic properties. This discovery opens new avenues for exploring mite-microbe interactions and developing innovative strategies for biological control and allergy mitigation.},
}

Animals
*Symbiosis
*Enterobacter/isolation & purification/genetics/classification/physiology
RNA, Ribosomal, 16S/genetics
Phylogeny
*Acaridae/microbiology
*Prunus armeniaca/parasitology
DNA, Bacterial/genetics/chemistry

@article {pmid41707590,
year = {2026},
author = {He, X and Liao, Z and Cai, X and Lin, J and Zhang, Y and Zeng, W and Feng, L and Mei, L and Liu, C},
title = {The oral-immune axis: neutrophil extracellular traps mediate the link between periodontitis and autoimmune diseases.},
journal = {International immunopharmacology},
volume = {174},
number = {},
pages = {116363},
doi = {10.1016/j.intimp.2026.116363},
pmid = {41707590},
issn = {1878-1705},
abstract = {Epidemiological and clinical evidence supports a strong association between periodontitis and autoimmune diseases. This review systematically elucidates the pivotal role of the "oral-immune axis" in this relationship, focusing on neutrophil extracellular traps (NETs) as key mediators. Periodontal pathogens can compromise the gingival epithelial barrier, induce excessive NETs formation within the periodontium, facilitate systemic dissemination of pathogens, and promote their ectopic spread to organs such as the joints, pancreas, and kidneys. These processes, in turn, may activate neutrophils to release additional NETs. NETs can aggravate the pathology of various autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, and type 1 diabetes mellitus, through mechanisms such as exposure of autoantigens, amplification of inflammatory cascades, and activation of adaptive immune responses. This article further discusses the reverse regulatory role of the oral-immune axis and compares the similarities and differences in NETs in periodontitis and autoimmune diseases. Reinforcing basic periodontal therapy may effectively reduce systemic inflammation and NETs levels, and therapeutic strategies targeting NETs formation, clearance, or function demonstrate potential in interdisciplinary disease management. Altogether, this review provides a novel perspective on the interplay between the oral microbiome and systemic immune diseases, highlighting its substantial translational medical implications.},
}

@article {pmid41707585,
year = {2026},
author = {Akoh-Arrey, T and Brooks, JF},
title = {Antimicrobial peptides and proteins as rheostats of intestinal homeostasis and immunity.},
journal = {Current opinion in immunology},
volume = {99},
number = {},
pages = {102738},
doi = {10.1016/j.coi.2026.102738},
pmid = {41707585},
issn = {1879-0372},
abstract = {Antimicrobial peptides and proteins (AMPs) function as molecular rheostats of host-microbe interactions and cell-intrinsic defense. Rather than being binary effectors, they act along a continuum. At basal levels, AMPs maintain harmony with the commensal members of the microbiome, and upon pathogen encounter, they induce levels that thwart bacterial invasion and dissemination. This duality arises from the mechanistic versatility and layered regulation by microbial, cytokine, and circadian cues. Importantly, this review is not intended to be a detailed catalog of all antimicrobial proteins, but rather a conceptual framework highlighting representative mechanisms that illustrate how AMPs function as adjustable regulators of intestinal homeostasis. Viewing AMPs as adjustable regulators of barrier integrity, rather than static effectors, reframes innate immunity as a dynamic system that balances microbial tolerance with host defense.},
}

@article {pmid41707528,
year = {2026},
author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y},
title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119865},
doi = {10.1016/j.ecoenv.2026.119865},
pmid = {41707528},
issn = {1090-2414},
abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.},
}

@article {pmid41707491,
year = {2026},
author = {Li, Z and Chen, S and Su, S and Wang, Y and Song, Y and Wu, H and Yi, X and Xiao, Z and Qin, Q},
title = {The impact of polystyrene nanoplastics on the chicken gut and liver: Based on transcriptomics and microbiomics.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106574},
doi = {10.1016/j.psj.2026.106574},
pmid = {41707491},
issn = {1525-3171},
abstract = {Nanoplastics, an emerging environmental pollutant, pose potential hazards to organisms. The impact of nanoplastics on poultry health, a crucial protein source for humans, has raised considerable concern. This study evaluated the multidimensional toxic effects of nanoplastic exposure on 240 Sanhuang chickens over a 21-day oral administration period followed by a 21-day recovery period. While nanoplastics did not affect average daily gain and average daily feed intake, they induced cardiac index elevation, indicating myocardial compensatory hypertrophy, with partial functional recovery post-exposure. Serum analysis revealed that reduced antioxidant enzyme activities and increased lipid peroxidation, and pro-inflammatory cytokines levels rose during exposure. Oxidative stress and inflammatory responses were alleviated, but IgG levels significantly declined in recovery. Transcriptome sequencing showed disrupted mitochondrial complex I function and inhibited cholesterol synthesis through abnormal expression of key genes, exacerbating cytotoxicity. Mechanistic studies confirmed toll-like receptor 4 (TLR4)/ nuclear factor kappa B (NF-κB) pathway activation driving hepatic/jejunal inflammation, alongside elevated pro-apoptotic Bax/Caspase-3, reduced anti-apoptotic B-cell lymphoma-2, and suppressed autophagy and nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. Post-exposure, the TLR4/NF-κB pathway remained activated, and autophagy and the Nrf2 pathway remained inhibited. Intestinal barrier function was impaired via downregulated tight junction proteins, increasing jejunal permeability. Jejunal villi height was abnormally elevated in the low-dose group during exposure, which decreased in the villus height / crypt depth ratio during recovery. Microbiome analysis revealed increased Proteobacteria/Escherichia-Shigella abundance during exposure and reduced beneficial bacteria. Harmful bacteria such as Flavobacteriaceae_uncultured remained highly abundant post-exposure. This study systematically demonstrates that NPs compromise avian health via two primary mechanisms: inducing inflammation, oxidative stress, apoptosis, and autophagy inhibition in the liver and jejunum; disrupting mitochondrial respiration in the liver and causing intestinal barrier dysfunction accompanied by dysbiosis. These findings offer critical evidence for evaluating the potential risks of environmental nano-pollutants in livestock and poultry industry.},
}

@article {pmid41707423,
year = {2026},
author = {Francés, Á and López, M and González-Raurich, M and Cobo-Díaz, JF and Prieto, M and Allende, A and Gil, MI and Truchado, P and Alvarez-Ordóñez, A and Oliveira, M},
title = {Characterization of microbial diversity, chemical hazards and antimicrobial resistant bacteria in wash water from a fresh-cut vegetable processing plant.},
journal = {International journal of food microbiology},
volume = {452},
number = {},
pages = {111667},
doi = {10.1016/j.ijfoodmicro.2026.111667},
pmid = {41707423},
issn = {1879-3460},
abstract = {This study investigated the quality of process wash water (PWW) in an industrial fresh-cut produce facility. Traditional microbiological and physico-chemical parameters, such as aerobic mesophilic counts, coliforms, molds and yeasts, pH, free chlorine, oxidation-reduction potential, and organic matter indicators, were monitored to contextualize water quality dynamics across the workday. Additionally, untargeted analyses were performed to characterize the microbiome and resistome and identify chemical hazards in PWW, highlighting the occurrence of antimicrobial-resistant bacteria and the presence of some pesticides at low levels, including chlorantraniliprole, cyprodinil, fludioxonil, and propyzamide, in a real-world processing environment. Antimicrobial susceptibility tests and whole genome sequencing of twelve coliform isolates revealed multidrug-resistant strains, including Enterobacter mori, Enterobacter ludwigii, and Klebsiella oxytoca, carrying resistance genes such as oqxB, fosA, and blaACT-12, as well as the plasmid-borne blaOXY-2-2. Metagenome analyses revealed a microbial community dominated by the genus Pseudomonas, together with high abundance of Rheinheimera mangrovi and Pantoea agglomerans. Moreover, resistome analysis disclosed that 83% of detected antimicrobial resistance genes were associated with beta-lactam resistance. Additionally, the efficacy of chlorine against one K. oxytoca isolate obtained from PWW using a dynamic system simulating a produce washing operation confirmed that maintaining pH at 6.5 and stable free chlorine levels of 6 mg/L was sufficient for complete inactivation. These findings demonstrate the importance of implementing proper wash water management practices in fresh produce processing, including preventing excessive organic matter accumulation through adequate water replenishment and maintaining chemical parameters within the validated operational range, supported by systematic verification and monitoring.},
}

@article {pmid41707393,
year = {2026},
author = {Tang, H and Du, S and Tan, Y and Su, W and Niu, Z and Sun, J and Shao, W and Fang, X and Tang, Z and Zhang, D and Chen, Z and Zhang, Z and Shao, J and Norback, D and Sun, Y and Fu, X and Lv, L and Zhao, Z},
title = {The role of the nasal microbiome in linking ozone pollution to allergic rhinitis in children.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141475},
doi = {10.1016/j.jhazmat.2026.141475},
pmid = {41707393},
issn = {1873-3336},
abstract = {Ambient ozone (O3) links to childhood allergic rhinitis (AR), but the nasal microbiome's role remains unclear. We did a case-control study in Shanghai (176 AR children, 114 controls). AR children had higher 12-month O3 (OR=1.21, 95 %CI:1.11-1.29 per 10 μg/m[3]) and reduced nasal microbial α-diversity (P < 0.05). Co-occurrence network analysis showed the nasal microbial community in AR children had reduced connectivity and lost keystone taxa compared to controls. O3 was negatively correlated with α-diversity (P < 0.05) which indices mediated annual (9.15 %, 95 %CI:3.17-18.45 %) and warm-season (14.21 %, 95 %CI:5.27-27.84 %) O3-AR links; predicted microbial functional pathways in particular steroid hormone biosynthesis (8.77 % for annual O3, 18.49 % for warm-season O3) and limonene/pinene degradation (7.46 % for warm-season O3) (P < 0.05) mediated the O3-AR link too. Our findings highlighted the nasal microbiome's potential role in mediating the link between O3 exposure and childhood AR. This fills gaps in the mechanism on ambient O3 and childhood AR in perspective of the mediation by nasal microbiome and its functional pathways and offers actionable insights for O3 - targeted environmental management and precise pediatric health protection.},
}

@article {pmid41707391,
year = {2026},
author = {Werid, GM and Hemmatzadeh, F and Batterham, T and Miller, D and Edwards, R and Trott, DJ and Petrovski, K},
title = {Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110926},
doi = {10.1016/j.vetmic.2026.110926},
pmid = {41707391},
issn = {1873-2542},
abstract = {Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.},
}

@article {pmid41707342,
year = {2026},
author = {Marino, AF and Marino, FE},
title = {Those ancient teeth and the endurance predator: Dentition and human heat adaptation.},
journal = {Journal of thermal biology},
volume = {136},
number = {},
pages = {104421},
doi = {10.1016/j.jtherbio.2026.104421},
pmid = {41707342},
issn = {0306-4565},
abstract = {Human thermoregulation is characterised by the ability to sustain endurance activities in hot environments through sweating and efficient heat dissipation. Combined with habitual bipedality, these adaptations enabled persistence hunting, where prey animals, constrained by panting, succumbed to hyperthermia during prolonged pursuit. This strategy offered early Homo access to calorie-dense animal foods, but it also imposed the critical requirement to consume prey rapidly under thermally stressful conditions. We argue that dentition was a key, though often overlooked, enabler of this thermoregulatory foraging niche. Fossil evidence demonstrates reductions in canine size, the disappearance of the honing complex, and modifications to molars and enamel thickness that enhanced versatility and durability in food processing. Teeth acted in concert with emerging tool use to minimise mastication time, reduce heat production, and accelerate nutrient intake. Alongside changes in gut morphology and microbiome composition, dentition formed part of an integrated system that linked diet, thermoregulation, and survival. Viewed in this light, dental evolution was not merely a dietary adaptation but a central contributor to Homo's ecological success as an endurance-adapted omnivore. We frame our hypothesis on heat and handling time: in hot-dry contexts, versatile human dentition together with stone tools and cooperation helped compress the post-kill processing, reducing on-site heat and dehydration; we avoid teleological 'optimization' and emphasize mosaic, trade-off responses.},
}

@article {pmid41707316,
year = {2026},
author = {Yang, J and Meng, X and Zhang, H and Sun, W and Yang, L and Li, S},
title = {Mobile genetic elements drive the assembly of high-risk resistance and virulence configurations at the riverine water-sediment interface.},
journal = {Environmental research},
volume = {296},
number = {},
pages = {124055},
doi = {10.1016/j.envres.2026.124055},
pmid = {41707316},
issn = {1096-0953},
abstract = {Riverine ecosystems are major conduits and repositories for microplastics, heavy metals and antibiotics yet how these co-occurring stressors jointly shape resistance and virulence risks across water and sediments remains unclear. Here we combined shotgun metagenomics with pollutant profiling along a representative rural-to-urban gradient during the dry season to resolve the distribution, mobility and drivers of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), virulence factors (VFs) and mobile genetic elements (MGEs) in paired surface waters and surficial sediments. Bacterial communities were dominated by Pseudomonadota and Actinomycetota while fungal communities were dominated by Ascomycota and Uroviricota respectively with stronger land-use effects observed in water than in sediments. Across all samples we detected 36 ARG classes and 1589 subtypes where multidrug and efflux or target alteration mechanisms predominated. Furthermore ARG richness, abundance and diversity increased from rural to urban reaches in both media. MGEs were dominated by transposases where ARG-MGE co-localization on 1474 contigs revealed dense transposase-centered networks in urban sediments that linked multidrug, peptide, glycopeptide and tetracycline resistance. Crucially we identified contigs co-harboring ARGs, MRGs, and VFs as multi-trait risk gene carriers. Urban reaches hosted diverse carrier lineages whereas rural reaches were dominated by the high abundance of specific carriers. SourceTracker and partial least squares path modeling together indicated that rural sediments are the principal upstream sources of microbes and risk genes while MGEs in urban sediments translate multi-pollutant stress into enlarged and more mobile risk gene pools. These findings highlight the need to jointly manage agricultural inputs and urban sediments under multi-stressor conditions.},
}

@article {pmid41707315,
year = {2026},
author = {Gaber, M and Moulden, LM and Wilson, AS and Payne, V and Holmes, J and Neary, K and Peoples, A and Duet, ML and Katz, AJ and Vidi, PA and Cook, KL},
title = {Microbe-associated molecular patterns differentially mediate carcinogenic alterations of the breast tissue in the context of obesity.},
journal = {Neoplasia (New York, N.Y.)},
volume = {73},
number = {},
pages = {101284},
doi = {10.1016/j.neo.2026.101284},
pmid = {41707315},
issn = {1476-5586},
abstract = {Obesity is a risk factor for breast cancer. Obesity alters the microbiome and microbiome perturbations are reported in breast cancer patients. Yet, the impact of obesity-mediated microbial shifts on breast cancer risk remains unclear. Here, we investigate the effect of microbial-associated molecular pattern (MAMP) signaling on genome instability and inflammation. We show in human samples that obesity chronically elevates breast tissue levels of two MAMPs: lipopolysaccharide (LPS) and flagellin. In contrast, obesity was not associated with chronic elevations in lipoteichoic acid (LTA). Injections of LPS and flagellin in mouse mammary glands (MG) were sufficient to induce DNA damage and inflammation. Moreover, DNA damage was reduced in MG of animals on a high-fat diet by knockdown of toll-like receptors for LPS and flagellin (TLR4 and TLR5), but not TLR2 (LTA receptor). Experiments with breast acini cultures demonstrated LPS and flagellin (but not LTA) induce DNA double-strand breaks via TLR and reactive oxygen species (ROS) generation. Similarly, LPS and flagellin mediated nuclear factor-kappa B (NF-κB) pathway activation and increased expression of inflammatory cytokines. Analyses of non-cancerous breast tissue microbiome revealed an enrichment of Proteobacteria in obese women. Proteobacteria often contain LPS and many of these bacteria are flagellated. Tissue-resident Proteobacteria abundance correlated with breast tissue DNA damage. Our findings show that LPS and flagellin are systemic and local mediators of obesity-induced microbiome alterations, predisposing the breast to pre-malignant changes. These results underscore the importance of considering the tissue-resident microbiome as a biomarker of risk to improve primary prevention of breast cancer. Significance: Obesity differentially modulates non-cancerous breast tissue microbial-associated molecular pattern signaling, enriching LPS and flagellin, to promote oxidative stress and DNA damage.},
}

@article {pmid41707175,
year = {2026},
author = {Huang, X and Deng, K and Zhu, G and Huang, W and Gong, G and Liu, H and Yang, T and Gui, Y and Li, W},
title = {Dynamics of soil microbiome throughout the cultivation life cycle of Phallus rubrovolvatus.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0279},
pmid = {41707175},
issn = {1480-3275},
abstract = {Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of P. rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during P. rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.},
}

@article {pmid41706615,
year = {2026},
author = {Hyoju, SK and Cira, K and McKinley, I and Faazal, R and Mailhiot, D and Ostdiek, A and Neumann, PA and Alverdy, JC},
title = {Feasibility and preliminary results of modeling a clinically meaningful anastomotic leak in pigs.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004959},
pmid = {41706615},
issn = {1743-9159},
abstract = {BACKGROUND: Animal models are essential for investigating the pathobiology of anastomotic leakage (AL). To be clinically meaningful, AL must occur despite a technically adequate anastomosis and reflect a phenotype relevant to surgical practice. This feasibility pilot study aimed to develop a clinically relevant porcine AL model by combining a Western diet (WD), segmental ischemia, perioperative antibiotic prophylaxis (PAP), and luminal exposure to pathogenic bacteria under optimal surgical conditions.

METHODS: Twenty-one female domestic pigs were randomized into four groups. Group 1 received standard chow, PAP, and underwent a stapled colorectal anastomosis. Group 2 received WD, PAP, and perioperative luminal exposure to viable human and murine pathogens via colonoscopy. Group 3 received the same treatment with added ischemia-reperfusion (I/R) injury. Group 4 served as a negative control, receiving all exposures with autoclaved pathogens. Animals underwent a technically optimal stapled colorectal anastomosis. Healing was assessed clinically, endoscopically, and macroscopically on postoperative days 3 and 7.

RESULTS: Gross healing (P = 0.0027) and adhesion scores (P = 0.0067) differed significantly between groups, with the highest scores in pigs exposed to WD, I/R, and viable pathogens. These changes did not reach the threshold of clinically overt anastomotic failure (Clavien-Dindo grade III), and endoscopic scores showed no significant intergroup differences. A strong association was observed between gross healing and adhesion scores (r = 0.909).

CONCLUSION: While the model did not progress to clinically overt AL (Clavien-Dindo grade III), it reproducibly induced subclinical impairment of anastomotic healing under compounded perioperative stress. These findings support its feasibility and biological relevance for studying early determinants of anastomotic integrity prior to clinical failure.},
}

@article {pmid41706443,
year = {2026},
author = {Khanna, S},
title = {What potential do DNA polymerase IIIC (PolC) inhibitors hold for the treatment of clostridioides difficile infection?.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14656566.2026.2634960},
pmid = {41706443},
issn = {1744-7666},
}

@article {pmid41706330,
year = {2026},
author = {Kovacs, ED and Kovacs, MH},
title = {Agrochemical mixture combination, dose, and exposure time differently modulate soil microbiome phenotypes.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {3},
pages = {59},
pmid = {41706330},
issn = {1573-3017},
support = {18PFE/30.12.2021//Ministry of Research, Innovation, and Digitization through Program 1-Development of the national research and development system, Subprogram 1.2-Institutional performance projects that finance RDI excellence/ ; 18PFE/30.12.2021//Ministry of Research, Innovation, and Digitization through Program 1-Development of the national research and development system, Subprogram 1.2-Institutional performance projects that finance RDI excellence/ ; Grant number 760104/23 May 2023, code CF 245/29, November 2022//European Union NextGeneration EU through the National Recovery and Resilience Plan, Component 9. I8., Romanian Government, Ministry of the Innovation and Digitization through the National Recovery and Resilience Plan (PNRR) PNRR-III-C9-2022-I8/ ; Grant number 760104/23 May 2023, code CF 245/29, November 2022//European Union NextGeneration EU through the National Recovery and Resilience Plan, Component 9. I8., Romanian Government, Ministry of the Innovation and Digitization through the National Recovery and Resilience Plan (PNRR) PNRR-III-C9-2022-I8/ ; },
}

@article {pmid41706260,
year = {2026},
author = {Matsumoto, M and Shiotani, A and Osawa, M and Handa, O and Matsumoto, H and Umegaki, E and Yonezawa, H and Osaki, T},
title = {Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {},
number = {},
pages = {},
pmid = {41706260},
issn = {1436-3305},
support = {Research Project Grant//Kawasaki Medical School/ ; },
}

@article {pmid41706019,
year = {2026},
author = {Rose, BD and Kreuch, D and Wu, T and Horowitz, M and Rayner, CK and Page, AJ and Miller, CL and Young, RL},
title = {Glycemic Impact of Non-Nutritive Sweeteners in Health and Type 2 Diabetes.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf313},
pmid = {41706019},
issn = {1753-4887},
abstract = {Foods and beverages sweetened with non-nutritive sweeteners (NNSs) are increasingly common in modern diets and widely promoted as healthy alternatives to their sugar-sweetened counterparts, with attendant benefits for individuals with preclinical or clinical metabolic disease. Despite this position, the evidence base supporting the purported health benefits of NNSs is limited and equivocal, particularly in individuals with type 2 diabetes. This review discusses the metabolic effects of NNSs from the standpoint of epidemiological studies and focuses on evidence from the hitherto limited number of prospective clinical trials, as well as potential modes of interaction. Non-nutritive sweeteners are capable of binding to sweet taste receptors (STRs, a heterodimer of T1R2-T1R3) in a wide variety of tissues, including the tongue, pancreas, and small intestine. In cellular, tissue and preclinical models, the binding of NNSs to intestinal STRs triggers the release of the incretin hormones glucagon-like peptide 1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), which, in turn, evoke pancreatic insulin release. Sweet taste receptor activation also triggers release of the intestinotrophic peptide, glucagon-like peptide 2 (GLP-2), which augments the expression and function of the primary apical glucose transporter in the intestine, sodium-glucose co-transporter-1 (SGLT-1). In addition, the NNSs saccharin and sucralose disrupt the composition of the gut microbiome in both pre-clinical and clinical settings in health, and do so in a manner that is individualized and causally related to glucose intolerance. Correspondingly, NNSs have the potential to impact metabolic outcomes directly via host-mediated pathways, as well as secondary to changes in the hosted microbiota. To date, most clinical trials have focused on the acute or subacute effects of NNSs on gut hormone release, glycemic control, and weight management. There is now broad recognition that longer-term, prospective randomized clinical trials are required to add mechanistic insight into how NNSs impact glycemic control in health and in type 2 diabetes.},
}

@article {pmid41705972,
year = {2026},
author = {Qiu, YZ and Yang, MT and Liu, Z and Chen, XY and Chen, JD and Huang, SY and Lan, QY and Hu, Y and Zhou, X and Wei, W and Wang, X and Ye, X and Zhu, HL},
title = {Impact of medium- and long-chain triacylglycerols and sn-2 palmitate on temperament development in term infants: potential role of gut Bifidobacterium.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03451e},
pmid = {41705972},
issn = {2042-650X},
abstract = {Background: Medium- and long-chain triacylglycerols (MLCTs) and sn-2 palmitate constitute 70-80% of human breast milk lipids. Our previous work showed that a formula supplemented with these structural lipids promoted adequate weight gain, but their effects on neuropsychological development and gut microbiome remain unclear. Therefore, this study aimed to investigate the effects of supplementation with MLCTs and sn-2 palmitate on temperament development and the gut microbiome in term infants. Methods: This was a prospective, parallel, open-label controlled trial. Infants were divided into three groups according to their feeding patterns at the 4[th] week postpartum: the intervention group received a formula supplemented with MLCTs and sn-2 palmitate (IG, n = 65), the control group received a formula without these lipids (CG, n = 48), and the breastfed group (BG, n = 66). Assessment of infant temperament was conducted at the baseline (1 month postpartum) and endpoint (3 months postpartum) using the Early Infancy Temperament Questionnaire. Stool samples were collected concurrently for microbiome analysis via 16S rRNA amplicon sequencing. Results: After two months of intervention, the IG exhibited significant improvements in temperament scores compared to the CG, including activity (p = 0.039), mood (p = 0.023), persistence (p = 0.001), and distractibility (p = 0.006), but similar changes to the BG. As for the gut microbiome, the relative abundance of Bifidobacterium in the IG was significantly increased compared to the CG (p = 0.011) and was comparable to the BG (p = 0.759). Conversely, the decrease in the relative abundance of Blautia was significantly more pronounced in the IG than in both the CG (p = 0.002) and BG (p = 0.048). Furthermore, temperament characteristics were associated with microbiome genera in early infancy. Notably, a positive correlation was observed between the changes in activity scores and the relative abundance of Bifidobacterium (r = 0.25, p = 0.002). Conclusions: The intervention involving MLCTs and sn-2 palmitate improves infant temperament, potentially mediated via increased Bifidobacterium. These findings highlight the potential of nutrition to alter the infant temperament by modulating the gut microbiome, offering valuable insights for the development of optimized nutritional strategies to support neurodevelopment. The clinical trial registry number is NCT05295030 (https://clinicaltrials.gov).},
}

@article {pmid41705833,
year = {2026},
author = {Troha, N and Zorec, TM and Hošnjak, L and Strašek Smrdel, K and Celar Šturm, A and Šalamun, V and Grazio Frković, S and Vrtačnik Bokal, E and Poljak, M},
title = {Bacterial microbiome analysis of vaginal, cervical, and endometrial samples in patients with adenomyosis during the window of implantation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0279125},
doi = {10.1128/spectrum.02791-25},
pmid = {41705833},
issn = {2165-0497},
abstract = {UNLABELLED: Adenomyosis is a chronic gynecological condition affecting a substantial portion of women of reproductive age. With symptoms including abnormal uterine bleeding, chronic pelvic pain (CPP), dysmenorrhea, and infertility, poor response to symptomatic treatment and unfavorable outcomes of assisted reproductive technologies, it remains a significant diagnostic and therapeutic challenge. Here, we analyzed microbial compositions of the reproductive tract of women with adenomyosis (n = 33) in comparison with healthy controls (n = 31). Vaginal, cervical, and endometrial samples were collected using minimally invasive transcervical sampling techniques on the 22nd day of the menstrual cycle, during the so-called window of implantation. 16S rRNA was amplified and recorded using the next generation sequencing. Bioinformatic and statistical analysis focused on quantitative taxonomical characterization of the specimens' microbiomes. Vaginal bacterial microbiome composition was consistent across the three anatomical sites. Compared with the control group, adenomyosis was associated with Lactobacillus iners, whereas Lactobacillus gasseri and Gardnerella vaginalis were negatively associated with adenomyosis and its clinical symptoms. G. vaginalis, typically considered a pathogen, was highlighted as an important dominant microbiome replacement for lactobacilli, more so in healthy women than in women with adenomyosis. Anaerococcus prevotii, Peptoniphilus grossensis, and Peptrostreptococcus anaerobius also showed weak correlation to adenomyosis. Differences in taxa abundance were detected in association with adenomyosis clinical symptoms. L. iners was associated with dysmenorrhea, heavy menstrual bleeding (HMB), as well as CPP. Prevotella disiens, Prevotella timonesis, and Dialister micraerophilus were associated with dysmenorrhea and Peptoniphilus grossensis with HMB, respectively. L. gasseri and L. jensenii appeared to anticorrelate with these symptoms.

IMPORTANCE: Adenomyosis poorly responds to treatment and assisted reproductive technologies. Here, we report a comprehensive 16S rRNA-based analysis of vaginal, cervical, and endometrial samples, obtained minimally invasively (transcervically) in a cohort of Caucasian women during the receptive phase of endometrium. Results revealed the least invasive option, vaginal microbiome sampling, reliably predicts the microbiome compositions of cervix and endometrium. We showed substantial variation in microbial composition of adenomyosis patients. L. iners, a species with specific functional traits, was consistently associated with adenomyosis presence and related symptoms. This finding suggests microbiome remodeling as a viable novel therapeutic option for adenomyosis. Furthermore, our findings indicate that the pathogenic role of G. vaginalis may be context-dependent. Ongoing genomic and ecological profiling is essential to clarify Gardnerella's dual commensal-pathogenic nature. Previous adenomyosis studies have mostly focused on the vaginal microbiome, whereas the endometrial microbiome has rarely been studied and never in the time of window of implantation.},
}

@article {pmid41705831,
year = {2026},
author = {Kato, H and Itakura, M and Sato, S and Wagai, R and Minamisawa, K},
title = {Higher-dimensional ordination analysis teases out impacts of Bradyrhizobium bioaugmentation on native soil microbial communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0288025},
doi = {10.1128/spectrum.02880-25},
pmid = {41705831},
issn = {2165-0497},
abstract = {Microbial inoculants are increasingly being used to enhance plant growth and soil environments, yet their ecological effects on native microbial communities remain unclear. We investigated the long-term dynamics of soybean-nodulating Bradyrhizobium strains carrying the nosZ gene encoding N2O reductase in microcosms comprising three different soils. Analysis of 16S rRNA amplicons revealed that bacterial community compositions were primarily driven by soil type and time, with inoculation having only minor effects. In contrast, nosZ clade I amplicon analysis showed high survivability of the dominant nosZ-sequence groups corresponding to the inoculant strains, which accounted for 20%-50% of the total nosZ community even 249 days after inoculation; despite this dominance, the overall community structures of indigenous nosZ-harboring Bradyrhizobium remained largely unchanged. This observation was further supported by a permutational multivariate analysis of variance, which showed a 90% reduction in R[2] when the inoculant sequence groups were excluded. Thus, it is possible to enhance N2O-reducing function through inoculation without drastically disrupting the indigenous microbial community. To explore the landscapes of inoculation effects obscured in two-dimensional mapping, we applied dimensionality-reduction tools such as principal coordinates analysis beyond their typical use for visualization by extending analyses into higher-dimensional spaces. Varying the number of dimensions revealed that the signal-to-noise ratio and clustering tendency peaked at 4-10 dimensions, with further increases in dimensions leading to homogenization of community patterns. This intermediate dimensional space also revealed differences in community succession by soil type. These findings demonstrate that careful selection of dimensionality can enhance the discovery of ecological patterns.IMPORTANCEDimensionality reduction is widely used to visualize microbiome data in two- or three-dimensional ordination spaces. However, its application in higher-dimensional analysis remains underexplored. We highlighted the use of dimensionality reduction not only as a visualization tool, but as a means of projecting microbiome data into ordination spaces for geometric analyses, which are not limited to two or three dimensions. Communities were projected beyond three dimensions to examine how dimensionality affects evaluation of inoculation effects through geometric analyses. Our findings show that dimension selection strongly influences the ability to detect and resolve ecological signals, which were distorted in low-dimensional spaces or homogenized in extremely high-dimensional spaces. Intermediate dimensionalities better retained the spatial fidelity needed to resolve soil-dependent responses to inoculation. By enhancing the resolution of small but meaningful effects, this approach provides a robust framework for guiding strain selection, application strategies, and risk assessment in microbial inoculation studies.},
}

@article {pmid41705617,
year = {2026},
author = {Gorelov, AV and Kozlov, RS and Andreeva, IV and Arova, AA and Bavykina, IA and Grigorovich, MS and Dovgan, EV and Ermolenko, KD and Zaytseva, OV and Zakharenko, SM and Zelenskaia, VV and Zyryanov, SK and Ilyenkova, NA and Kachkovskii, MA and Kogut, TA and Kondyurina, EG and Krasnov, VV and Lokshina, EE and Privorotsky, VF and Repetskaya, MN and Rzyankina, MF and Serikova, SN and Stetsiouk, OU and Usenko, DV and Khanipova, LV and Shabalov, AM and Shevyakov, MA and Yakovleva, LV},
title = {[Probiotics' position in clinical practice: focus on the combination of Lactobacillus acidophilus (LA-5) and Bifidobacterium animalis subsp. lactis (BB-12). A review].},
journal = {Terapevticheskii arkhiv},
volume = {97},
number = {12},
pages = {1037-1043},
doi = {10.26442/00403660.2025.12.203481},
pmid = {41705617},
issn = {0040-3660},
mesh = {*Probiotics/therapeutic use/pharmacology ; Humans ; *Lactobacillus acidophilus ; *Bifidobacterium animalis ; *Diarrhea/prevention & control/chemically induced ; Anti-Bacterial Agents/adverse effects ; },
abstract = {Probiotics are currently widely used in clinical practice to prevent and treat a wide range of diseases. The purpose of our review is to highlight what we consider to be the most significant clinical studies on the use of probiotics for preventing antibiotic-associated diarrhea, clostridial diarrhea and pseudomembranous colitis. The article also presents the results of studies confirming the efficacy of probiotics in Helicobacter pylori eradication therapy. The review focuses on Linex[®] Forte, medicinal product containing the combination of Lactobacillus acidophilus (LA-5) and Bifidobacterium animalis subsp. lactis (BB-12).},
}

*Probiotics/therapeutic use/pharmacology
Humans
*Lactobacillus acidophilus
*Bifidobacterium animalis
*Diarrhea/prevention & control/chemically induced
Anti-Bacterial Agents/adverse effects

@article {pmid41705405,
year = {2026},
author = {Wetthasinghe, L and Ng, HF and Chew, KS and Ranai, NM and Ngeow, YF and Lee, WS},
title = {Paediatric Crohn's Disease Management: A Mini Review Exploring Conventional and Innovative Therapies With Promising Potential.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70307},
pmid = {41705405},
issn = {1440-1746},
support = {//UTAR Research Scholarship Scheme/ ; 6274/0016//UTAR Research Fund/ ; 6555/1L02//UTAR Research Fund/ ; 4417/0004//Toray Science Foundation Japan/ ; },
abstract = {Pediatric Crohn's disease (pCD) is a chronic, relapsing inflammatory bowel disease with increasing incidence worldwide, including in Asia where it was once rare. Affected children often experience gastrointestinal symptoms, growth failure, malnutrition, and psychosocial impacts that significantly impair quality of life. This review summarizes current knowledge on the epidemiology and pathogenesis of pCD, highlighting the role of dysbiosis, environmental triggers, and immune dysregulation. Conventional management strategies, including aminosalicylates, corticosteroids, immunomodulators, biologics, surgery, and nutritional interventions such as exclusive enteral nutrition, are discussed, alongside their limitations in efficacy, tolerability, or long-term safety. The paper further explores emerging therapeutic approaches, including helminthic therapy, fecal microbiota transplantation, and synthetic biotics, which aim to modulate the gut microbiome or immune response more precisely. Although early data from clinical trials are promising, these novel modalities require further investigation, particularly in pediatric populations, to establish optimal protocols, safety profiles, and long-term outcomes. The integration of established and innovative strategies, informed by ongoing research, offers the potential for more personalized and effective care in managing pCD.},
}

@article {pmid41705261,
year = {2026},
author = {Fentie, EG and Lim, K and Andargie, YE and Park, S and Shin, JH},
title = {Preserving fermented-foods microbial diversity through systematic culturomics for the discovery of multi-strain probiotic candidates.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101318},
pmid = {41705261},
issn = {2665-9271},
abstract = {Fermented foods (FFs) represent complex living ecosystems that deliver viable microbes and bioactive metabolites linked to human health benefits. However, many probiotic strains isolated from FFs fail to reproduce these effects in vivo, likely due to the disruption of their natural ecological synergy during isolation. Here, we employed a systematic, ecology-aware culturomics framework to transform the Kimchi microbiome into genome-vetted, multi-species probiotic candidates while preserving ecological fidelity. Specifically, 56 distinct enrichment culture conditions were established using six liquid media (In-situ, MRS, NB, TSB, BHI, BB) across varied redox states (aerobic, anaerobic, microaerophilic), incubation periods (12 h, 66 h), and selective suppressants (CHIR-090, nalidixic acid). Results indicated that In-situ and MRS media under microaerophilic conditions effectively preserved the lactobacilli core, whereas generalist media and aeration expanded taxonomic breadth to include rare taxa. Furthermore, extended incubation (66h) successfully unlocked 107 unique taxa compared to the limited diversity of short incubation (12h). Shotgun metagenomic mining further revealed promising functional properties, including acid tolerance, adhesion modules, and diverse bacteriocin-skewed biosynthetic gene clusters. Crucially, the collection exhibited a strong safety profile: only 1 % of identified risk factors were antibiotic resistance genes (ARGs) on mobile genetic elements (MGEs), and only 4 % represented colocalized ARGs, virulence factors, and MGEs. Systematic-culturomic isolation later yielded over 90 strains, including Weissella, Bacillus, and Lactococcus, significantly expanding beyond standard lactobacilli-centric portfolios. Overall, this study confirms that ecology-aware culturomics captures the functional diversity of the Kimchi microbiome, providing a scalable model for realizing the full therapeutic potential of FFs.},
}

@article {pmid41705247,
year = {2026},
author = {Kovaleva, OV and Sinyov, VV and Rashidova, MA and Malashenko, OS and Gratchev, A},
title = {Tumor-associated neutrophils in renal cell carcinoma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1755401},
pmid = {41705247},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Renal Cell/immunology/pathology/metabolism ; *Kidney Neoplasms/immunology/pathology/metabolism ; *Neutrophils/immunology/metabolism ; Tumor Microenvironment/immunology ; Animals ; Extracellular Traps/immunology/metabolism ; },
abstract = {Renal cell carcinoma (RCC) is an immunogenic tumor in which tumor-associated neutrophils (TANs) and neutrophil extracellular traps (NETs) represent a functionally important component of the tumor microenvironment. Recent studies have revealed pronounced phenotypic heterogeneity of RCC-infiltrating neutrophils, including interferon-responsive, immunosuppressive PMN-MDSC-like, pro-angiogenic, and NET-forming subsets that cannot be adequately described by the classical N1/N2 model. Their polarization is shaped by ELR[+] CXC chemokines (CXCL1, CXCL8), cytokine signals, systemic inflammation, hypoxia driven by VHL/HIF pathways, and tumor-intrinsic oncogenic alterations such as PTEN loss, ERβ- and c-Myc-dependent programs, as well as epigenetic remodeling. TANs exert predominantly pro-tumor functions in RCC, promoting T-cell exclusion and exhaustion, supporting angiogenesis and stromal remodeling, and facilitating epithelial-mesenchymal transition, venous invasion and metastasis. NETs, enriched in hypoxic and necrotic tumor regions and in venous tumor thrombi, further contribute to vascular occlusion, metastatic dissemination and local immune dysfunction, and are reflected by distinct transcriptional signatures. Clinically, high TAN density, activation markers and neutrophil/NET-associated gene signatures are consistently associated with aggressive tumor behavior, early recurrence, poor survival and resistance to VEGF-TKIs and immune checkpoint inhibitors. Emerging data also link neutrophil-rich stromal inflammation with the tumor resident microbiome, suggesting composite TAN-microbiome biomarkers for refined risk stratification. In this review, we summarize current knowledge on phenotypic diversity, regulatory circuits and functional programs of TANs and NETs in RCC, and discuss their prognostic and predictive significance, as well as therapeutic strategies aimed at chemokine blockade, complement modulation, NET inhibition and neutrophil re-education.},
}

Humans
*Carcinoma, Renal Cell/immunology/pathology/metabolism
*Kidney Neoplasms/immunology/pathology/metabolism
*Neutrophils/immunology/metabolism
Tumor Microenvironment/immunology
Animals
Extracellular Traps/immunology/metabolism

@article {pmid41705232,
year = {2026},
author = {Yuan, Y and Zhang, W and Wang, D},
title = {Targeting the gut-pancreatic axis: microbial modulation of immunotherapy in pancreatic cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1682390},
pmid = {41705232},
issn = {1664-3224},
mesh = {Humans ; *Pancreatic Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; *Pancreas/immunology/microbiology ; Animals ; },
abstract = {With advances in microbial sequencing technology, the role of microorganisms in cancer development and treatment has been increasingly explored. The gut microbiota, as a key shaper of both innate and adaptive immunity, is believed to migrate from the gut and colonize the pancreas, thereby influencing the tumor microenvironment(TME) of pancreatic cancer. Pancreatic cancer exhibits treatment resistance due to its immunosuppressive TME and high interstitial density. Multiple sequencing analyses of pancreatic tumor tissues have revealed that alterations in the tumor-associated microbiota are associated with prognosis and treatment response, suggesting that the microbiota may serve as a complementary modality in immunotherapy. This paper describes potential pathways by which the gut microbiota can migrate to the pancreas and analyzes changes in tumor microbiota composition. It also identifies microbiota types associated with prognosis, and summarizes treatment strategies leveraging the gut-pancreas axis to enhance the personalization and precision of care. It critically examines the limitations of existing research, and aims to leverage microbiome ecology to overcome the immune -suppressive barrier in pancreatic cancer and improve patient outcomes.},
}

Humans
*Pancreatic Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Tumor Microenvironment/immunology
*Immunotherapy/methods
*Pancreas/immunology/microbiology
Animals

@article {pmid41705204,
year = {2026},
author = {Verbunt, J and Mennens, L and Jocken, J and Blaak, EE and Savelkoul, P and Stassen, FRM},
title = {From food to vesicle: nutritional influences on gut microbial inflammatory signaling.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1756462},
pmid = {41705204},
issn = {2296-861X},
abstract = {Diet is a pivotal determinant of gut microbial ecology, giving not only rise to specific bacterial compositionality but also its functional output. Studying functional readouts-such as microbial metabolite production-could provide a more accurate and mechanistically informative measure of intervention outcome than traditional compositional profiling alone. Bacterial membrane vesicles (bMVs) are gaining attention as mediators of microbial metabolism and output. These nanoparticles are selectively released as carriers of bioactive proteins, lipids, nucleic acids, and metabolites reflective of the activity of the parent bacteria. Importantly, bMVs are rigid, can efficiently be isolated from feces, and are able to stably transport their cargo to interact with the host. In interacting with immune cells or pathogen recognition receptors, they can potentiate inflammatory responses. Given their extensive, multifaceted involvement in inter-Kingdom communication, bMVs represent an important biomarker for evaluating dietary modulation of gut microbial function. We propose that characterization of gut-derived bMVs offers a highly sensitive, mechanistically grounded approach to titrating impact of dietary interventions. By capturing shifts in microbial metabolic activity and inflammatory potential, bMV-based assessments could complement or surpass traditional measures of microbiome compositional change. Integrating bMV profiling into dietary intervention studies may therefore provide new insight into the functional consequences of diet-microbiome interactions and help refine strategies aimed at reducing inflammation and promoting host health.},
}

@article {pmid41705029,
year = {2026},
author = {Ghavi Hossein-Zadeh, N},
title = {Advancing climate-resilient livestock systems: Next-generation emission mitigation strategies and integrated technological innovations.},
journal = {Veterinary and animal science},
volume = {31},
number = {},
pages = {100588},
pmid = {41705029},
issn = {2451-943X},
abstract = {Livestock production significantly contributes to global greenhouse gas (GHG) emissions, particularly methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2), posing challenges to climate change mitigation and environmental sustainability. This review explores advanced, system-wide approaches to reduce emissions from livestock systems while enhancing productivity, resilience, and resource efficiency. It covers short-term mitigation strategies such as dietary interventions-including methane inhibitors, microbial modulators, and natural compounds-that target enteric fermentation. Long-term solutions involve genetic and breeding innovations, such as microbiome-genome interaction analyses, CRISPR-based editing, and low-methane phenotyping, supported by genomic selection and precision phenotyping tools. The review also assesses advanced manure management technologies like anaerobic digesters and nutrient recovery systems, and examines precision livestock farming tools, including real-time sensors, machine learning models, UAVs, and IoT-based monitoring systems. Emerging digital tools, blockchain, augmented reality, and AI-assisted diagnostics are highlighted for enhancing traceability and decision-making. The potential of integrated energy systems, such as microbial fuel cells, hydrogen electrolysis, algae-based bioenergy, and thermal gasification, is discussed alongside traditional renewables, enabling livestock farms to become clean energy hubs. Circularity is emphasized through silvopasture, algal bioremediation, insect bioconversion, and integrated crop-livestock systems. Environmental assessment tools and the socio-political dimensions of technology adoption, including policy, education, and farmer behavior, are also considered. Future research directions, such as atmospheric methane oxidation, 4D-printed feed additives, and quantum modeling, are proposed. Overall, the review calls for a transdisciplinary, integrated approach to transform livestock systems into climate-smart, low-emission food production networks.},
}

@article {pmid41704943,
year = {2026},
author = {Narulla, RS and Ting, R and Sima, S and Diwan, AD and Smith, GCS},
title = {Shoulder surgery preparation: a systematic review and meta-analysis.},
journal = {JSES reviews, reports, and techniques},
volume = {6},
number = {2},
pages = {100637},
pmid = {41704943},
issn = {2666-6391},
abstract = {BACKGROUND: Shoulder infections are an unfortunate and serious complication of surgery. The prevention strategy for infections is multimodal, with a strong reliance on surgical preparation solutions. There is great variability in the use of and effectiveness of surgical preparation solutions; this review aims to identify the most effective methods of shoulder surgical site preparation in the literature.

METHODS: A systematic review and meta-analysis was conducted by 2 independent reviewers in accordance with the PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analyses) framework. Articles were screened by title, then abstract, and finally by full text by each clinician independently. A third orthopedic clinician adjudicated any disagreement on the application of the inclusion criteria. Studies included were human clinical studies utilizing skin preparation methods for the shoulder in a simulated or real primary surgery setting. English language databases from 1980 until the first of January 2025 were accessed. The terms searched included "shoulder," combined with each of the terms "skin," "wound," "antibiotic," "decolonization," "topical," "eradication," "preparation," and "sterilization." The results were pooled and then analyzed in subgroups according to the timing of skin preparation, the solution used, and the area of sampling.

RESULTS: The search found 13,154 articles, of which 31 studies were included in the final study and captured a total of 2,115 patients who were cultured for organisms. The lowest rates of culture positivity at the time of surgery were associated with the use of benzoyl peroxide (27.1% culture positive) and prior-to-day-of-surgery preparation solution administration (30.5% culture positive). Patients who received preparation solutions with alcohol numbered 1,551, of which 577 (37.2%) had positive cultures. Patients who received preparation solutions without alcohol numbered 564, with 140 (24.8%) culture positive, P < .0001, chi-square = 28.285. Patients who had shoulder preparation only on the day of surgery numbered 2,067 with a total of 703 (34%) with positive cultures. The patients who did not have day-of-surgery preparation were numbered at 39, with 9 (23%) positive cultures, P = .027, chi-square = 4.89.

CONCLUSION: There is a wide range of available surgical preparation solutions to attempt to prevent day-of-surgery culture positivity. However, even the most robust regiments still have a substantially high culture positivity rate at the time of surgery. Further trials are warranted to unify protocols for the management of perioperative shoulder preparation.},
}

@article {pmid41704904,
year = {2025},
author = {Av, EZ and Greenberg, A and Knaan, T and Melanson, EL and Youngster, I and Dubnov-Raz, G and Borenstein, E and Gepner, Y},
title = {The associations between physical activity, microbiome and metabolic adaptation in sedentary overweight adults.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1722274},
pmid = {41704904},
issn = {2296-861X},
abstract = {Despite well-established benefits of exercise on metabolic regulation and the gut microbiome (GM), its impact on body composition is inconsistent and often attenuated by metabolic adaptation. This compensation mechanism adjusts energy expenditure including total daily energy expenditure (TDEE) and resting metabolic rate (RMR). Intra-individual variation in exercise response remains unclear, but might be explained by the GM. In this well-controlled study, we investigated the relationship between aerobic exercise, GM composition, and metabolic adaptation in a cohort of 16 sedentary overweight adults (ages 21-45, 50% female) over a 12-week moderate-intensity intervention (65-75% HRmax; 20 kcal/kg/week). Pre- and post-intervention RMR was measured via whole-room calorimetry, TDEE by doubly labeled water, and GM composition via shotgun metagenomics. While body composition did not change at the group-level, a subset of participants ("responders") showed improved body composition and aerobic capacity. Using machine learning, we identified bacterial species, including Faecalibacterium prausnitzii species, whose abundance pre-training is predictive of response. Additionally, we found that responder GM communities are more compositionally cohesive and post-training increases in GM diversity are associated with higher TDEE and RMR. These findings highlight the complex interaction between exercise, metabolism and the GM, and suggest that baseline GM characteristics may contribute to individual variability in metabolic adaptation. This insight may help guide microbiome-informed strategies to enhance exercise efficacy. Clinical trial registration: ClinicalTrials.gov, identifier NCT04460040.},
}

@article {pmid41704851,
year = {2025},
author = {Soriano, S and Marshall, A and Holcomb, M and Flinn, H and Burke, M and Kara, G and Scalzo, P and Villapol, S},
title = {Sex-specific effects of fecal microbiota transplantation on TBI-exacerbated Alzheimer's disease pathology in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1703708},
pmid = {41704851},
issn = {1664-302X},
abstract = {BACKGROUND: Traumatic brain injury (TBI) accelerates Alzheimer's disease (AD) pathology and neuroinflammation, potentially via gut-brain axis disruptions. Whether restoring gut microbial homeostasis mitigates TBI-exacerbated AD features remains unclear, particularly with respect to sex differences.

OBJECTIVE: The goal of our study was to test whether fecal microbiota transplantation (FMT) modifies amyloid pathology, neuroinflammation, gut microbial composition, metabolites, and motor outcomes in male and female 5xFAD mice subjected to TBI.

METHODS: Male and female 5xFAD mice received sham treatments or controlled cortical impact, followed 24 h later by vehicle (VH) or sex-matched FMT from C57BL/6 donors. Assessments at baseline, 1-, and 3-days post-injury (dpi) included Thioflavin-S and 6E10 immunostaining for Aβ, Iba-1 and GFAP for glial activation, lesion volume, rotarod performance, 16S rRNA sequencing for microbiome profiling, serum short-chain fatty acids (SCFAs), and gut histology.

RESULTS: TBI increased cortical and dentate gyrus Aβ burden, with females showing greater vulnerability. FMT reduced Aβ deposition in sham animals and shifted plaque morphology but did not attenuate TBI-induced amyloid escalation. FMT differentially modulated glial responses by sex and region (reduced microgliosis in males) without altering lesion volume at 3 dpi. Rotarod performance was better in sham females compared to males and declined in FMT-treated TBI females. Fecal microbiome alpha diversity and richness were unchanged, while beta diversity revealed marked, time-dependent community shifts after TBI that were slightly altered by FMT. Gut morphology remained broadly intact, but crypt width increased after TBI, particularly in males.

CONCLUSION: In 5xFAD mice, TBI drives sex-dependent worsening of amyloid pathology, neuroinflammation, and dysbiosis. Acute FMT partially restores microbial composition and plaque features in sham animals but fails to reverse TBI-induced neuroinflammation or motor deficits. These findings underscore the context- and sex-dependence of microbiome interventions and support longer-term, sex-specific strategies for AD with comorbid TBI.},
}

@article {pmid41704794,
year = {2025},
author = {Basu, U and Ahanger, SA and Gai, X and Hu, X},
title = {Longitudinal metagenomics reveals continuous restructuring of soil pathobiome under persistent Phytophthora pressure.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1749879},
pmid = {41704794},
issn = {1664-462X},
abstract = {Soil borne pathogen, Phytophthora nicotianae causes black shank disease in tobacco, present a pervasive threat to global agriculture, with conventional control strategies often proving inadequate. A critical gap exists in our understanding of the long-term, dynamic interplay between the pathogen and the soil microbiome. To address this, we conducted a six-year longitudinal metagenomic study in a monocultured tobacco field, revealing a pathobiome in constant, non-equilibrium adaptation. Our analysis uncovered profound microbial restructuring, beginning with cumulative transcriptional reprogramming of highly significant genes. Functional profiling showed a critical metabolic shift toward anabolic capacity, with a 66.7% increase in KEGG orthologs and enrichment of amino acid biosynthesis (+8.9%), ribosomes (+13.0%), and quorum sensing (+11.0%). The soil resistome underwent dramatic succession, featuring an initial coordinated defense (R[2]=0.825), a comprehensive collapse in Year 3-4 (917 downregulated genes), and a resilient recovery that drove a net increase in antibiotic resistance, indicating a lasting ecosystem alteration. Virulence factor evolution revealed strategic trade-offs, with flagella systems dominating (2,583 occurrences) while more costly energy consuming secretion systems declined, and 87 core virulence factors persisted across time. Crucially, we observed a widespread decoupling between genetic potential and functional expression; key categories for defense and signal transduction declined in abundance (slopes of -150.4 and -264.9, respectively) despite stable gene counts, suggesting a systemic, energy conserving survival strategy. Concurrently, the community experienced progressive diversity loss (Shannon index slope = -0.0464/yr at genus level) despite maintained species richness (717 species), indicating restructuring was driven by shifting evenness rather than species loss. Our findings exhibit that persistent pathogen pressure drives the soil microbiome into a continuous state of adaptive restructuring, prioritizing coordinated defensiveness and metabolic efficiency over stability. This time resolved framework challenges static views of soil ecosystems and provides a foundational dataset for developing predictive, microbiome informed strategies to manage soil borne diseases sustainably.},
}

@article {pmid41704789,
year = {2025},
author = {Panchal, K and Sudhir, A and Prajapati, AS},
title = {Engineering the plant microbiome: synthetic community approaches to enhance crop protection.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1705289},
pmid = {41704789},
issn = {1664-462X},
abstract = {The plant microbiome is essential for plant health; in particular, synthetic microbial communities (SynComs) offer a scalable, sustainable alternative to chemical pesticides. The concept has moved beyond single-strain inoculants, with SynComs being rationally designed using ecological principles, computational tools, and an understanding of how plants shape their microbial niche through root exudates and chemotaxis. Indeed, effective SynCom design requires a mechanistic understanding of microbe-microbe and host-microbe interactions. In real field settings, SynComs have been shown to suppress diseases in tomato, rice, wheat, and maize while enhancing yield. Inconsistent field performance, instability in formulation, regulatory challenges, and farmer adoption are among the pressing issues related to SynComs. In the foreseeable future, the integration of machine learning and gene-editing tools is expected to enable SynCom formulation with greater precision and impact. Favorable labor division and mutualistic relationships within a SynCom make it a more controlled and ecologically informed tool for modern agriculture.},
}

@article {pmid41704769,
year = {2026},
author = {Yinhang, W and Xueli, J and Zheng, W and Xiaojian, Y and Shu, X and Qingjie, Z and Ying, L and Shuwen, H},
title = {Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114664},
pmid = {41704769},
issn = {2589-0042},
abstract = {The gut microbiota is a key hallmark of colorectal cancer (CRC), yet gut fungi remain understudied. We characterized the gut fungal landscape and its associations with bacteria, metabolites, and trace elements in CRC using fecal samples from healthy controls (n = 401), colorectal polyp patients (n = 162), and CRC patients (n = 253). Fungal annotation was performed using genomic data from NCBI (PRJNA833221) as reference. Fungal diversity increased in CRC patients, with seven genera showing differential abundance. Rhizopus was specifically enriched in CRC, while Sporisorium, etc. enriched in polyps. Ablation study identified an optimal 31-microbial-marker panel (28 bacteria and three fungi) that effectively distinguished intestinal disease groups (AUC = 0.89). Structural equation modeling revealed three fungal markers-Penicillium citrinum, Penicillium sp. PG10607D, and Rhizopus stolonifera-that influence bacterial-metabolite-trace element networks. This study delineates the gut fungal atlas in CRC and reveals complex cross-kingdom interactions, offering new insights into CRC pathogenesis.},
}

@article {pmid41704763,
year = {2026},
author = {Turroni, S and Günther, K and D'Amico, F and Veidebaum, T and Kourides, Y and Molnár, D and Lissner, L and Foraita, R and Barone, M and Mora-Martínez, C and Sanz, Y and Fraterman, A and Wolters, M and Brigidi, P and Candela, M and Ahrens, W and Rampelli, S},
title = {Disrupted gut microbiome networks and unhealthy behaviors predict metabolic dysfunction in children and adolescents in the long term.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114763},
pmid = {41704763},
issn = {2589-0042},
abstract = {We recently showed that the individual gut microbiome (GM) configuration in children and adolescents, together with long-term dietary habits, can predict the development of obesity. Here, we expanded our previous cohort to include 218 individuals and used 16S rRNA amplicon sequencing, shotgun metatranscriptomics, and a network approach to analyze fecal samples collected at a baseline survey and after a 4-year follow-up, investigating associations with health status, dietary intake, and other health-related behaviors. Our results showed that an unbalanced GM profile in children/adolescents, with few represented species, poor connectivity, and low transcriptional activity (especially in relation to molecular effectors that positively influence gut and immune health), combined with unhealthy behaviors (i.e., low-fiber diet and reduced physical activity), may favor the onset of obesity. This knowledge may pave the way for the development of adjunct GM-based precision intervention strategies aimed at rewiring microbial networks to promote long-term health.},
}

@article {pmid41704756,
year = {2026},
author = {Liang, N and Zhang, K},
title = {Factors influencing the proliferation of keratinocytes in psoriasis.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114745},
pmid = {41704756},
issn = {2589-0042},
abstract = {The pathogenesis of psoriasis is extremely complex, and abnormal proliferation of keratinocytes (KCs) is one of its key pathological features. During the disease process, multiple factors can induce KC proliferation. This article reviews the mechanisms by which inflammatory cytokines, immune microenvironment, microbiome, epigenetics, metabolism, and the autophagy influence KC proliferation, aiming to provide insights for further research into the pathogenesis of psoriasis and the development of precise clinical treatments.},
}

@article {pmid41704732,
year = {2026},
author = {Bian, R and Zhang, L and Zhu, J and Xu, X},
title = {Multi-Omics Evidence Linking Gualou Xiebai Banxia Decoction Intervention to Atherosclerosis Mitigation and Gut Microbiota-Bile Acid Signatures in ApoE[-/-] Mice.},
journal = {Food science & nutrition},
volume = {14},
number = {2},
pages = {e71543},
pmid = {41704732},
issn = {2048-7177},
abstract = {Atherosclerosis presents a persistent health challenge, with limited therapies addressing residual cardiovascular risk. Gualou Xiebai Banxia Decoction (GXBD), a classical Chinese herbal formula traditionally used for chest obstruction syndromes, was evaluated as a dietary-style intervention in ApoE[-/-] mice fed a high-fat diet for 14 weeks. Using a multi-omics strategy that combined UHPLC-QE-MS/MS chemical profiling, network pharmacology, 16S rRNA sequencing, targeted bile acid metabolomics, and biological validation, we assessed vascular and metabolic outcomes alongside gut ecology. Chemical profiling identified 348 constituents, including bioactive flavonoids and saponins. In vivo, GXBD intervention significantly improved lipid profiles by reducing serum TC, TG, and LDL-C, and by raising HDL (p < 0.05). It markedly reduced aortic plaque burden and alleviated hepatic steatosis (p < 0.05). Mechanistically, GXBD reshaped the gut microbiota, characterized by the enrichment of beneficial Bacteroides and Alloprevotella and the depletion of pro-inflammatory Blautia and Bilophila. This microbial shift coincided with significantly higher levels of protective secondary bile acids, such as 11-LCA and 23-DCA, and fewer cytotoxic chenodeoxycholic acid-derived metabolites (p < 0.05). Correlation and constrained ordination analyses linked these microbial-bile acid signatures to the concordant modulation of vascular hub targets, including the downregulation of MMP9 and CASP3 and upregulation of PPARG and SIRT1. These findings suggest that GXBD mitigates atherosclerosis in this murine model through a coordinated remodeling of the gut microbiota-bile acid-host axis, supporting its potential as a microbiome-informed, multi-component adjunct for cardiometabolic health.},
}

@article {pmid41704685,
year = {2026},
author = {Andus, I and Büttner, J and Bochow-Fitzner, B and Tacke, F and Jochum, C},
title = {Intestinal permeability correlated with chronic fatigue in a patient with long COVID-A case report and overview of the literature.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1725242},
pmid = {41704685},
issn = {2296-858X},
abstract = {BACKGROUND: Long COVID is a complex condition characterized by persistent symptoms such as chronic fatigue, cognitive impairment, and autonomic dysfunction. Emerging evidence suggests that the gut may play a role in the pathophysiology of long COVID, potentially contributing to systemic inflammation and symptom severity. Prior studies indicate intestinal permeability (IP) alteration in patients with long COVID. To date, there have been no reports on the assessment of intestinal permeability via carbohydrate absorption in individuals with long COVID.

CASE PRESENTATION: We present a 60-year-old female with long COVID who exhibited chronic fatigue and autonomic dysfunction for more than 3 years following SARS-CoV-2 infection. IP was assessed at five time points using a carbohydrate absorption test. Results revealed significantly elevated lactulose/mannitol (L/M) ratios during episodes of symptom exacerbation, including a second SARS-CoV-2 infection. Notably, clinically observed improvement in fatigue correlated with a reduction in IP. A probiotic regimen with Bacillus coagulans and Bacillus subtilis, combined with a second intervention using medicinal clay, led to further clinical improvement.

CONCLUSIONS: This case report demonstrates a correlation between intestinal permeability alterations and long COVID symptom severity. Notably, to our knowledge, this is the first report assessing intestinal permeability in a long COVID patient using a carbohydrate absorption-based permeability test. It reinforces the emerging link between gut barrier integrity and long COVID pathophysiology and emphasizes the need for further studies to assess IP as a potential disease marker. Furthermore, the observed improvement with probiotic therapy highlights the need for further research into microbiome-targeted interventions for long COVID management. Larger studies are required to explore the mechanistic link between gut permeability and long COVID pathophysiology.},
}

@article {pmid41704669,
year = {2026},
author = {Yelleti, G and Maripini, N and Bolar Suryakanth, V},
title = {Preeclampsia and environmental epigenomics: the emerging role of air pollution, gut microbiome, and maternal exposures in disease programming.},
journal = {Environmental epigenetics},
volume = {12},
number = {1},
pages = {dvag001},
pmid = {41704669},
issn = {2058-5888},
abstract = {Preeclampsia (PE) remains a major contributor of maternal and fetal morbidity and mortality worldwide, affecting 2%-8% of pregnancies. While genetic predisposition, placental dysfunction, and angiogenic imbalance remain central to PE pathophysiology, emerging observational evidence suggests potential associations between environmental factors, epigenetic modifications, and PE development. This review consolidates available research linking environmental exposures, particularly air pollution, maternal gut microbiome composition, and dietary habits, with changes in epigenetic markers during pregnancy that may influence PE susceptibility. We synthesize findings from epidemiological studies, mechanistic research, and biomarker studies across this research area. However, definitive causal evidence linking specific environmental exposures to PE through epigenetic mechanisms remains limited. The majority of existing studies employ observational designs or focus on biological mechanisms; well-designed prospective cohorts incorporating direct environmental measurements and randomized intervention trials are lacking. Circulating biomarkers, including microRNAs and DNA methylation patterns, show associations with both PE status and prior environmental exposure, providing biological support for the concept that environmental factors may influence PE development. The maternal gut microbiome demonstrates dysbiosis in PE patients, and mechanistic studies in animal models suggest that microbiota-derived metabolites may influence placental development through epigenetic pathways; however, clinical evidence in humans remains preliminary. Integration of environmental exposure assessment with multi-omics profiling in large prospective studies is necessary to establish whether environmental factors causally contribute to PE pathogenesis. Future research combining detailed environmental characterization, longitudinal epigenomic profiling, and rigorous causal inference methods will be essential to translate these mechanistic insights into prevention and therapeutic strategies.},
}

@article {pmid41704661,
year = {2026},
author = {Coraça-Huber, DC and Spiegel, C and Moraes, BF and Arora, R},
title = {Beyond the germ: Rethinking implant-related infections as a host-microbiota-biomaterial ecosystem.},
journal = {Biofilm},
volume = {11},
number = {},
pages = {100352},
pmid = {41704661},
issn = {2590-2075},
abstract = {Implant-related infections remain one of the most challenging complications in modern medicine, often leading to implant failure, revision surgery, significant patient morbidity and high rate of patient mortality. Traditionally framed within the germ theory paradigm, their pathogenesis has been attributed primarily to microbial contamination and biofilm formation. However, growing evidence reveals a far more complex picture in which infection susceptibility emerges from the dynamic interplay between host biology, microbiota composition, biomaterial properties, and environmental influences . Host immune tone, metabolic status, and systemic exposures shape the tissue environment in ways that either resist or facilitate microbial colonization. The microbiota contributes to this balance not only by mediating immune responses and providing colonization resistance but also through metabolites and detoxification mechanisms that influence local and systemic immunity. Biomaterials themselves are active participants in this ecosystem: metal ion release, corrosion, and surface properties modulate both host responses and microbial behavior. A particularly intriguing concept is the potential dual role of biofilms - not only as pathogenic reservoirs but also as detoxification systems that sequester metal ions and buffer oxidative stress at the host-implant interface. Recognizing this duality reframes biofilms as biological structures that may, in part, participate in protective containment, albeit at the cost of sustaining low-grade inflammation and risk of septicemia. Looking forward, the integration of systems biology approaches promises to transform our understanding and management of implant-associated infections. Multi-omics profiling, predictive modeling, engineered probiotics, dietary modulation, and novel implant surface designs represent emerging strategies that target the entire host-microbe-material interface. By bridging insights from immunology, microbiome science, biomaterials research, and digital technologies, a new paradigm is emerging - one that views infection prevention and treatment not simply as microbial eradication, but as the cultivation of a resilient biological and material ecosystem around the implant.},
}

@article {pmid41704660,
year = {2026},
author = {Visser, K and Wang, Y and Laman, JD and de Koning, ME and Xu, X and Vakhtin, AA and Mayer, AR and Kremer, D and Bakker, SJL and van Goor, H and van der Naalt, J and Bourgonje, AR and van der Horn, HJ},
title = {Stable serum peptidoglycan fragment levels do not support leaky gut in the acute phase or at one month following "mild" traumatic brain injury: A preliminary study.},
journal = {Brain, behavior, & immunity - health},
volume = {52},
number = {},
pages = {101192},
pmid = {41704660},
issn = {2666-3546},
abstract = {The gut-brain axis is increasingly recognized as contributor to the pathophysiology of brain disorders, in part through its influence on inflammation. Impaired gut health can lead to so-called leaky gut, allowing bacterial cell wall fragments such as peptidoglycan-derived muramyl dipeptide (MDP) to translocate to the circulation. MDP can activate microglia, key mediators of neuroinflammation, via the intracellular receptor nucleotide-binding oligomerization domain-containing protein 2 (NOD2). Although neuroinflammation is a hallmark of "mild" traumatic brain injury (mTBI), the link between leaky gut and mTBI remains largely unexplored. This preliminary prospective study investigated whether mTBI leads to increased MDP levels and NOD2 activation in the acute phase (N = 246; median 106 min post-injury) and at a ∼1-month follow-up visit (N = 140; median 32 days) in an emergency department cohort, relative to healthy controls (HC; N = 31, with N = 26 at ∼1-month). Serum MDP concentration was measured using an indirect competitive ELISA. Engagement of the pro-inflammatory nuclear factor (NF)-κB pathway was measured in NOD2-transfected cells. Additionally, blood interleukin (IL)-6 and IL-10 levels were quantified. Clinical outcome was measured at six months post-injury using the extended Glasgow Outcome Scale and a symptom questionnaire. Linear mixed effects models showed that concentrations of MDP remained stable across visits in both mTBI and HC (P = 0.62), with no significant main effect of group (P = 0.16) or group × visit interaction (P = 0.25). In contrast, for engagement of NF-κB signaling in NOD2-expressing cells, a significant group × visit interaction (P = 0.004) was observed, with an elevation in mTBI relative to HC at ∼1-month post-injury (P = 0.01, Cohen's d = 0.48), but not in the acute phase (P = 0.22, d = 0.22). This elevation was associated with higher IL-6 (β = 0.16, P = 0.02) and IL-10 (β = 0.17, P = 0.006) levels in the acute phase. No associations with clinical outcome were observed. In conclusion, our preliminary null findings for serum MDP do not directly support the emergence of leaky gut in either the acute phase or at ∼1-month following mTBI. However, transient increases in MDP occurring during the first month cannot be ruled out based on our findings. Increased engagement of the NF-κB pathway in NOD2-expressing cells likely reflects (damage-associated) mechanisms other than MDP. Assessment of NF-κB signaling may serve as a useful marker for studying chronic (neuro)inflammation following mTBI, complementing interleukin responses in the acute phase, an avenue warranting further investigation.},
}

@article {pmid41704593,
year = {2026},
author = {El Houssni, I and Zahidi, A and Mortada, S and El-Mrabet, A and Faouzi, MEA and Haoudi, A and Khedid, K and Hassikou, R},
title = {Wheat landraces and microbiome endophytic phytases: In vitro/in silico study for iron bioavailability.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100363},
pmid = {41704593},
issn = {2666-5662},
abstract = {This study proposes an innovative biotechnological strategy to enhance iron bioavailability in wheat by leveraging the untapped potential of phytase-producing endophytic lactic acid bacteria and yeasts isolated from Moroccan wheat landraces. The research was predicated on the hypothesis that the endophytic microbiota of indigenous wheat landraces possesses a specialized and highly efficient catalytic profile capable of surpassing the structural and kinetic limitations of endogenous wheat enzymes. To validate this hypothesis, the investigation involved: (i) molecular characterization of endophytes via 16S and 18S rRNA sequencing; (ii) quantification of specific phytase activity for ferric phytate degradation; (iii) identification of phytase-encoding genes; and (iv) molecular docking simulations to elucidate enzyme-substrate interactions. Findings confirmed the hypothesis, demonstrating that these microbial phytases possess a superior capacity for ferric phytate hydrolysis, significantly exceeding endogenous wheat activity. Three distinct microbial phytase classes were identified - Histidine Acid Phosphatase (HAP), Protein Tyrosine Phosphatase (PTP), and β-Propeller Phosphatase (βPP) - which complement the native Purple Acid Phosphatase (PAP) found in wheat. Molecular docking results further substantiated the hypothesis by revealing high binding affinities and identifying key catalytic residues within these microbial taxa. These results suggest that the identified strains can be utilized as bio-priming agents or functional fermentation starters to naturally biofortify wheat-based products, providing a scalable biotechnological solution to mitigate global iron deficiency.},
}

@article {pmid41704576,
year = {2026},
author = {Wang, Y and Luo, X and Ping, M and Wang, H and Bao, Y and Zhao, C and Li, X and Chen, J},
title = {Ecological composite fertilizer application enhances wheat yield and optimizes rhizosphere microbial community under reduced fertilization.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1771450},
pmid = {41704576},
issn = {1664-462X},
abstract = {Excessive fertilization poses a major threat to sustainable agriculture, resulting in resource waste and environmental degradation. The ecological composite fertilizer (ECF) combined with fertilizer reduction represents a promising strategy to improve rhizosphere microbial diversity in wheat systems. A field experiment, containing six treatments, namely traditional compound fertilizer (TF, applied at the conventional rate) with a 10% reduction (TF90), TF90 plus ECF application (TF90+ECF), TF with a 15% reduction (TF85), TF85 plus ECF application (TF85+ECF), TF with a 20% reduction (TF80), and TF80 plus ECF application (TF80+ECF), was conducted to explore the influences of fertilizer reduction combined with ECF application on wheat yield and rhizosphere soil microbial diversity. Results showed that the TF85+ECF treatment achieved the highest wheat yield at 8,717.33 kg ha[-1], which was significantly greater than all other treatments and represented a 30.63% increase over the TF85 treatment. The TF85+ECF group significantly enhanced the activities of the carbon and nitrogen cycling enzymes β-1, 4-glucosidase glucosidase (BG) and urease (UE), and increased the abundances of the functional genes cbbLR and amoA. In the +ECF treatment groups (TF90+ECF, TF85+ECF, and TF80+ECF), linear discriminant analysis effect size (LEfSe) and specialization-occupancy (SPEC-OCCU) analyses identified keystone microbial taxa, including positively correlated taxa with biocontrol and metabolic versatility (e.g., Trichoderma, Solicoccozyma) and negatively correlated potential pathogens (e.g., Alternaria). Co-occurrence network analysis revealed that the TF85+ECF group streamlined bacterial network architecture while enhanced fungal network complexity and connectivity. Mantel tests and correlation analyses indicated that soil organic carbon, BG activity, and cbbLR gene abundance were significantly linked to microbial community structure, and keystone taxa were strongly correlated with soil nutrient cycling functions. Our findings provide a microbiome-based strategy and a novel perspective for sustainable wheat production and targeted microbial management in agriculture.},
}

@article {pmid41704320,
year = {2025},
author = {Mason, L and Osire, E and Awiti, E and Akinyi, C and Akello, C and Zulaika, G and Otieno, FO and Phillips-Howard, PA and Mehta, SD},
title = {"Should I tell him I have something in my vagina?" Female sex workers' perceptions and experiences of using a menstrual cup, and client reactions: A qualitative study in Western Kenya.},
journal = {Frontiers in reproductive health},
volume = {7},
number = {},
pages = {1740096},
pmid = {41704320},
issn = {2673-3153},
abstract = {INTRODUCTION: The menstrual cup is worn intravaginally, holding blood up to 12 h before emptying and reinserting. It offers protection from sexually transmitted infections and bacterial vaginosis, whilst preserving a Lactobacillus crispatus-dominant vaginal microbiome. The menstrual disc, a type of menstrual cup, is positioned near the cervix and can remain in place during sex, enabling female sex workers (FSWs) to avoid unsafe practices to conceal menstruation during work. In this study, we aim to examine the perceptions and experiences of a convenience sample of FSWs 6 months after they received a menstrual disc, along with client views.

METHODS: In a qualitative design, our Kenyan study recruited 38 FSWs in 4 focus group discussions (FGDs) and 86 clients in 9 FGDs. Using a semi-structured guide, a Kenyan moderator and note-taker facilitated audio-recorded discussions. Following translation and transcription, the discussions were analysed using deductive thematic analysis.

RESULTS: Six themes emerged: Anticipation and reaction to seeing the menstrual cup, Apprehension and determination to use, Benefits, Challenges, Secrecy, and Use during sex. Some FSWs were able to insert the cup on initial attempt, typically others encountered discomfort, pain, or misalignment during insertion or difficulty in removing. By the end of the third month, the majority were using the cup without experiencing any leakage, pain, or concerns. Benefits noted included ease, convenience, reduced leakage, and comfort. Financial advantage over pads and ability to work regularly were also noted. Nearly all FSWs used the cup during sex, despite prior anxiety that a client would detect it and react negatively. In three instances, the FSWs reported that a client "may" have felt the disc, whilst noting just two clients "may" have felt something. None reacted badly. In summing up their experience, the FSWs spoke very positively about the disc, with the intention to keep wearing it in the future. Many clients were supportive of the disc but did not want to know whether an FSW was wearing it.

CONCLUSIONS: The FSWs quickly adapted to using the disc, finding it a comfortable, reliable menstrual product with financial advantages. With clients remaining mostly unaware of its use, the FSWs enthusiastically embraced the disc with the intention to keep using it. These positive outcomes have implications for future scale-up and roll-out to other vulnerable female populations.},
}

@article {pmid41704316,
year = {2026},
author = {Wang, Y and Yang, Z and Liu, C and Liu, Y and Bai, Z and Miao, W and Zhang, T and Wang, Y and Li, X and Lai, Z and Xu, J},
title = {Gut microbial signatures of advanced hepatocellular carcinoma and their potential diagnostic value.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1760859},
pmid = {41704316},
issn = {1664-302X},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) is a prevalent and lethal malignancy worldwide. Gut microbiota play crucial roles in liver disease progression and may offer noninvasive diagnostic value, yet microbial signatures specific to advanced HCC remain unclear.

METHODS: Seventy-six participants, including early-stage HCC (HCC12), advanced HCC (HCC34), liver cirrhosis (LC), and healthy controls (CG), were prospectively enrolled. Fecal samples underwent 16S rRNA sequencing to characterize microbial diversity and community composition. Differential taxa were identified using Kruskal-Wallis tests, linear discriminant analysis effect size (LEfSe), and zero-inflated negative binomial regression (ZINB). Machine learning models were constructed using clinical features, representative microbiota, and their combination. External validation was performed using 74 published HCC cases.

RESULTS: Advanced HCC exhibited reduced microbial richness and diversity, accompanied by substantial community structure alterations. Enterococcus, Enterococcaceae, Enterobacteriaceae, and Escherichia-Shigella were enriched in HCC34, whereas Ruminococcus and Blautia were depleted. These taxa correlated strongly with liver injury markers and HCC-specific biomarkers. The extreme gradient boosting model showed high diagnostic potential when using either clinical or microbial features alone, while the combined model achieved improved accuracy (AUC = 1.0 in the primary test set). External validation supported the good generalizability of the model (AUC = 1.0 in the external cohort). Feature importance analysis identified Enterococcus as the most influential discriminator of advanced HCC.

CONCLUSION: This study reveals distinct gut microbial signatures associated with advanced HCC and suggests that Enterococcus may serve as a potentially important microbial marker linked to disease severity. Integrating gut microbiota profiling with clinical features may offer a promising noninvasive strategy for the accurate identification of advanced HCC and provides hypothesis-generating insights for microbiome-based therapeutic interventions.},
}

@article {pmid41580828,
year = {2026},
author = {Yi, S and Zhuang, X and Luo, L and Fu, L and Dong, Z and Wang, K and Jiang, Y and Yang, X and Hei, F},
title = {Gut microbiota and metabolites in acute lung injury: mechanisms and therapeutic perspectives.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {82},
pmid = {41580828},
issn = {1465-993X},
support = {Grant CX24PY21//Chinese Institutes for Medical Research/ ; },
abstract = {UNLABELLED: Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), represent a clinical syndrome with high mortality, characterized by excessive pulmonary inflammation and oxidative stress. Despite advancements in conventional supportive care, mortality rates for ALI/ARDS remain persistently high (30%-50%). In recent years, increasing attention has focused on the regulatory mechanisms of the gut microbiota and their metabolites in ALI through the bidirectional ‘gut-lung axis’ interaction. This paper systematically reviews the mechanisms by which gut dysbiosis exacerbates lung inflammation and barrier damage via immune cell migration, inflammatory pathway activation, and metabolite imbalance. It also explores the potential of microbiome-based interventions—including probiotics, fecal microbiota transplantation (FMT), and dietary modification—for ALI treatment. This review not only elucidates the complex link between the gut microbiota and lung disease but also provides a theoretical basis for developing novel diagnostic and therapeutic approaches targeting the gut-lung axis. These insights hold significant implications for improving ALI patient prognosis and advancing precision medicine.

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

@article {pmid41704312,
year = {2026},
author = {Zhang, X and Sha, L and Mai, Y and Xu, J and Nizamani, MM and Fang, F},
title = {Coastal gradients and human disturbance shape bacterial and fungal rhizosphere microbiomes of Heliotropium arboreum in Hainan, China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1774048},
pmid = {41704312},
issn = {1664-302X},
abstract = {Coastal ecosystems in Hainan exhibit steep sea-land gradients in salinity and nutrient availability, yet the rhizosphere microbiome of the pioneer shrub Heliotropium arboreum remains poorly understood. We investigated bacterial and fungal communities across seven coastal sites using replicated transects from seaward to shrub-belt to inland zones, and linked community patterns to soil physicochemical properties and human disturbance. Bacterial communities consistently showed higher richness, evenness, and compositional stability than fungal communities. Alpha diversity increased from seaward to inland zones for both groups, with a stronger gradient in fungi. Community composition was dominated by Proteobacteria and Planctomycetota in bacteria and Ascomycota in fungi, with distinct dominant genera across zones and sites. β-diversity analyses revealed clear differentiation of microbial communities among zones and locations, with fungi showing stronger turnover and site separation than bacteria, indicating higher sensitivity to environmental filtering and disturbance. Redundancy analysis indicated that fungal communities were primarily structured by available potassium, total nitrogen, and soil organic carbon, whereas bacterial communities were most strongly associated with soil pH (7.468-9.613 across sites) and nitrate concentrations. Functional profiling suggested complementary roles in decomposition and nitrogen cycling, and human-disturbed sites showed higher predicted pathogenic potential. Overall, H. arboreum hosts an environmentally filtered rhizosphere microbiome shaped jointly by coastal gradients and disturbance, with fungi responding more strongly than bacteria to spatial and environmental variation.},
}

@article {pmid41704310,
year = {2026},
author = {Romero-Rivera, M and Fernández-de-Bobadilla, MD and Beltrán, M and Del Campo, R and Avendaño-Ortiz, J and Herencias, C},
title = {Genome assembly and functional predation analysis of novel Bdellovibrio isolates from human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752098},
pmid = {41704310},
issn = {1664-302X},
abstract = {INTRODUCTION: Predatory bacteria of the Bdellovibrio and like organisms (BALOs) have long been postulated as living antimicrobials, yet their occurrence and ecological roles within human-associated microbiota have remained uncertain due to the absence of culturable human-derived isolates. Here, we report the first successful isolation and comprehensive characterization of viable Bdellovibrio bacteriovorus from human fecal samples.

METHODS: Targeted enrichment was applied to five pooled fecal samples to facilitate predator recovery. We performed whole-genome sequencing on the isolates and conducted comparative genomics across 162 publicly available Bdellovibrio genomes. Additionally, pangenome analysis of 22 high-quality genomes and phenotypic assays against clinical pathogens were conducted to assess genomic diversity, prey specificity, and biosafety profiles.

RESULTS: Despite extremely low natural abundance, targeted enrichment recovered predators in two of five pooled samples, which produced characteristic lytic plaques. Sequencing revealed >99% average nucleotide identity to reference strain HD100 with only 26 core single-nucleotide polymorphisms across both isolates, indicating minimal divergence between human-associated and environmental lineages. Comparative genomics showed that only 10.4% of public genomes fulfill criteria for B. bacteriovorus sensu stricto. Pangenome analysis revealed a stable, highly conserved core (~2,500-2,650 genes) and an expanding accessory genome. Phenotypically, the human-derived isolates displayed narrower prey ranges concentrated on Pseudomonas spp., including multidrug-resistant clinical strains, and no acquired virulence factors were detected.

DISCUSSION: Collectively, these findings suggest predation in the human gut and that viable Bdellovibrio could be natural, genomically conserved members of the intestinal ecosystem. This work advances a testable keystone-predator framework for human microbiome ecology and opens an ecologically informed therapeutic pathway in which human-associated Bdellovibrio may help control multidrug-resistant pathogens while supporting microbiota homeostasis.},
}

@article {pmid41704005,
year = {2026},
author = {Shi, W and Xie, R and Zhang, H and Su, S and Tan, J and Sun, Y and Guo, J},
title = {Additive effects of nitrogen deficiency and water stress on reassembly of the rhizosphere microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71010},
pmid = {41704005},
issn = {1469-8137},
support = {32372808//National Natural Science Foundation of China/ ; 32202468//National Natural Science Foundation of China/ ; 32102401//National Natural Science Foundation of China/ ; JCYJ20220530145216037//Shenzhen Science and Technology Program/ ; JCYJ20230807111217035//Shenzhen Science and Technology Program/ ; JCYJ20250604174526034//Shenzhen Science and Technology Program/ ; JCYJ20250604174524032//Shenzhen Science and Technology Program/ ; 2024SKLBC-KF05//State Key Laboratory of Biocontrol (Sun Yat-sen University)/ ; },
abstract = {Rhizosphere microbial symbioses confer advantages to host plants under environmental stress. However, the effect of multiple stressors on triggering rhizomicrobiome reassembly remains poorly understood, as stress effects can be additive, antagonistic, or synergistic. Tomato was used as a model plant to investigate the interactions between nitrogen deficiency and two contrasting water stresses (drought and waterlogging) on the reassembly of rhizosphere bacterial and fungal communities through quantitative microbiome profiling. The combination of nitrogen deficiency with drought or waterlogging increased α-diversity, except for bacteria under the combined stress of nitrogen deficiency and drought. Nitrogen deficiency generally reduced the abundance of taxonomic groups, with this reduction exacerbated under drought but reversed under waterlogging, particularly for bacteria. Similar results were observed for the abundance of bacterial functional guilds and dominant microbial taxa. The interactive effects of nitrogen deficiency and water stress on microbial α-diversity, as well as on the abundance of taxonomic groups, functional guilds, and dominant taxa were predominantly additive. Additive interactions dominated rhizomicrobiome reassembly in response to nitrogen deficiency and water stress, with distinct response patterns observed between bacterial and fungal communities. This study provides new insights into rhizomicrobiome dynamics under multiple abiotic stressors.},
}

@article {pmid41703989,
year = {2026},
author = {Wang, Q and Hu, Z and Wang, Y and Guo, S and Zhang, X and Ren, Y and Li, J and Li, X and Cui, H},
title = {Lactobacillus paragasseri LG-1 Alleviates Urticaria-Like Symptoms in Mice via Modulation of Gut Microbiota, Hypoxanthine and Uric Acid.},
journal = {Microbial biotechnology},
volume = {19},
number = {2},
pages = {e70316},
doi = {10.1111/1751-7915.70316},
pmid = {41703989},
issn = {1751-7915},
support = {202303021221224//Fundamental Research Program of Shanxi Province/ ; J202301E036//Bethune Charitable Foundation/ ; 2023RC009//The Youth Science and Technology Innovation Talent Project Four Batches of Shanxi Province/ ; 2025C02080//The Key Research and Development Plan of Zhejiang Province/ ; 2021DG700024-ZZ202210//The State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ ; },
mesh = {Animals ; *Uric Acid/blood/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Lactobacillus/growth & development/metabolism/physiology ; *Hypoxanthine/blood/metabolism ; Disease Models, Animal ; *Probiotics/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Female ; DNA, Ribosomal/chemistry/genetics ; },
abstract = {Chronic Spontaneous Urticaria (CSU) is an immunoinflammatory disorder with complex pathogenesis. Emerging evidence implicates that gut microbiota dysbiosis plays a pivotal role in this pathological network. Integrated 16S rRNA sequencing and untargeted metabolomics revealed distinct CSU-associated signatures, including significant reductions in Lactobacillus abundance and elevated serum uric acid (UA) and hypoxanthine levels. Functional screening identified Lactobacillus paragasseri LG-1 from breast milk as a potent purine-metabolising strain, demonstrating significant hypoxanthine and UA degradation in vitro. In an ovalbumin (OVA)-induced urticaria murine model, LG-1 administration demonstrated marked reductions in serum UA and hypoxanthine concentrations, alleviated clinical manifestations, and suppressed inflammation via TLR4-NF-κB pathway inhibition. Moreover, it modulated gut microbial composition by promoting Lactobacillus proliferation while restraining pathogenic bacteria. These findings collectively established that LG-1 exerted dual therapeutic effects through uric acid/hypoxanthine degradation and microbiome remodelling. Our study provides compelling evidence for microbiome-targeted strategies in CSU management, highlighting LG-1 as a promising therapeutic candidate.},
}

Animals
*Uric Acid/blood/metabolism
*Gastrointestinal Microbiome
Mice
*Lactobacillus/growth & development/metabolism/physiology
*Hypoxanthine/blood/metabolism
Disease Models, Animal
*Probiotics/administration & dosage
RNA, Ribosomal, 16S/genetics
Female
DNA, Ribosomal/chemistry/genetics

@article {pmid41703963,
year = {2026},
author = {Skoog, T and Yang, Y and Olah, P and Katayama, S and Karisola, P and Smith, C and Weidinger, S and Barker, J and Lauerma, A and Andersson, B and Homey, B and Fyhrquist, N and Kere, J and Alenius, H and , },
title = {Integrated Methylome-Transcriptome Analysis Reveals Epigenomic Remodeling and Rho GTPase-Linked Immune-Epithelial Crosstalk in Atopic Dermatitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70259},
pmid = {41703963},
issn = {1398-9995},
support = {//Seventh Framework Programme/ ; //Innovative Medicines Initiative/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by immune dysregulation and epithelial barrier dysfunction. Although transcriptional changes in AD skin are increasingly well characterized, DNA methylation patterns remain less well understood.

METHODS: Here, we present an integrated analysis of matched DNA methylomes, transcriptomes, and microbiomes from lesional (n = 40), adjacent non-lesional (n = 38), and healthy control (n = 40) skin, using complementary cell-type-adjusted models.

RESULTS: We identified thousands of differentially methylated regions (DMRs) across all pairwise contrasts (lesional vs. healthy: n = 13,514; lesional vs. non-lesional: n = 4591; non-lesional vs. healthy: n = 1716), including both hyper- and hypo-methylated regions with balanced effect sizes. A core subset of DMRs persisted after methylation-based adjustment, whereas the extensive lesional vs. non-lesional set was largely composition-driven. Integration with transcriptomic co-expression networks linked DMRs to immune-epithelial modules, and 225 DMR-gene pairs showed significant anti-correlation (FDR < 0.05). Lesional skin with dominant Staphylococcus aureus colonization differed at 92 DMRs compared with absent-colonized skin, of which 70 also overlapped with local severity. Pathway analyses consistently highlighted Rho GTPase and actin-junctional programs across analytic layers, suggesting that Rho GTPase signaling is a central integrator of immune, epithelial, and microbial interactions in AD.

CONCLUSIONS: Our study underscores the importance of epigenomic remodeling in AD and highlights potential avenues for precision intervention in chronic inflammatory skin disease.},
}

@article {pmid41703894,
year = {2026},
author = {Kamath, S and Chan, NSL and Joyce, P},
title = {GLP-1 agonists and the gut microbiome: A bidirectional relationship.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70487},
pmid = {41703894},
issn = {1365-2125},
support = {2022-CF-EMCR-004-25314//Hospital Research Foundation/ ; },
abstract = {Glucagon-like peptide-1 (GLP-1) receptor agonists have transformed the management of type 2 diabetes mellitus (T2DM) and obesity, yet their interactions with the gut microbiome remain an emerging frontier in pharmacological and metabolic research. Mounting evidence suggests that the gut microbiota modulates GLP-1 secretion via microbial metabolites, including short-chain fatty acids and bile acid derivatives, while GLP-1 agonists reciprocally reshape microbial composition, influencing metabolic outcomes beyond their classical incretin functions. This bidirectional interplay has profound implications for precision medicine, as gut microbial signatures have been associated with variability in therapeutic response, raising the possibility that microbiome features could contribute to response stratification in future studies. Advances in pharmacomicrobiomics, multiomics integration and computational modelling now enable a more refined dissection of these interactions, illuminating potential microbial targets for intervention. Study discrepancies may arise from variations in host diet, baseline microbiome composition and genetic factors influencing GLP-1 signalling. Future studies should incorporate stratified analyses accounting for these confounders to understand causative mechanisms. This review collates current evidence on the microbiome-mediated modulation of GLP-1 dynamics, evaluates the pharmacomicrobiomic impact of GLP-1 agonists and outlines future research directions at the interface of gut microbiota and incretin biology. By unravelling the complexities of this host-microbe-drug axis, the field moves closer to a paradigm of personalized metabolic medicine, where future GLP-1 therapeutic strategies may consider host metabolic and microbial context, optimizing efficacy and minimizing variability in patient response.},
}

@article {pmid41703879,
year = {2026},
author = {Gialluisi, K and De Vero, L and Petruzzino, G and Verrone, L and Perrone, G and Moretti, A and Capozzi, V and Ferrara, M},
title = {Cryopreservation of fermented table olives microbiomes: an integrative case study on viability, functional stability, and biobanking applications.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118430},
doi = {10.1016/j.foodres.2026.118430},
pmid = {41703879},
issn = {1873-7145},
mesh = {*Cryopreservation/methods ; *Olea/microbiology ; *Microbiota ; Fermentation ; Biological Specimen Banks ; Cryoprotective Agents ; Microbial Viability ; *Fermented Foods/microbiology ; Glycerol ; *Food Microbiology ; Dimethyl Sulfoxide ; Food Storage ; Iridoids ; },
abstract = {Microorganisms and their assembly in composite microbiomes play a crucial role in food fermentation, significantly influencing product quality, safety, and nutritional value. Preserving these microbiomes in culture collections is essential for maintaining biodiversity and supporting bio-based innovation in sustainable food systems. However, the long-term conservation of complex microbiomes remains challenging due to microbial heterogeneity and sensitivity to preservation methods. This study evaluated the effectiveness of two cryopreservation protocols for the long-term storage of microbiomes from naturally fermented table olives (cv. Leccino), a traditional Mediterranean diet staple food. Glycerol and dimethyl sulfoxide (DMSO), both at 15% (v/v), were used as cryoprotectants and microbiome samples were stored at -140 °C. Microbial viability, taxonomic composition, and metabolic functionality were assessed over one year using culture-dependent techniques, RNA-based metabarcoding, and Biolog® EcoPlate profiling. Moreover, the oleuropein degradation was evaluated in microbiome samples recovered after one year of cryopreservation. Results indicated that the viability of the microbial consortium slightly decreased, regardless of the cryoprotectant used, and no significant changes in the metabolic profile were observed. In addition, the metabarcoding analysis revealed no significant differences in relative abundances after the storage period. The study confirmed the effectiveness of the cryopreservation method, proper maintenance of the microbial consortium viability and functionality after long-term storage. These findings support the feasibility of microbiome biobanking for fermented foods and highlight the importance of tailored preservation strategies to ensure the stability and functionality of microbial consortia. This approach contributes to the conservation of microbial resources, reproducibility in microbiome science, and the development of high-quality standardisation in fermented products.},
}

*Cryopreservation/methods
*Olea/microbiology
*Microbiota
Fermentation
Biological Specimen Banks
Cryoprotective Agents
Microbial Viability
*Fermented Foods/microbiology
Glycerol
*Food Microbiology
Dimethyl Sulfoxide
Food Storage
Iridoids

@article {pmid41703844,
year = {2026},
author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y},
title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118381},
doi = {10.1016/j.foodres.2026.118381},
pmid = {41703844},
issn = {1873-7145},
mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; },
abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.},
}

*Fermentation
*Phenols/metabolism/analysis
*Plant Leaves/microbiology/metabolism/chemistry
*Microbiota
*Tea/microbiology/chemistry/metabolism
*Metabolome
Anaerobiosis
Metabolomics/methods
Bacteria/metabolism
*Camellia sinensis/microbiology
Flavonoids/metabolism

@article {pmid41703840,
year = {2026},
author = {Mo, Q and Qin, M and Liang, H and Wei, L and Li, Y and Qin, Y and Tang, L and Liang, J and Qian, C and Liang, Y and Luo, S and Wei, Y and Kong, L and Cheng, J},
title = {Lactiplantibacillus pentosus JWN01 and Lactiplantibacillus plantarum JWN02 attenuate renal fibrosis and pathological autophagy in hyperuricemic nephropathy via gut-kidney axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118376},
doi = {10.1016/j.foodres.2026.118376},
pmid = {41703840},
issn = {1873-7145},
mesh = {Animals ; *Probiotics/pharmacology ; *Hyperuricemia/complications ; *Autophagy/drug effects ; Gastrointestinal Microbiome ; Fibrosis ; Mice ; *Kidney Diseases/pathology ; *Kidney/pathology ; Male ; Uric Acid/blood ; Humans ; *Lactiplantibacillus plantarum ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Hyperuricemic nephropathy (HN) is a worldwide metabolic disorder marked by uric acid (UA) imbalance and renal tubulointerstitial fibrosis, yet therapies that both lower UA and prevent fibrosis remain limited. Targeting the gut-kidney axis with probiotics is a promising strategy, but most candidates are food-derived and not human-adapted. We isolated two Lactiplantibacillus strains, Lactiplantibacillus pentosus JWN01 and Lactiplantibacillus plantarum JWN02, from the healthy newborn skin representing a relatively unperturbed, early-life human microbiome. In vitro, these two human-derived probiotic strains showed robust survival under simulated gastrointestinal conditions and efficiently degraded UA precursors (inosine, guanosine). In Uox[-]/[-] mice, oral supplementation with these probiotics for 12 weeks significantly reduced serum UA levels, improved renal function, and regulated key urate transporters, such as ABCG2, GLUT9, and OAT1, in kidney and ileum. The treatment also reinforced intestinal barrier integrity by upregulating tight junction proteins (Claudin-1, Occludin, ZO-1) and alleviated renal fibrosis by inhibiting the TGF-β1/SMAD3 signaling pathway. Gut microbiome analysis showed that JWN01 and JWN02 administration reshaped the microbial composition by decreasing potentially harmful genera (Mammaliicoccus, Staphylococcus, Corynebacterium) and enriching beneficial taxa (Muribaculaceae, Lactiplantibacillus, Akkermansia). This microbial shift was accompanied by partial restoration of disturbed gut metabolites, including Coenzyme Q10 and p-cresol sulfate. Proteomic profiling of proximal tubules, along with subsequent validation, demonstrated that intervention with JWN01 and JWN02 suppressed pathological autophagy-evidenced by reduced ULK1, LC3A/B, and Beclin-1 expression, and increased P62 levels. Notably, the potential inflammation-related biomarkers MSP and IBA1, elevated in HN, were reversed following probiotic treatment. Together, these findings indicate that L. pentosus JWN01 and L. plantarum JWN02 confer protective effects against HN through modulation of the gut-kidney axis, supporting their potential as functional probiotics for dietary management of hyperuricemia.},
}

Animals
*Probiotics/pharmacology
*Hyperuricemia/complications
*Autophagy/drug effects
Gastrointestinal Microbiome
Fibrosis
Mice
*Kidney Diseases/pathology
*Kidney/pathology
Male
Uric Acid/blood
Humans
*Lactiplantibacillus plantarum
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid41703759,
year = {2026},
author = {Gigl, F and Abdullahi, M and Benkwitz-Bedford, S and Eastwood, N and Zhou, J and Hollert, H and Orsini, L},
title = {Challenging Evolutionary Paradigms: Daphnia Populations Resurrected From Unpolluted Environments Show Enhanced Detoxification Ability to Aromatic Pollutants.},
journal = {Molecular ecology},
volume = {35},
number = {4},
pages = {e70272},
doi = {10.1111/mec.70272},
pmid = {41703759},
issn = {1365-294X},
support = {101112877//Horizon Europe HORIZON-IA/ ; 101057014//Horizon Europe Partnership for the assessment of Risk of Chemicals/ ; //Goethe University Academy for Early Career Researchers/ ; //RobustNature Excellence Cluster Initiative/ ; },
mesh = {Animals ; *Daphnia/genetics/drug effects/microbiology ; *Water Pollutants, Chemical/toxicity ; Gastrointestinal Microbiome/drug effects/genetics ; *Polycyclic Aromatic Hydrocarbons/toxicity ; Transcriptome ; Phenanthrenes/toxicity ; Inactivation, Metabolic/genetics ; *Biological Evolution ; },
abstract = {Understanding how organisms respond to chemical stress requires disentangling genetically encoded (constitutive) adaptations from environmentally induced (plastic) responses. This challenge is particularly acute for polycyclic aromatic hydrocarbons (PAHs), widespread aquatic pollutants with well-documented toxicity, where mechanisms of tolerance, including host-microbiome interactions, are unexplored. We used Daphnia magna, a keystone freshwater species with clonal reproduction and dormant egg banks to test population-specific (constitutive) responses to phenanthrene (PHE), a common PAH. Populations resurrected from contrasting historical environments were exposed to sub-lethal PHE concentrations, and both host transcriptomes and gut microbiomes were profiled to assess induced responses. Transcriptomic analysis revealed distinct, population-specific responses in detoxification, stress signalling, and endocrine regulation. Unexpectedly, the semi-pristine (pollution-naïve) population showed higher tolerance, with robust induction of cytochrome P450 and hormonal pathways, while populations historically exposed to pollution exhibited chronic stress signatures and reduced plasticity. Gut microbiome profiling revealed PHE-induced functional shifts across populations, with the pollution-naïve population showing broader stress-associated responses and historically exposed populations to pollutants exhibiting more detoxification-focused microbiome profiles. Both host and microbial datasets consistently showed enrichment in pyruvate and carbon metabolism, indicating coordinated energy mobilisation and detoxification responses. Our results show that historical exposure to chemical stress and wider pollution does not necessarily confer enhanced physiological tolerance to PHE. Instead, hydrocarbon stress elicits coordinated, functionally linked responses across the host and its associated microbiome. By leveraging Daphnia's unique ecology and evolutionary history, we disentangle constitutive from plastic responses and show that microbiome functional reconfiguration under PHE exposure is coordinated with host responses, contributing to population-specific profiles.},
}

Animals
*Daphnia/genetics/drug effects/microbiology
*Water Pollutants, Chemical/toxicity
Gastrointestinal Microbiome/drug effects/genetics
*Polycyclic Aromatic Hydrocarbons/toxicity
Transcriptome
Phenanthrenes/toxicity
Inactivation, Metabolic/genetics
*Biological Evolution

@article {pmid41703668,
year = {2026},
author = {Rezaei Somee, M and González-Rosales, C and Gralka, M and Turner, S and Bertilsson, S and Dopson, M and Mehrshad, M},
title = {Cross-feeding options define genome evolution and community assembly of deep groundwater microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00865-z},
pmid = {41703668},
issn = {2524-6372},
abstract = {BACKGROUND: Deep groundwaters populated by diverse and active microbes are among the most energy and nutrient-limited ecosystems. Characteristics of this ecosystem (including nutrient and dispersal limitations, low cell densities, and an episodic growth strategy) interactively underpin the so far elusive eco-evolutionary dynamics of its microbiome. Here, we used genome-resolved modular metabolic analyses of disconnected deep groundwater sites in the Fennoscandian Shield to test how eco-evolutionary constraints in these deep groundwater ecosystems shape microbial genome architecture, metabolic versatility, and community assembly at different depths.

RESULTS: The analysis revealed that lineages with larger genomes (≥ 2.6 Mb) maintained higher population sizes in the deepest and most oligotrophic groundwaters, whereas lineages with known metabolic dependencies, such as and DPANN, declined in relative abundance with depth. This pattern was interpreted as consistent with limited opportunities for sustained metabolic cross-feeding in these ecosystems. Moreover, while similar ecological niches based on cross-feeding interactions and potential primary production were available across different boreholes, distinct microbial lineages appeared to occupy these niches at each site.

CONCLUSION: The findings provided new insights into the role of metabolic cross-feeding in genome evolution and community assembly of deep groundwater microbiomes. By extending the streamlining theory, this study underscores the critical influence of ecological interactions, particularly metabolic exchanges, in shaping microbial life under severe nutrient limitation, offering new insights into subsurface microbial communities.},
}

@article {pmid41703218,
year = {2026},
author = {Warp, PV and Bilik, SM and Ferrari, LM and Keri, JE},
title = {Prebiotics, Probiotics, and Postbiotics for Acne Vulgaris: A Systematic Review.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {41703218},
issn = {2193-8210},
abstract = {INTRODUCTION: Microbiome-modulating therapies including prebiotics, probiotics, and postbiotics have been increasingly investigated as adjuncts or alternatives for managing acne vulgaris through effects on the gut-skin axis, inflammation, and barrier function. The objective of this systematic review is to characterize the safety and efficacy of oral and topical prebiotics, probiotics, and postbiotics in managing acne vulgaris.

METHODS: We conducted a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)-guided systematic review of randomized controlled trials, cohort studies, and case-control studies evaluating oral and topical prebiotics, probiotics, and postbiotics for acne vulgaris from inception to August 2025 in PubMed, Embase, Web of Science, and Cochrane. Inclusion criteria comprised clinical studies reporting on safety and/or efficacy of topical and/or oral prebiotic, probiotic, and postbiotic therapy in patients with acne vulgaris.

RESULTS: In total, 33 studies evaluating 2112 total patients were included, with treatment durations of 4-25 weeks; 5 prebiotic, 24 probiotic, and 7 postbiotic studies were included, with 2 studies comparing prebiotics and probiotics and 1 study comparing prebiotics and postbiotics against each other. Safety was favorable across all modalities with no serious adverse events reported. Pooled mean total lesion reductions were -37.2% for prebiotics, -45.2% for probiotics, and -49.5% for postbiotics, versus -37% for controls.

CONCLUSIONS: Prebiotic, probiotic, and postbiotic therapies appear to be safe and associated with clinically meaningful lesion reductions in acne. They may increase tolerability and add additional efficacy to standard acne treatments including topical and oral antibiotics and retinoids. Probiotics currently have the strongest evidence base, while prebiotics and postbiotics are promising adjuncts. Larger, standardized randomized trials are needed to clarify comparative efficacy, optimal formulations, and durability.},
}

@article {pmid41703109,
year = {2026},
author = {Preissner, R and Yang, Z and Preissner, S and Thöne-Reineke, C},
title = {Contact with dogs is associated with improved survival in cancer patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39952-z},
pmid = {41703109},
issn = {2045-2322},
abstract = {For cardiovascular diseases, diabetes, and asthma, the positive effects of dog ownership are shown. Cancer is a leading cause of death, but the influence of dogs on cancer incidence and survival is not well examined. As modifiable lifestyle factors gain importance in cancer survivorship research, the potential protective role of dog ownership warrants systematic investigation. We retrospectively analyzed clinical data from a federated global health research network, focusing on patients diagnosed with cancer (International Classification of Diseases (ICD-10): C00-D49). From these, we generated two cohorts with contact with dogs (cohort 1) and one without (cohort 2). After propensity score matching for age and sex, a total of about 55,000 patients were included. Analysis of the matched cohort demonstrated that dog ownership was significantly associated with reduced 5-year all-cause mortality in cancer patients compared to non-owners (RR = 0.44). Survival analysis revealed a significantly higher 5-year cumulative survival rate among dog-owning patients versus non-owners, with a hazard ratio (HR) of 0.36. Contact with dogs is associated with a 64% relative risk reduction in cancer mortality, potentially mediated by increased physical activity, psychosocial support, and microbiome modulation. While retrospective design precludes causal inference, this first large-scale matched cohort study provides compelling epidemiological evidence warranting prospective validation.},
}

@article {pmid41702954,
year = {2026},
author = {Maranha, A and Leal, EC and Alarico, S and Tiago, I and Pereira, SG and Empadinhas, N and Carvalho, E},
title = {Neuropeptides neurotensin and substance P accelerate diabetic wound healing by modulating immunity and the skin microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30723-w},
pmid = {41702954},
issn = {2045-2322},
support = {PTDC/BIA-MIC/0122/2021//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1448/CT0024//Fundação para a Ciência e a Tecnologia/ ; 10.54499/DL57/2016/CP1448/CT0017//Fundação para a Ciência e a Tecnologia/ ; CEECINST/00051/2018//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-MIC/0122/2021//Fundação para a Ciência e a Tecnologia/ ; UIDB/04539/2020//Fundação para a Ciência e a Tecnologia/ ; FIS-2015-01_DIA_20150630-144//INFARMED - National Authority for Medicines and Health Products/ ; },
}

@article {pmid41702871,
year = {2026},
author = {Wen, M and Ma, X and Chen, J and Wu, J and Wu, F and Ma, R and Peng, R},
title = {Composition, Structure, and Diversity of Rhizosphere Soil Microbial Community in Saffron (Crocus sativus) Affected by Root Bulb Rot.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-07-25-1456-RE},
pmid = {41702871},
issn = {0191-2917},
abstract = {Fusarium oxysporum, first identified in Yunnan Province as the causal agent of saffron corm rot, causes a destructive soil-borne disease that has become a devastating threat to saffron cultivation in Shangri-La, causing over 50% mortality. This pathogen infects saffron corms, leading to vascular browning and rot, ultimately causing plant death and severe production losses. Given the crucial role of the rhizosphere microbiome in plant immunity and soil ecology, deciphering pathogen-microbiome interactions is essential for developing sustainable disease-control strategies. High-throughput sequencing of ITS/16S rRNA (Illumina MiSeq) was combined with arbuscular mycorrhizal fungi (AMF) analysis to compare the community structures of fungi, bacteria, and AMF in the rhizosphere of healthy and diseased saffron. The effects of soil physicochemical factors on microbiome assembly were systematically evaluated. The rhizosphere microbiome of diseased plants was significantly dysregulated: (1) pathogen-related taxa (e.g., Lauriomyces) proliferated, while saprotrophic functional taxa (e.g., Mortierella elongata) underwent community restructuring; (2) disease-suppressive taxa (e.g., fususidium) were enriched, while symbiotic mycorrhizal fungi (AMF) essential for nutrient acquisition sharply declined; (3) the soil parameter-microbiome relationship changed under different health conditions:available phosphorus (AP) and available potassium (AK) drove the aggregation of pathogenic soil fungi, while pH/organic matter (OM) dominated the aggregation of healthy soil fungi; (4) Knufia and Phomopsis were important taxa regulating soil ammonia oxidation and plant vitality. Fusarium infection disrupts the rhizosphere balance by inhibiting beneficial symbionts and promoting the colonization of pathogenic or saprotrophic microorganisms, ultimately compromising the innate resistance of saffron. Our findings reveal the rhizosphere ecological mechanism underlying corm rot progression and provide a microbiome informatics framework for the selection of biocontrol agents and rhizosphere engineering. Moreover, the worker safety benefits from the reductions in psychic emanations mandate industry adoption.},
}

@article {pmid41702355,
year = {2026},
author = {Katayama, Y and Fukuda, A and Inoue, R and Kawachi, H and Sawada, R and Harada, T and Yoshimura, A and Okada, A and Shiotsu, S and Chihara, Y and Takemura, Y and Yamada, T and Nishioka, N and Iwasaku, M and Tokuda, S and Takagi, T and Kumagai, S and Koyama, S and Takayama, K and Yamada, T},
title = {Gut microbiome-driven modulation of the tumor immune microenvironment optimizes dual checkpoint blockade in advanced non-small-cell lung cancer.},
journal = {ESMO open},
volume = {11},
number = {3},
pages = {106077},
doi = {10.1016/j.esmoop.2026.106077},
pmid = {41702355},
issn = {2059-7029},
abstract = {BACKGROUND: Dual checkpoint blockade with ipilimumab plus nivolumab (I-N), with or without chemotherapy, has shown clinical efficacy for treating advanced non-small-cell lung cancer (NSCLC); however, its benefits are limited to a subset of patients. The gut microbiome influences immune responses and may impact the efficacy of immune checkpoint inhibitors, thus warranting further investigation.

MATERIALS AND METHODS: This prospective study enrolled 50 patients with NSCLC who were treated with I-N, with and without chemotherapy. Gut microbiota diversity and composition were assessed from fecal samples collected before treatment initiation, and tumor-infiltrating lymphocytes (TILs) were evaluated using multiplex immunofluorescence staining. Progression-free survival (PFS), overall survival (OS), and objective response rate were analyzed alongside gut microbiota characteristics and treatment regimens.

RESULTS: High gut microbiota diversity was associated with improved outcomes in patients receiving I-N alone and with greater CD8+ TIL infiltration, particularly PD-1+CD8+ TILs. Responders receiving I-N alone showed enrichment of short-chain fatty acid (SCFA)-producing bacteria, which were linked to favorable metabolic pathways associated with antitumor immune responses. In contrast, the association between gut microbiota diversity and treatment efficacy was not observed in patients treated with I-N plus chemotherapy. Antibiotic use before treatment was independently associated with shorter PFS and OS across all treatment regimens.

CONCLUSIONS: Gut microbiota diversity and SCFA-producing bacteria are associated with improved efficacy of I-N. Baseline gut microbiota diversity may help identify patients who are more likely to have improved outcomes with I-N plus chemotherapy than with I-N alone. These findings highlight the potential of gut microbiota as a novel biomarker for dual checkpoint blockade in NSCLC may contribute to advancing personalized medicine.},
}

@article {pmid41702202,
year = {2026},
author = {Zhang, Z and Chen, H and Fu, Y},
title = {Deciphering antibiotic resistome characteristics and dissemination risks in fertilized and irrigated agricultural soils.},
journal = {Waste management (New York, N.Y.)},
volume = {214},
number = {},
pages = {115409},
doi = {10.1016/j.wasman.2026.115409},
pmid = {41702202},
issn = {1879-2456},
abstract = {While applying animal manure remain widespread agricultural practices for resources recycling, it risks unintentionally transferring antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) from manure to soils. Despite the recognized environmental implications, limited research has systematically investigated the risk characteristics of ARGs linked to the combined application of manure as base fertilizer and routine irrigation practices. The question of which practice, fertilization or irrigation, more significantly contributes to the spread of ARGs remains unresolved. To bridge the gap, this study comprehensively investigates the characteristics and dissemination risks of ARGs in agricultural soils treated with chicken/cattle manure fertilization alongside groundwater irrigation. The characteristics, differences, and interactions among the resistome, microbiome, mobilome, and virulome across irrigation systems are systematically analyzed and compared. A novel non-negative matrix factorization-based microbial source tracking approach, NMF-SourceID, with superior accuracy in tracking low-abundance sources is used to quantify the source-sink relationship of ARGs in irrigated agroecosystems. The results revealed that combined fertilization and irrigation significantly enhanced both the abundance and diversity of ARGs in agricultural soils (p < 0.05). Importantly, these practices increased environmental risks by introducing emerging ARGs, mobile genetic elements, opportunistic human pathogens, virulence factors, and promoting their ecological co-occurrence. Comparative analysis showed no significant difference (p > 0.05) in ARG levels between chicken manure-treated strawberry soils and cattle manure-amended wheat cultivation soils. Source apportionment indicated that irrigation contributed 16-26% of ARGs while manure contributed 2.7-3.8%, suggesting the impact of base fertilizer on the dissemination of ARGs is much smaller than that of irrigation. The findings of this study provide essential theoretical groundwork for guiding agricultural fertilization and irrigation practices to mitigate environmental risks associated with antibiotic resistance dissemination in agroecosystems.},
}

@article {pmid41702193,
year = {2026},
author = {Liu, J and Ugwah-Oguejiofor, CJ and Zhu, L},
title = {Granulocytic myeloid derived suppressor cells derived extracellular vesicles ameliorate DSS-induced colitis via modulation of Th17/Treg balance.},
journal = {Pathology, research and practice},
volume = {281},
number = {},
pages = {156405},
doi = {10.1016/j.prp.2026.156405},
pmid = {41702193},
issn = {1618-0631},
abstract = {Colitis is closely associated with immune system dysregulation in the gastrointestinal tract. The present study aimed to evaluate the impact of Granulocytic Myeloid-Derived Suppressor Cells (G-MDSCs)-derived extracellular vesicles (EVs) on disease activity and the immunologic profile in a murine model of colitis. G-MDSCs-EVs were administered to colitis-bearing mice and were evaluated for changes in body weight, disease activity index, colon histopathology, frequencies of Th17 and Tregs, and cytokine release from lymphocytes. The impact of G-MDSCs-EVs was also evaluated on the expression of immune-response-related genes and the intestinal microbiome. G-MDSCs-EVs prevented body weight loss and controlled the disease activity index on day 10. This treatment improved the Treg population along with a decrease in the release of IL-6, IL-17A, and IFN-γ from lymphocytes. Treatment with G-MDSCs-EVs modulated immune-response-related gene expression and influenced the gut microbiota and colon histopathology. G-MDSCs-EVs demonstrated a preliminary potential in expanding the Treg population and upregulating immunoregulatory cytokines, which contributed to improvements in disease activity index and histopathology of the affected tissue.},
}

@article {pmid41702132,
year = {2026},
author = {Maji, C and Kokiwar, PR and Biradar, A and Jauhari, R},
title = {Comment on 'Feasibility Study Exploring the Effect of Pelvic Radiotherapy on the Intestinal Microbiome and Metabolome to Improve the Detection and Management of Gastrointestinal Toxicity'.},
journal = {Clinical oncology (Royal College of Radiologists (Great Britain))},
volume = {52},
number = {},
pages = {104060},
doi = {10.1016/j.clon.2026.104060},
pmid = {41702132},
issn = {1433-2981},
}

@article {pmid41702067,
year = {2026},
author = {Guo, X and Peng, L and Zhu, Z and Fan, S and Feng, J and Fang, X and Guo, D and Yang, P},
title = {Combined effects of polystyrene micro-/nano-plastics and imidacloprid on Gut-Brain axis and neurotoxicity in juvenile Carassius auratus.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128998},
doi = {10.1016/j.jenvman.2026.128998},
pmid = {41702067},
issn = {1095-8630},
abstract = {Polystyrene micro/nanoplastics (PS-MPs/NPs) and the neonicotinoid imidacloprid (IMI) frequently co-occur in freshwater ecosystems, yet their combined toxicity profiles remain distinct and unresolved. Here, we exposed juvenile crucian carp (Carassius auratus) to PS-MPs (5 μm), PS-NPs (60-100 nm), and IMI, alone or in combination, to unravel their interactive mechanisms via a multi-omics approach. Results revealed a clear size-dependent toxicity pattern: while PS-NPs (especially with IMI) preferentially targeted the brain, PS-MPs (with or without IMI) induced the most severe intestinal histological injury, characterized by extensive intestinal fold atrophy and goblet cell depletion. In the brain, co-exposure to PS-NPs and IMI elicited potentiated neurotoxicity, manifesting as blood-brain barrier (BBB) breakdown, neuroinflammation, and a specific disruption of the glutamate-glutamine-γ-aminobutyric acid (Glu-Gln-GABA) metabolic cycle, which coincided with hyperactive and asocial behaviors. Microbiome analysis highlighted distinct dysbiotic signatures. Integrated network analyses further linked these gut microbial shifts to central neurochemical imbalances, implicating the microbiota-gut-brain axis as a potential pathway involved in systemic toxicity. In summary, this study differentiated between gastrointestinal damage caused by MPs and systemic combined toxicity caused by the penetration of NPs and IMI across biological barriers. It emphasizes the importance of size-specific assessment in understanding the complex risks of combined exposure to plastics and pesticides, providing insights for pollution management in agricultural hotspots.},
}

@article {pmid41701663,
year = {2026},
author = {Zhou, H and Chen, J and Zhang, X},
title = {Correction: BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data.},
journal = {PLoS computational biology},
volume = {22},
number = {2},
pages = {e1013974},
pmid = {41701663},
issn = {1553-7358},
abstract = {[This corrects the article DOI: 10.1371/journal.pcbi.1013124.].},
}

@article {pmid41701630,
year = {2026},
author = {Wang, G and Luo, Y and Song, S and Li, X and Pan, Y and Zhao, Z and Wang, B and Yang, Q and Yang, F and Fang, T},
title = {Role of the Gut Microbiome in Modulating Interactions Between β-Lactam Antibiotics and Statins in Coronary Heart Disease.},
journal = {Journal of cardiovascular pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1097/FJC.0000000000001805},
pmid = {41701630},
issn = {1533-4023},
abstract = {Clinical evidence suggests that the lipid-lowering efficacy of statins may be diminished by concurrent β-lactam administration in patients with coronary heart disease (CHD), yet the mechanisms driving this potential drug-drug interaction, particularly the role of gut microbiota as a mediator, remain undefined. To address this gap, we conducted a retrospective analysis of data from a tertiary hospital spanning 5 years, enrolling 436 CHD patients on statin therapy who had two hospital admissions within a 3-month window. Patients were stratified into β-lactam-treated and antibiotic-free cohorts to assess the correlation between β-lactam exposure and statin efficacy. Additionally, 16S ribosomal RNA gene sequencing was employed to characterize and compare gut microbiota profiles between CHD patients receiving combined rosuvastatin and β-lactam therapy versus those on rosuvastatin monotherapy. Our findings demonstrated that β-lactam exposure was associated with elevated low-density lipoprotein cholesterol and total cholesterol levels. Both rosuvastatin and β-lactams induced significant alterations in gut microbiota composition, with distinct shifts in bacterial taxa abundances: rosuvastatin increased the relative abundance of Faecalibacterium and Dysosmobacter, whereas β-lactams disrupted the abundance of Faecalibacterium, Roseburia, and Dysosmobacter. Collectively, these results indicate that concomitant β-lactam use impairs rosuvastatin efficacy in CHD patients, likely via perturbation of gut microbiota composition. Rosuvastatin may exert a portion of its cardioprotective effects through modulation of gut microbiota, and β-lactams may abrogate this benefit by depleting key bacterial taxa linked to statin-mediated lipid regulation. Notably, Dysosmobacter emerges as a potential mediating species in this interaction, supporting a microbiome-dependent mechanism underlying the reduced lipid-lowering efficacy of rosuvastatin during β-lactam co-administration.},
}

@article {pmid41701442,
year = {2026},
author = {Zhang, R and Zhu, J and Qu, S and Chen, X and Wang, Y and Sun, L and Zhang, X and Lu, Z and Wang, X},
title = {S1P2 Reduces Mast Cell Activation and Colonic Inflammation of L-Arginine-Induced Acute Pancreatitis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41701442},
issn = {1573-2568},
support = {82371241, 82171232, 31900716//the National Natural Science Foundation of China/ ; 82274171//the National Natural Science Foundation of China/ ; 22XD1404900//the Program of Shanghai Academic/Technology Research Leader/ ; 20204Y0047//the Shanghai Municipal Health Commission/ ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) is a serious pancreatic disorder and colonic inflammation is involved in the progression of AP. However, the role of mast cells in the regulation of colonic inflammation in AP has been less studied; thus, we explored the role of mast cells in the regulation of colonic inflammation.

METHODS: An AP model was established by intraperitoneal injection of L-arginine or caerulein. Colonic inflammation in AP was tested using H&E staining. The mRNA levels were quantified using qRT-PCR. The protein level of sphingosine-1-phosphate receptor 2 (S1P2) was quantified using western blotting or immunohistochemistry. The gut microbiota was analyzed using 16S rRNA sequencing.

RESULTS: The Western blot analysis revealed that S1P2 expression was decreased by 0.63-fold in L-arginine-AP-induced colonic inflammation. Ketotifen, a second-generation H1-antihistamine and mast cell stabilizer, increased the survival rate (90%) in the L-arginine-AP model and increased the mRNA level of S1P2 by 1.33-fold and protein expression by 1.47-fold, suggesting that ketotifen inhibited mast cell activation through the S1P2 pathway. Similarly, treatment with the S1P2 agonist CYM-5520 in the L-arginine-AP model did not result in death and decreased the proportion of mast cells in the spleen by 1.58-fold. Moreover, gut microbiome analysis revealed that the abundance of proteobacteria decreased in L-arginine-AP mice pretreated with CYM-5520. In vitro experiments revealed a 2.1-fold decrease in S1P2 expression following mast cell stimulation, and the absence of S1P2 promoted mast cell degranulation.

CONCLUSION: This study provides evidence that S1P2 can ameliorate colonic inflammation in an L-arginine-induced AP mouse model by inhibiting mast cell activation.},
}

@article {pmid41701340,
year = {2026},
author = {Li, H and Yang, Z and Li, M and Yang, H and Liu, D and Bi, Y and Dai, X and Chen, X and Miao, L and Yang, F and Chen, Z},
title = {Causal association between gut microbiota and osteonecrosis in European populations: a two-sample Mendelian randomization analysis.},
journal = {Journal of bone and mineral metabolism},
volume = {},
number = {},
pages = {},
pmid = {41701340},
issn = {1435-5604},
support = {XDYC-QNRC-2024-163//Yunnan Revitalization Talent Support Program/ ; 2024SCP001//Spring City Plan: The High-level Talent Promotion and Training Project of Kunming Yunnan Revitalization Talent Support Programme Young Talent Project/ ; 82360480//National Natural Science Foundation of China/ ; 202301AU070104//Applied Basic Research Foundation of Yunnan Province/ ; 202301AY070001-180//Applied Basic Research Foundation of Yunnan Province and Kunming Medical University/ ; 202401AY070001-330//Applied Basic Research Foundation of Yunnan Province and Kunming Medical University/ ; 2023-SW-65//Kunming Health Commission Health Science and Technology Talent Project/ ; },
abstract = {INTRODUCTION: Recent studies have linked gut microbiota composition to osteonecrosis, but the causal relationship remains unclear. Clarifying this relationship is clinically important because osteonecrosis currently lacks early biomarkers and etiology-targeted therapies; if causal, the gut microbiome would offer a readily modifiable intervention target.

METHODS: We conducted a two-sample Mendelian randomization analysis to explore this relationship. Exposure data were sourced from the MiBioGen consortium (N = 18,340), while outcome data on osteonecrosis were obtained from FinnGen (N = 392,580). The Inverse Variance Weighted method was used as the primary analytical approach, supplemented by comprehensive sensitivity analyses to assess the robustness of our findings.

RESULTS: Our analysis screened 196 microbial taxa and identified seven taxa associated with osteonecrosis risk in European populations. Protective effects were noted for the genus Odoribacter (OR = 0.579; P = 0.027) and family Alcaligenaceae (OR = 0.703; P = 0.049). Conversely, increased risk was linked to the genus Eubacterium fissicatena group (OR = 1.272; P = 0.046), genus Bifidobacterium (OR = 1.372; P = 0.038), order Bifidobacteriales (OR = 1.412; P = 0.023), family Bifidobacteriaceae (OR = 1.412; P = 0.023) and phylum Actinobacteria (OR = 1.750; P = 0.001). Sensitivity analyses confirmed the robustness of these findings, with no evidence of pleiotropy or heterogeneity.

CONCLUSION: This study establishes a causal link between gut microbiota composition and osteonecrosis, suggesting that gut microbiota may be a modifiable factor in its pathogenesis. Further research is needed to elucidate underlying mechanisms and evaluate microbiota-targeted interventions for prevention and treatment.},
}