@article {pmid41865111,
year = {2026},
author = {Oliveira, AGG and Dias, MF and Haq, IU and Ferreira, JFG and Silva, CP and Moreira, M and da Silva Lanna, MC and Santos Rodrigues, LD and de Mâcedo Farias, L and Magalhães, PP},
title = {Seasonal and Source-Associated Microbiome Dynamics in Brazilian Drinking Water.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02735-0},
pmid = {41865111},
issn = {1432-184X},
}

@article {pmid41865193,
year = {2026},
author = {Mathkor, DM and Aldairi, AF and Faidah, H and Babalghith, AO and Johargy, AK and Ahmad, F and Haque, S and Bantun, F},
title = {The role of breastfeeding in modulating antimicrobial resistance in neonates: a systematic review.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41865193},
issn = {1530-0447},
abstract = {Antimicrobial resistance (AMR) is a growing health concern in neonates. Breastfeeding potentially plays a pivotal role in modulating neonatal gut microbiota, thereby influencing the acquisition and transmission of AMR genes (ARGs). This systematic review evaluates the links between breastfeeding and the origin of neonatal gut microbiota and AMR. Selection of pertinent studies published between 2015 and 2025 focusing on major outcome measures of neonatal AMR and ARG transfer was performed on scholarly databases. Following quality assessment, 22 studies met the inclusion criteria for further consideration. Evidence consistently demonstrates that breast milk is an active contributor to the microbial and genetic landscape of the neonatal gut microbiome. Further, studies implicated breast milk as a source of ARG transfer in neonates. Other reports indicated that exclusive breastfeeding and human milk-associated bioactive compounds promoted the colonization of beneficial commensals, limited colonization of multidrug-resistant species, and suppressed horizontal transfer of ARGs. Interestingly, maternal factors, such as maternal antibiotic history, lifestyle, and overall health status, appeared to influence the links between breast milk and transmission and impact of ARGs in neonates. In conclusion, while breastfeeding-based strategies are important to neonatal AMR mitigation, further mechanistic studies are required to establish causal pathways. IMPACT: Breastfeeding has an active role in altering neonatal gut microbiota and influences antimicrobial resistance (AMR) acquisition. This review synthesizes evidence from 2015-2025 indicating that breastfeeding is both a source of antimicrobial resistance genes (ARGs) and contains bioactive components that suppress ARG transmission and promote beneficial colonization. Maternal factors, such as antibiotic exposure, lifestyle, and overall health, potently influence these links. Mechanistic comprehension of the links between breastfeeding, neonatal microbiome, and AMR acquisition may allow identification of prevention strategies against neonatal infections. The analyses underscore the need for longitudinal, mechanistic studies to determine causal relationships and long-term effects of breastfeeding on neonatal AMR.},
}

@article {pmid41865545,
year = {2026},
author = {Yu, F and Feng, H and Yu, Z and Jiang, J and Li, S and Meng, J},
title = {Dissolved nitrogen and phosphorus trigger Euglena sanguinea blooms via Burkholderiaceae enrichment and extracellular polymeric substance stimulation.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129428},
doi = {10.1016/j.jenvman.2026.129428},
pmid = {41865545},
issn = {1095-8630},
abstract = {As representative landscape water bodies, urban park ponds are typically shallow and hydrologically isolated, making them highly susceptible to algal blooms. This study focused on recurrent summer-autumn blooms of Euglena sanguinea in Hefei Binhu Forest Park. These blooms form thin, red, oil-slick-like surface scums that severely suppress aquatic photosynthesis. We investigated phytoplankton community succession and its drivers by collecting surface biofilm, mid-depth water, and bottom sediment samples from three representative ponds during the 2024 bloom season. Results revealed extensive E. sanguinea blooms in July-August, with surface cell density reaching 9.86 × 10[6] cells/L (42% of total) and biomass attaining 98.61 mg/L (94% of total). This bloom peak coincided with a 2.5-fold increase in surface dissolved total nitrogen (DTN) and phosphorus (DTP). Concurrently, the surface biofilm exhibited a peak extracellular polymeric substance (EPS) concentration of 43.92 mg/L and a film-forming rate of 90.73%, structurally supported by the predominance of large algal-bacterial aggregates (>64 μm), which accounted for nearly 80% of the particulate composition. The bounding EPS (BEPS), rich in tryptophan-like proteins, corresponded with peak biofilm hydrophobicity. Critically, this nutrient-enriched microenvironmental transformation selected for a low-diversity, high-dominance microbiome. Burkholderiaceae dominated the August biofilm (23%), contrasting sharply with sediment communities (dominated by Steroidobacteraceae, 7%) and post-bloom October biofilms (dominated by Sporichthyaceae, 21%). Mechanistic path analysis revealed that DTN and DTP stimulated bloom expansion not by directly promoting algae, but by enriching Burkholderiaceae and stimulating EPS production. These findings elucidate a microbially mediated pathway linking nutrient enrichment to E. sanguinea bloom formation, challenging the conventional direct nutrient-bloom paradigm. The study provides mechanistic blueprint for targeted, microbiome-informed management of urban landscape water blooms.},
}

@article {pmid41865546,
year = {2026},
author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C},
title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129432},
doi = {10.1016/j.jenvman.2026.129432},
pmid = {41865546},
issn = {1095-8630},
abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.},
}

@article {pmid41865576,
year = {2026},
author = {Wu, Y and Qin, L and Zhang, Y and Jia, Y and Lü, Y and Wang, N and Zheng, H and Li, L and Zhang, Z},
title = {Co-exposure to polystyrene microplastics and glyphosate induces gut microbiota dysbiosis and cognitive impairment in honeybees.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141796},
doi = {10.1016/j.jhazmat.2026.141796},
pmid = {41865576},
issn = {1873-3336},
abstract = {Microplastics, as emerging persistent environmental contaminants, can act as vectors for the absorption of other pollutants in ecosystems, such as pesticide residues. However, the combined toxicological effects of microplastics and pesticides on pollinators remain poorly understood. Here, we evaluated the toxicity of polystyrene microplastics (PS) and glyphosate (GLY), both individually and in combination, in honeybees (Apis mellifera). While no significant changes in body weight gain or food consumption were observed after 20 days of exposure, co-exposure to PS and GLY significantly increased bee mortality and induced midgut damage and microbial dysbiosis. In the gut, pathways associated with cell proliferation and differentiation, along with genes related to oxidative stress, detoxification, and immunity, were significantly downregulated. Furthermore, the combination of PS and GLY impaired sucrose responsiveness, a key cognitive behavior in bees. Brain transcriptomics indicated a downregulation of serotonergic synapse-related genes, which were correlated with shifts in core gut bacteria such as Snodgrassella and Lactobacillus. Our findings demonstrate that co-exposure to PS and GLY exacerbates gut homeostasis disruption and impairs cognitive behavior, suggesting a potential role of the gut-brain axis. This study extends our understanding of the combined ecological risks posed by multiple environmental contaminants to bees as insect pollinators and emphasizes the need for comprehensive hazard assessments in insect conservation.},
}

@article {pmid41865725,
year = {2026},
author = {Wang, S and Sun, H and Lv, X and Li, J and Du, D and Guo, F and Zhang, C},
title = {Ultrasound-assisted extraction optimization of Fructus Tribuli polysaccharides: How stir-frying processing alters structures and enhances antihypertensive efficacy.},
journal = {Ultrasonics sonochemistry},
volume = {128},
number = {},
pages = {107829},
doi = {10.1016/j.ultsonch.2026.107829},
pmid = {41865725},
issn = {1873-2828},
abstract = {Fructus Tribuli (FT), the dried ripe fruit of Tribulus terrestris L., is recognized for its antihypertensive properties, which are enhanced by stir-frying without adjuvants. However, research on its polysaccharides with therapeutic potential remains limited. This study optimized the ultrasound-assisted extraction (UAE) of FT polysaccharides (FP) using response surface methodology, yielding a maximum extraction yield of 2.182 ± 0.29% under the conditions of liquid-solid ratio 20:1 mL/g, 51 min, 62 °C, and precipitation ethanol concentration of 95%. Subsequently, FP and stir-fried FT polysaccharides (SFP) were isolated, and their structural differences and antihypertensive effects were systematically compared. Structural analysis revealed notable differences between FP and SFP. Furthermore, the extraction resulted in a higher polysaccharide yield for SFP. In spontaneously hypertensive rats, both FP and SFP attenuated hypertension and vascular injury, modulated gut microbiota, increased short-chain fatty acids, and enhanced intestinal barrier function effects that were more pronounced with SFP. Mechanistically, both polysaccharides inhibited the aortic TLR4/MyD88 pathway. These results suggest that stir-frying modifies polysaccharide structure, thereby improving gut microbiome regulation, barrier protection, and vascular outcomes, highlighting the value of processing in enhancing polysaccharide efficacy. Thus, stir-frying amplifies therapeutic effects through bioactive macromolecular remodeling, advancing the understanding of Traditional Chinese medicine processing principles.},
}

@article {pmid41865866,
year = {2026},
author = {Wang, Y and Wang, D and Wang, H},
title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {},
number = {},
pages = {111996},
doi = {10.1016/j.cbpa.2026.111996},
pmid = {41865866},
issn = {1531-4332},
abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.},
}

@article {pmid41865944,
year = {2026},
author = {Zou, C and Liang, L and Zhao, M and Lin, L},
title = {Chlorogenic acid enhances gut microbiota regulatory effect and anti-inflammatory of Lycium barbarum polysaccharide by simulated fermentation.},
journal = {International journal of biological macromolecules},
volume = {356},
number = {},
pages = {151538},
doi = {10.1016/j.ijbiomac.2026.151538},
pmid = {41865944},
issn = {1879-0003},
abstract = {The intricate interplay between dietary components, the gut microbiome, and host immunity is a core of intestinal immune research. Lycium barbarum polysaccharide (LBP)-chlorogenic acid (CGA) complex exhibits proliferative activity of Bacteroides and strong inhibitory effect on Staphylococcus aureus, but lacks of the microbial fermentation characteristics and immunomodulatory effect. Herein, in vitro fecal bacteria microbiota and macrophages models were employed to investigated the regulatory capacity of the LBP-CGA complex on intestinal microbiota and immunomodulatory activities of its metabolites. Results showed that LBP and LBP-CGA both readily fermentable. Fermentation led to significant molecular weight and pH reductions, nearly 85% polysaccharide degradation. Notably, LBP-CGA complex was more favorable to increase the relative abundance of Sutterella, Veillonella, Faecalibacterium and contents of SCFAs than LBP. Interesting, LBP fermentation product possessed the potential for immune-enhancing, with the polysaccharide fraction was the key active component. Conversely, LBP-CGA complex fermentation product elicited the potential for immune-suppressive response, with dihydrocaffeic acid of CGA metabolites was critical contributors. The data further indicated LBP-CGA exhibited better immunomodulatory of intestinal microbiota probably due to the proliferation of Bacteroides. Bacteroides may improve the bio-transformation of CGA and produce more dihydrocaffeic acid, which may in turn potentiate the immunosuppressive activity of the LBP-CGA complex fermentation product. To summarize, the results revealed that CGA elevated the ability of LBP to regulate the intestinal microbiota and to potential exert immunosuppression. This study offers profound insights into the development of LBP-CGA complex as a prebiotic with excellent anti-inflammatory effect.},
}

@article {pmid41866241,
year = {2026},
author = {Chauhan, S and Kumari, P and Deepa, N and Chanotiya, J and Trivedi, PK and Singh, A},
title = {Proteomic insights into plant-endophyte interactions: advancing understanding of mutualistic symbiosis and plant resilience.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/07388551.2026.2618190},
pmid = {41866241},
issn = {1549-7801},
abstract = {Endophytic microorganisms are a vital part of the plant microbiome, contributing significantly to the plant's growth, development, and stress tolerance. Proteomics investigations have significantly enhanced our comprehension of the interactions between plants and endophytes, illuminating the complex molecular mechanisms that govern these mutually beneficial relationships. The review aims to integrate the latest developments in proteomic research concerning endophyte-plant interactions, emphasizing on elucidating the molecular mechanisms that underlie the benefit imparted to the host plant by the symbionts. The special focus of the review is to discuss the proteome level changes happening at the early recognition events, primary and secondary metabolism, signaling pathways, and defense mechanisms. By underscoring critical proteomic signatures, the review aspires to offer insights into how these interactions enhance plant health, increase stress resilience, and promote overall growth. The article discusses the potential applications of proteomics in agriculture and environmental sciences, emphasizing its role in crop resilience against biotic and abiotic stresses, optimizing biocontrol strategies, and improving nutrient use efficiency. The article also highlights that despite the advancements, critical gaps persist including the necessity for a deeper understanding of the temporal dynamics of proteomic responses, the specificity of protein-protein interactions, and the influence of environmental factors on the proteome induced by the endophytes. The review concludes by proposing future directions for proteomics research in plant-endophyte interactions for developing a more comprehensive understanding of the intricate molecular dialogues for developing a more sustainable and resilient agricultural systems.},
}

@article {pmid41866413,
year = {2026},
author = {Berkelmann, D and Zuñiga-Umaña, JM and Chaverri, P and Solano, W and Gatica-Arias, A},
title = {Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866413},
issn = {1573-0972},
support = {111-C1-472//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; },
mesh = {*Plant Diseases/microbiology ; *Coffea/microbiology ; Plant Leaves/microbiology ; *Basidiomycota/genetics/classification/isolation & purification ; DNA, Fungal/genetics ; Costa Rica ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; *Fungi/genetics/classification/isolation & purification ; Coffee/microbiology ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.},
}

*Plant Diseases/microbiology
*Coffea/microbiology
Plant Leaves/microbiology
*Basidiomycota/genetics/classification/isolation & purification
DNA, Fungal/genetics
Costa Rica
Phylogeny
Sequence Analysis, DNA
Biodiversity
*Fungi/genetics/classification/isolation & purification
Coffee/microbiology
DNA, Ribosomal Spacer/genetics

@article {pmid41866421,
year = {2026},
author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R},
title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866421},
issn = {1573-0972},
}

@article {pmid41866543,
year = {2026},
author = {Lu, Q and Chen, S and Shan, B and Wei, A and Luo, Y and Wu, L and Jiang, Q and Chen, Z},
title = {Rhizosphere microbiome dynamics and hormonal interactions regulating tiller development in sugarcane cultivars.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38474-y},
pmid = {41866543},
issn = {2045-2322},
support = {32201392//National Natural Science Foundation of China/ ; 2024GXNSFBA010329//Natural Science Foundation of Guangxi Province/ ; Guike AA24263045//Guangxi Major Science and Technology Program/ ; },
abstract = {Sugarcane tillering is a key determinant of crop productivity, yet the integrated roles of rhizosphere microbiome dynamics, nutrient status, and hormone signaling in regulating tiller development remain poorly understood. Here, we compared rhizosphere microbial communities, endogenous hormone profiles, and nutrient element concentrations in sugarcane cultivars with contrasting tillering capacities. High-tillering varieties exhibited significantly greater microbial diversity and more complex co-occurrence network structures in the rhizosphere, characterized by enrichment of Acidobacteriota, Chloroflexi, and Planctomycetes and functional pathways related to nitrogen fixation, phosphorus solubilization, and auxin biosynthesis. In contrast, low-tillering varieties harbored simplified, stress-adapted microbial consortia and prioritized pathways linked to oxidative stress response and heavy metal detoxification. Hormonal analysis revealed that high-tillering cultivars maintained higher levels of growth-promoting hormones-particularly auxin (IAA) and active cytokinins-in tiller buds while low-tillering cultivars accumulated elevated abscisic acid (ABA) and inactive cytokinin conjugates. Nutrient analysis indicated that high-tillering genotypes possessed higher nitrogen and phosphorus contents, supporting vigorous axillary bud activation and shoot proliferation, whereas low-tillering varieties accumulated more zinc and manganese, potentially reflecting stress adaptation. Network-level integration of microbial, hormonal, and nutrient profiles underscored genotype-specific feedback between rhizosphere microbiota and plant physiological states, highlighting modular associations that link microbial hubs with tissue-specific nutrient and hormone signatures. Our findings reveal a systems-level mechanism by which rhizosphere microbial community structure and function interact with plant-nutrient-hormonal status to regulate tillering in sugarcane. These insights provide a basis for microbiome-informed strategies to enhance sugarcane productivity through integrated nutrient-hormonal-microbe management.},
}

@article {pmid41866581,
year = {2026},
author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW},
title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45459-4},
pmid = {41866581},
issn = {2045-2322},
support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; },
}

@article {pmid41866722,
year = {2026},
author = {Chen, SJ and Wayne, CD and Jacobs, TH and Besner, GE},
title = {Rethinking probiotic delivery: new hope for preventing necrotizing enterocolitis.},
journal = {Expert opinion on drug delivery},
volume = {},
number = {},
pages = {},
doi = {10.1080/17425247.2026.2648748},
pmid = {41866722},
issn = {1744-7593},
abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is a devastating disease of the gastrointestinal tract that mainly affects premature newborns, with mortality rates exceeding 50% in the most severe cases. Despite decades of research the disease persists, there is no known cure, and treatment consists of supportive care only. Dysbiosis of the gut microbiome has been implicated as a contributing factor to the development of NEC. With a deepening understanding of the therapeutic efficacy of probiotics in reversing intestinal dysbiosis, a potential avenue to prevent this disease has emerged.

AREAS COVERED: Through review of the literature related to probiotics in NEC and novel oral delivery methods for probiotics, we will discuss what is known about preventing NEC with commercially available probiotics. We will discuss the challenges imposed on probiotic therapy by the September 2023 FDA warning on probiotic administration to premature babies. We will also examine novel delivery methods for probiotics that can enhance their beneficial capabilities.

EXPERT OPINION: By obtaining approval for novel oral probiotic delivery technologies including biofilm formation and prebiotic co-ride, the risk of NEC in premature infants could be significantly decreased.},
}

@article {pmid41866998,
year = {2026},
author = {Ebigbo, N},
title = {The esophageal microbiome: mechanisms and clinical implications.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000001170},
pmid = {41866998},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: Interest in the esophageal microbiome has expanded rapidly, yet its functional and clinical relevance remains incompletely defined. This review synthesizes emerging evidence on host-microbe interactions in esophageal diseases, with a focus on mechanistic pathways and translational potential.

RECENT FINDINGS: Recent studies demonstrate that esophageal microbes influence epithelial differentiation, barrier integrity, and inflammatory signaling in conditions such as eosinophilic esophagitis and Barrett's esophagus. Microbial metabolism, particularly bile acid transformation, links microbial composition to epithelial stress responses and neoplastic progression. In esophageal cancer, tumor-associated microbes modulate epigenetic regulation and suppress antitumor immunity. Integrative multiomics approaches have further identified microbial signatures associated with disease progression and treatment response.

SUMMARY: The esophageal microbiome influences disease pathogenesis and has potential for risk stratification and therapeutic targeting. Future progress will depend on longitudinal studies, improved functional resolution, and integration of microbial data with epithelial and immune biology to enable clinical translation.},
}

@article {pmid41867064,
year = {2026},
author = {Nikam, R and Pax, K and Beverly, ML and Kumar, PS},
title = {Mapping the subgingival HerBiome and HisBiome over the human healthspan.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70098},
pmid = {41867064},
issn = {1943-3670},
support = {/DE/NIDCR NIH HHS/United States ; },
abstract = {BACKGROUND: Understanding the intricate relationship between sex, age, and the oral microbiome is crucial for deciphering the onset and progression of numerous age-related oral and systemic diseases.

METHODS: Subgingival plaque was collected from 781 periodontally and systemically healthy females and 160 males spanning 0 to 80 years. 16S amplicon sequencing was performed. 80 million sequences were annotated and analyzed through the QIIME pipeline, principal components analysis (PCA) used for dimensionality reduction, LefSe to identify driver species, beta dispersion to measure inter-subject variability, and machine learning algorithm (RandomForest package in R [RF]) to validate the results. Causal mediation models were implemented to investigate the influence of aging on the male and female microbiomes.

RESULTS: PCA demonstrated significant class separation based on sex (p < 0.001, permutational multivariate analysis of variance [PERMANOVA]). Males demonstrated higher alpha diversity (p < 0.001, Wilcoxon signed-rank test of the Shannon diversity index), but also higher inter-subject heterogeneity p < 0.001, ANOVA). RF identified males with 0.99 sensitivity, 0.15 specificity, and accuracy of 85%. Age exerted an almost complete mediation effect, with significant differences in the trajectory and pattern of aging between males and females. Females > 30 demonstrated a lower microbial diversity (p < 0.001) and higher levels of Fusobacterium nucleatum (p < 0.001), while the male microbiome remained highly personalized throughout the lifespan, without defined patterns of aging.

CONCLUSIONS: Sex and age interact to influence the subgingival microbiome. These findings might explain differing disease susceptibilities in either sex, as well as informing personalized prevention and intervention based on age and sex. Further studies using granular -omics approaches are needed to advance our knowledge.

PLAIN LANGUAGE SUMMARY: Periodontal (gum) diseases are caused by a breakdown in the intricate balance between bacteria that live under the gumline and the local immune response. Since periodontal diseases have been reported to be more common in men than in women, we set out to investigate whether these bacterial communities are intrinsically different between the 2 sexes, and whether these differences are sustained over the lifespan. Using deep-sequencing technology to analyze the microbiomes of 941 individuals, we discovered that sex at birth is indeed a determining factor in the types of bacteria that live under the gums. Aging trajectories and patterns also differ between men and women, with women demonstrating a distinct shift after 30 years of age, and men showing no definite age-based change. These findings have important implications for the cause of periodontitis in either sex, as well as the potential to personalize therapy based on age and sex.},
}

@article {pmid41867134,
year = {2026},
author = {Piraccini, BM and Micali, G and Fulgione, E and Guida, S and Caldarola, G},
title = {Experts' view on the management of scalp seborrheic dermatitis in Italy.},
journal = {The Journal of dermatological treatment},
volume = {37},
number = {1},
pages = {2644012},
doi = {10.1080/09546634.2026.2644012},
pmid = {41867134},
issn = {1471-1753},
mesh = {Humans ; *Dermatitis, Seborrheic/diagnosis/drug therapy ; Italy ; Antifungal Agents/administration & dosage/therapeutic use ; Algorithms ; *Scalp Dermatoses/diagnosis/drug therapy ; *Dermatologic Agents/administration & dosage/therapeutic use ; Severity of Illness Index ; Acne Vulgaris/drug therapy/diagnosis/complications ; Adolescent ; Diagnosis, Differential ; },
abstract = {BACKGROUND: Acne vulgaris is a common skin disorder that negatively affects adolescents' quality of life. Recent evidence suggests that combining isotretinoin with desloratadine may enhance treatment outcomes.

OBJECTIVES AND METHODS: This study aimed to develop a practical algorithm for SSD management in Italy, by gathering insights from Italian dermatology experts on diagnosis, treatment and long-term management of SSD.

RESULTS: According to literature review and clinical experience, accurate diagnosis of SSD requires medical history, clinical evaluation, disease severity assessment and trichoscopy. The differentiation of SSD from psoriasis, eczema, and tinea capitis is essential to guide appropriate treatment, which should counteract the main pathogenic mechanisms underlying the disease and be tailored to the severity of clinical manifestations. Topical antifungals are the first-line treatments due to their efficacy in reducing Malassezia colonization. The use of topical anti-inflammatory agents, including corticosteroids, is useful for moderate-to-severe cases, but should be limited due to potential adverse effects. Selenium disulfide may be a useful option for both acute symptom control and long-term maintenance because of its antifungal, sebostatic, keratolytic, and microbiome-restoring properties, associated with a high degree of patient satisfaction. Systemic antifungals may be considered in refractory cases.

CONCLUSION: This experts' view provides a structured approach to SSD management in Italy, integrating clinical experience and scientific evidence.},
}

Humans
*Dermatitis, Seborrheic/diagnosis/drug therapy
Italy
Antifungal Agents/administration & dosage/therapeutic use
Algorithms
*Scalp Dermatoses/diagnosis/drug therapy
*Dermatologic Agents/administration & dosage/therapeutic use
Severity of Illness Index
Acne Vulgaris/drug therapy/diagnosis/complications
Adolescent
Diagnosis, Differential

@article {pmid41867523,
year = {2026},
author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S},
title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.},
journal = {ACS omega},
volume = {11},
number = {10},
pages = {16913-16921},
pmid = {41867523},
issn = {2470-1343},
abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.},
}

@article {pmid41867679,
year = {2026},
author = {Biagioli, V and Matera, M and Cavecchia, I and Illiceto, M and Pennazzi, L and Luongo, G and Lugli, S and Striano, P},
title = {Beyond breastfeeding: a One Health Decalogue for nurturing the infant microbiota.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1784544},
pmid = {41867679},
issn = {2296-861X},
abstract = {BACKGROUND: Early-life nutrition is a key determinant of infant gut microbiota development, immune maturation, and long-term health outcomes. Although breastfeeding is widely recognized as the optimal feeding strategy, many mothers are unable to breastfeed, underscoring the need for practical, evidence-based guidance to support infant health beyond breastfeeding. A One Health approach enables the integration of nutritional, microbial, clinical, environmental, and socio-cultural factors that influence maternal-infant dyads.

METHODS: A narrative review of the literature was conducted using PubMed, Scopus, and Google Scholar, focusing more on works published from 2020 to 2026. Evidence was synthesized on maternal and infant nutrition, breast milk bioactive components, infant formula feeding, gut microbiota development, and short- and long-term health outcomes in non-breastfed infants. Based on this interdisciplinary evidence, a translational "One Health Decalogue" was developed for mothers who are unable to breastfeed.

FINDINGS: The reviewed literature highlights that infant nutrition, particularly in the absence of breastfeeding, significantly influences gut microbiota composition, immune programming, metabolic regulation, and neurodevelopment. Key modifiable factors include formula composition, feeding practices, maternal health status, environmental exposures, caregiver education, and psychosocial support. The proposed One Health Decalogue synthesizes these elements into 10 actionable principles aimed at supporting microbial resilience, promoting healthy development, and reducing health inequalities when breastfeeding is not possible.

CONCLUSION: Translating scientific evidence into practical tools is essential to support infants who cannot be breastfed. The One Health Decalogue presented in this review provides a comprehensive, interdisciplinary, and translational framework for healthcare professionals, families, and public health policies, fostering informed nutritional choices and holistic strategies to optimize infant health beyond breastfeeding.},
}

@article {pmid41867689,
year = {2026},
author = {Zhong, L and Qing, Y and Liu, J},
title = {The role of enteral nutrition and parenteral nutrition in the management of inflammatory bowel disease: a bibliometric analysis (1999-2025).},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1767514},
pmid = {41867689},
issn = {2296-861X},
abstract = {OBJECTIVES: As a chronic disease often accompanied by malnutrition, Inflammatory Bowel Disease (IBD) has encountered many difficulties in long-term management. Enteral nutrition (EN) and parenteral nutrition (PN) are important methods to help improve nutritional status and support the remission of the disease. However, although increasing attention has been directed toward this kind of nutritional therapy, there is still a lack of detailed and accurate bibliometric analysis in this field. Therefore, the goal of this study is to find out the research trends and hot spots, and provide reference for future academic exploration and clinical practice.

METHODS: On November 26th, 2025, publications concerning EN, PN in IBD published from 1999 to 2025 were retrieved from two databases: Web of Science Core Collection and Scopus. In this study, R software, Microsoft Excel, VOSviewer and CiteSpace are used to measure and visually analyze the articles.

RESULTS: A total of 3,245 documents were reviewed, indicating a trend of power-law growth. The USA and UK lead in global collaboration, with China being third in volume but with less cooperative intensity. The study identifies a clear progression from early "total parenteral nutrition" and "corticosteroids" to "exclusive enteral nutrition". Citation bursts occurring in the years 2020 to 2025 included "Mediterranean diet," "gut microbiome," and "Crohn's disease exclusion diet," pointing to an emerging focus in personalized, whole-food-based therapies and microbiome modification.

CONCLUSION: The research on nutritional therapy of IBD demonstrates a rapid increase, which shows that it is becoming more and more important in helping patients control their illness. In the future, we need more high-quality research to turn these data into useful and multidisciplinary treatment guidelines.},
}

@article {pmid41867705,
year = {2026},
author = {Barrodia, P and Saw, AK and Jeter-Jones, SL and Chang, CC and Shao, J and Arslan, E and Singh, AK and Satpati, S and Jenq, RR and Rai, K and Piwnica-Worms, H},
title = {Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.06.710208},
pmid = {41867705},
issn = {2692-8205},
abstract = {UNLABELLED: Fasting enhances small intestinal regeneration after radiation but the contribution of the gut microbiome to this process remains uncharacterized. We identify Akkermansia muciniphila (AKK) as a key mediator of this response. AKK was enriched in fasted mice and its antibiotic depletion abrogated radioprotection whereas reintroduction restored both organismal survival and intestinal integrity. Fasting elevated propionic acid, consistent with AKK 's metabolic output. AKK -conditioned medium and propionate induced histone H3 acetylation in intestinal stem cell cultures while in vivo fasting induced AKK -dependent H3K27ac and H3K9ac, remodeling promoter-enhancer landscapes in crypt epithelial cells. Epigenetic profiling revealed a rewired core regulatory program enriched for pioneer transcription factors (Foxa, Gata, Klf), architectural organizers (Ctcf, Boris), and lineage-defining and metabolic regulators (Cdx2, Hnf4). This program supports expansion of a population of persister stem cells characterized by open chromatin accessibility at key stem and regenerative-associated loci including Clu , Olfm4 , Lgr5, Ascl2, Lrig1, Sox9, Rnf43, and Axin2. These findings define a fasting-induced microbiome-metabolite-chromatin axis that epigenetically primes highly plastic persister stem cells for rapid regeneration of the intestinal epithelium following radiation-induced injury.

SIGNIFICANCE STATEMENT: Fasting changes the gut microbiome, but how these changes help the body recover from damage is not well understood. We found that fasting increases a helpful bacterium, Akkermansia muciniphila , which produces propionate, which drives epigenetic changes by modifying histones and regulating gene activity. These changes promote the expansion of persister stem cells that help the intestine recover after radiation. This study shows how fasting and gut bacteria work together to protect healthy tissue and suggests that diet or microbial treatments could help reduce side effects of cancer radiotherapy.},
}

@article {pmid41867794,
year = {2026},
author = {Alviter-Plata, A and Ahmari, N and Gadient, J and Brammer-Robbins, E and Martyniuk, CJ and Zubcevic, J},
title = {Loss of Bone Marrow β1/β2-Adrenergic Receptors Reprograms Host-Microbiota Interactions and Protects Against Diet-Induced Obesity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.05.707516},
pmid = {41867794},
issn = {2692-8205},
abstract = {The gut ecosystem is shaped by multiple factors with the immune system being one of the major determinants in shaping its composition in health and disease. On the other hand, the immune system regulates its responses through the action of the sympathetic nervous system (SNS) in part through beta-adrenergic receptors 1/2 (ADRB1/2). In the past years, a clear link has been established between the immune system, SNS, and the modification of nutrient absorption by the gut microbiota in the development of diet-induced obesity. We have previously shown in male mice transplanted with bone marrow cells ADRB1/2 knock-out mice (KD) showed mild immunosuppression and microbiota changes. Post-recovery, mice were challenged with high-fat diet (HFD) for two weeks ad libitum . Our findings show that KD mice are protected against diet-induced adiposity and weight gain. Additionally, these mice showed an increase in residual calorific values and a decreased expression of the fatty acid transporter FAT/CD36. Suggesting a decreased absorption of lipids in the KD mice. Gut microbiota analysis showed that KD microbiota composition on a HFD remained stable with a significant enrichment in the Bacteroidetes phylum , which is depleted in obesity. This was associated with a switch from triglycerides to diglyceride fecal profile. Moreover, microbiome culture showed a decrease in triglycerides after an incubation with 0.1% of HFD lipid extract. Suggesting a potential role of the Bacteroidetes phylum in the metabolism of these lipids. Our findings demonstrate not only that the gut microbiota can modify nutrient absorption and susceptibility to diet-induced obesity but also that the immune system contributes to selective depletion of microbial members that would otherwise thrive on dietary lipids. Revealing a novel mechanism by which host immunity sculpts the gut ecosystem in ways that influence metabolic outcomes.},
}

@article {pmid41867919,
year = {2026},
author = {Morrin, ST and Buck, RH and Hill, DR},
title = {A unique blend of five human milk oligosaccharides supports recovery of infant microbiome composition and function after ex vivo antibiotic use.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1765159},
pmid = {41867919},
issn = {2296-2360},
abstract = {Human milk oligosaccharides (HMOs) are the third most abundant solid component of human breast milk, with well-established prebiotic and immunomodulatory functions. HMOs serve as selective substrates to support the growth of beneficial microbes in the developing gastrointestinal tract. At the same time individual HMOs have been shown to also exert selection against pathogens via direct anti-adhesive mechanisms. A longstanding hypothesis has held that HMOs act in concert and with other bioactive components of milk, and that this complex matrix of milk components collectively accounts for both the benefits to microbiome development and reduced risk of infectious disease associated with breastfeeding. The prebiotic activity of a diverse blend of fucosylated, acetylated, and sialylated HMOs was examined using microbiota cultured in an ex vivo model of the infant gastrointestinal tract before, during and after the supplementation of common childhood antibiotics. The anti-adhesive activity of this blend against infant-prevalent bacterial pathogens was tested using in vitro cultured intestinal epithelial cells. Taken together, this data suggests that a blend of 5 specific HMOs acts through multiple selection mechanisms to shape the development of the microbiota and interrupt opportunistic microbial pathogenesis.},
}

@article {pmid41868041,
year = {2026},
author = {Yu, S and Shu, W and Zhang, J and Cheng, S and Shen, X and Chen, G and Zhang, T and Dong, K and Zhang, J and Wang, H},
title = {Gut Microbiota-Immune Interactions in Endometrial Cancer: Causal Mediation and Subtype-Specific Mechanisms.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {583327},
pmid = {41868041},
issn = {1179-1411},
abstract = {PURPOSE: In this study, we applied two-sample Mendelian randomization (MR) to explore the causal effects between gut microbiota (GM), immune cells, and endometrial cancer (EC) subtypes and to assess whether immune cells mediate the impact of GM on EC.

PATIENTS AND METHODS: Using two-sample Mendelian randomization and mediation analysis, we analyzed GWAS data: GM (Dutch Microbiome Project; N=7738), EC subtypes (IEU Open GWAS; N=331,588), and immune traits (N=3757). We assessed the effects of the causal gut microbiota on EC subtypes and immune trait mediation.

RESULTS: Subtype-specific causal relationships were identified.Overall EC: Four positive (e.g. genus Erysipelotrichaceae noname) and three negative (e.g. species Bacteroides faecis) microbial causal effects; three mediated by immune traits (e.g. Ruminococcus obeum via CD86+ myeloid DC AC). Endometrioid EC: Five negative (e.g. class Bacilli) and two positive (e.g. species Aspergillus senegalensis) effects; three immune-mediated (e.g. Bacilli via IgD+ CD38br % lymphocytes). Non-endometrioid EC: Two positive (e.g. species Bacteroides stercoris) and one negative (species Ruminococcus bromii) effect; one mediated (Ruminococcus bromii via CD8br NKT % lymphocytes).

CONCLUSION: Immune traits significantly mediated causal pathways from GM to EC development. It also highlighted the distinct causal relationships and immune-mediated mechanisms across the three major EC subtypes (overall, endometrioid, and non-endometrioid). These subtype-specific insights into the gut-immune-cancer axis provide novel perspectives for developing therapeutic strategies targeting GM and the immune microenvironment in different EC subtypes.},
}

@article {pmid41868135,
year = {2026},
author = {Wen, P and Zhuo, X and Xue, S},
title = {Fatty acid-related immune network in psoriasis: metabolic regulation of innate and adaptive immunity.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1731683},
pmid = {41868135},
issn = {1663-9812},
abstract = {Psoriasis is a chronic inflammatory skin disorder driven by dysregulation of the Treg/Th17 axis, where enhanced Th17 activity promotes keratinocyte proliferation and inflammation, while impaired Treg function exacerbates immune dysregulation. Emerging evidence highlights peroxisome proliferator-activated receptor γ (PPARγ) as a key regulator of fatty acid oxidation (FAO), a metabolic pathway critical for Treg differentiation and function. PPARγ activation enhances FAO via upregulation of CD36, CPT1, and AMPK signaling, while suppressing glycolysis, thereby skewing the Treg/Th17 balance toward immune tolerance. Concurrently, short-chain fatty acids (SCFAs), microbial metabolites with immunomodulatory properties. ameliorate psoriatic inflammation by promoting Treg expansion, inhibiting Th17 polarization, and modulating innate immune cells (neutrophils, dendritic cells, and macrophages). SCFAs exert their effects through receptor-dependent signaling and epigenetic mechanisms (HDAC inhibition), while derivative compounds and probiotic interventions enhance therapeutic potential. This review summarizes mechanistic insights into PPARγ-driven FAO and SCFA-mediated immunomodulation, proposing novel metabolic and microbiome-targeted strategies for psoriasis treatment.},
}

@article {pmid41868170,
year = {2026},
author = {Zhang, J and Zhang, M and Wu, X and Jing, H and Li, P and Wang, W and Guo, X and Zhao, Z and Zhu, S and Wang, Y},
title = {Circulating Butyrate Attenuates Cetuximab Efficacy in Colorectal Cancer Through EGFR and AMPK-Wip1 Signaling.},
journal = {Drug design, development and therapy},
volume = {20},
number = {},
pages = {574116},
pmid = {41868170},
issn = {1177-8881},
mesh = {*Colorectal Neoplasms/drug therapy/pathology/metabolism ; *Cetuximab/pharmacology ; Humans ; ErbB Receptors/metabolism/antagonists & inhibitors ; Signal Transduction/drug effects ; *AMP-Activated Protein Kinases/metabolism ; *Butyrates/pharmacology/blood ; Animals ; Mice ; Cell Proliferation/drug effects ; Drug Screening Assays, Antitumor ; *Adaptor Proteins, Signal Transducing/metabolism ; *Antineoplastic Agents, Immunological/pharmacology ; Neoplasms, Experimental/drug therapy/pathology/metabolism ; Dose-Response Relationship, Drug ; Mice, Nude ; Tumor Cells, Cultured ; },
abstract = {BACKGROUND: Cetuximab is an approved therapy for metastatic colorectal cancer (CRC) with wild-type RAS and BRAF; however, additional resistance mechanisms beyond genetic mutations remain poorly understood. Butyrate, a key metabolite produced by the gut microbiome and present in the circulatory system, has been reported to supply cellular energy and modulate the epidermal growth factor receptor (EGFR) downstream signaling pathway. However, whether butyrate affects the resistance to cetuximab is still unknown.

METHODS: In this work, Cell Counting Kit-8 (CCK-8) and colony formation assays were used to evaluate the efficacy of cetuximab. Glycolysis/oxidative phosphorylation (OXPHOS) Assay Kit was applied to assess metabolic activity. Human Phospho-Kinase Array and RNA sequencing were employed to screen targets of butyrate. Overexpression plasmids and short hairpin RNAs (shRNAs) targeting these molecules were transfected into cells for further validation. Subcutaneous tumor and pulmonary metastasis models were used for in vivo studies.

RESULTS: The findings showed that physiological concentrations of butyrate increased cetuximab resistance in KRAS wild-type cells only. Further investigation found that butyrate upregulated EGFR signaling through facilitating the binding reaction between epidermal growth factor (EGF) and EGFR. In parallel, butyrate activated AMP-activated protein kinase (AMPK)-wild-type p53-induced phosphatase 1 (Wip1) signaling, leading to suppression of p53 and p38 mitogen-activated protein kinase (p38 MAPK)-mediated pro-apoptotic signaling. These two mechanisms are the reason that butyrate attenuates the efficacy of cetuximab. Results of subcutaneous tumor and pulmonary metastasis models exhibited a similar conclusion to in vitro experiments.

CONCLUSION: Butyrate reduces cetuximab efficacy in KRAS wild-type colorectal cancer through EGFR and AMPK-Wip1 signaling, and may represent a candidate predictive biomarker for treatment response.},
}

*Colorectal Neoplasms/drug therapy/pathology/metabolism
*Cetuximab/pharmacology
Humans
ErbB Receptors/metabolism/antagonists & inhibitors
Signal Transduction/drug effects
*AMP-Activated Protein Kinases/metabolism
*Butyrates/pharmacology/blood
Animals
Mice
Cell Proliferation/drug effects
Drug Screening Assays, Antitumor
*Adaptor Proteins, Signal Transducing/metabolism
*Antineoplastic Agents, Immunological/pharmacology
Neoplasms, Experimental/drug therapy/pathology/metabolism
Dose-Response Relationship, Drug
Mice, Nude
Tumor Cells, Cultured

@article {pmid41868349,
year = {2026},
author = {Liang, J and Huang, T and Li, J and Yang, Z and Ni, J and Wang, Y},
title = {The chemistry of the nitrate-nitrite-nitric oxide pathway: regulating muscle oxygenation and exercise performance.},
journal = {RSC advances},
volume = {16},
number = {17},
pages = {15723-15735},
pmid = {41868349},
issn = {2046-2069},
abstract = {Nitric oxide (NO) is a pleiotropic signaling molecule fundamentally involved in regulating skeletal muscle physiology, including blood flow, contractility, and metabolism. For decades, the synthesis of NO was attributed solely to the l-arginine-dependent nitric oxide synthase (NOS) enzymes. However, the discovery and characterization of the nitrate-nitrite-NO pathway have revealed an alternative, NOS-independent mechanism for NO generation. This pathway is particularly significant under hypoxic and acidic conditions, which are characteristic of exercising skeletal muscle. Dietary inorganic nitrate, abundant in green leafy vegetables and beetroot, is sequentially reduced to nitrite and then to bioactive NO. This review critically examines the intricate chemistry underpinning this pathway, from the initial enzymatic reduction of nitrate by both mammalian and microbial reductases to the diverse chemical routes of nitrite reduction to NO within the muscle milieu. We delve into the specific roles of key proteins such as xanthine oxidoreductase, deoxyhemoglobin/deoxymyoglobin, and mitochondrial complexes in catalyzing these transformations. Furthermore, we explore how NO generated via this pathway modulates muscle oxygenation through vasodilation and regulation of mitochondrial respiration. The ergogenic potential of dietary nitrate supplementation is discussed in the context of human exercise performance, highlighting the significant controversies, methodological challenges, and sources of inter-individual variability, including genetics and the microbiome. This review aims to provide a comprehensive, chemistry-focused perspective on the nitrate-nitrite-NO pathway, bridging fundamental biochemical mechanisms with their physiological consequences in exercise.},
}

@article {pmid41868361,
year = {2026},
author = {Zhang, Y and Pang, Y and Tan, H and Xian, R and Liang, J and Wen, Q and Li, Z and Yan, L and Xie, Z and Li, J and Fu, W and Zhou, P},
title = {Electroacupuncture alleviates comorbid obesity and depression via the gut-brain axis: orchestrating SCFA-producing bacteria and hippocampal synaptic plasticity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1772788},
pmid = {41868361},
issn = {1664-302X},
abstract = {INTRODUCTION: Comorbid obesity and depression (COMBD) represents a complex metabolic-neuropsychiatric challenge with limited therapeutic options. While Electroacupuncture (EA) is effective for both metabolic and mood disorders, the systemic mechanisms-particularly the interplay between the gut microbiome and hippocampal plasticity-remain elusive.

METHODS: We established a COMBD rat model using a high-fat diet combined with chronic unpredictable mild stress (CUMS). An integrated multi-omics approach comprising 16S rDNA sequencing, LC-MS/MS serum metabolomics, and hippocampal transcriptomics was utilized to decipher the therapeutic mechanisms of EA.

RESULTS: EA treatment significantly attenuated body weight gain and reversed depressive-like behaviors. Crucially, EA restructured the dysbiotic gut microbiota, specifically increasing the abundance of short-chain fatty acid (SCFA)-producing bacteria. This microbial restoration was strongly correlated with a reprogrammed serum metabolic profile. In the hippocampus, transcriptomic analysis identified Cd74 as a pivotal upstream regulator modulated by EA. Furthermore, EA mitigated hippocampal oxidative stress and restored synaptic plasticity, evidenced by increased dendritic spine density and upregulated synaptic protein expression.

CONCLUSION: Our findings suggest that EA ameliorates COMBD via a coordinated "Microbiota-Metabolism-Brain" axis. Specifically, EA creates a neuroprotective milieu by promoting beneficial SCFA-producing bacteria and regulating metabolic signals, which subsequently targets hippocampal Cd74 to restore synaptic plasticity. This study provides a novel mechanistic basis for the clinical application of EA in treating complex metabolic-mood comorbidities.},
}

@article {pmid41868364,
year = {2026},
author = {Yin, J and Wang, H and Cui, Y and Zhou, X and Zhang, S and Yin, H},
title = {Bacteriophage-mediated gut microbiota regulation: a bibliometric landscape analysis (2005-2024).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768117},
pmid = {41868364},
issn = {1664-302X},
abstract = {OBJECTIVE: This study systematically evaluates the current situation, knowledge structure and development trend of bacteriophage-mediated intestinal microbiota regulation research from 2005 to 2024 through literature measurement analysis.

METHOD: Retrieve relevant research from the Web of Science core collection, Scopus and PubMed databases. After screening according to inclusion criteria, CiteSpace, VOSviewer, and R-bibliometrix were employed for bibliometric and visualization analysis. This systematically mapped publication trends, collaboration networks among countries/institutions/authors, core journals, and research hotspots.

RESULTS: Thousands of relevant studies were included. From 2005 to 2024, the number of papers published in microbiology journals showed a step-by-step increase, reaching a peak of 355 articles in 2022. The United States and China are the main contributors. University College Cork in Ireland and San Diego State University in the United States have become core research institutions, and Colin Hill is listed as the most influential author. The Frontiers in Microbiology has published the largest number of papers, and Microbiome and Nature Communications have become platforms for the publication of high-impact research results. The research focus has shifted from the description of early bacteriophage-bacterial binary interaction to exploring the ternary relationship of "bacteriophage-microbiota-host health." In recent years, short-chain fatty acids, microbiota disorders and clinical intervention have become the core research directions. This study included 16 clinical trials on phage-mediated gut microbiota regulation, 14 of which were based on moderate to high-quality clinical evidence, indicating that research design in this field has advanced from the initial observational stage to the intervention verification stage.

CONCLUSION: This research systematically sorts out the research progress of 20 years in the field of bacteriophage-mediated intestinal microbiota regulation through the method of literature metrology. The research clearly outlines the evolutionary trajectory of this field from basic description to mechanism exploration to clinical transformation. Future research should focus on the following directions: clarifying the molecular mechanism of the interaction of core diseases, establishing a standardized research framework, and carrying out large-scale multi-center clinical trials to promote the transformation of this field from basic research to clinical application.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

TRIAL REGISTRATION NUMBER: ISRCTN23947730.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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