@article {pmid41676100,
year = {2026},
author = {Liu, C and Chen, Y},
title = {The current consensus on ulcerative colitis, and the evidence and perspectives on the influence of gut microbiota on it.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1735850},
pmid = {41676100},
issn = {2296-858X},
abstract = {Ulcerative colitis (UC) is a chronic non-specific inflammatory disease, the pathogenesis is not clear, there is no clinical cure. The number of cases of UC has increased worldwide in recent years due to industrialization and social pressures. At present, the therapeutic effectiveness of UC remains controversial. Although researchers have conducted certain studies on the pathogenesis of UC, its pathogenesis and anti-UC pathogenesis have not been fully revealed. Previous studies have found a close relationship between human gut microbes and UC, and may be the most important measure of UC for clinical judgment. Many studies have linked UC to disruption of the gut microbiome, which is one of the most important features of UC. This paper reviews the clinical characteristics, pathogenesis and current treatment strategies of UC, and reviews the interaction between intestinal flora and UC as well as the therapeutic effects of intestinal flora, providing reference for the prevention and treatment of UC.},
}

@article {pmid41676065,
year = {2026},
author = {Liu, Y and Huang, S and Zhang, Y and Zhang, Y and Xu, Y and Tang, Y and Guo, S and Zhang, Z},
title = {Microbial dysbiosis in cholangiocarcinoma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1727736},
pmid = {41676065},
issn = {1664-302X},
abstract = {Cholangiocarcinoma (CCA) is a highly aggressive malignancy of the biliary epithelium, with its incidence and mortality rates continuing to rise worldwide. Advances in high-throughput sequencing and metabolomic technologies have intensified interest in elucidating the role of the microbiome in CCA. Microbial dysbiosis may contribute to tumor initiation and progression by inducing chronic inflammation, altering metabolic pathways, and modulating the immune microenvironment. Moreover, these microbial alterations have been associated with therapeutic resistance, underscoring their potential impact on disease progression and treatment outcomes. This review summarizes the potential origins of intratumoral microorganisms and the microbiome alterations associated with distinct CCA subtypes. Crucially, we critically evaluate the methodological challenges inherent to low-biomass biliary samples-including contamination risks and confounding factors such as cholestasis and medical interventions-and distinguish between associative and causal evidence in current literature. Collectively, this work aims to provide a rigorous theoretical framework and novel insights for microbiome-based strategies in the early diagnosis and treatment of CCA.},
}

@article {pmid41676061,
year = {2026},
author = {Qiao, X and Yan, X and Dong, C and Tao, L and Aili, A and Waheed, A},
title = {From microbiome collapse to recovery: a roadmap for microbiome-informed grassland restoration under global change.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741287},
pmid = {41676061},
issn = {1664-302X},
abstract = {Grassland ecosystems depend on soil- and plant-associated microbiomes that regulate nutrient cycling, soil structure formation, plant health, and stress tolerance. This review synthesizes recent progress on how grassland microbiomes are assembled across rhizosphere, endosphere, and bulk soil niches, and how degradation drivers (e.g., overgrazing, drought, salinization, and nutrient enrichment) disrupt microbial diversity, network stability, and functional guilds, often shifting communities toward reduced mutualist capacity and greater disease risk. We then evaluate restoration strategies that aim to re-establish beneficial microbial functions through practices such as organic amendments, inoculation with mycorrhizae or plant growth-promoting microbes, and management approaches that promote habitat recovery and microbial recolonization. Despite rapid advances in sequencing and observational studies, major gaps remain: (i) limited causal evidence linking microbiome changes to process rates (e.g., nitrification, phosphorus mobilization) across field gradients; (ii) underrepresentation of soil viral ecology and its consequences for microbial regulation and ecosystem function; (iii) inconsistent persistence and context-dependence of introduced inoculants; and (iv) a lack of standardized, outcome-oriented indicators for "restoration-ready" microbiomes. Future research should integrate multi-omics with process-based measurements and long-term field experiments, develop locally adapted microbial consortia with monitoring of non-target effects, and strengthen risk assessment and governance frameworks to enable safe, scalable microbiome-informed grassland restoration under global change.},
}

@article {pmid41676058,
year = {2026},
author = {Sivamaruthi, BS and Kesika, P and Chaiyasut, C and Ragu Varman, D},
title = {Gut dysbiosis in neurodevelopmental disorders: linking microbiota signatures to cognitive rigidity in autism spectrum disorder.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1760635},
pmid = {41676058},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterised not only by social-communication difficulties but also by restricted interests, stereotyped behaviours, and marked cognitive rigidity. Over the past decade, converging lines of evidence have implicated gut dysbiosis, an imbalance in intestinal microbial composition and function, as a potentially important modulator of these behavioural phenotypes via the microbiota-gut-brain axis. In this narrative review, we integrate preclinical and clinical data to examine how specific microbial signatures, metabolic pathways, and immune and synaptic mechanisms may contribute to inflexible cognition in ASD. The manuscript outlines the organisation of the microbiota gut-brain axis in neurodevelopment and summarises reproducible microbial alterations reported in ASD cohorts. We then discuss how microbial metabolites, including short-chain fatty acids and tryptophan-derived neuroactive molecules, as well as immune mediators and neurotransmitter precursors, converge on pathways regulating excitatory-inhibitory balance, synaptic plasticity, and corticostriatal circuit function. Evidence from germ-free, genetic, and environmental rodent models provides causal support for microbiota-dependent modulation of repetitive and rigid behaviours, whilst clinical studies reveal associations between dysbiosis, metabolomic profiles, gastrointestinal symptoms, and ASD severity. Finally, we consider the translational landscape of microbiota-targeted interventions, probiotics, prebiotics, dietary strategies, and faecal microbiota transplantation and highlight key methodological and ethical challenges for moving toward precision microbiome-based therapies. Taken together, current data support gut dysbiosis as both a mechanistic contributor and a tractable therapeutic target for cognitive rigidity in ASD.},
}

@article {pmid41675883,
year = {2026},
author = {Amjad, A and Batool, ST and Ali, U and Mahato, RK},
title = {Gut microbiome metaproteomics for colorectal cancer risk stratification: moving from taxonomic signatures to functional protein biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2112-2113},
doi = {10.1097/MS9.0000000000004567},
pmid = {41675883},
issn = {2049-0801},
}

@article {pmid41675866,
year = {2026},
author = {Mehmood, MS and Qamar, T and Amjad, F and Danaf, N},
title = {Bacterial co-infection as a catalyst in HPV-associated cervical carcinogenesis.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {1176-1177},
pmid = {41675866},
issn = {2049-0801},
abstract = {Cervical cancer remains a preventable yet persistent global burden, with more than 660 000 new cases and 360 000 deaths reported in 2024. While high-risk HPV is the central driver of malignant transformation, growing evidence shows that bacterial co-infection can intensify HPV persistence and promote genomic instability. Meta-analyses now indicate that pathogens such as Chlamydia trachomatis, Mycoplasma genitalium, Gardnerella vaginalis, and diverse anaerobic microbiota markedly increase the risk of persistent HPV infection and cervical lesions. These microbes disrupt epithelial barriers, fuel chronic inflammation, and enhance the oncogenic activity of HPV E6/E7. Studies also show that Lactobacillus-depleted vaginal communities carry higher viral loads and increased CIN2[+] progression. A 2024 review from sub-Saharan Africa further highlights frequent bacterial co-infections among HPV-positive women, particularly in settings with limited vaccination and screening. Together, these findings support a dual-pathogen model of cervical carcinogenesis and underscore the need to integrate microbiome-focused strategies into prevention efforts.},
}

@article {pmid41675854,
year = {2026},
author = {Imtiaz, E and Mahato, RK and Tahir, A},
title = {Patient-specific precision microbiome modulation: rethinking therapeutic strategies in IBD.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2138-2139},
pmid = {41675854},
issn = {2049-0801},
}

@article {pmid41675847,
year = {2026},
author = {Ali, MR and Devi, S and Jawed, M and Irshad, NUN and Imran, SB},
title = {Gut-brain axis in neurology: microbiome as a modifiable risk factor for multiple sclerosis.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2158-2159},
pmid = {41675847},
issn = {2049-0801},
}

@article {pmid41675768,
year = {2026},
author = {Beniwal, SS and Janu, Y and Cummings, K and Syed, S and Everton Assunção Ribeiro da Costa, R and Dahiya, P and Jeong, Y and Cabe Cacas, A and Mwaanga, C and Kotaich, J},
title = {Sex steroid receptors in colorectal cancer: implications for tumor progression, therapeutic opportunities, and sex-specific outcomes.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {1427-1436},
pmid = {41675768},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) is a common malignancy with high incidence and mortality. Hormone signaling pathways, including estrogen, progesterone (P4), and androgen receptors (ARs), influence tumor development and progression and offer potential therapeutic opportunities. This study investigates the role of sex steroid receptors in CRC, explores therapeutic strategies, and considers sex-specific implications. Multiple cohort studies were analyzed based on gender, age, clinical stage, and tumor location. A structured literature search was conducted across PubMed, Web of Science, and Google Scholar, selecting studies with relevant sex-specific data and study designs. ERβ exhibits antitumor effects, with lower levels linked to tumors in females, while ERα and AR promote growth, particularly in postmenopausal women. Progesterone receptors (PGRs) are associated with poorer prognosis, though P4 treatment inhibits CRC cell proliferation. Malignant tissues show increased ERα and AR but decreased ERβ and PGR. ER isoforms' mRNA is lower in malignant females, and AR expression is higher in males. Women more often develop proximal colon tumors (reduced ERβ) and men develop distal tumors, reflecting nuanced gene transcription modulation by ERα, ERβ, and G-protein coupled estrogen receptor (GPER). The mechanism of P4's protective effect remains unclear. Variability in cell lines, hormone concentrations, receptor expression, and hormone replacement therapy outcomes complicates interpretation, as do interactions between cytokines and estrogen signaling in the tumor microenvironment. Future strategies include combined ERβ and PGR activation, sequential estrogen-P4 therapy for early stage CRC, and simultaneous therapy for advanced cases. Research should clarify sex hormone roles, advance prognostic markers, explore selective estrogen receptor modulators, target ERβ pharmacologically, and investigate gut microbiome influences for tailored interventions.},
}

@article {pmid41675731,
year = {2026},
author = {Mehmood, MS and Iqbal, I and Hajj, F},
title = {Microbial metabolites from gut bacteria as novel anti-cancer agents.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2096-2097},
pmid = {41675731},
issn = {2049-0801},
abstract = {Recent evidence highlights the potential of gut microbial metabolites as promising anticancer agents, with mechanisms distinct from those of conventional chemotherapeutics. Short-chain fatty acids, particularly butyrate, exhibit histone deacetylase inhibitory activity, leading to apoptosis and cell-cycle arrest in colorectal and breast cancers. Reuterin, a redox-active metabolite of Lactobacillus reuteri, selectively induces oxidative stress and suppresses tumo growth in vivo. Likewise, secondary bile acids such as lithocholic acid demonstrate dose-dependent antineoplastic properties, while inosine has been shown to potentiate PD-1 blockade efficacy by enhancing T-cell activation. Additionally, bacteriocins derived from lactic acid bacteria reveal selective cytotoxicity and immunomodulatory effects, representing biocompatible therapeutic scaffolds. The novelty of these metabolites lies in their ability to target epigenetic, metabolic, and immune pathways simultaneously, offering a multidimensional approach to tumor control. Harnessing these microbial molecules through synthetic optimization, delivery innovations, and integrative clinical trials could revolutionize cancer therapeutics by merging microbiome science with precision oncology.},
}

@article {pmid41675714,
year = {2025},
author = {Wang, C and Lin, J and Duan, M and He, J and Halizere, S and Chen, N and Chen, X and Jiao, Y and He, W and Dyar, KA and Yang, F and Zhu, S},
title = {Multi-omics reveals different signatures of obesity-prone and obesity-resistant mice.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e59},
pmid = {41675714},
issn = {2996-9514},
abstract = {Obesity-prone (OP) and obesity-resistant (OR) individuals demonstrate significant metabolic differences, potentially influenced by variations in the gut microbiome. However, the influence of host-microbiota interactions on obesity susceptibility remains unknown. We performed an integrative multi-omics approach to explore microbial, metabolic, and genetic differences in high-fat diet (HFD)-fed OP and OR mice, with additional analyses of gut microbiota variations in humans. In OP mice, the dynamic gut microbiota was characterized by a stable presence of Longibaculum, while Kineothrix predominated in OR mice. We termed both as keystone bacteria. Beyond these, eight dominant bacterial genera were significantly associated with bile acid metabolites and amino acids. Three of these genera were also identified in OR humans and showed positive correlations with genes that may support intestinal barrier function. We identified 22 specific amino acid profiles as potential biomarkers for obesity susceptibility, along with significantly increased levels of ten non-12-OH bile acids in fecal of OR mice. In vivo, mouse experiments demonstrated that ursodeoxycholic and hyodeoxycholic acids could reduce HFD-induced obesity. Additionally, the colon of OP mice displayed a higher presence of inflammatory cells. These findings suggest that host-microbiota interactions may contribute to phenotypic differences between OP and OR. Our study offers insights into crucial intestinal markers associated with obesity, providing a valuable resource for advancing the understanding of obesity-prone and obesity-resistant phenotypes.},
}

@article {pmid41675707,
year = {2025},
author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L},
title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e62},
pmid = {41675707},
issn = {2996-9514},
abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.},
}

@article {pmid41675303,
year = {2026},
author = {Siani, R and Si, Y and Thaqi, SK and Stabl, G and Gutjahr, C and Schloter, M},
title = {Loss of the flagellar regulator FlhC changes the transcriptional response of plant-associated Acidovorax delafieldii strains to metabolites from Rhizophagus irregularis-colonized Lotus japonicus roots.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf235},
pmid = {41675303},
issn = {2730-6151},
abstract = {Acidovorax is a cosmopolitan bacterial genus comprising both beneficial and pathogenic plant-associated species. In plant-associated bacteria, flagella can facilitate colonization but also trigger plant immune responses driving mutation or loss of flagella in some strains. FlhC is an important transcriptional regulator of flagella assembly genes. Here, we investigated whether it modulates root colonization and the transcriptional response of plant-commensal Acidovorax strains to different plant cues. As model cues, we used root extracts from Lotus japonicus that forms symbioses with arbuscular mycorrhiza fungi (AMF), which strongly change root metabolism and add their own metabolites. To offer different stimuli to Acidovorax bacteria, we used extracts from L. japonicus roots colonized or not with the AMF Rhizophagus irregularis. We investigated two Acidovorax delafieldii strains with almost identical genomes but differences in the presence or absence of flhC. Overall, loss of flhC resulted in distinct expression profiles and a more modular transcriptional network. Pathway analysis linked flhC to genes associated with stress tolerance, nutrient mobilization, biofilm formation, secretion, surface attachment, and quorum sensing. Root extracts from mycorrhizal roots induced increased expression of genes associated with substrate preference and downregulation of genes involved in biofilm formation and secretion. flhC-deficient strains also responded with increased expression of genes related to surface attachment and vitamin biosynthesis. The absence of flhC correlated with increased root colonization and influenced the response of Acidovorax to R. irregularis in planta. Our findings highlight that a flagellar regulator in root-associated bacteria influences root colonization and transcriptional responses to host cues.},
}

@article {pmid41675273,
year = {2025},
author = {Yue, H and Shen, P and Huang, Q and Lin, S and Shen, J and Wang, Y and Sun, Z and Qi, X and Jiang, Y and Yuan, C and Zou, D and Zheng, Y and Yang, C},
title = {Associations Between Dietary Habits, Oral Microbiota, and Dental Caries in Adolescents.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {6},
pages = {633-645},
pmid = {41675273},
issn = {2730-5848},
abstract = {UNLABELLED: Suboptimal dietary habits, such as excessive consumption of sugary foods and beverages, have been associated with a higher risk of dental caries. While known cariogenic species enrichment in the oral microbiome correlating with dental caries, the complex interactions between dietary habits, the oral microbiota, and dental caries among adolescents remain underexplored. Here, we examined the comprehensive associations between dietary habits, oral microbiota, and dental caries among 421 adolescents (mean age: 12.9 years, 28% having dental caries). The dietary data were collected via a food frequency questionnaire, dental health was examined by a skilled dentist, and the saliva microbiota was profiled by 16S ribosomal RNA sequencing. Significant difference in the oral microbial composition was observed between participants with and without dental caries (p-value < 0.05), which was replicated in an external adult population (n = 580). The relative abundances of 19 genera were associated with dental caries in adolescents independent of gender (all FDR-adjusted p-values < 0.20). For example, dental caries was linked with a higher abundance of Prevotella and Veillonella, both of which were also enriched in higher consumer of sugary food and beverage. In mediation analysis, certain caries-related genera, including Staphylococcus and Paludibacteraceae F0058, might partially mediate the associations between dietary habits and dental caries (p-mediation < 0.05). This research highlighted the role of oral microbiota in the association between dietary intakes and dental caries and may explain the potential mechanisms by which diet affects dental caries.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00208-3.},
}

@article {pmid41675168,
year = {2025},
author = {Qin, F and Zhang, M and Yang, Q and Wu, L and Mao, T and Zhou, X and Li, J and Lai, M},
title = {Interactions between Parabacteroides goldsteinii CCUG 48944 and diet ameliorate colitis in mice via regulating gut bile acid metabolism.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70008},
pmid = {41675168},
issn = {2996-9514},
abstract = {Inflammatory bowel disease (IBD) is a chronic disorder linked to an increased risk of colorectal cancer (CRC) and is characterized by significant dysbiosis in the gut microbiota. The commensal bacterium Parabacteroides goldsteinii (P. goldsteinii) has shown potential in modulating host metabolism and inflammatory responses. In this study, we investigated the probiotic properties of P. goldsteinii and its mechanism of action in IBD models, with a particular focus on bile acid metabolism and diet-microbiota interactions. Fecal samples from patients with ulcerative colitis (n = 14), Crohn's disease (n = 22), and healthy controls (n = 13) were analyzed to assess P. goldsteinii relative abundance. In dextran sulfate sodium (DSS)-induced colitis and azoxymethane (AOM)/DSS-induced CRC mouse models, administration of P. goldsteinii significantly attenuated inflammation and tumorigenesis, particularly under fiber-free diet conditions. Metabolomic profiling revealed an enrichment of secondary bile acids in P. goldsteinii-treated mice, suggesting a link between bile acid metabolism and its anti-inflammatory effects. Further mechanistic studies using bile salt hydrolase inhibitors and Tgr5 knockout mice confirmed the role of bile acid regulation in mediating the therapeutic benefits of P. goldsteinii. Additionally, we found that dietary factors significantly influenced the colonization and metabolic activity of P. goldsteinii, thereby modulating its probiotic efficacy. This highlights the potential for microbiome-based therapies tailored to specific dietary contexts in the treatment of IBD. Our findings demonstrate that P. goldsteinii can modulate gut bile acid metabolism to alleviate colitis, making it a promising candidate for probiotic applications in IBD management, with dietary modulation enhancing its therapeutic potential.},
}

@article {pmid41675166,
year = {2025},
author = {Shao, MW and Chen, HJ and Huang, AQ and Zheng, L and Li, CJ and Qin, D and Sun, YH and Lin, Z and Fu, G and Chen, YH and Li, YJ and Dong, ZY and Cheng, P and Pramono, H and Yu, GH and Xu, ZM and Miao, S and Hyde, KD},
title = {Modulation of rhizosphere microbiota by Bacillus subtilis R31 enhances long-term suppression of banana Fusarium wilt.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70006},
pmid = {41675166},
issn = {2996-9514},
abstract = {Continuous cropping of bananas leads to Fusarium wilt, affecting crop health, yet employing biocontrol bacteria to modulate rhizosphere microbial communities may offer effective disease suppression. This study revealed the secondary succession characteristics of rhizosphere microbiota in banana fields after more than 5-year continuous cropping and assessed the suppressive effects induced by biocontrol strain Bacillus subtilis R31. Through high-throughput sequencing, we observed a convergent enrichment of core bacterial genera Burkholderia-Dyella and Arthrobacter-Ralstonia in naturally suppressive and R31-treated suppressive soils, indicating broad-spectrum disease-suppressive soil traits induced by R31. R31 significantly enhanced associations between Streptomyces and the rhizosphere core community while weakening Burkholderia's linkage with membrane transport and energy metabolism pathways; moreover, it strengthened positive correlations between Rhizobium and terpenoid and polyketide metabolism (r = 0.65, p < 0.01). Culture-dependent assays showed that among 46 isolates from root and rhizosphere, those with high activities of indole-3-acetic acid, protease, cellulase, chitinase, and β-1,3-glucanase exhibited pronounced antagonistic activities against Fusarium oxysporum. Although R31 was undetectable in the rhizosphere in the second year, its modulation of rhizosphere function persisted, displaying a "legacy effect" consistent with the priority effects theory, whereby early colonizing beneficial communities resist subsequent pathogen invasions. R31 induced functional bacteria colonization in nascent banana root hair tissues, establishing new microbiome patterns that contributed to long-term disease suppression. Pot experiments further indicated that endophytic bacteria within roots exhibited stronger Fusarium wilt control than rhizosphere isolates. However, single-strain treatments frequently led to sheath rot co-infection, suggesting that synergistic actions of multiple strains might be more effective for disease suppression. This study highlighted R31's potential to sustainably modulate the rhizosphere microbiome, enhance enzyme activity, and promote beneficial bacteria colonization, laying the groundwork for constructing efficient synthetic bacterial communities for biocontrol.},
}

@article {pmid41675162,
year = {2025},
author = {Lyu, Y and Shen, J and Che, Y and Dai, L},
title = {Skin microbiome engineering: Challenges and opportunities in skin diseases treatment.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70012},
pmid = {41675162},
issn = {2996-9514},
abstract = {The skin microbiome, consisting of a vast array of microorganisms, is essential for human skin health, aiding in barrier protection, immune regulation, wound repair, and defense against pathogens. Disruptions in this microbial balance are closely linked to the onset and worsening of various skin disorders. This review evaluates the potential of skin microbiome engineering as a therapeutic strategy for treating skin diseases. We discuss nontargeted approaches like probiotics and fecal microbiota transplantation that aim to reshape the microbial community, as well as targeted methods such as phage therapy, phage lysins, and engineered bacteria, which specifically modulate microbial populations or influence the skin environment. These approaches open new avenues for personalized dermatological treatments. Despite significant progress, challenges remain in the clinical translation of microbiome-based therapies. Safety, standardization, regulatory approval, and long-term ecological stability must be addressed to ensure efficacy and reproducibility in clinical settings, underscoring the critical need for further research in their dermatological applications.},
}

@article {pmid41675159,
year = {2025},
author = {Zhang, Q and Wang, N and Zhang, F and Chen, B and Wang, Y and Wang, Z and Zhao, C and Jin, C and Sheng, D and Yue, K and Jiang, D and Gao, L and Zhang, H and Kang, Z and Cheng, M and Ma, X and Wang, H and Hu, D and Wang, J and Liu, Y and Zhou, C and Yao, M and Zhao, G and Wang, Y and Wang, Z and Ning, K and Zhang, L},
title = {Transfer learning identifies bacterial signatures for cross-regional diagnosis of type 2 diabetes and enable stage-sensitive dietary fiber intervention.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70021},
pmid = {41675159},
issn = {2996-9514},
abstract = {DeepMicroFinder is a deep learning framework designed to update the existing disease diagnosis model to generate a transfer model by leveraging region-specific microbiome datasets and transfer learning approach. This framework effectively overcomes the limitation of regional effects in the gut microbiome, enabling accurate cross-regional disease detection. Microbial markers related to type 2 diabetes (T2D) were identified by DeepMicroFinder, and subsequently validated in independent T2D cohorts undergoing dietary fiber interventions.},
}

@article {pmid41675154,
year = {2025},
author = {Liu, Y and Li, Z and Zhang, C and Li, B and Jiang, W and Li, H and Zhang, L and Zhen, H and Bao, S and Li, X and Liu, Y and Chen, X and Du, J and Xia, J and Wang, J and Guo, R and Sun, Y and Pan, B and Lei, W and Xiao, L and Zhao, J and Jin, X and Zhang, W and Liu, X and Wang, J and Chen, M and Liao, W and Fang, W and Nie, C and Pan, W},
title = {A human skin microbiome reference catalog and the skin microbial landscape of plateau adults.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70000},
pmid = {41675154},
issn = {2996-9514},
abstract = {Comprehensive reference genomes are needed for the classification and functional characterization of the human skin microbiota. Here, we established human skin microbiome genome (HSMG) and protein (HSMP) catalogs by integrating 739 newly sequenced and 2,520 published samples, along with two published microbial genome catalogs. The HSMG includes 3547 prokaryotic species, of which 1556 (43.87%) are unidentified, and the HSMP contains 39,283,339 nonredundant proteins, with 64.8% of which are poorly characterized. Using the HSMG as a reference, we identified distinct features and biogeographical traits of the skin microbiome in plateau adults, revealing significant differences between sebaceous and dry skin, with 1784 of 3547 inferred prokaryotes showing considerable variation. Additionally, host characteristics, skincare, and daylight habits were found to shape the skin microbiome. This work expands our understanding of the diversity of uncultured skin bacteria and provides a comprehensive characterization of the human skin microbiome in plateau environments.},
}

@article {pmid41675153,
year = {2025},
author = {Ye, L and Hu, Q and Zang, T and Wang, Y and Heng, H and Chan, EWC and Chen, S},
title = {Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70004},
pmid = {41675153},
issn = {2996-9514},
abstract = {The pork microbiome was investigated using an integrated approach combining isolation and metagenomic sequencing methods to comprehensively analyze the pathogens and resistome on pork surfaces. The study revealed a large number and diversity of pathogens and resistance genes, potentially originating from air, transportation, water, or cross-contamination. These findings underscore the importance of implementing multifaceted food surveillance strategies to monitor and mitigate these risks effectively.},
}

@article {pmid41675150,
year = {2025},
author = {Du, Y and Wang, Z and Liu, K and Chai, G and Chi, Y and Li, T and Duan, Y and Xia, T and Liu, D and Che, R},
title = {The performance of different methods in characterizing soil live prokaryotic diversity and abundance is highly variable.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70011},
pmid = {41675150},
issn = {2996-9514},
abstract = {The long-term persistence of extracellular DNA in soils is well-documented, yet its impacts on analyzing soil microbial abundance and diversity remain controversial. This primarily arises from our limited comprehension regarding the reliability of various methods for studying soil live microbiotas. In this study, we systematically compared and assessed commonly used methods for studying live soil microbial abundance and diversity, including alkaline buffer washing, propidium monoazide (PMA) treatment, DNase pre-digestion, and rRNA-based analysis, using soils collected from a wide range of locations across China. We found that the elimination of extracellular DNA substantially influenced the analysis of soil prokaryotic abundance, diversity, community profiles, and co-occurrence patterns, but not community assembly mechanisms. However, the effects varied considerably across different methods. DNase pre-digestion and PMA treatment led to significant decreases in prokaryotic abundance, while alkaline buffer washing and rRNA-based analysis had negligible effects. As for prokaryotic richness, DNase pre-digestion and rRNA-based analysis significantly decreased and increased it, respectively. Although 67.8% of amplicon sequence variants were shared, significant differences in their relative abundance were observed across various methods. While the removal of extracellular DNA simplified the co-occurrence network, it also enhanced its robustness. According to the assessment experiments, DNase pre-digestion showed the highest extracellular DNA removal efficiency and live prokaryotic characterizing accuracy. Concerns for other methods include low DNA removal efficiency, instability, and uncertainties in result explanation. This study suggests that soil live prokaryotic diversity and abundance characterized by different methods exhibit high variability, and DNase pre-digestion is recommended for characterizing soil live prokaryotic communities. These findings provide crucial information for optimizing soil microbiome research methodologies.},
}

@article {pmid41675055,
year = {2026},
author = {Matthews, JL and Ferrier-Pagès, C and Moorhead, J and Peixoto, RS and Raubenheiemer, D and Roger, LM and Suggett, DJ and Tresguerres, M and van Oppen, MJH and Voolstra, CR and Camp, EF},
title = {Advancing reef recovery through insights into coral nutrition.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114747},
pmid = {41675055},
issn = {2589-0042},
abstract = {Coral reefs support immense biodiversity and human well-being, yet accelerating environmental change demands new strategies to strengthen reef resilience. Across ecological systems, balancing nutritional supply with organismal demand is fundamental to performance and persistence, but this principle has been rarely applied to corals. We propose a nutritional ecology framework that links coral physiological requirements with environmental nutrient supply and quality. By systematically addressing critical knowledge gaps of coral physiological requirements - including nutrient balance, quality, acquisition, and allocation - and integrating these with environmental nutrient data, a nutritional ecology framework can identify mismatches between nutritional requirements and availability that impact coral performance under stress. These insights provide a foundation for advancing restoration practices, from site selection to propagation effectiveness, while opening opportunities for interventions such as targeted nutrient supplementation or microbiome-based nutrient enhancement.},
}

@article {pmid41675043,
year = {2026},
author = {Zeng, S and Xie, Q and Zhang, R and Yang, T and Liu, D and Zhang, J and Ma, S and Qiu, X},
title = {Butyrate ameliorates doxorubicin-induced heart failure by inhibiting cardiomyocyte ferroptosis through the gut-heart axis.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114754},
pmid = {41675043},
issn = {2589-0042},
abstract = {Doxorubicin (DOX), a widely used chemotherapeutic agent, is clinically limited by DOX-induced heart failure (DIHF). Emerging evidence links gut microbial dysbiosis to exacerbating DIHF progression, yet the mechanisms remain elusive. Herein, we established a rat DIHF susceptibility model to investigate the gut microbiota's regulatory role. Multi-omics analyses indicated that DIHF severity was associated with reduced butyrate-producing bacteria and systemic butyrate levels. Sodium butyrate (NaB) significantly alleviated DOX-induced cardiomyocyte toxicity and DIHF. Mechanistically, NaB strengthened the colonic and cardiac barrier functions and reduced gut microbiota translocation to the heart and cardiac lipopolysaccharide (LPS) accumulation. NaB altered cardiac bacterial composition and functions, reduced cardiac Fe[2+] levels, and inhibited cardiomyocyte ferroptosis. Further results confirmed that NaB mitigated DOX-induced ferroptosis via the GPX4/GSH pathway. Collectively, this study indicated that butyrate ameliorates DIHF by inhibiting cardiomyocyte ferroptosis through the gut-heart axis, providing translational potential for microbiota-targeted cardioprotective strategies in DIHF.},
}

@article {pmid41675042,
year = {2026},
author = {Lung, CF and Lu, HH and Chung, CY and Lin, PT and Hsu, YC},
title = {A systematic review of microgravity on reproductive systems: Implications for space biology and human health.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114663},
pmid = {41675042},
issn = {2589-0042},
abstract = {Microgravity poses risks to mammalian reproductive health by altering gametogenesis, fertilization, and embryonic development. This review summarizes evidence from spaceflight and ground-based microgravity analogs, together with radiation exposures, showing disruptions in spermatogenesis, oogenesis, and pre-implantation embryo development that depend on cell type, exposure duration, and experimental platform. Mechanistic studies indicate that microgravity and radiation can trigger oxidative stress, DNA damage, mitochondrial dysfunction, and epigenetic alterations, potentially reducing gamete quality and embryo viability. We also highlight extracellular vesicles as key mediators of gamete maturation, fertilization, and implantation; microgravity-related changes in EV biogenesis or cargo may further impair reproductive success. In addition, spaceflight-associated microbiome shifts-including emerging evidence on reproductive-tract microbiomes-may influence fertility via immune dysregulation and inflammation. Finally, we discuss countermeasures such as artificial gravity, dietary and antioxidant/radioprotective strategies, and reproductive technologies, and outline priorities for future research to safeguard reproductive health in space and advance reproductive medicine on Earth.},
}

@article {pmid41674906,
year = {2025},
author = {Hoy, P and Hassenrück, C and Mittermayer-Schmittmann, F and Schmittmann, L and Jürgens, K},
title = {Microbiome changes in the sponge Halichondria panicea along the Baltic Sea salinity gradient.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1723082},
pmid = {41674906},
issn = {1664-302X},
abstract = {The Baltic Sea is characterized by a strong salinity gradient, which impacts the diversity and composition of free-living macro- and microorganisms. Much less is known about how host-associated microorganisms are affected by decreasing salinities. Marine sponges are known to harbor complex prokaryotic communities, relevant for the host's health and functions. This raises the question of whether and how the sponge microbiomes are also subject to changes along the declining salinity of the South-western Baltic Sea. We analysed the microbiome of the dominating sponge, the marine demosponge Halichondria panicea, from high saline conditions (28.3 PSU) in the Kattegat to the Eastern limit of its distribution at lower salinities (11.4 PSU). We utilized a dual approach of 16S rRNA gene metabarcoding of sponge and seawater microbiomes, together with the absolute quantification of the total prokaryotic sponge community and the main bacterial symbiont, the alpha-proteobacterium Ca. Halichondribacter symbioticus (Ca. H.s.), by digital droplet PCR (ddPCR). All sponge microbiomes originating from the same location shared a highly similar prokaryotic community, clearly different from the surrounding water, and dominated by the known symbiont Ca. H.s. In addition, location-specific bacterial genera, enriched in the sponge microbiomes, were also found (e.g., Endozoicomonas, Shewanella, Ekhidna). Sponge microbiomes at the Eastern limit of the distribution of H. panicea, with the lowest salinity, showed a higher sponge microbiome diversity and an increased similarity between sponge and water microbiomes. Furthermore, at the lowest salinity, absolute bacterial abundance increased while Ca. H.s. remained at relatively stable absolute abundances. These observations were paired with a notable trend of decreasing body volume of sponge individuals, indicating lower fitness at the lowest salinities. We hypothesize that the observed shifts under low salinity conditions, with an increased occurrence of bacterial taxa from the surrounding water, reflect potential early signs of dysbiosis of the sponge microbiome, coinciding with the occurrence at their distribution limit. This study provides a first insight into the effects of changing salinity on the microbiome of H. panicea in the Baltic Sea, and on the shifts in sponge microbiomes that occur in environmental gradients such as the challenging environment of the Baltic Sea.},
}

@article {pmid41674903,
year = {2025},
author = {Ding, Z and Ren, K and Xu, Y and Feng, T and Cui, K and Liu, Q and Liao, C},
title = {Disease-driven restructuring of the gut microbiome underlies inflammatory bowel disease dysbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1744574},
pmid = {41674903},
issn = {1664-302X},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent intestinal disorder with rising global incidence, yet its complex pathogenesis remains poorly understood, underscoring the need to clarify the microbial mechanisms underlying intestinal inflammation. IBD is associated with a profound imbalance of the gut microbial ecosystem. However, the ecological and functional remodeling of the gut microbiota during IBD progression remains unclear. This study used metagenomic sequencing to investigate microbial composition, functional capacity, and ecological interactions in the gut microbiota of IBD patients compared with healthy individuals.

RESULTS: The IBD group exhibited significantly reduced microbial diversity and a distinct community structure compared with healthy controls. Pro-inflammatory genera such as g_Fusobacterium (p < 0.001) and g_Morganella (p < 0.001) were enriched, whereas short-chain fatty acid producing bacteria, including g_Ruminococcus (p < 0.0001) and g_Agathobacter (p < 0.0001), were markedly depleted. Functional annotation revealed decreased abundance of carbohydrate-active enzymes (GH3, GH44, GH53, and GH77; all p < 0.05) associated with polysaccharide degradation, together with enrichment of pathways related to immune activation and inflammation, such as the JAK-STAT and chemokine signaling pathways (p < 0.05). Co-occurrence network analysis further showed that IBD-associated microbes formed positively correlated clusters dominated by inflammatory taxa, whereas healthy microbiota were organized around SCFA-producing commensals.

CONCLUSION: Compared with healthy individuals, the gut microbiota of IBD patients undergoes functional reprogramming characterized by loss of metabolic versatility and enrichment of inflammation-related pathways. These findings provide new insights into the ecological and metabolic mechanisms through which the gut microbiota contribute to intestinal inflammation and disease progression.},
}

@article {pmid41674859,
year = {2026},
author = {Wang, Z and Kumar, A and Singh, R and Azevedo, LCB and Solanki, MK},
title = {Editorial: Engineering plant-microbiomes to improve the health of economic crops.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1782531},
pmid = {41674859},
issn = {1664-462X},
}

@article {pmid41674758,
year = {2026},
author = {Nadella, H and Armstrong, JL and Greenwald, R and Johnson, K and Kesselman, MM},
title = {Microbiome Differences in Preeclampsia Versus Lupus Nephritis.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e101296},
pmid = {41674758},
issn = {2168-8184},
abstract = {Preeclampsia (PE) and lupus nephritis (LN) share clinical features of hypertension, proteinuria, and systemic inflammation, reflecting overlapping immune dysregulation. Both conditions involve activation of pro-inflammatory cytokines and endothelial dysfunction, which contribute to organ damage. They also exhibit similarities in their microbiomes, including reduced diversity and loss of beneficial immunoregulatory taxa, which may exacerbate systemic inflammation. Despite similarities, they differ in etiology. PE results from placental dysfunction, whereas LN arises from autoimmune-driven renal injury. PE is associated with enrichment of pro-inflammatory microbes, which contribute to endothelial dysfunction and impaired trophoblast invasion. In contrast, LN exhibits gut dysbiosis involving expansion of pro-inflammatory species and depletion of protective immunoregulatory taxa, promoting intestinal permeability and renal inflammation. These shared, disease-specific microbiome features suggest potential for diagnostic differentiation and help guide future microbiome-targeted therapies.},
}

@article {pmid41674736,
year = {2026},
author = {Mukenschnabl, K and Humpel, O and Abdalla, TE and Wood, E},
title = {An Unusual Case of Unexplained Infertility: Co-colonization of the Uterus and Seminal Fluid.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e101251},
pmid = {41674736},
issn = {2168-8184},
abstract = {Chronic endometritis (CE) is defined as a persistent, mild inflammation of the endometrium induced by intrauterine bacterial infection. CE has been associated with infertility in patients with recurrent in vitro fertilization (IVF) failure. We report an unusual case of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility. A 35-year-old woman presented to the office for infertility evaluation after 16 months of inability to conceive naturally using ovulation kits. Initial workup revealed adequate ovarian reserve with an anti-Müllerian hormone (AMH) level of 4.8 ng/mL, tubal patency on hysterosalpingogram, and normal semen analysis. The patient and her partner failed to conceive following three cycles of ovulation induction with intrauterine insemination (IUI). In preparation for IVF, an endometrial biopsy (EMB) was performed, and five CD138+ plasma cells per 10 high-power fields suggested CE. The patient underwent antibiotic therapy, yet EMB remained positive. At this time, the partner's semen culture was positive for Enterococcus faecalis and Escherichia coli. Endometrial microbiome metagenomic analysis (EMMA) and analysis of infectious chronic endometritis (ALICE) demonstrated co-colonization with the same bacteria seen on her partner's semen culture. Both the patient and her partner required multiple rounds of antibiotic therapy before successful conception via IVF. This case demonstrates an unusual occurrence of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility, suggesting a potential pathway for CE development from bacteriospermia. The patient's EMMA/ALICE tests and the partner's semen cultures revealed the presence of the same bacteria. While current literature does not identify the development of CE from the bacteria in a partner's semen, there is an association between bacteria in semen and infertility. In couples with unexplained infertility, thorough evaluation for CE with EMB and EMMA/ALICE can be performed in conjunction with a semen culture on the partner to explore potential co-colonization and guide dual-partner treatment.},
}

@article {pmid41674645,
year = {2026},
author = {Kusters, C and Santos Cabrera, J and Zhang, Y and Zhang, Y and Huang, T and Chung, J and Yu, B and Qi, Q and Alcantara, C and Tarraf, W and Perreira, KM and Arens, R and Ramos, AR and Daviglus, ML and Zee, PC and González, HM and Isasi, CR and Redline, S and Sofer, T},
title = {Insomnia-Related Metabolomic Profiles Reflect Antioxidant Deficits and Relate to Cognitive Decline Through a Metabolic Risk Score in HCHS/SOL.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.04.26345594},
pmid = {41674645},
abstract = {BACKGROUND: We aimed to identify metabolites and create risk scores for insomnia symptoms in U.S. Hispanic/Latino adults.

METHODS: We analyzed data from 6,107 participants in the Hispanic Community Health Study/Study of Latinos, split into discovery (n=3,932) and replication datasets (n=2,175). Serum metabolites and the Women's Health Initiative Insomnia Rating Scale (WHIIRS) were collected at baseline. We examined the relationships between 768 metabolites and insomnia symptoms and suspected insomnia (WHIIRS≥9) using the discovery dataset, followed by replication. Metabolite risk scores (MRSs) were generated with LASSO regression and evaluated for replication. We assessed the relationships of replicated metabolite measures and MRS with sleep, cognitive, and psychological traits (cross-phenotypes).

FINDINGS: Nine metabolites were associated with insomnia symptoms in the discovery study, with two of these being replicated. Lower levels of hydrocinnamate and indolepropionate correlated with increased insomnia symptoms. We developed MRS for insomnia symptoms with replication. Various associations were observed between the two metabolites, 2 MRS, and cross-phenotypes. For instance, the WHIIRS MRS was associated with a higher risk of mild cognitive impairment (MCI) seven years later (OR:1.58, 95%CI:1.43-1.74 per 1 SD increase in MRS).

INTERPRETATION: The metabolomic profile associated with insomnia symptoms encompasses diet and gut microbiome metabolites. This study identified specific metabolites linked to insomnia that are also related to comorbidities, such as a higher risk of developing MCI during follow-up, suggesting a shared mechanism.

FUNDING: Grants from various National Institutes of Health and the JLH Foundation supported the work.

RESEARCH IN CONTEXT: Evidence before this study: Insomnia affects 30-36% of individuals, with clinical insomnia estimated at 6-10%, and it is more severe among Hispanics, who also face higher risks for cognitive decline and cardiovascular disease. While previous metabolomics studies have investigated sleep disorders, most have focused on sleep apnea or sleep duration, not insomnia. The few studies that focus on insomnia were limited by small sample sizes or co-occurring psychiatric conditions. Only two large-scale studies linked insomnia symptoms to specific metabolites, but neither examined these associations in Hispanics or their connection to cognitive decline-gaps this study aims to address using data from the HCHS/SOL cohort.Added value of this study: We identified nine metabolites related to insomnia symptoms, with two-hydrocinnamate and indolepropionate-being replicated. We also created and validated metabolite risk scores (MRS), which predicted a higher likelihood of developing mild cognitive impairment (MCI) seven years later. These results provide new insights into the metabolic pathways connecting insomnia and cognitive decline in a high-risk Hispanic population.Implications of all the available evidence: Our findings indicate that insomnia symptoms are linked to specific metabolic changes, some of which may also play a role in cognitive decline. Identifying metabolites related to diet and the gut microbiome points to biological pathways that could be modified through lifestyle or therapeutic interventions. The metabolite risk scores (MRS) developed in this study showed links with mild cognitive impairment (MCI) over time, suggesting their potential usefulness in understanding long-term health risks associated with sleep disturbances. These results encourage further research into the role of metabolomics in sleep and cognitive health, especially in high-risk populations like Hispanics.},
}

@article {pmid41674640,
year = {2026},
author = {Nirmalan, S and Arif, S and Wei, J and Priya, S and Blekhman, R and Pique-Regi, R and Luca, F},
title = {Host genotypes interact with microbial communities to modulate gene expression in the human intestine.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.30.26344673},
pmid = {41674640},
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is characterized by chronic intestinal inflammation and is associated with both altered gut microbiome composition and host genetic risk. Both host genetic variants and the gut microbiome can affect host gene expression in the colon; however, it remains unclear whether interactions between the two (genotype x microbiome, GxM) shape intestinal gene regulation in humans and their contribution to IBD risk.

METHODS: We analyzed publicly available data for 86 individuals (64 patients with IBD and 22 controls) in the Inflammatory Bowel Disease Multi'omics Database consisting of host genotype, host gene expression, and mucosal gut microbiome (16S rRNA) data from rectal and ileum biopsies. We performed expression Quantitative Trait Locus (eQTL) mapping and then used computational fine-mapping to identify likely causal variants. We tested whether microbial taxa modify genetic effects on host gene expression. We then integrated GxM eQTLs with IBD, Crohn's Disease (CD) and Ulcerative Colitis (UC) Genome-Wide Association Study results by leveraging Transcriptome-Wide Association Studies and colocalization methods.

RESULTS: We found 3,777 and 3,694 host genes with eQTLs in the rectum and in the ileum, respectively (FDR = 10%). Using the fine-mapped eQTLs, we found 36 GxM interactions for 31 host genes with 22 microbial taxa in the rectum and 30 GxM interactions in the ileum for 15 host genes and 20 taxa (FDR = 10%). Taxa with GxM interactions clustered into two distinct groups with opposing effects on host gene regulation and reflected distinct functions of microbes in the gut. i.e, butyrate producers versus sulfate reducers. Integration with IBD GWAS revealed that 23 variants with GxM regulated the expression of host genes putatively causal for IBD, CD or UC (FDR = 10%), thus identifying microbes that can either amplify or buffer genetic risk.

CONCLUSIONS: Our results show evidence of genetic effects on host gene expression that are modulated by microbiome composition, and provide insight into how IBD risk could be reduced by targeting specific microbial taxa contingent on host genotype.},
}

@article {pmid41674628,
year = {2026},
author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA},
title = {Plant-based whole-food diets are feasible during autologous stem cell transplantation and are associated with dose-dependent microbiome modulation: Results from a pilot clinical trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.26345403},
pmid = {41674628},
abstract = {Plant-based dietary strategies may offer a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked to infectious complications and inferior survival. We conducted a single-arm study to test the feasibility and biological activity of a high-fiber, plant-based, whole-food meal delivery intervention during the peri-transplant period. Adults with multiple myeloma (n = 22) received fully prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting consumption of nutrient-dense, high-fiber foods despite transplant-related symptoms that often limit oral intake. The primary endpoints were feasibility and tolerability, defined by successful enrollment, adherence to study procedures, and patient-reported intake of study meals; diet was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming at least some proportion of delivered meals and with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. Larger randomized trials are warranted to determine whether microbiome-targeted nutrition can reduce transplant-related toxicities, enhance immune recovery, and improve disease control in multiple myeloma. The trial is registered at ClinicalTrials.gov (NCT06559709).},
}

@article {pmid41674595,
year = {2026},
author = {Liang, N and Mahmoudiandehkordi, S and Heston, MB and Kaushik, P and Powell, WR and Karu, N and Dempsey, DA and Labus, JS and Schimmel, L and Blach, C and Kueider-Paisley, A and Brydges, C and Huynh, K and Mandal, R and Quirke, MV and Brewer, JB and Henderson, VW and Chen, DS and Swerdlow, RH and Taylor, M and Wisniewski, T and Roberson, ED and Craft, S and Miller, JB and Foroud, TM and Faber, KM and Amin, N and Wishart, DS and Saykin, AJ and Bendlin, BB and Brosch, JR and Meikle, PJ and Kind, AJ and Borkowski, K and Kaddurah-Daouk, RF and , and , },
title = {The Metabolome as a Readout for Adverse Social Exposome Influences on Human Health - A Roadmap for Modifiable Factors and Proactive Health.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.26344798},
pmid = {41674595},
abstract = {The exposome factors, such as diet, lifestyle, microbiome, chemical exposures and social exposome, shapes human health beyond genetic influences, but the mechanisms remain only partially understood. Leveraging the Area Deprivation Index (ADI) of Neighborhood Atlas, a validated measure of the US social exposome, we derive molecular insights on how adverse social exposome (ASE) may impact cardiometabolic and brain health. Using complementary metabolomics platforms, we measured blood metabolome as readouts on net influences of exposome factors. Participants from six Alzheimer's disease research centers (n=449) were studied with generalizability confirmed in the UK Biobank using its harmonizable metric for ASE (n=380,943). Our results suggest that participants living in ASE have metabolic features often shown to predispose individuals to higher risks for cardiovascular diseases and cognitive decline, with impaired mitochondrial energetics, amino acid and lipid metabolism. Diet, microbiome and chemical exposures may contribute to these metabolic features. Molecular insights from metabolic signatures for ASE allows us to map potential modifiable risk factors that can impact and sustain health including brain health.},
}

@article {pmid41674575,
year = {2025},
author = {Zhang, Z and Xu, Y and Pang, K and Wu, C and Zhao, C and Lei, T and Zhang, J and Hai, T and Zhao, F and Zhao, Y},
title = {Microbiota humanization drives human-like metabolic and immune transcriptomic shifts in pigs.},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70034},
pmid = {41674575},
issn = {2996-9514},
abstract = {Pigs are increasingly recognized as promising candidates for clinical xenotransplantation and as large-animal models for biomedical research; however, interspecies differences in gut microbiota, immune function, and metabolism remain major barriers. To address this, we established gut microbiota-humanized (GMH) pigs by transplanting human fecal microbiota into antibiotic-treated pigs. We systemically evaluated alterations in microbiota composition, serum metabolites, and immune cell profiles using integrated metagenomic, quasi-targeted metabolomic and single-cell transcriptomic (scRNA-seq) analyses. Metagenomic profiling revealed a shift in the intestinal microbiota of GMH pigs toward a human-like composition, characterized by enrichment of Bacteroidia and depletion of Bacilli. Metabolomic analysis showed that GMH pigs exhibited serum metabolite profiles more closely resembling those of humans. Among 423 detected serum metabolites, 136 that were lower in control pigs than in humans were upregulated in GMH pigs, whereas 79 that were elevated in control pigs decreased post-transplantation. Notably, pathways related to tryptophan metabolism, bile acid biosynthesis, and fatty acid metabolism were enhanced in GMT pigs, while carbon-related and glycolytic pathways were attenuated, indicating partial convergence toward human metabolic phenotype. Integration of microbial and metabolite data identified 20 and 33 metabolites associated with Bacteroidia and Bacilli, respectively. scRNA-seq profiling of peripheral blood mononuclear cells demonstrated transcriptional and compositional remodeling of T cells, monocytes, and B cell subsets in GMH pigs. These findings demonstrated that human fecal microbiota can reshape both systemic metabolic and immune artitecture in pigs, offering a robust large-animal platform for studying host-microbiota interactions and advancing translational application in xenotransplantation and microbiome-based therapeutics.},
}

@article {pmid41674572,
year = {2025},
author = {Foxx, AJ and Rivers, AR},
title = {A cautionary tale of batch corrections on confounded microbiome community profiles.},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70025},
pmid = {41674572},
issn = {2996-9514},
abstract = {We use a case study of seed microbiomes to assess the performance of five batch effects correction algorithms (BECAs) (zero-mean centering (ZMC), Ratio-A, conditional quantile regression (ConQuR), partial least squares discriminant analysis (PLSDA), and weighted PLSDA on a confounded data set in which the covariate of interest (plant species) does not appear in all batches (studies). We show incomplete batch effects removal in all cases, which calls for careful application of and future work on BECAs.},
}

@article {pmid41674571,
year = {2025},
author = {},
title = {Correction to "Multiomics integration unravels genotype-microbiome interactions shaping the conjunctival transcriptome".},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70033},
doi = {10.1002/imo2.70033},
pmid = {41674571},
issn = {2996-9514},
abstract = {[This corrects the article DOI: 10.1002/imo2.37.].},
}

@article {pmid41674568,
year = {2025},
author = {Sun, X and Zhang, J and Chen, J and Yang, L and Pang, X and Chen, X and Chen, Y and Zhang, Y and Chen, A},
title = {A portable device for probiotic counting and viability assessment based on microfluidic chip and image recognition.},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70045},
pmid = {41674568},
issn = {2996-9514},
abstract = {Probiotics play a critical role in maintaining or improving gut microbiome balance, offering numerous health benefits. Therefore, the accurate quantification of viable probiotics is essential for ensuring the efficacy of probiotic products. However, traditional culture-based methods are cumbersome and time-intensive, limiting their applications in scenarios requiring real-time decisions. Here, we report a portable, cost-effective system (approximately $2 per test, including reagents and one-time microfluidic chip usage) that enables rapid (3 min) on-site quantification of viable probiotics through a microfluidic chip integrated with a fluorescent biosensor and advanced image recognition technology. The system's reliability and accuracy were validated by comparison with the standard flow cytometry and plate counting, with results showing no significant differences in viable probiotics numbers. Furthermore, the platform demonstrated excellent specificity in distinguishing dead probiotics from viable ones with a large quantification range of 10[7]-10[11] colony-forming units (CFU) mL[-1], which encompasses the concentration range of commonly encountered probiotics, thereby meeting practical detection requirements. In summary, this portable system offers an innovative solution for rapid, on-site identification, and precise quantification of live and dead probiotics. Given these attributes, the system demonstrates significant commercial potential, particularly in situations requiring immediate results and efficient decision-making.},
}

@article {pmid41674565,
year = {2025},
author = {Jiang, CH and Fang, X and Huang, W and Wang, YH and Kang, L and Wang, PY and Xu, C and Li, ZS and Zou, WB and Liao, Z},
title = {A reciprocal interaction between L-lysine and Holdemanella biformis modulates intestinal barrier function and anxiety in irritable bowel syndrome.},
journal = {iMetaOmics},
volume = {2},
number = {3},
pages = {e70042},
pmid = {41674565},
issn = {2996-9514},
abstract = {Irritable bowel syndrome (IBS) is a prevalent stress-associated disorder characterised by gut barrier dysfunction and gut-brain axis disturbances. However, the interplay between host metabolites and gut microbes in IBS pathogenesis remains incompletely understood. Here, through integrated microbiome and metabolome profiling of faecal sample from seafarers before and after long-term voyages, we identify a reciprocal interaction between the essential amino acid l-lysine and the gut bacterium Holdemanella biformis (H. biformis). l-lysine was depleted in individuals with voyage-induced IBS, whereas H. biformis abundance increased concurrently. In a mouse model of diarrhoea-predominant IBS, l-lysine supplementation restored intestinal barrier integrity, reduced visceral hypersensitivity, and alleviated anxiety-like behaviours through modulation of tryptophan metabolism. In contrast, oral administration of H. biformis improved tight junction protein expression but paradoxically worsened anxiety-like phenotypes. In vitro, both l-lysine and H. biformis supernatant promoted epithelial wound healing and ZO-1 expression. Mechanistically, H. biformis degrades l-lysine via lysine degradation pathway, while l-lysine suppresses H. biformis growth possibly by downregulating pathways involved in carbohydrate and energy metabolism. These findings reveal a stress-sensitive, bidirectional metabolic loop in between l-lysine and H. biformis, with complementary but opposing effects on gut and neurological function. Targeting this axis may offer new strategies for IBS and other gut-brain axis disorders.},
}

@article {pmid41674531,
year = {2026},
author = {Barry, N and Landreville, KD and Blackwood, D and Yard, JK and Noble, R and Kuzma, J},
title = {Experiences with household mold and perceptions of microbiome engineering to mitigate mold.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1725172},
pmid = {41674531},
issn = {2296-2565},
mesh = {Humans ; *Fungi ; Male ; Female ; *Microbiota ; North Carolina ; Middle Aged ; Adult ; *Family Characteristics ; Qualitative Research ; Aged ; Interviews as Topic ; *Air Pollution, Indoor/prevention & control ; Housing ; },
abstract = {BACKGROUND: Mold, biologically defined as fungal mold, is frequently identified as a household concern, especially in humid and coastal regions where conditions favor growth. Yet, the ways residents recognize, experience, and manage mold in their daily lives remain understudied. In recent years, emerging mold-control strategies, such as microbiome-engineering technologies, are increasing in application and attracting the interest of homeowners. However, these technologies raise important questions about community perceptions, trust, and acceptance. Understanding how people navigate everyday mold management and views on novel interventions is essential for guiding effective, market-relevant, socially-responsive solutions.

METHODS: This qualitative study draws on 22 interviews with residents of eastern North Carolina, an area with climate conditions that favor fungal molds. Using the Health Belief Model (HBM) as a framework, we explored participants' conceptualizations of mold, perceived health and structural impacts, prevention strategies, and views on microbiome-engineering remediation technologies.

RESULTS: Residents understood mold in diverse ways, as a fungus, a dampness-driven growth, and a sensory presence tied to smell and sight. Mold was linked to respiratory illness, systemic health effects, property damage, and financial burdens. Participants employed layered strategies such as ventilation, dehumidification, cleaning, and occasional professional remediation, though cost, trust, and perceived effectiveness of these strategies remained barriers. Analysis through the HBM revealed high perceived severity of the mold problem and related health illness but underestimation of susceptibility due to reliance on visible cues. Reactions to microbiome-engineered tools showed cautious interest: while residents acknowledged potential benefits, they expressed concerns about unintended consequences, invisibility, and loss of control. Conditional acceptance was contingent on rigorous testing, transparent regulation, and proven safety and efficacy.

CONCLUSION: Mold is experienced by Eastern NC residents not only as a biological contaminant but as a lived, socio-environmental challenge shaped by health, housing, and financial vulnerabilities. Participants in this study indicated serious health concerns related to mold, including after specific events such as large storms and flooding. Acceptance of microbiome-engineering solutions will depend on building trust, addressing equity, and ensuring accessibility. By bridging environmental science, social science, and residents' lived experiences, policies and technologies can more effectively strengthen resilience against one of the most persistent risks in the built environment.},
}

Humans
*Fungi
Male
Female
*Microbiota
North Carolina
Middle Aged
Adult
*Family Characteristics
Qualitative Research
Aged
Interviews as Topic
*Air Pollution, Indoor/prevention & control
Housing

@article {pmid41674481,
year = {2026},
author = {Ben Yahia, S and Lam, AVW and Cabuta, M and Nielsen, M and Helderman, NC},
title = {A multilevel perspective on MSH6-associated Lynch syndrome: Integrating molecular, biological, and clinical insights.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70381},
pmid = {41674481},
issn = {1097-0215},
abstract = {Lynch syndrome (LS) is the most common hereditary colorectal cancer syndrome, caused by a germline pathogenic variant in one of the mismatch repair (MMR) genes. Among these, MSH6-associated LS represents a distinct subtype with unique molecular and clinical characteristics. Despite its relatively high prevalence (~1 in 758 individuals) compared with MLH1- (1 in 1946) and MSH2-associated LS (1 in 2841), MSH6-associated LS remains underrepresented in research and clinical guidelines. To bridge this knowledge gap, we reviewed current literature on molecular, biological, and clinical aspects of MSH6-associated LS. From a biological perspective, loss of MSH6 function results in a relatively low degree of microsatellite instability and potentially slower tumor progression compared with other LS subtypes. Nevertheless, tumor immunogenicity of MSH6-associated colorectal cancers appears preserved, supporting responsiveness to immune checkpoint inhibitors. Clinically, pathogenic MSH6 (path_MSH6) variant carriers have a unique tumor spectrum, characterized by a relatively lower colorectal cancer penetrance (~8.1%-44%) compared with path_MLH1 and path_MSH2 carriers, but a relatively high endometrial cancer risk (~16%-44%), with a median age of onset approximately a decade later than that observed for path_MLH1 or path_MSH2 carriers. Phenotypic heterogeneity among path_MSH6 carriers may reflect contributions from modifier genes, environmental exposures, microbiome composition and/or the individual's HLA type. Recognition of the distinct biology of MSH6-associated LS and its clinical implications highlights the importance of gene-specific precision in clinical care, such as initiating colonoscopy surveillance at a later age (30-35 years) and performing it every 2-3 years.},
}

@article {pmid41674471,
year = {2026},
author = {Figura, M and Milanowski, Ł and Nowak, JM and Antoniak, A and Kopczyński, M and Zając, W and Sadowski, K and Hołubiuk, Ł and Walęcik-Kot, W and Szlufik, S and Friedman, A and Kaczmarczyk, B and Biliński, J and Koziorowski, D},
title = {Safety and Efficacy of Fecal Microbiota Transplantation in Alleviating Symptoms of Parkinson's Disease: A Randomized, Placebo-Controlled, Double-Blinded Study.},
journal = {Annals of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ana.78153},
pmid = {41674471},
issn = {1531-8249},
support = {2021//Biocodex Microbiota Foundation National Grant/ ; NZP/1/Z/GW/N/21//Medical University of Warsaw/ ; 09/M/MBS/N/21//Medical University of Warsaw/ ; 1/Z/MG/24//Medical University of Warsaw/ ; NZP/1/Z/MG/N/23//Medical University of Warsaw/ ; M/MG/77/22//Medical University of Warsaw/ ; },
abstract = {OBJECTIVES: Changes in the gut microbiome may be involved in the pathogenesis and progression of Parkinson's disease (PD). This randomized, placebo-controlled, double-blinded study aimed to assess the effects of fecal microbiota transplantation (FMT) on the manifestation of the motor symptoms of PD (The Movement Disorders Society - Unified Parkinson's Disease Rating Scale Part III [MDS-UPDRS III]) over a 12 month long observation and non-motor symptoms as secondary objectives: the Movement Disorders Society-Non-Motor Rating Scale; EuroQol-5 Dimension; PD Quality-of-Life Questionnaire; Montreal Cognitive Assessment (MoCA); UPDRS I, II, and IV; Gastrointestinal Dysfunction Scale for PD; modified Constipation Assessment Scale; and levodopa equivalent dose.

METHODS: The patients were randomly assigned to receive either fecal microbiota (Mbiotix, Human Biome Institute) or placebo (auto-fecal microbiota, prepared from the patient's stool) in a 1:1 ratio. The fecal microbiota transplantation was performed via colonoscopy. Assessments were performed before and after 12 months for the MoCA and at 1, 3, 6, and 12 months for the other scales. Intention-to-treat analysis was performed using a multivariable mixed regression model.

RESULTS: Of the 59 patients included, 28 were randomly assigned to the Mbiotix group (median age = 65 years; 15 male patients) and 31 to the placebo group (median age = 63 years; 14 male patients). No significant differences were observed in the MDS-UPDRS III "OFF" state score at 12 months between groups (1.50 points, 95% confidence interval [CI] = -4.28 to 7.28, p = 1.00), however, some non-motor symptoms improved in different study timepoints.

INTERPRETATION: A single FMT does not influence motor symptoms manifestation in patients with PD but could improve non-motor functioning via gut-brain axis. Trial registration information: Clinical Trial ID NCT05204641 was submitted on November 29, 2021. The first patient was enrolled on January 4, 2022. ANN NEUROL 2026.},
}

@article {pmid41674277,
year = {2026},
author = {Alarcón-Sánchez, MA and Henao-Díaz, V and Escoto-Vasquez, LS and Martínez-Nieto, M and González-Alvarez, GE and Muradyan, AA and Heboyan, A and Lomelí-Martínez, SM},
title = {Impact of hepatitis C virus on oral health: Clinical lesions, immunopathology, and dental management: A narrative review.},
journal = {International journal of immunopathology and pharmacology},
volume = {40},
number = {},
pages = {3946320261419189},
doi = {10.1177/03946320261419189},
pmid = {41674277},
issn = {2058-7384},
mesh = {Humans ; *Oral Health ; *Hepacivirus/immunology/pathogenicity ; *Hepatitis C/immunology/drug therapy/virology/complications ; Antiviral Agents/therapeutic use ; Periodontal Diseases/virology/immunology ; *Mouth/virology/immunology/pathology ; *Mouth Diseases/virology/immunology ; },
abstract = {Hepatitis C virus (HCV) infection is a major global public health problem. Although it has traditionally been linked to liver damage, several studies have demonstrated its extrahepatic impact, specifically in the oral cavity. Oral manifestations can be considered early signs of infection or contribute to clinical progression. This narrative review aims to describe the oral alterations associated with HCV, integrating the pathophysiological mechanisms and clinical implications for dental management. The most prevalent manifestations include periodontal disease, oral lichen planus, Sjögren's syndrome-like sialadenitis, and squamous cell carcinoma of the oral cavity. Recent findings suggest that HCV triggers dysbiosis of the oral microbiome, promotes exacerbated immune responses with overproduction of pro-inflammatory cytokines, and disrupts the homeostatic environment, thereby promoting the progression of inflammatory and neoplastic diseases. In addition, viral RNA has been identified in saliva and gingival crevicular fluid, which could be considered a non-parenteral route of transmission, particularly important in dental interventions. In parallel, direct-acting antiviral therapy, in addition to achieving virus elimination, could also partially correct immunological and microbial disruptions in the cavity, with favorable clinical responses. Understanding these oral alterations can guide dentists in early detection and improve systemic outcomes.},
}

Humans
*Oral Health
*Hepacivirus/immunology/pathogenicity
*Hepatitis C/immunology/drug therapy/virology/complications
Antiviral Agents/therapeutic use
Periodontal Diseases/virology/immunology
*Mouth/virology/immunology/pathology
*Mouth Diseases/virology/immunology

@article {pmid41674227,
year = {2026},
author = {Nguyen, TT and Dao, T and Nguyen, HT and Park, JH and Jeong, SJ and Kim, S and Jo, Y and Thieu, NTH and Zhao, J and Ding, F and Yu, Y and Dung, VC and Gariani, K and Kim, BJ and Ryu, D},
title = {Sarcopenia and Muscle Aging: Updated Insights into Molecular Mechanisms and Translational Therapeutics.},
journal = {Endocrinology and metabolism (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.3803/EnM.2025.2656},
pmid = {41674227},
issn = {2093-5978},
abstract = {Sarcopenia is a progressive, age-related condition characterized by the loss of skeletal muscle mass, strength, and function, which increases the risk of falls, frailty, and loss of independence. Despite growing recognition and its incorporation into geriatric assessments, there is still no approved pharmacological treatment. This review provides an updated overview of sarcopenia, encompassing diagnostic criteria, biological mechanisms, and emerging therapeutic strategies. Key molecular features include mitochondrial dysfunction, nicotinamide adenine dinucleotide (NAD[+]) decline, fiber-type alterations, and dysregulation of myokines. Recent singlecell and multi-omics studies have revealed the heterogeneity of muscle tissue and distinct cell-type-specific aging patterns. Therapeutic efforts are evolving beyond lifestyle interventions toward targeted approaches, including myostatin inhibitors, NAD[+] boosters, senolytics, and microbiome modulators. However, clinical translation remains constrained by heterogeneity in trial design and the absence of standardized outcome measures. Future sarcopenia care will likely involve precision medicine guided by biomarkers and supported by digital monitoring tools. Progressing from molecular discovery to clinical application will be essential for preserving muscle health and function in aging populations.},
}

@article {pmid41674171,
year = {2026},
author = {Qiao, Y and Gao, X},
title = {Investigating the Interplay between the Gut Microbiota and Host Immunity in Gastroenteric Disorders: The Potential of Combined Drug Therapies to Restore Microbial-immune Homeostasis.},
journal = {Iranian journal of allergy, asthma, and immunology},
volume = {25},
number = {1},
pages = {32-44},
doi = {10.18502/ijaai.v25i1.20434},
pmid = {41674171},
issn = {1735-5249},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Gastrointestinal Diseases/drug therapy/immunology/microbiology ; Retrospective Studies ; Homeostasis ; Adult ; Drug Therapy, Combination ; *Irritable Bowel Syndrome/drug therapy/immunology/microbiology ; Treatment Outcome ; Aged ; },
abstract = {This study examines the interaction between the microbiota and the immune system in diseases of the gastrointestinal tract, with a special emphasis on the synergistic use of pharmacological agents. This was a retrospective, observational study of 100 patients with moderate to severe gastrointestinal disorders, including irritable bowel syndrome and inflammatory bowel disease, receiving control, monotherapy, or combination therapy. Over 12 weeks, combination therapy demonstrated superior efficacy in enhancing gut microbial diversity. Improvements were achieved in alpha diversity, and a decrease in inflammatory indices and a shift in the immune phenotype were observed. Patients experienced significant improvements in symptom severity, pain, and general health. In addition, the general health of patients also improved. Importantly, the combination therapy group had better responses compared with the other groups. With respect to the identified factors, regression analysis revealed that microbial diversity, immune system regulation, and inflammation had positive effects on disease symptom alleviation. These findings therefore help support the perspective of combination therapy as a more comprehensive mode of approaching and treating gastroenteric diseases.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
Male
Female
Middle Aged
*Gastrointestinal Diseases/drug therapy/immunology/microbiology
Retrospective Studies
Homeostasis
Adult
Drug Therapy, Combination
*Irritable Bowel Syndrome/drug therapy/immunology/microbiology
Treatment Outcome
Aged

@article {pmid41674105,
year = {2026},
author = {Song, B and Zeb, J},
title = {The midgut of Aedes albopictus shapes its bacteriome but not its mycobiome.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70505},
pmid = {41674105},
issn = {1526-4998},
support = {//City University of Hong Kong/ ; },
abstract = {BACKGROUND: Midgut microbiota consists mainly of bacteria and fungi and can interact directly or indirectly with ingested pathogens. However, both the specific microbes that stably colonize the mosquito midgut and how the midgut shapes their microbiome remain poorly understood. In this study, we analyzed the midgut microbiome of the insect vector Aedes albopictus at three different developmental stages collected from the field. Additionally, we reared field-collected larvae under laboratory conditions, using either field water from the breeding habitat or sterilized water, to track the linear evolution of the microbiome from larvae to adulthood.

RESULTS: Our metagenomic analysis revealed that the mosquito host selected specific bacterial species, while the mycobiome remained virtually identical to that of the surrounding water. We identified 42 core bacterial species that form a highly interactive network, as well as two core fungal species, both of which were consistently more abundant in the mosquito gut than in the surrounding water across all life stages in both laboratory and field conditions. Furthermore, we successfully assembled 271 bacterial genomes de novo, 14 of which belonged to core species. These 14 bacterial genomes were enriched in genes associated with antioxidant function and cAMP metabolism.

CONCLUSION: This study uncovers fluctuating bacterial dynamics alongside conserved fungal communities in the mosquito gut, suggesting distinct mechanisms that shape the bacteriome and mycobiome. This study highlights the antioxidant function in stabilizing bacteria in Aedes albopictus. © 2026 Society of Chemical Industry.},
}

@article {pmid41674065,
year = {2026},
author = {Jo, S and Seo, H and Lee, KA and Kim, S and Rahim, MA and Barman, TI and Kim, HS and Song, HY},
title = {Skin Microbiome Profiling in Patients with Primary Sjögren Disease Compared to Healthy Individuals.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510010},
doi = {10.4014/jmb.2510.10010},
pmid = {41674065},
issn = {1738-8872},
mesh = {Humans ; *Sjogren's Syndrome/microbiology ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Female ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification ; Adult ; DNA, Bacterial/genetics ; Aged ; Biodiversity ; Case-Control Studies ; Sequence Analysis, DNA ; Skin Microbiome ; },
abstract = {Primary Sjögren disease (SjD) is a systemic autoimmune disease characterized by inflammation of exocrine glands, most commonly leading to dry mouth and dry eyes. Although the etiology of SjD remains unclear, emerging evidence suggests that the microbiome modulates immune homeostasis. This study aimed to compare the skin microbiomes of SjD patients with those of healthy controls (HCs) using 16S rRNA gene sequencing. Taxonomic composition, alpha and beta diversity, and predicted functional profiles were evaluated. We observed a significant depletion of Cutibacterium and a marked reduction in microbial diversity in SjD patients. Beta diversity analyses revealed distinct clustering among groups. Functional prediction suggested the downregulation of metabolic pathways associated with microbial homeostasis. Our findings propose that alterations in the skin microbiota may contribute to SjD pathogenesis and serve as potential biomarkers or therapeutic targets.},
}

Humans
*Sjogren's Syndrome/microbiology
*Skin/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Female
Middle Aged
Male
*Bacteria/classification/genetics/isolation & purification
Adult
DNA, Bacterial/genetics
Aged
Biodiversity
Case-Control Studies
Sequence Analysis, DNA
Skin Microbiome

@article {pmid41674063,
year = {2026},
author = {Asahi, Y and Kuriki, N and Okamoto, M and Motooka, D and Nakamura, S and Maezono, H and Klanliang, K and Shimaoka, T and Iida, T and Ebisu, S and Noiri, Y and Hayashi, M},
title = {Microbiome of Apical Intracanal and Extraradicular Biofilms From the Same Roots of Teeth With Persistent Apical Periodontitis: An Observational Study.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70113},
pmid = {41674063},
issn = {1365-2591},
support = {JP23K09198//Japan Society for the Promotion of Science/ ; JP20K09953//Japan Society for the Promotion of Science/ ; },
abstract = {AIM: Bacterial biofilms around the apex are crucial in disease progression and persistence of apical periodontitis. While intracanal biofilms initiate infection, extraradicular biofilms contribute to treatment resistance and persistence. Thus, a comprehensive understanding of these biofilms may help elucidate mechanisms underlying persistent apical periodontitis. Therefore, in this study, we aimed to compare the microbiome and predicted functional profiles in matched apical root canals with those of extraradicular biofilms associated with persistent apical periodontitis.

METHODOLOGY: Seventeen root apices from patients with persistent apical periodontitis were collected via surgery. After extraradicular biofilm was collected, intracanal biofilm was obtained by cryopulverisation. Bacterial communities were detected by amplicon sequencing of the V1-V2 region of the 16S rRNA gene. Diversity, microbial composition and predicted bacterial functions were compared between matched intracanal and extraradicular biofilms.

RESULTS: Alpha diversity analysis of the microbiome revealed no significant differences between the two sampling sites. In contrast, the beta diversity of the microbiota of the same root (matched samples) was significantly lower than that of the microbiota of unpaired samples. There were no statistically significant differences in permutational multivariate analysis of variance for the microbiome between paired extraradicular and intracanal biofilms, regardless of the presence of the sinus tract. The abundances of the predominant genera, namely Fusobacterium, Treponema, Prevotella, Porphyromonas and Bacteroides as well as gram-positive bacteria, including Actinomyces, were similar between extraradicular and intraradicular biofilms. Linear discriminant analysis effect size analysis identified bacterial taxa significantly enriched in extraradicular biofilms, whereas no taxa were significantly enriched in intraradicular biofilms. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis revealed several differences in Kyoto Encyclopaedia of Genes and Genomes pathways between these biofilms.

CONCLUSION: While comparison of the microbiome between extraradicular and intracanal biofilms of the same root apices revealed differences in bacterial composition, certain similarities were noted, particularly in dominant bacterial species abundance, indicating a close microbial relationship between intracanal and extraradicular biofilms, with some exceptions. Additionally, some differences in predicted functional profiles were observed between the two biofilm types. Thus, the characterisation of bacterial communities around the apical foramen may guide the development of appropriate antimicrobial strategies.},
}

@article {pmid41673713,
year = {2026},
author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ},
title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {65},
pmid = {41673713},
issn = {2049-2618},
support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Biofilms/growth & development ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Droughts ; *Microbiota ; *Rivers/microbiology ; Metagenomics/methods ; Metagenome ; Switzerland ; Diatoms/genetics ; Viruses/classification/genetics/isolation & purification ; Cyanobacteria/genetics/classification ; },
abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.

RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.

CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.},
}

*Biofilms/growth & development
*Bacteria/classification/genetics/isolation & purification/metabolism
*Droughts
*Microbiota
*Rivers/microbiology
Metagenomics/methods
Metagenome
Switzerland
Diatoms/genetics
Viruses/classification/genetics/isolation & purification
Cyanobacteria/genetics/classification

@article {pmid41673679,
year = {2026},
author = {Liao, J and Mou, H and Luo, S and Shen, L and Jiao, B},
title = {Microbiota and Alzheimer's disease: mechanistic insights from a multi-organ perspective.},
journal = {Translational neurodegeneration},
volume = {15},
number = {1},
pages = {3},
pmid = {41673679},
issn = {2047-9158},
support = {82371434//National Natural Science Foundation of China/ ; 2024JJ2097//Outstanding Youth Fund of Hunan Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology/therapy ; *Dysbiosis/microbiology ; *Microbiota/physiology ; Probiotics/therapeutic use ; *Gastrointestinal Microbiome/physiology ; Animals ; Fecal Microbiota Transplantation/methods ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder driven by multifactorial mechanisms. Increasing evidence suggests that dysbiosis, a term denoting an imbalance in the composition of the microbiota, may play a pivotal role in the pathogenesis of AD across multiple bodily sites, including the gut, oral cavity, nasal passages, lungs, and skin. Microbial imbalances may promote neuroinflammation, immune dysfunction, and metabolic disturbances through complex host-microbiota networks. This review synthesizes current advances in the understanding of microbiota-driven modulation of AD, introduces the "Multi-Axis Co-Regulation" concept, and evaluates microbial biomarkers for early diagnosis. Finally, the translational potential of microbiota-targeting interventions, including probiotics, dietary modulation, fecal microbiota transplantation, and oral microbiome-based therapies, are discussed, which represent novel strategies for precision prevention and treatment of AD.},
}

Humans
*Alzheimer Disease/microbiology/therapy
*Dysbiosis/microbiology
*Microbiota/physiology
Probiotics/therapeutic use
*Gastrointestinal Microbiome/physiology
Animals
Fecal Microbiota Transplantation/methods

@article {pmid41673480,
year = {2026},
author = {},
title = {Babies at nursery shape each other's microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41673480},
issn = {1476-4687},
}

@article {pmid41673465,
year = {2026},
author = {Widdowson, M and Shah, S and Thorsen, J and Poulsen, CS and Rosenberg, JB and Mohammadzadeh, P and Jepsen, JRM and Vinding, R and Poulsen, CE and Rodriguez, CL and Pedersen, CT and Wang, T and Zachariasen, T and Ottosson, F and Werge, TM and Ernst, M and Sørensen, SJ and Chawes, B and Bønnelykke, K and Trivedi, U and Ebdrup, BH and Stokholm, J},
title = {Neonatal gut Bifidobacterium associates with indole-3-lactic acid levels in blood and risk of ADHD at age 10.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {41673465},
issn = {1476-5578},
support = {NNF22OC0073817//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; R269-2017-5//Lundbeckfonden (Lundbeck Foundation)/ ; },
abstract = {The gut microbiome has been associated with brain health. The neuromodulatory effects of microbial-derived metabolites is supported by experimental evidence, and alterations of gut microbiota have been associated with the pathophysiology of certain neuropsychiatric disorders.Research on the gut microbiome's role in attention-deficit/hyperactivity disorder (ADHD) have been predominantly cross-sectional and seldomly within the neonatal period, missing its potential impact on critical periods shaping long-term neurodevelopmental outcomes. This study addresses how initial colonization and timing of specific gut bacteria, and their metabolic byproducts, may influence the risk of future ADHD. Using the highly-phenotyped COPSAC2010 birth cohort, we show that a higher level of Bifidobacterium in the child's one-week gut microbiome, after extensively adjusting for genetic and early-life factors, is associated with ADHD at age 10. Our analyses also reveal that the tryptophan-derived metabolite indole-3-lactic acid (ILA) in the neonatal dried blood spot (DBS) mediates the relationship between Bifidobacterium and ADHD risk. The association between neonatal DBS ILA and ADHD was replicated in two independent cohorts. Bifidobacterium is known to promote healthy neurodevelopmental outcomes; however, these findings suggest that the initial temporal colonization pattern of Bifidobacterium may be particularly important for neurodevelopment. In particular, elevated Bifidobacterium-derived metabolite ILA levels may have adverse consequences on the child's neurodevelopment during the first week of life. This suggests that by promoting a suitable temporal colonization pattern for Bifidobacterium and its production of ILA in the newborn may represent potential strategies for clinical interventions for supporting adequate neurodevelopment, and mitigating the risk of future ADHD.},
}

@article {pmid41673237,
year = {2026},
author = {Gao, J and Abriat, C and Laekas-Hameder, M and Virgilio, N and Dozois, CM and Quach, C and Heuzey, MC and Lemay, G and Daigle, F},
title = {Microbiological and rheological dynamics of mixed biofilms formed by bacteria and eukaryotic virus.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39314-9},
pmid = {41673237},
issn = {2045-2322},
support = {NFRFE-2022-00464//New Frontiers in Research/ ; },
abstract = {Biofilms are structured microbial communities embedded within an extracellular matrix that confers protection against environmental stresses. In both natural and clinical settings, biofilms are rarely composed of a single species and may also involve interactions with bacteriophages or even eukaryotic viruses. Since both biofilms and viruses are ubiquitous, and viruses remain among the neglected components of the microbiome, understanding their interactions is essential. In hospitalized patients, catheter colonization by biofilms markedly increases the risk of bacteremia and septicemia, and biofilm formation is almost inevitable during long-term catheterization. In this study, we investigated biofilm-forming capacities of uropathogenic Escherichia coli (UPEC) and clinical strains associated with catheter-related systemic infections. Selected strains were further examined to evaluate the influence of the ubiquitous mammalian reovirus on bacterial biofilm formation and to evaluate biofilm entrapment of viral particles and its impact on viral infectivity. Bacterial growth, survival and biofilm production were measured in the presence or absence of the virus. While reovirus exhibited no bactericidal effects and biofilm biomass remained largely unchanged, rheological and microscopic analyses revealed strain-specific alterations in biofilm properties. Remarkably, reovirus retains infectivity after release from biofilms, indicating that bacterial biofilms may serve as reservoirs or shelters for eukaryotic viruses.},
}

@article {pmid41673107,
year = {2026},
author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG},
title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39378-7},
pmid = {41673107},
issn = {2045-2322},
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.},
}

@article {pmid41672982,
year = {2026},
author = {D'Onofrio, AM and Gomez-Nguyen, A and Camardese, G and Scaldaferri, F and Burberry, A and Cominelli, F},
title = {Fecal microbiota transplantation from psychiatric patients to mice - systematic review of methodologies and a call for standardization.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-03847-4},
pmid = {41672982},
issn = {2158-3188},
support = {NIDDK097948//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; NIDDK097948//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01AG085316//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has emerged as a key tool to explore the role of the microbiome-gut-brain axis in psychiatric disorders. However, the field is hindered by significant methodological inconsistencies.

METHODS: A comprehensive literature search identified 31 studies performing FMT from human patients with psychiatric conditions into rodent models.

RESULTS: None of the 31 studies followed an identical FMT protocol. Significant heterogeneity was observed across studies in rodent model selection, including germ-free, antibiotic-pretreated, or specific pathogen-free approaches, in antibiotic regimens, timing and microbiota depletion verification, as well as in FMT donor strategy, dosage, frequency, engraftment assessment, and behavioral testing schedules.

CONCLUSIONS: This review highlights the necessity for standardized methodologies in microbiome research. Evidence-based recommendations are provided to promote reproducibility in future work. Investigators are encouraged to publish transparent and rigorous protocols, to enhance the translational potential of microbiome-gut-brain axis research.},
}

@article {pmid41672513,
year = {2026},
author = {Nishijima, S and Hattori, M and Nagata, N},
title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {102},
number = {2},
pages = {82-103},
doi = {10.2183/pjab.102.006},
pmid = {41672513},
issn = {1349-2896},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Japan ; *Health ; *Disease ; East Asian People ; },
abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.},
}

Humans
*Gastrointestinal Microbiome/genetics
Japan
*Health
*Disease
East Asian People

@article {pmid41672407,
year = {2026},
author = {Furst, AJ and Johnson, KE and Nagel, EM and Yerabandi, N and Kats, AM and Gallagher, TT and Gale, CA and Palmsten, K and Pierce, S and Hoffman, S and Jacobs, K and Fields, DA and Isganaitis, EM and Bode, L and Demerath, EW},
title = {Gestational diabetes, human milk oligosaccharide (HMO) concentrations, and their links to infant weight gain and the gut microbiome in a United States observational cohort.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101235},
doi = {10.1016/j.ajcnut.2026.101235},
pmid = {41672407},
issn = {1938-3207},
abstract = {BACKGROUND: Gestational Diabetes Mellitus (GDM) increases offspring obesity risk, but whether this occurs via changes in human milk composition, including alterations in human milk oligosaccharides (HMOs), is unknown.

OBJECTIVE: To identify differences in HMO concentrations in mothers with and without GDM and test whether GDM-associated HMOs are associated with infant growth, body composition, and fecal microbiome characteristics over the first 6-months of life.

METHODS: Human milk was collected at 1- month postpartum from 337 females (49 with GDM) who fed their infants breastmilk exclusively. HMOs were quantified by high performance liquid chromatography and multivariate regression models were used to test differences in HMO concentrations by GDM status (false discovery rate adjustment for multiple testing set at q<0.05). HMOs associated with GDM were then tested for associations with infant growth, body composition, and 1 and 6-months infant fecal microbial abundances measured by metagenomic whole-genome sequencing.

RESULTS: Participants with GDM had approximately 1 standard deviation higher milk 6'SL (β (95% Confidence interval): 0.58 (0.20, 0.96)) and LNFP III (0.55 (0.16, 0.94) compared to those without GDM and 6'SL concentration was also positively associated with weight and length gain. While infants of mothers with GDM had lower 1-month fecal alpha-diversity and altered abundances of 6/56 microbial species detected compared to those without GDM, microbial features were not associated with the concentration of either 6'SL or LNFP III and evidence for mediation of GDM-growth and GDM-microbiome by HMOs was not found.

CONCLUSIONS: Mothers with a GDM diagnosis had higher milk concentrations of LNFP III and 6'SL, and 6'SL was in turn associated with increased infant growth rate, but neither HMO was associated with differential infant gut microbial abundances. The results suggest that the link between 6'SL and faster infant growth, if causal, occurs via mechanisms independent of the infant gut microbiome.

CLINICAL TRIALS REGISTRATION: The study is registered with ClinicalTrials.gov under NCT03301753.},
}

@article {pmid41672375,
year = {2026},
author = {Hillier, K and Kim, T and Pincez, T},
title = {Immunopathology of Immune Thrombocytopenia.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2026.01.011},
pmid = {41672375},
issn = {1538-7836},
abstract = {Immune thrombocytopenia (ITP) is an acquired bleeding disorder caused by complex immune dysregulation. ITP is a rare disorder with significant morbidity; patients can suffer from bleeding symptoms and reduced quality of life. The pathogenesis of ITP can be observed at several levels: the mechanisms of thrombocytopenia, the loss of tolerance mechanisms, and underlying factors that drive its occurrence. Several mechanisms of platelet destruction and impaired platelet production are recognized as driving the disease. These mechanisms range from autoantibody-mediated platelet destruction, T cell-mediated cytotoxicity, complement-mediated destruction, and platelet desialylation leading to platelet clearance, to thrombopoietin consumption. These alterations are driven by a loss of tolerance with impaired T regulatory and myeloid derived suppressor cell surveillance. Several underlying factors may contribute to ITP pathogenesis by promoting this loss of tolerance, including genetic susceptibility, infections, the gut microbiome, and environmental influences. The numerous alterations described may be heterogeneous across patients with ITP, contributing to disease heterogeneity. Many patients will require treatment of ITP, which may target one or more of these mechanisms, with new therapies being developed to focus on specific pathways. Ultimately, identifying the main mechanism(s) driving ITP in a patient may allow individualized management. This review will highlight the major mechanisms of ITP immunopathology to deepen understanding of important pathways and therapies modulating these pathways.},
}

@article {pmid41672331,
year = {2026},
author = {Yu, J and Allela, OQB and Alkhazali, WH and Bishoyi, AK and Oweis, R and Varma, P and Kashyap, A and Panigrahi, R and Chauhan, AS and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M},
title = {The Gut Microbiome as a Modulator of Antibiotic Resistance: Mechanisms, Dynamics, and Therapeutic Interventions.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108357},
doi = {10.1016/j.micpath.2026.108357},
pmid = {41672331},
issn = {1096-1208},
abstract = {The gut microbiome is increasingly recognized as a critical factor in the dynamics of antibiotic resistance, influencing the acquisition, persistence, and dissemination of antibiotic resistance genes (ARGs) among both commensal and pathogenic bacteria. This research focuses on elucidating the mechanisms by which the gut microbiome modulates the horizontal gene transfer (HGT) of ARGs, a key driver of the global antibiotic resistance crisis. By employing advanced metagenomic sequencing and functional assays, this study aims to identify specific microbial species, genetic elements, and metabolic pathways that either facilitate or inhibit the transfer of ARGs within the gut environment. Particular attention is given to the role of microbial metabolites, interspecies interactions, and environmental factors that shape the resistome the collection of all resistance genes within the microbiome. Additionally, this research explores innovative microbiome-based interventions, such as the use of probiotics, prebiotics, and bacteriophage therapy, to disrupt the transmission of ARGs and restore microbial balance. These interventions are designed to target the gut microbiome as a reservoir of resistance genes, offering a novel approach to curbing the spread of antibiotic resistance. The significance of this work lies in its potential to provide actionable insights into microbiome-mediated resistance mechanisms and to develop targeted strategies that complement traditional antibiotic therapies. By addressing the gut microbiome as a modifiable factor in the resistance landscape, this research could contribute to mitigating the global burden of antibiotic resistance, preserving the efficacy of existing treatments, and improving public health outcomes in the face of this pressing challenge.},
}

@article {pmid41672231,
year = {2026},
author = {Yu, X and Zhang, K and Kan, C and Ma, Y and Sheng, S and Zheng, T and Sun, X},
title = {The gut-brain axis in diabetic neuropathy, cognitive impairment, and emotional disorders.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.02.006},
pmid = {41672231},
issn = {1873-7544},
abstract = {Diabetes mellitus has become a global public health challenge, with a steadily rising prevalence that imposes substantial socioeconomic burdens. Over recent years, the gut-brain axis (GBA) has garnered significant attention as a crucial biological framework. GBA denotes the intricate network of bidirectional signaling between the gut and the brain via neuronal, endocrine, and immunological pathways, with the connections among gut bacteria, gut barrier function, and neuroendocrine factors significantly influencing the progression of diabetes mellitus. Studies indicate that disruptions in gut microbiota balance and compromised intestinal barrier integrity are significantly associated with the onset of insulin resistance and diabetes mellitus. Gut flora regulates energy metabolism, insulin sensitivity, and immune responses via the generation of metabolites (e.g., short-chain fatty acids), while impaired gut barrier function can trigger systemic chronic inflammation, which in turn promotes insulin resistance. The GBA also influences appetite, energy balance and insulin secretion through neuroendocrine pathways. Imbalances in the gut microbiota may lead to neuroendocrine dysregulation, thereby accelerating diabetes pathogenesis. New diabetes treatment strategies are being explored based on research on the GBA. Modulation of the intestinal microbiome, restoration of gut barrier integrity, and correction of neuroendocrine dysregulation may offer novel avenues for managing diabetes and its associated complications. In conclusion, revealing the multidimensional pathogenesis of diabetes mellitus from the perspective of the GBA will help to develop more effective therapeutic strategies.},
}

@article {pmid41672156,
year = {2026},
author = {Ma, J and To, SKY and Zhang, X and Zhao, W and Zhang, P and Wong, AST},
title = {Emerging perspectives on metabolic reprogramming in the microenvironment of ovarian cancer metastasis.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {1881},
number = {2},
pages = {189554},
doi = {10.1016/j.bbcan.2026.189554},
pmid = {41672156},
issn = {1879-2561},
abstract = {Ovarian cancer (OC) is one of the most lethal malignancies in females, mainly due to the aggressive metastasis at the late stage and the unsatisfactory of current therapies. OC cells exhibit a special metastatic behavior compared to other common epithelial tumors, primarily spreading within the peritoneal cavity. Due to the complexity of tumor microenvironment, physical factors induce significant metabolic changes in OC cells, thereby enhancing their metastatic ability. Key cellular components, such as cancer-associated fibroblasts and adipocytes, act synergistically to support metastasis through metabolic interactions. Recent efforts in tumor immunometabolism showed that metabolic reprogramming of immune cells can also significantly impact metastatic progression. Moreover, the microbiome and cellular senescence are emerging as important factors that alter the metabolic landscape. This review provides a systematic review of metabolic reprogramming in the OC microenvironment and highlights the most recent clinical trials targeting metabolic pathways. By increasing our understanding of these metabolic interactions, we can develop innovative metabolism-targeting interventions for this devastating gynecological malignancy.},
}

@article {pmid41672080,
year = {2026},
author = {Zeilstra, D and Te Velde, AA and Remmers, G and Besseling-van der Vaart, I and Brummer, RJ and Kraneveld, AD},
title = {A pragmatic approach to integrate evidence-based medicine and personalized medicine: the example of personalized microbiome-targeting interventions.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-25},
doi = {10.1163/18762891-bja00110},
pmid = {41672080},
issn = {1876-2891},
abstract = {Health care practitioners (HCPs) strive to provide the best medical care for each individual patient. The question as to what constitutes 'the best' does, however, not have a single straightforward answer. Evidence-based Medicine (EBM) and Personalized Medicine (PM) are two paradigms that have emerged as means to improve intervention selection. Both paradigms have their own strengths and weaknesses that affect their use in clinical decision-making. In this review we discuss the strengths and weaknesses from the patient's and HCP perspective: how to find the best intervention for a particular patient. We review methodological and practical aspects, and zoom out from the scientific level to the epistemological level to integrate EBM and PM. Both EBM and PM are based on a realist worldview and by adopting a pragmatist worldview the strengths of both paradigms can be combined. We apply this pragmatic approach, called Evidence-based Personalized Medicine (EBPM), to microbiome-targeting interventions. The example EBPM implementation uses four steps. First, it allows HCPs to provide information (clinical diagnosis, complaints, patient needs, laboratory measures) about an individual patient. Second, it uses a GRADE-based system to grade evidence of specific intervention components. Next, it combines the patient profile data and preferences with the graded evidence, to come to a suggestion for a personalized intervention. Finally, this method enables gathering of treatment effects providing feedback into the system and further improve suggestions for future patients.},
}

@article {pmid41672068,
year = {2026},
author = {Pellow, D and Geva, GA and Godneva, A and Reisner, Y and Talmor-Barkan, Y and Segal, E},
title = {Analysis of biomarkers in the Human Phenotype Project using disease models from UK Biobank.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100993},
doi = {10.1016/j.medj.2025.100993},
pmid = {41672068},
issn = {2666-6340},
abstract = {BACKGROUND: We integrate longitudinal health outcomes from the UK Biobank (UKBB) with our own Human Phenotype Project (HPP) cohort. The HPP contains a range of data per participant that are not found in the UKBB, including microbiome, liver ultrasound, continuous glucose monitoring, and more. Conversely, the UKBB includes a much larger cohort and longer follow-up durations with large numbers of disease outcomes already tracked.

METHODS: To leverage the scale and extended follow-up of the UKBB in our study, we model disease outcomes in the UKBB to predict pseudo-outcomes in the HPP. Correlating these predicted pseudo-outcomes with unique measurements in the HPP study, we identify individual biomarkers for those conditions, including those from gut microbiome, liver ultrasound, and other modalities. Multivariate analysis identifies the contribution of each modality in predicting each pseudo-outcome.

FINDINGS: Our method enabled us to recapitulate known biomarkers across the spectrum of diseases studied as well as to reveal less-attested biomarkers in a range of different modalities. We further identify systemic biomarkers correlated with many diseases and sex-specific biomarkers with higher correlation to a pseudo-outcome for one sex as compared to the other.

CONCLUSIONS: Our method enables analysis of biomarkers leveraging both the scale and follow-up of the UKBB and the unique measurements of the HPP. This analysis provides a broad perspective across the landscape of many diseases through the lens of many modalities, providing a framework for transferring knowledge from large longitudinal cohorts to smaller, more deeply phenotyped cohorts, advancing discovery across modalities.

FUNDING: E.S. is supported by the European Research Council and the Israel Science Foundation.},
}

@article {pmid41671957,
year = {2026},
author = {Wu, J and He, C and Wu, K and Feng, W and Yang, Y and Zhou, Q and Mao, P and Xiao, X},
title = {Silver sulfide nanoparticles amplify earthworm gut denitrification and elevate N2O emissions in subtropical forest soils under nitrogen deposition.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119853},
doi = {10.1016/j.ecoenv.2026.119853},
pmid = {41671957},
issn = {1090-2414},
abstract = {Silver sulfide nanoparticles (Ag2S-NPs), commonly introduced into forest soils via sewage sludge, may disrupt nitrogen (N) cycling under elevated N deposition. This study examined how Ag2S-NPs and earthworms (Eisenia fetida) interact to influence N2O emissions in subtropical forest soils subjected to long-term simulated N deposition. A 60-day incubation was conducted using soils treated with low (1 mg Ag kg[-1]) and high (30 mg Ag kg[-1]) Ag2S-NP doses. Nitrogen deposition alone suppressed N2O emissions by acidifying soil and inhibiting nitrification. In contrast, earthworm activity enhanced emissions by stimulating organic matter turnover and N-cycling gene expression. Under N deposition, Ag2S-NPs significantly increased N2O emissions in a dose-dependent manner, with the high dose raising emissions by 68 % compared to earthworm-only treatments. Metagenomic analysis revealed that this effect was driven by increased gut-associated denitrification, with notable enrichment of narG/H/I and nirK/S genes, and denitrifiers such as Microbacterium and Bacillus. Conversely, soil nitrification declined, as reflected by reduced NO3[-] levels and amoA gene abundance. Multivariate models identified gut denitrification genes as key predictors of N2O flux. These findings highlight the synergistic impact of Ag2S-NPs and earthworms on greenhouse gas emissions in N-deposited soils and underscore the importance of considering nanomaterial-fauna-microbe interactions in forest ecosystems.},
}

@article {pmid41671864,
year = {2026},
author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H},
title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141429},
doi = {10.1016/j.jhazmat.2026.141429},
pmid = {41671864},
issn = {1873-3336},
abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.},
}

@article {pmid41671814,
year = {2026},
author = {Xu, M and Chen, L and Zou, H},
title = {Plant-mediated niche differentiation promotes comammox-dominated nitrification in aquaponic rhizospheres.},
journal = {The Science of the total environment},
volume = {1018},
number = {},
pages = {181517},
doi = {10.1016/j.scitotenv.2026.181517},
pmid = {41671814},
issn = {1879-1026},
abstract = {Sustainable aquaculture requires efficient nitrogen management and reduced N2O emissions. Integrating plants into these systems (aquaponics) represents a promising strategy to achieve these goals. In this study, a tilapia-chive aquaponics model was used to investigated the mechanisms by which plant root exudates regulate rhizosphere nitrifier microbial communities, with a focus on complete ammonia oxidizers (comammox). Over 70 days, we probed how aquaponics and hydroponic conditions reshape the rhizosphere microbiome using qPCR, qFISH, and selective inhibitor assays to quantify the functional contributions of comammox, AOA, and AOB to nitrification and N2O production. Results showed that the aquaponics system enhanced root exudation, increasing rhizosphere total organic carbon and creating a mildly acidic micro-environment that selectively enriched comammox. Comammox ultimately dominated the ammonia-oxidizing community (99% in abundance) and activity (98% of nitrification capacity) by the end of the experiment. Consequently, the aquaponics system achieved a sustained reduction in the N2O conversion rate compared to the hydroponic controls, exceeding 50% in all sampling stages after day 7. This mitigation is attributed to minimized nitrite (NO2[-]-N) accumulation and the inherently low N2O-yielding potential of comammox. These findings reveal a plant-driven mechanism that selects for comammox-dominated nitrification, effectively curbing N2O emissions while maintaining efficient N conversion. The results offer a potential strategy for improving nitrogen use efficiency and emission control in integrated aquaculture systems.},
}

@article {pmid41671813,
year = {2026},
author = {Wang, N and Jin, M and Zhu, Z and Wang, Y and Li, X and Xu, J and Cheng, S and Zhu, Y and Wang, R and Xu, T and Yin, F and Li, X and Ke, Y and Yue, H},
title = {Ecological distribution and functional characterization of polyethylene-degrading enzymes from diverse metagenomes.},
journal = {The Science of the total environment},
volume = {1018},
number = {},
pages = {181486},
doi = {10.1016/j.scitotenv.2026.181486},
pmid = {41671813},
issn = {1879-1026},
abstract = {Polyethylene (PE), the most widely produced synthetic polymer, is highly resistant to degradation and poses long-term ecological risks due to its accumulation in terrestrial and aquatic ecosystems. Although biological degradation pathways have been investigated, research has primarily concentrated on heavily polluted environments, leaving the ecological distribution of PE-degrading enzymes largely unknown. In this study, we systematically screened more than 4.57 billion metagenomic sequences from diverse ecological sources-including farmland soils, Przewalski's horse gut microbiota, insect symbionts, and human oral microbiomes-for homologs of known PE-degrading enzymes. A total of 701 candidate sequences were identified using an integrated pipeline combining sequence homology, structural modeling, and molecular docking. Thirty-two representative enzymes were heterologously expressed and tested on pristine PE films and microspheres, among which 25 exhibited measurable activity, inducing surface erosion, up to ∼1.5% mass loss (w/w) of PE films over 30 days, and oxidative modifications. These degradative effects were validated by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), and stable carbon isotope (δ[13]C) analysis, collectively supporting molecular-level oxidation and early-stage carbon turnover associated with enzymatic PE degradation. Notably, PE-degrading activity was observed in microbiomes from relatively minimally disturbed environments, suggesting that microbial communities may adaptively evolve plastic-degrading capabilities in response to chronic, low-level exposure. These findings expand our understanding of plastic pollution's ecological footprint and highlight naturally occurring enzymes as promising candidates for sustainable bioremediation.},
}

@article {pmid41671795,
year = {2026},
author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B},
title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134181},
doi = {10.1016/j.biortech.2026.134181},
pmid = {41671795},
issn = {1873-2976},
abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.},
}

@article {pmid41671698,
year = {2026},
author = {Derrick, A and Fred, B and Zheng, Y and Boateng, AG and Wang, H and Biney, E and Azupio, S and Zhang, S},
title = {Toxicological responses of Litopenaeus vannamei to short-term ferric chloride exposure: implications for histopathology, oxidative stress, and intestinal microbiota.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119408},
doi = {10.1016/j.marpolbul.2026.119408},
pmid = {41671698},
issn = {1879-3363},
abstract = {Iron (Fe) contamination in aquaculture environments threatens marine species, particularly Litopenaeus vannamei, with ferric chloride (FeCl3) from industrial uses being a major potential source. This study examines the acute toxicity of FeCl3 in juvenile shrimp through bioaccumulation, histopathology, oxidative stress biomarkers, immune gene expression, and microbiome alterations. Following the determination of the 96-h median-lethal concentration (LC50) of FeCl3 for L. vannamei as 1.194 mg/L, two exposure groups were established; FeC1 (1%) and FeC2 (10%) 96-h LC50 to model low and high sublethal toxicity levels. Bioaccumulation analysis revealed that Fe primarily concentrated in the hepatopancreas, with significantly higher concentrations in Fe-exposed groups compared to controls. Histological analysis showed dose-dependent hepatopancreatic damage, including cell degeneration, lumen collapse, and epithelial necrosis, especially in the FeC2 group. Oxidative stress biomarkers (ROS and MDA) were significantly elevated in Fe-treated groups, with a notable reduction in antioxidant enzyme activities (T-SOD, CAT), and immune parameters (PO, LZM) showed initial activation followed by significant decline. Gene expression analysis indicated transient upregulation of immune (Relish, Toll-2) and antioxidant (Nrf2, GPx, MnSOD) genes, but expression levels of ferritin and lysozyme were suppressed in Fe-exposed shrimp. Microbiome analysis revealed a significant shift towards opportunistic genera such as Enterococcus and Ruegeria in high-dose groups. Functional prediction based on KEGG-pathways indicated enrichment of pathways related to xenobiotic degradation and immune dysfunction, while energy metabolism and immune-related pathways were suppressed. These findings emphasize the significant impact of FeCl3 pollution on shrimp health, indicating the need for strict regulation of iron levels in aquaculture systems.},
}

@article {pmid41671649,
year = {2026},
author = {Zhang, J and Liu, W and Wang, B and Zhai, Q and Bai, Y},
title = {Plant microbiome regulation for sustainable agriculture.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103444},
doi = {10.1016/j.copbio.2026.103444},
pmid = {41671649},
issn = {1879-0429},
abstract = {Plant-associated microbiomes are vital for sustainable agriculture, enhancing crop nutrient uptake, stress resistance, and yield while reducing agrochemical reliance. Microbial regulation, the targeted manipulation of these microbiomes, bridges microbial ecological potential and agricultural application. Currently, this regulation is categorized by whether microbial genomes are modified, encompassing two core strategies: external conditioning and internal engineering. External conditioning is a genome-unaltered approach that reshapes microbial communities via environmental cues, host traits, and agronomic practices, enabling rapid, low-regulatory tuning of microbiome function. In contrast, internal engineering alters microbial genomes via CRISPR-based tools, synthetic communities, and in situ editing to lock in stable beneficial traits for consistent field performance. Emerging technologies like AI-powered predictive models and advanced delivery systems support both strategies by boosting microbial regulation precision and scalability. Ultimately, microbial regulation optimizes plant-microbe interactions, expediting sustainable agricultural solutions to enhance climate resilience and global food security.},
}

@article {pmid41671385,
year = {2026},
author = {Wang, J and Nan, Y and Liu, Q and Ding, T and Liu, D and Duo, L and Zhao, J and Gao, S and Zhang, Y and Dai, Z and Yan, S and Zhang, W and Li, Z and Liu, W and Han, B and Zhao, Y and Yu, Y and Zhao, E and Li, X and You, B},
title = {Tumor-Resident Streptococcus pneumoniae Promotes Malignant Progression and Pazopanib Resistance in Clear Cell Renal Cell Carcinoma.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-25-3780},
pmid = {41671385},
issn = {1538-7445},
abstract = {Persistent drug resistance to tyrosine kinase inhibitors has become a hurdle in extending the survival of patients with clear cell renal cell carcinoma (ccRCC). Through microbiome screening of patient samples from a ccRCC cohort treated with the tyrosine kinase inhibitor pazopanib, we identified Streptococcus pneumoniae (S. pneumoniae) as the dominant intratumoral microbiota in pazopanib-resistant ccRCC samples. Further investigation revealed that S. pneumoniae reprogramed lipid metabolism in ccRCC cells by depleting manganese (Mn2+) from the tumor microenvironment, consequently facilitating malignant progression and development of pazopanib resistance. S. pneumoniae suppressed S-nitrosylation of tripartite motif containing protein 28 (TRIM28) by diminishing Mn2+ levels, allowing TRIM28 to physically interact with the transcription factor SP1 to promote the transcription of solute carrier family 27 member 1 (SLC27A1) and lipid deposition. Taken together, these findings indicate that tumor-resident S. pneumoniae plays an important role in conferring pazopanib resistance, suggesting that S. pneumoniae could serve as a potential biomarker of pazopanib response in ccRCC.},
}

@article {pmid41671169,
year = {2026},
author = {Saati-Santamaría, Z and Pérez-Mendoza, D and Khashi U Rahman, M and de Sousa, BFS and Montero-Calasanz, MDC and Rey, L and Roy, S and Sanjuán, J and García-Fraile, P},
title = {Evolutionary mechanisms underlying bacterial adaptation to the plant environment.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag005},
pmid = {41671169},
issn = {1574-6976},
abstract = {Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that are essential for plant survival and ecosystem function. Bacterial adaptation to plant environments involves dynamic evolutionary mechanisms including horizontal gene transfer, gene regulation, and metabolic specialization, enabling bacteria to persist and specialize within diverse plant-associated niches. Here we review how evolutionary forces such as selection, drift, and gene flow shape bacterial genomes, regulatory networks, and ecological strategies in response to plant-imposed pressures, underpinning both beneficial and pathogenic lifestyles. Understanding these processes provides a unified evolutionary framework for bacterial adaptation to plants and highlights their implications for sustainable agriculture and microbiome-based innovations.},
}

@article {pmid41671163,
year = {2026},
author = {He, T and Jansonius, K and Li, X and Reilly, AM and Sevgin, B and Setroikromo, R and Hackl, T and Haslinger, K},
title = {A discriminative primer design workflow enables selective metabarcoding, demonstrated using long-read sequencing of endophytic fungi.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag014},
pmid = {41671163},
issn = {1574-6941},
abstract = {Metabarcoding is a powerful tool to simultaneously identify multiple taxa within a habitat. However, its application to host-associated microbiomes is challenged by substantial co-amplification of host DNA. Here we developed a host-exclusive primer design workflow, to selectively generate amplicons from target taxa while excluding the host. This workflow is centered around a new computational tool, mbc-prime, that can generate a list of discriminative candidate primers and score them. We showcase the use of this tool in the design of primers for long-read metabarcoding of endophytic fungi in Vinca minor. Mbc-prime streamlines the design of fungus-specific primers, enabling efficient and plant-free amplification of fungal rDNA from mixed DNA samples. Our workflow can be used to study the composition of complex host-associated microbiomes. It should be universally applicable for the design of discriminative primers in a user-friendly and practical manner and thus be of use for various researchers in microbiome research.},
}

@article {pmid41671097,
year = {2026},
author = {Cadavid, IC and Capelari, ÉF and Salvati, C and Margis, R},
title = {Phyllosphere microbiomes uncovered: Research trends, geographic disparities, and key microbial players.},
journal = {Genetics and molecular biology},
volume = {49Suppl 1},
number = {Suppl 1},
pages = {e20250083},
pmid = {41671097},
issn = {1415-4757},
abstract = {In recent years, significant efforts have been made to understand the phyllosphere microbiome. To clarify current research trends and identify knowledge gaps, we conducted a systematic review of the literature and investigated the methodologies used to analyze microbiome communities associated with plants, along with the objectives of these studies. Applying systematic review principles, we assessed 333 reports from the Web of Science database for eligibility. Articles were included if they presented original research on microbiomes associated with phyllosphere tissues identified by next-generation sequencing. Of these, 268 reports, published from 2009 to March 2025, were retrieved. These reports were used to extract data in a controlled and methodical manner. The analyses identified the most frequently studied plant species and primary tissues, the geographical locations sampled, the variables investigated in the phyllosphere microbiome, and the methodologies and tools employed. A comparison of the number of studies on below-ground (n=1562) versus above-ground tissue (n=375) underscores the relatively unexplored nature of above-ground research. We notice a surprisingly low number of studies from the Southern Hemisphere. Additionally, through data mining, we identify the most dominant bacteria and fungi reported in phyllosphere studies. Based on these findings, we offer recommendations for future research on the phyllosphere.},
}

@article {pmid41670382,
year = {2026},
author = {Qin, Y and Hu, Z and Dong, Z and Shen, J and Han, Y and Wu, J and Lan, Y and Zhong, C and Ou, Y and Sun, J and Luo, J and Li, C and Gao, Z and Wu, Q and Zhang, Y and Wen, L and Qiu, X and Liang, W and Nong, Q and Wang, P and Huang, Y and Zhao, N},
title = {Integrated analysis of gut microbiome and fecal metabolome reveals potential non-invasive biomarkers for early-stage silicosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297725},
doi = {10.1128/spectrum.02977-25},
pmid = {41670382},
issn = {2165-0497},
abstract = {Silicosis is an irreversible and progressive form of pulmonary fibrosis resulting from inhalation of silica particles, representing a persistent global health concern. Although the gut microbiota has been implicated in chronic lung diseases, its role in silicosis remains largely unexplored. Here, we performed 16S ribosomal RNA (rRNA) gene sequencing on fecal samples from 78 silicosis patients (27 stage I, 24 stage II, 27 stage III) and 30 matched healthy controls (HCs), and further conducted untargeted fecal metabolomics profiling in stage I patients, the critical point for microbial dysbiosis. Silicosis patients exhibited significantly altered beta diversity compared with HCs. At the phylum level, a progressive increase in Proteobacteria and a decline in Bacteroidota were observed. Notably, Pantoea, Kluyvera, and unclassified Pasteurellaceae were significantly enriched in stage I patients, with persistent alterations across later stages, suggesting stage I as a key turning point of microbial dysbiosis. Metabolomic analysis of stage I patients revealed distinct profiles enriched in tyrosine, histidine, purine metabolism, and arginine biosynthesis pathways. Correlation analysis identified strong associations between specific taxa and metabolites, and combined microbial-metabolite signatures such as Lactobacillus with N-succinyl-2-amino-6-ketopimelate (N-Succinyl-AKP) achieved an area under the curve (AUC) of 0.84 in distinguishing stage I patients from HCs.IMPORTANCEThis study systematically characterizes gut microbial changes across different stages of silicosis and integrates microbiome-metabolome data specifically in early-stage patients. We demonstrate that stage I is a critical point for gut microbiome alterations and identify microbe-metabolite signatures with diagnostic potential. These findings highlight the gut microbiome-metabolome combination as a promising source of non-invasive biomarkers for the early detection of silicosis.},
}

@article {pmid41670341,
year = {2026},
author = {Spooren, J and Shao, Y and Tarrant, T and Ploemacher, H and Qi, R and Hopkoper, S and Yüce, UG and Dong, H and Goossens, P and van Wees, SCM and Pieterse, CMJ and Berendsen, RL},
title = {Downy mildew disease-suppressive soils transmit a protective core microbiome to the phyllosphere.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag016},
pmid = {41670341},
issn = {1751-7370},
abstract = {Plants can respond to pathogen attack by assembling disease-suppressive microbiomes. In Arabidopsis thaliana, infection by the obligate foliar downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) consistently led to the formation of a soil microbial community, referred to as "soilborne legacy" (SBL), that enhanced resistance in subsequent plant populations grown in the same soil. Previous work identified an enrichment of specific "Hpa-associated microbiota" (HAM) in the phyllospheres of infected plants, which suppressed pathogen proliferation. Here, we demonstrate how the assembly of protective HAM in the phyllosphere contributes to a disease-suppressive SBL. We identified a community of 25 core-HAM that consistently dominated the phyllospheres of 14 sets of distinct Hpa-infected plant populations across six independent experiments. Using HAM-free, gnotobiotic Hpa spores, the infection-driven assembly of a core-HAM representative was recapitulated, showing de novo and progressive enrichment under sustained disease pressure. Despite being transmitted via soil as SBL, HAM are phyllosphere specialists with infected leaves as their primary niche. Disease-induced HAM assembly is initiated in the phyllosphere rather than the rhizosphere, and once transmitted, they particularly accumulate on aboveground tissues. Leaf wash-offs from plant populations that inherited SBL, were shown to effectively suppress downy mildew disease when applied to leaves of plants grown in unconditioned soil. These findings reveal that downy mildew disease-suppressive soils transmit a protective core microbiome to the phyllosphere, highlighting a crucial link between belowground and aboveground plant-driven microbiome assembly processes. Paradoxically, the phyllosphere thus emerges as a key assembly hub for disease-suppressive soil microbiomes.},
}

@article {pmid41670327,
year = {2026},
author = {Hu, Y and Ye, C and Liu, Y and Yang, S and Zhou, X and Zeng, L and Liu, Y and Huang, H and Mei, X and Zhu, Y and Yang, M and Zhu, S},
title = {Plant Reproductive Suppression Triggers Fatty Acid-Mediated Enrichment of Mortierella for Enhanced Stress Resilience.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag019},
pmid = {41670327},
issn = {1751-7370},
abstract = {Reproductive growth suppression enhances plant productivity, yet its effects on the health and survival strategies of perennial flowering plants remain underexplored. This study investigates the trade-offs between growth and reproduction in Panax notoginseng, focusing on its relationship with rhizosphere microbiome. Through three-year, multi-site field experiments coupled with metabolomic and microbiome analyses, we demonstrate that suppressing reproductive growth significantly increases biomass, particularly in underground tissues. Mechanistically, this suppression activates fatty acid biosynthesis pathways, leading to the reallocation of fatty acid metabolites from aboveground to belowground tissues and enhancing the rhizospheric secretion of palmitic acid, oleic acid, linoleic acid, and stearic acid. These fatty acids specifically promote the growth of beneficial fungus Mortierella, which supports plant health and progeny development. Exogenous application of these fatty acids in field conditions further confirmed their role in enriching Mortierella, thereby improving plant productivity. Our findings uncover a microbial-mediated survival strategy in plants under reproductive suppression, offering mechanistic insights for sustainable rhizosphere management in perennial crops.},
}

@article {pmid41670230,
year = {2026},
author = {Bissonnette, R and Salem, Y and Palijan, A and Maari, C and Proulx, ES and Prifti, DK and Hunter, S and Routy, B and Elkrief, A},
title = {The Gut Microbiome of Non-Atopic Chronic Hand Eczema (CHE) Subjects is Distinct and Enriched in Immuno-Modulatory Bacteria Species compared to Atopic-CHE and Healthy Subjects.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljag048},
pmid = {41670230},
issn = {1365-2133},
}

@article {pmid41669916,
year = {2026},
author = {Vílchez, B and Chamorro, C and Figuero, E and Marín, MJ and Arce, M and Kumar, PS and Sanz, M},
title = {Longitudinal Changes in the Peri-Implant Microbiome Following Implant Placement: A 3-Year Follow-Up Study.},
journal = {Clinical oral implants research},
volume = {},
number = {},
pages = {},
doi = {10.1111/clr.70101},
pmid = {41669916},
issn = {1600-0501},
support = {527-2023//Institut Straumann AG (Basel, Switzerland)/ ; },
abstract = {AIM: To investigate longitudinal changes in the submucosal peri-implant microbiome during early healing and long-term maturation, and their association with clinical and radiographic outcomes.

MATERIALS AND METHODS: This is the 3-year follow-up of a subset of individuals from a randomized controlled clinical trial. Marginal bone level changes (MBL) were measured at implant placement, loading, 12 months, and 3 years; clinical parameters were recorded at 12 months and 3 years. Submucosal plaque samples were collected at 1 week, 4 weeks, and 3 years post-implantation and analyzed by 16S rRNA gene sequencing. Microbial diversity, composition, and co-occurrence networks were evaluated.

RESULTS: Twenty-seven patients (64 implants) completed the 3-year visit. At 3 years, peri-implant clinical conditions and MBL remained stable across visits, although early supracrestal remodeling was observed. The incidence of peri-implant mucositis was 14.8% and peri-implantitis 11.1% at patient-level. Microbiome richness and phylogenetic diversity increased over time (p < 0.0001). Early biofilms were dominated by facultative anaerobes (e.g., Haemophilus parainfluenzae, Neisseria elongata), which declined at 3 years, when anaerobic/proteolytic taxa (e.g., Prevotella, Porphyromonas gingivalis, Fusobacterium nucleatum) became more prominent. Presence/absence analyses at 3 years showed persistence of early colonizers alongside the integration of later-arriving species. Lactococcus lactis and Enterococcus italicus increased in abundance and occupied more central positions in co-occurrence networks.

CONCLUSIONS: Over 3 years, the peri-implant microbiome matured into a more diverse and structured community, while MBL remained stable with physiological early supracrestal remodeling. These longitudinal findings suggest that early colonization and its subsequent evolution may influence long-term peri-implant health.},
}

@article {pmid41669888,
year = {2026},
author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004254},
pmid = {41669888},
issn = {1473-5598},
abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.

AIM: This study assessed the association between gut microbiome and incident hypertension.

METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74  years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.

RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster, Bariatricus, CAG-317-146760, and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.

CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.},
}

@article {pmid41669854,
year = {2026},
author = {Fu, Y and Zhang, K and Miao, Z and Yang, G and Huang, Y and Zheng, JS},
title = {Advancing Precision Nutrition Through Multimodal Data and Artificial Intelligence.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e21111},
doi = {10.1002/advs.202521111},
pmid = {41669854},
issn = {2198-3844},
support = {82574077//National Natural Science Foundation of China/ ; U21A20427//National Natural Science Foundation of China/ ; 92374112//National Natural Science Foundation of China/ ; 82404243//National Natural Science Foundation of China/ ; 2024SSYS0032//'Pioneer' and 'Leading goose' R&D Program of Zhejiang/ ; 2024SSYS0035//'Pioneer' and 'Leading goose' R&D Program of Zhejiang/ ; },
abstract = {Interindividual variability in metabolic responses to diets complicates the relationship between nutrition and metabolic health, which highlights the existence of metabolic heterogeneity across populations. This variability challenges the conventional "one-size-fits-all" approach to dietary recommendations and underscores the need for precision nutrition. In the current era, characterized by breakthroughs in sophisticated data collection technologies, the explosion of big data, and progress in artificial intelligence, the implementation of precision nutrition is becoming increasingly feasible. This review aims to summarize potential sources of metabolic heterogeneity from the angle of the host genome, gut microbiome, and brain connectome to explore the implications of their interactions with diet. Furthermore, we discuss the application of artificial intelligence in leveraging multimodal data for predicting individualized dietary responses. Aggregating data on host genetics, gut microbes, and brain activity profiling offers profound insights into the personalized response to diets. We also highlight the development of individual-specific predictive models that combine n-of-1 study designs with advanced wearable technologies and machine learning algorithms, thereby placing the individual at the center of nutritional decision-making. Finally, this review summarizes current challenges in the field and outlines potential directions for advancing precision nutrition.},
}

@article {pmid41669634,
year = {2025},
author = {Wang, B and Wang, Z and Chen, Z and Zhang, J and Wang, X},
title = {Deciphering the profiles of grapevine microbiomes from rhizosphere-to-leaf compartments using multi-omic analysis.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1734057},
pmid = {41669634},
issn = {1664-462X},
abstract = {INTRODUCTION: Root- and leaf-associated microbiomes are crucial for plant health and influence the yield and quality of the products. The composition of microbes and their association with the host depend on different factors that must be continuously investigated.

RESULTS: We examined the composition and structure of bacterial and fungal communities in four compartments (root, rhizoplane, rhizosphere, and leaf endosphere) of two grapevine varieties ('Alachua' and 'Noble') targeting the 16S rRNA V5-V7 and ITS regions.

RESULTS AND DISCUSSION: A comparison of the effects of the varieties and compartments showed that they were the major factors contributing to variations in the microbial structures. Bacterial alpha diversity significantly decreased from the rhizosphere to leaf endosphere, while the fungal alpha diversity did not show linear variations. According to normalized stochastic ratio analysis, deterministic processes dominated the bacterial and fungal assemblies of the leaf endosphere while stochastic processes in the rhizosphere and rhizoplane dominated the microbial assemblies. Assembly processes in bacterial and fungal roots differed (stochastic processes in bacteria and deterministic processes in fungi). Twenty shared core operational taxonomic units (OTUs) (bacteria, 13; fungi, 7) were identified across all compartments. Various stilbene compounds in leaf were significantly correlated with these shared core microbes, and weighted gene co-expression network analysis revealed that some hub genes were correlated with these metabolites. Thus, their role as regulators of grapevine microbiome interactions needs to be further evaluated. This study provided new profiles of the microbiota in different grapevines compartments, which suggested their association with grape metabolites and plant genes, representing a major development for further studies focused in understanding the role of these microorganisms for grapevine production.},
}

@article {pmid41669552,
year = {2026},
author = {Hearne, G and S Refahi, M and Duan, HN and Brown, JR and Rosen, GL},
title = {Normalized compression distance for DNA classification.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20677},
pmid = {41669552},
issn = {2167-8359},
mesh = {Humans ; *Data Compression/methods ; Algorithms ; *Genomics/methods ; *Sequence Analysis, DNA/methods ; Open Reading Frames ; Neural Networks, Computer ; *DNA/classification/genetics ; },
abstract = {Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.},
}

Humans
*Data Compression/methods
Algorithms
*Genomics/methods
*Sequence Analysis, DNA/methods
Open Reading Frames
Neural Networks, Computer
*DNA/classification/genetics

@article {pmid41669550,
year = {2026},
author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A},
title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20648},
pmid = {41669550},
issn = {2167-8359},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Nutrients ; *Stress, Physiological ; Phylogeny ; Biodegradation, Environmental ; },
abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Araceae/microbiology
*Bacteria/genetics/classification
*Nutrients
*Stress, Physiological
Phylogeny
Biodegradation, Environmental

@article {pmid41669382,
year = {2026},
author = {Yao, Y and Zhao, L and Zhang, Y and Duan, A and Yang, Y and Wang, A and Xue, C and Zhang, J and Zhao, M},
title = {Comparative analysis of the seed microbiome in four major oilseed crops (rapeseed, sunflower, soybean, sesame) reveals host-specific assembly and potential application of seed core microbes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1721916},
pmid = {41669382},
issn = {1664-462X},
abstract = {The oilseeds are abundant in oils and proteins, and the production of high-quality oilseeds represents a major objective in modern agriculture. However, oilseed production is constrained by biotic and abiotic stresses, resulting in the decreasing in yield and quality. The seed microbiome has been recognized as a critical determinant of plant health. However, its composition and functional roles in various oilseed crops remains poorly explored. In this study, we utilized 16S rRNA gene amplicon sequencing to compare the bacterial component of seed microbiome and predict their metabolic potential in four oil crops (rapeseed, sunflower, sesame, soybean). Our results revealed that the oilseed harbored high diverse of microbes, and the assembly of microbial community was not random but driven by species and cultivar. From the perspective of microbial functions, the lipid metabolism and other secondary metabolites of seed microbes were associated with corresponding metabolic processes in seeds, such as glucosinolate and linoleic acid, reflecting the functional connection between seed metabolites and seed microbes. Furthermore, the core microbiome was obtained among four oilseed groups, consisting of 18 bacterial amplicon sequence variants (ASVs), including putative plant-beneficial resources, such as Sphingomonas. Notably, strain SE-S32 (Sphingomonas endophytica) isolated from rapeseed seed, one of the core microbes, could improve the resistance of various crops, indicating that seed core microbes could serve as a microbial inoculant among multiple crops. These results provide new insights into the correlation between seed microbiome and seed metabolites, establishing a theoretical foundation for developing microbial strategies to improve oilseed quality and plant health.},
}

@article {pmid41669238,
year = {2025},
author = {Benavides-Infante, AP and Fresno-Rueda, AM and Rodrigues, LA and Socha, MT and Fernandes, T and St-Pierre, B and Perez-Palencia, JY and Levesque, CL},
title = {Interactive effects of dietary protein and fiber levels on total tract and apparent ileal nutrient digestibility, microbiota profiling, and fermentation products in pigs fed a blend of branched-chain volatile fatty acids.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1731832},
pmid = {41669238},
issn = {2297-1769},
abstract = {INTRODUCTION: The experiment investigated the interactions between diet protein and fiber and branched-chain volatile fatty acids (BCVFA) on nutrient digestion, fermentation products, and microbiome modulation in pigs.

METHODS: Fourteen cannulated pigs (body weight 20.4 ± 1.4 kg) were used in a replicated 6 × 5 Youden square design with 6 diets and 5 periods for at least 11 observations per dietary treatment. Experimental diets were 2 × 2 + 2 arrangement, consisting of 4 BCVFA-diets (isobutyrate, isovalerate, and 2-methyl butyrate, 1:1:1) supplemented at 1%, with varying protein [low (LP; 15%) or normal (NP; 19%) protein] and fiber [low (LF: 11%) neutral detergent fiber (NDF) or high (HF: 17% NDF)]. The '+2' diets were a positive LP-LF (PC) and a negative NP-HF (NC) control without BCVFA. Diets, fecal, and ileal digesta samples were analyzed for nutrients, fiber composition, AA, and titanium. Fecal samples were analyzed for bacterial composition.

RESULTS: Pigs fed BCVFA-supplemented NP-HF diets had the greatest AID for acid detergent fiber (ADF), acid detergent lignin, cellulose, and hemicellulose, and the greatest ATTD for ADF (p < 0.05). The AID of AA was greater (p < 0.05) in pigs fed LP-LF PC diet compared to LP-LF BCVFA-supplemented diet (p < 0.05). There were no interactions (p > 0.05) between fiber and protein levels for volatile fatty acids (VFA) concentration in ileal and fecal samples. Feeding high fiber diets supplemented with BCVFA resulted in greater (p < 0.05) concentration of acetic, propionic, butyric, and total VFA production in fecal samples. Fecal bacteria affiliated to Erysipelotrichaceae were found in higher abundance in the BCVFA-supplemented NP-HF diet compared to its non-supplemented control (p < 0.05). Similarly, candidate bacterial strains of Turicibacter sanguinis (OTU Ssd-110) and Romboutsia timonensi (OTU Ssd-23) were more highly represented in the fecal microbial communities of pigs fed the BCVFA-supplemented NP-HF diet compared to its non-supplemented control (p < 0.05).

CONCLUSION: Supplementation of 1% BCVFA in swine diets containing higher fiber and typical crude protein can optimize digestive efficiency, particularly at the ileal level, which was associated with improvements in nutrient digestibility potentially mediated by microbiome modulation. This may represent an opportunity to feed simpler diets, improving the efficiency and sustainability of swine production.},
}

@article {pmid41668960,
year = {2026},
author = {Yang, J and Zhu, H and Yao, B and Zhang, W and Xing, X and Cheng, W and Dong, C},
title = {The impact of caffeine-mediated gut microbiota regulation on the athletic performance of football players.},
journal = {Biology of sport},
volume = {43},
number = {},
pages = {115-125},
pmid = {41668960},
issn = {0860-021X},
abstract = {Caffeine is widely utilized as an ergogenic aid in sports, yet its interaction with gut microbiota - a key modulator of metabolic and physiological processes - remains underexplored in athletic populations. This study aimed to investigate whether caffeine supplementation enhances the athletic performance of football players through gut microbiota regulation, thereby bridging the gap between caffeine's ergogenic effects and microbial mediation mechanisms. A 7-day randomized, double-blind, placebo-controlled trial was conducted with 32 male national-level football players. Participants were allocated to either a caffeine group (3 mg/kg body mass) or a placebo group. Performance assessments included agility tests, 30-m repeated sprints, technical dribbling tasks, and aerobic endurance evaluations. Fecal samples were analyzed via 16S rRNA sequencing to assess microbial diversity and composition. Structural equation modeling (SEM) was employed to evaluate the mediating role of gut microbiota. Caffeine supplementation significantly improved agility (p < 0.001, Cohen's d = 1.1), sprint performance (p = 0.007, d = 0.7), and technical execution (p = 0.003, d = 0.7) compared to placebo. Gut microbiota alpha diversity (Chao1, Shannon) increased in the caffeine group (p < 0.05), with enrichment of Prevotella, Bacteroides, and Veillonella. SEM revealed that 33.3% of caffeine's performance-enhancing effect was mediated by microbial diversity (β = 0.2, p = 0.01), while no direct caffeine-performance pathway was observed (p = 0.2). These findings demonstrate that caffeine enhances football-specific performance partially through gut microbiota modulation, emphasizing the microbiome's role in translating nutritional interventions into athletic gains. Future research should explore long-term microbial adaptations and personalized strategies combining caffeine with microbiome-targeted therapies.},
}

@article {pmid41668881,
year = {2026},
author = {Chen, S and Cui, L and Zuo, B and Zhao, J and Walker, ED},
title = {Tannic acid shaped microbiome composition in midguts and rearing microcosms of Aedes triseriatus (Say).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755894},
pmid = {41668881},
issn = {1664-302X},
abstract = {INTRODUCTION: Tannic acid (TA), a polyphenol derived from plants, often accumulates in water-holding containers where mosquitoes develop. Yet, its effects on mosquito gut microbiota remain poorly understood, representing an important knowledge gap. Because mosquito-associated microbiota are vital for host development, nutrition, and immunity, uncovering how TA shapes these microbial communities may yield new insights into mosquito biology and vector control strategies.

METHODS: In this study, we conducted a comparative analysis of bacterial communities in Aedes triseriatus midguts and rearing microcosms with or without TA supplement.

RESULTS: Addition of TA at 0.35 mg/mL caused up to 50% larval Ae. triseriatus mortality, whereas combined supplementation with TA and kanamycin (100 μg/mL) increased mortality to 75% relative to controls. TA treatment significantly reduced microbial Chao 1 richness and Shannon diversity in larval and adult mosquito guts, while water and leaf samples were not affected. Distinct microbial community structures were observed between TA-treated and control groups across larvae, adults, water, and leaf surfaces. Pseudomonadota and Bacteroidota dominated all samples, with TA increasing the relative abundance of Pseudomonadota while decreasing Bacteroidota. Notably, Pseudomonas was enriched in TA-treated water, leaf surfaces, and larval midguts. PICRUSt functional predictions indicated enrichment of carbohydrate and amino acid metabolism and membrane transport pathways under TA exposure, reflecting adaptive microbial responses to TA stress.

CONCLUSION: Our findings highlight how TA shapes mosquito microbiota and habitat quality, offering potential avenues to manipulate microbial communities as a biocontrol strategy for mosquito larvae.},
}

@article {pmid41668803,
year = {2026},
author = {Mousa, HRF and Abiko, Y and Washio, J and Sato, S and Takahashi, N},
title = {Characteristics of Candida albicans metabolism of glucose and two sugar substitutes, xylose and xylitol and effect of these substitutes on glucose metabolism from a cariogenic perspective.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2626130},
pmid = {41668803},
issn = {2000-2297},
abstract = {OBJECTIVES: Carbohydrate metabolism and subsequent acid production of Candida albicans remain insufficiently understood. C. albicans may utilize xylitol, but its cariogenic implications are understudied. This study examined growth and metabolism of glucose, xylitol and precursor xylose by C. albicans and their effects on glucose metabolism.

METHODS: C. albicans JCM1537 was cultured in YNB medium containing 1% glucose, xylose, xylitol or xylose- or xylitol-glucose combinations. Acid production from cells grown on each substrate was assessed by pH-stat system at pH 7.0 using 10 mM substrates. Metabolic end-products were quantified by HPLC and enzymatic methods. Carbon recovery and redox balance of glucose metabolism were calculated stoichiometrically.

RESULTS: Growth and acid production on xylose or xylitol were much lower than on glucose, with no inhibitory effect of xylose or xylitol observed. Glucose carbon was distributed as 50.48% ethanol, 21.95-24.72% bicarbonate, 5.70% glycerol, 2.88% organic acids and 0.12% acetaldehyde, yielding 81.07-84.48% recovery and 93.26-93.97% reduction-oxidation balance.

CONCLUSIONS: Although xylose and xylitol did not inhibit C. albicans glucose metabolism, their limited growth and acidogenicity suggest low cariogenic potential. The overall view of glucose metabolism, including high ethanol production, provides new insights into the metabolic impact of C. albicans within the oral microbiome.},
}

@article {pmid41668733,
year = {2025},
author = {Sui, Q and Yu, J and Cui, S},
title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1707599},
pmid = {41668733},
issn = {2235-2988},
mesh = {Humans ; Middle Aged ; Male ; Female ; Aged ; Retrospective Studies ; *Atherosclerosis/microbiology/diagnosis ; *Microbiota ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Risk Factors ; Bacteria/classification/genetics/isolation & purification ; *Cardiovascular Diseases/microbiology/diagnosis ; Metagenomics ; },
abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.

METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).

RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.

CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.},
}

Humans
Middle Aged
Male
Female
Aged
Retrospective Studies
*Atherosclerosis/microbiology/diagnosis
*Microbiota
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
ROC Curve
Risk Factors
Bacteria/classification/genetics/isolation & purification
*Cardiovascular Diseases/microbiology/diagnosis
Metagenomics

@article {pmid41668721,
year = {2025},
author = {Mahalak, KK and Narrowe, AB and Firrman, J and Lemons, JMS and Liu, L},
title = {The ginger polyphenol 6-gingerol elicits minimal changes in an ex vivo human gut microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1711783},
pmid = {41668721},
issn = {2296-861X},
abstract = {Ginger (Zingiber officinale) has a long history of use in traditional medicine and the modern world to alleviate health conditions, particularly those related to indigestion and nausea. Gingerols are phenolic bioactive compounds found in ginger. It has been suggested that health benefits associated with gingerols may be due to modification of the gut microbiome, especially in disease models. However, the impact of gingerol on a healthy human gut microbiome, and whether age affects gingerol activity, is not well understood. To address this, the impact of 6-gingerol, the most abundant polyphenol found in ginger, on the gut microbiomes of four age groups (infants, children, adults (22-40), and adults (60+)) was determined using SIFR® technology. Following a 24-h incubation with 6-gingerol, microbial community genomic analysis was performed together with metabolic analysis to determine the impact of 6-gingerol on the gut microbiota ex vivo. Using this method, 6-gingerol was determined to have no significant impact on the gut microbiota in terms of community density, community diversity, or short-chain fatty acid production. This study found that, in healthy gut microbiota, 6-gingerol did not have a strong effect within a 24-h period of treatment.},
}

@article {pmid41668505,
year = {2026},
author = {Baek, J and Choi, DH and Park, BE and Cho, E and Kim, K and Lee, JY and Shin, JW and Kim, W},
title = {Synbiotic Combination of Lactococcus lactis LB1022 and Fructo-Oligosaccharides Mitigates the Atopic March by Modulating the Microbiota-Gut-Skin-Lung Axis.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2511044},
doi = {10.4014/jmb.2511.11044},
pmid = {41668505},
issn = {1738-8872},
mesh = {Animals ; *Synbiotics/administration & dosage ; *Oligosaccharides/administration & dosage/pharmacology ; Female ; Mice, Inbred BALB C ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Dermatitis, Atopic/microbiology/immunology/therapy/prevention & control ; *Lactococcus lactis ; Lung/immunology/pathology/microbiology ; Disease Models, Animal ; Skin/pathology/immunology ; Asthma ; Cytokines/metabolism ; Fatty Acids, Volatile/metabolism ; Ovalbumin ; Probiotics ; Immunoglobulin E/blood ; Feces/microbiology/chemistry ; Immunoglobulin G/blood ; },
abstract = {Dysregulated gut microbiota is increasingly recognized as a major contributor to allergic diseases and their progression. A key clinical manifestation of this progression is the atopic march, in which atopic dermatitis (AD) precedes the development of allergic airway disease. Although prebiotics and probiotics individually improve AD symptoms, their combined use as synbiotics, especially with regard to preventing the progression from cutaneous inflammation to airway hypersensitivity, has not been clearly established. In this study, we assessed the biological activity of a synbiotic composed of fructo-oligosaccharides (FOS) and Lactococcus lactis LB1022 in an ovalbumin (OVA)-induced murine model of AD and asthma-like inflammation. Female BALB/c mice were treated for eight weeks with FOS, L. lactis LB1022, or their combination following OVA sensitization. The synbiotic formulation produced the strongest protective effects, markedly reducing AD-like skin pathology, suppressing airway inflammatory cell influx, and lowering Th2-skewed cytokine responses. These protective effects were further supported by significant reductions in serum IgE and Th2-associated IgG1 levels. Synbiotic treatment also enriched multiple short-chain fatty acid (SCFA)-producing taxa, including Lactobacillus and Bifidobacterium species, resulting in increased fecal SCFA concentrations that were closely associated with improvements in systemic and mucosal immunity. These results demonstrate that the FOS-L. lactis LB1022 synbiotic mitigates both epidermal and respiratory allergic inflammation through coordinated regulation of the microbiota-gut-skin-lung axis. The findings highlight a promising dietary approach for reducing the risk of progression along the atopic march and address an important gap in current allergy-related microbiome research.},
}

Animals
*Synbiotics/administration & dosage
*Oligosaccharides/administration & dosage/pharmacology
Female
Mice, Inbred BALB C
*Gastrointestinal Microbiome/drug effects
Mice
*Dermatitis, Atopic/microbiology/immunology/therapy/prevention & control
*Lactococcus lactis
Lung/immunology/pathology/microbiology
Disease Models, Animal
Skin/pathology/immunology
Asthma
Cytokines/metabolism
Fatty Acids, Volatile/metabolism
Ovalbumin
Probiotics
Immunoglobulin E/blood
Feces/microbiology/chemistry
Immunoglobulin G/blood

@article {pmid41668329,
year = {2026},
author = {Tingga, RCT and Ampeng, A and Liam, J and Deli, B and Anuar, ML and Abang-Abdillah, DN and Johari, N and Mohd-Ridwan, AR and Md-Zain, BM},
title = {First Gut Microbiome Profiling of the Critically Endangered Tricolour Langur (Presbytis chrysomelas cruciger) and Vulnerable Silvery Langur (Trachypithecus cristatus) in Sarawak, Malaysia.},
journal = {Journal of medical primatology},
volume = {55},
number = {1},
pages = {e70065},
doi = {10.1111/jmp.70065},
pmid = {41668329},
issn = {1600-0684},
support = {ST-2022-027//The National Conservation Trust Fund for Natural Resources/ ; B210//Sarawak government project/ ; P23//Sarawak government project/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Malaysia ; *Endangered Species ; DNA Barcoding, Taxonomic ; *Cercopithecidae/microbiology ; },
abstract = {DNA metabarcoding is used to explore the gut microbiome of Presbytis chrysomelas cruciger and Trachypithecus cristatus from the Jemoreng Protected Forest. Phylum Firmicutes, family Lachnospiraceae, and genus Shuttleworthia are suggested as the key microbiome components for both species. The microbiome was primarily composed of beneficial bacteria essential for food digestion.},
}

Animals
*Gastrointestinal Microbiome
Malaysia
*Endangered Species
DNA Barcoding, Taxonomic
*Cercopithecidae/microbiology

@article {pmid41668221,
year = {2026},
author = {Peng, X and Xue, Y and Wang, H and Nan, S and Qi, Y and Nie, C and Zhang, W},
title = {Maternal supplementation with rumen-protected arginine reshapes the ileal microbiome and enhances neonatal lamb growth.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {18},
pmid = {41668221},
issn = {2524-4671},
support = {2024D14009//Xinjiang Production and Construction Corps/ ; 2022B02029//Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND: The nutritional status of ewes during gestation and lactation is a key determinant of lamb growth performance. Supplementation with rumen-protected L-arginine (RP-Arg) during these stages induces maternal metabolic adaptation, thereby maintaining fetal developmental homeostasis. However, the sustained effects of such metabolic regulation on postnatal lamb growth and immune functions are currently unclear. Twenty-seven pregnant Chinese Merino ewes (at 60 days of gestation) were randomly assigned to one of three dietary treatments: (1) grazing only (control, CON), (2) grazing plus 300 g/day of concentrate feed (SF), or (3) SF diet supplemented with 30 g/day of RP-Arg (ARG). When the lambs reached 14 days of age, ileal and liver tissues were collected. The ileal microbiota was characterized using 16S rRNA gene amplicon sequencing, and untargeted metabolomics was used to examine the hepatic metabolism in the lambs.

RESULTS: Compared with the CON group, both SF and ARG group lambs showed significantly improved early growth performance (P < 0.05), and the ARG group exhibited significantly higher average daily gain and total weight gain (net weight gain) than the SF group (P < 0.05). Milk protein content was significantly higher in the SF and ARG groups than in the CON group (P < 0.05). Notably, compared with the SF group, ARG supplementation elevated colostrum lactoferrin and insulin-like growth factor-1 (IGF-1) concentrations by 28.4% and 34.1%, respectively (P < 0.05). Compared with SF group, ARG group showed a higher relative abundance of ileal Bacteroidota (+ 40%, P < 0.05) and Prevotella (+ 96%, least discriminant analysis > 3.2), increased hepatic glutamine, methionine, and malate (variable importance in projection > 1.3, P < 0.05), and upregulated arginine-proline metabolism and ABC transporters, indicating that RP-Arg was associated with a shift in both the ileal microbiota and hepatic metabolite profile, suggestive of a modest gut-liver metabolic interaction to enhance nitrogen and energy flux, resulting in superior lamb growth.

CONCLUSIONS: RP-Arg specifically elevates colostrum IGF-1 and lactoferrin levels, enriches ileal Bacteroidota and Prevotella, and reprograms hepatic arginine-proline and ABC transporter metabolism. Overall, these changes were associated with an increased early growth rate of lambs without affecting milk protein production.},
}

@article {pmid41668172,
year = {2026},
author = {Kim, DY and Youn, J and Kang, N and Cho, SI and Ha, IH},
title = {Potential application of brain-gut axis-based treatments in Long COVID and ME/CFS: a case-based systematic review.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07807-w},
pmid = {41668172},
issn = {1479-5876},
abstract = {BACKGROUND: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and Long COVID share clinical features including persistent fatigue, post-exertional malaise (PEM), and gastrointestinal (GI) dysfunction. Growing evidence implicates brain-gut axis dysregulation, characterized by dysbiosis, neuroinflammation within the central nervous system (CNS), increased intestinal permeability, and microbial translocation in their pathophysiology. However, therapeutic strategies targeting these pathways remain poorly defined.

METHODS: We report a case of post-COVID ME/CFS successfully treated with electroacupuncture (EA)-based deep peroneal nerve stimulation which was employed to potentiate the vagal reflex. Fatigue trajectories were assessed using the Multidimensional Fatigue Inventory over 12 weeks. Based on the case, a systematic review of randomized controlled trials (RCTs) evaluating brain-gut axis-modulating interventions in ME/CFS or Long COVID was conducted.

RESULTS: The patient exhibited a significant reduction in total fatigue, with early improvements in motivation and mental fatigue, and delayed improvement in physical fatigue following transient systemic symptom flares. Across included RCTs (n = 8, 790 participants), four investigated gut microbiome-modulating therapies and four employed nerve stimulation. Synbiotic and herbal interventions demonstrated benefits for fatigue or PEM, accompanied by alterations in specific bacterial populations or CNS metabolisms. Regarding nerve stimulation, transcranial direct current stimulation (tDCS) combined with exercise program improved fatigue, whereas standalone tDCS, auricular or peripheral TENS showed limited efficacy.

CONCLUSION: Brain-gut axis-based interventions may alleviate fatigue in ME/CFS and Long COVID by potentially modulating neuroinflammation, restoring microbiome balance, and improving epithelial barrier function. EA-based vagal stimulation represents a feasible option for patients with severe or treatment-resistant symptoms. Larger mechanistic studies and rigorously designed RCTs are needed to establish therapeutic targets and optimize intervention strategies.},
}

@article {pmid41668157,
year = {2026},
author = {Yau, PT and Taketani, RG and Bonnin, JM and Stewart, H and Thompson, CMA and Clark, IM and Mauchline, TH and Malone, JG and Ryan, MJ and Jones, S and Holden, N},
title = {Correction: Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {27},
pmid = {41668157},
issn = {2524-6372},
}

@article {pmid41668155,
year = {2026},
author = {Tiwary, P and Oswal, K and Tzvetkov, NT and Litvinova, O and Atanasov, AG and Varghese, R},
title = {Travel microbiota: a novel frontier in travel medicine exploring microbial shifts across transportation modes.},
journal = {Tropical diseases, travel medicine and vaccines},
volume = {12},
number = {1},
pages = {9},
pmid = {41668155},
issn = {2055-0936},
abstract = {BACKGROUND: Between 2010 and 2019, international travel increased by approximately 52.2%, highlighting the world's dependence on transportation for global connectivity. Although travel enhances global interactions, it also poses risks to public health through the potential transmission of diseases. The rapid global transmission of infectious diseases, exemplified by the outbreaks of COVID-19 and Zika virus, underscores the critical need for in-depth research into travel-associated disease dissemination. When individuals travel, they are exposed to a variety of diverse microbial environments, which can affect their healthy microbiome. In this review, we introduce the concept of "travel microbiota" to encapsulate the dynamic shifts in human microbial communities induced by travel across different transportation modes. This disruption can affect metabolic and immune functions and potentially facilitate the spread of diseases. Given these implications, it is crucial to investigate how different modes of transportation affect the human microbiota. Our study reviews the impact of travel on the human microbiota, highlighting differences across transportation modes. The objective is to establish a framework for understanding travel health and the role of microbiota in managing travel-related health risks. A comprehensive understanding of this relationship is essential for developing preventive strategies to safeguard and restore the human microbiota.

METHODS: To provide the specific content, relevant publications were identified on Google Scholar, PubMed, and Science Direct using specific keywords such as dysbiosis, gut, health, microbiome, microbiota, pathogens, travel, and transportation. We did not add any limits to the publication date during the inclusion of papers. However, it is noteworthy that the initial reports, including the aforementioned keywords, have been published starting from 2015.

CONCLUSION: Travel has a profound impact on the human microbiota, and it is essential to consider the implications associated with various modes of transportation. Traveling through various modes of transportation, such as roadways, airways, and maritime, has significantly influenced human microbiota. Moreover, it acts as a dynamic interface for microbial exchange driving rapid shift in microbial diversity, community convergence, and the diversification of resistant genes. However, the underlying mechanism of these changes remains elusive. By integrating evidence across multiple modes of transportation, this review highlights travel as an underrecognized determinant of microbiome variability and introduces the term "Travel microbiota". Moreover, this review is pivotal for understanding the ways in which travel alters microbial diversity and developing effective interventions. It is imperative to conduct future research that focuses on conducting large-scale longitudinal studies to assess the effects of traveling on microbial composition and to develop potential preventive measures.},
}

@article {pmid41667953,
year = {2026},
author = {Guccione, C and Sfiligoi, I and Gonzalez, A and Shaffer, JP and Kazachkova, M and Weng, Y and McDonald, D and Shah, SC and Minot, SS and Paulson, TG and Grady, WM and Alexandrov, LB and Knight, R and Curtius, K},
title = {Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12545-w},
pmid = {41667953},
issn = {1471-2164},
support = {R01 CA270235/NH/NIH HHS/United States ; 5K12GM068524-17/NH/NIH HHS/United States ; P30 CA023100/NH/NIH HHS/United States ; RG103468//University of California, San Diego/ ; 2019-67013-29137//National Institute of Food and Agriculture/ ; ICX002027A//U.S. Department of Veterans Affairs/ ; AGA2022-13-05//AGA Research Foundation/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; },
}

@article {pmid41667763,
year = {2026},
author = {Bian, H and Li, Y and Zhang, Y and Shen, Y and Hao, J and Wang, S and Li, J},
title = {Coupled rhizosphere application of cyanobacteria-bamboo acid hydrolysis extract and cyanobacterial biochar enhances soil health and crop quality.},
journal = {Bioresources and bioprocessing},
volume = {13},
number = {1},
pages = {22},
pmid = {41667763},
issn = {2197-4365},
support = {2023YFC3207602//National Key Research and Development Program of China/ ; BE2022030//Jiangsu Special Funding of Science and Technology Innovation for Carbon Emission Peaking and Carbon Neutrality/ ; },
abstract = {UNLABELLED: Driven by waste resource utilization and carbon neutrality imperatives, this study synthesized cyanobacterial growth elicitor (CGE) and cyanobacterial-bamboo growth elicitor (CBGE) via acid-hydrothermal hydrolysis. The coupling potential of cyanobacterial biochar (CB) for improving rhizosphere soil and crop quality was investigated through four pot trial treatments: (1) CK (control), (2) BR (rhizospheric CB), (3) LBR (rhizospheric CB with CGE), (4) LZBR (rhizospheric CB with CBGE). Integration of phenotypic analyses, microbiome profiling, functional gene predictions, and risk assessment elucidated biostimulant mechanisms. Compared to CK, all treatments elevated soil nutrient levels. BR exhibited superior nitrogen enrichment (15 ± 3 g/kg), while LBR and LZBR—particularly LZBR—enhanced phosphorus/potassium bioavailability and maximized soil organic carbon (SOC). LZBR treatment markedly increased Chryseobacterium abundance (an organic matter-decomposing genus). Functional verification confirmed enhanced C-N-P cycling activity, minimized environmental nutrient leakage, and improved plant nutrient assimilation. Specifically, LZBR increased soybean grain protein content by 37.0 g/kg and plant nitrogen accumulation by 5.4 g/kg compared to CK, and risk assessments indicated no detectable ecotoxicological effects. Consequently, the coupled application of CGE and CBGE derived from cyanobacteria and bamboo powder simultaneously improves soil quality and crop performance. This approach establishes a novel waste valorization pathway, suitable for partial replacement of chemical fertilizers and carbon emission reduction.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40643-026-01016-5.},
}

@article {pmid41667443,
year = {2026},
author = {Chen, D and Li, D and Su, L and Wang, DY and Ren, Y and van der Mei, HC and Shi, L and Chen, T and Busscher, HJ},
title = {Stimuli-responsive, antimicrobial-loaded nanocarriers for oral biofilm control and microbiome restoration.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {17},
pmid = {41667443},
issn = {2049-3169},
mesh = {*Biofilms/drug effects ; Humans ; *Microbiota/drug effects ; *Drug Carriers ; *Anti-Infective Agents/administration & dosage/pharmacology ; *Mouth/microbiology ; Animals ; *Nanoparticles ; Anti-Bacterial Agents/administration & dosage ; },
abstract = {Nanotechnology has provided thousands of novel nano-antimicrobials possessing features uncommon in clinically available antimicrobials. Here, nanocarriers loaded with conventional antimicrobials and responding to environmental changes upon entry into oral biofilms are reviewed. Supra-gingival biofilms are characterized by acidic pH, the presence of bacterial enzymes, and the development of hypoxia in deeper layers. Sub-gingival biofilms are slightly alkaline, with hypoxia occurring over their entire depth. Upon entering biofilms, negatively charged, pH- and/or hypoxia-responsive nanocarriers become positively charged. This charge reversal leads to electrostatic double-layer attraction between positively charged nanocarriers towards negatively charged, water-filled channel walls in biofilms, enhancing their accumulation in a biofilm. Degradation of bacterial enzyme-responsive nanocarriers causes in-biofilm release of antimicrobial cargo, yielding higher local antimicrobial concentrations than can be achieved through their direct, oral administration without harming soft tissues. Enhanced antibiofilm activity after in-biofilm antimicrobial release from biofilm-responsive micelles and liposomes has been demonstrated in vitro towards single-species Streptococcus mutans and Staphylococcus aureus biofilms or in vivo using specific-pathogen-free rodents inoculated with selected pathogens. This preferential antibacterial activity regulated the microbial composition of ex vivo human oral biofilm towards a more healthy microbiome composition. Although clinical confirmation is limited, the potential benefits of stimuli-responsive, antimicrobial-loaded nanocarriers for oral biofilm control and microbiome restoration are worth further investigation towards clinical translation.},
}

*Biofilms/drug effects
Humans
*Microbiota/drug effects
*Drug Carriers
*Anti-Infective Agents/administration & dosage/pharmacology
*Mouth/microbiology
Animals
*Nanoparticles
Anti-Bacterial Agents/administration & dosage

@article {pmid41667397,
year = {2026},
author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E},
title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2627692},
pmid = {41667397},
issn = {1949-0984},
mesh = {Humans ; *Ceftriaxone/therapeutic use/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy ; Aged ; *Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification ; Genetic Variation ; Adult ; Rectum/microbiology ; },
abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.},
}

Humans
*Ceftriaxone/therapeutic use/pharmacology
*beta-Lactamases/genetics/metabolism
*Anti-Bacterial Agents/therapeutic use/pharmacology
Male
Female
Middle Aged
Prospective Studies
*Gastrointestinal Microbiome/drug effects
*Enterobacteriaceae Infections/microbiology/drug therapy
Aged
*Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification
Genetic Variation
Adult
Rectum/microbiology