@article {pmid41930959,
year = {2026},
author = {Horinouchi, M},
title = {Identification of the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings in steroid degradation by Comamonas testosteroni TA441.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0233125},
doi = {10.1128/aem.02331-25},
pmid = {41930959},
issn = {1098-5336},
abstract = {Comamonas testosteroni TA441 is a model aerobic steroid-degrading bacterium whose sterane degradation pathway has been elucidated in the greatest detail to date. Similar pathways have been identified in many genera of bacteria, including both proteobacteria and actinobacteria, such as Mycobacterium tuberculosis. However, the genes encoding the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA, also known as HIP) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings had not been identified. In this study, we identified these missing genes, located adjacent to the chsE1E2H1H2ltp2 cluster involved in C17 side-chain degradation, and designated them scdB and scdH, respectively. This finding completes the elucidation of all degradation steps of 9,17-DOHNA prior to D-ring cleavage. AlphaFold models showed that ScdB and at least five hydrogenases/dehydrogenases involved in steroid degradation in TA441 share a similar dimer structures with Rossmann fold motif. In contrast, ScdH was predicted to form a homohexameric structure similar to ScdY and ScdN, involved in B-, C-, and D-ring degradation in TA441. Furthermore, AlphaFold modeling revealed that SteC, the dehydratase responsible for removing the C12β-hydroxyl group from 9,17-DOHNA derivatives, exhibits strong structural similarity to BaiE, the bile acid 7α-dehydratase of Clostridium scindens JCM 10418/VPI 12708, despite sharing only ~28% amino acid sequence identity.IMPORTANCEResearch on bacterial aerobic steroid degradation began more than 70 years ago, initially to produce intermediates for steroid drug synthesis. Recently, this field has gained renewed attention due to its implications for human health-for example, the role of cholesterol import and degradation in the persistence of Mycobacterium tuberculosis H37Rv within chronically infected lungs. Comamonas testosteroni TA441 serves as a key model organism for elucidating aerobic steroid degradation, with pathways for cleavage of the A-, B-, C-, and D-rings already well established. The functions and structures of the enzymes identified in TA441 display striking similarities to those in actinobacteria, such as M. tuberculosis. In this study, we identified two enzymes indispensable for initiating β-oxidation of the B-, C-, and D-rings, thereby filling the last remaining gaps for initiating this pathway. Our AlphaFold-based structural analysis of these enzymes not only provides new insights into the steroid metabolism of M. tuberculosis but also broadens understanding of the ecological and physiological significance of bacterial steroid degradation.},
}

@article {pmid41930960,
year = {2026},
author = {Nan, F and Song, H and Sun, M and Cui, L and Bian, Z and Yin, J and Lin, Z and Wang, Y},
title = {Hijacking competitor-derived signals: RcsB/C drives Lysobacter enzymogenes to exploit farnesol for enhanced antifungal capacity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030426},
doi = {10.1128/aem.00304-26},
pmid = {41930960},
issn = {1098-5336},
abstract = {Microbial antagonism is a fundamental ecological process that shapes community composition and maintains ecosystem balance. However, the molecular signals, such as cross-kingdom interactions between bacteria and fungi in natural environments, remain largely unexplored. Lysobacter enzymogenes is a widespread predatory bacterium that produces the antifungal secondary metabolite heat-stable antifungal factor (HSAF), which enables interactions with diverse fungi. Here, we investigated the interkingdom interactions between L. enzymogenes and the environmental fungus Candida krusei, both of which are widely distributed, to elucidate the bacterial-fungal communication. We found that the antagonistic effect of bacteria-fungi was significant under both contact and non-contact co-culture conditions, indicating the involvement of diffusible metabolites. Given that farnesol is a common quorum-sensing (QS) molecule in Candida, metabolite profiling combined with exogenous addition and biosynthesis inhibition experiments demonstrated that farnesol functions as a cross-kingdom signal regulating HSAF production and bacterial antagonism. Further mechanistic analysis of the intrinsic mechanism revealed that the two-component system (TCS) RcsB/C in L. enzymogenes can sense farnesol and activate the production of HSAF through the MarR family regulators, mediating the antagonistic pathway. In addition, our work identified the key amino acid residues in RcsC of L. enzymogenes responsible for recognizing farnesol. In summary, we report the bacterial TCS involved in farnesol sensing and reveal a novel bacterial-fungal antagonistic mechanism, in which L. enzymogenes "hijacks" a fungal QS molecule to enhance its antifungal capacity, uncovering a previously unrecognized strategy of cross-kingdom communication.IMPORTANCEBacteria and fungi frequently interact in shared habitats, yet the chemical cues that shape these cross-kingdom relationships remain poorly defined. Farnesol is a well-known quorum-sensing molecule in Candida, but its ecological roles beyond fungal communication are unclear. Here, we show that Lysobacter enzymogenes directly senses fungal-derived farnesol through the RcsB/C two-component system, which activates the downstream regulator MarR-2 and induces the production of the antifungal metabolite heat-stable antifungal factor (HSAF). This signal hijacking strategy allows L. enzymogenes to convert a fungal communication molecule into a cue that strengthens its antagonistic capacity. We further identify key amino acid residues in RcsC responsible for farnesol recognition, revealing the bacterial two-component system (TCS) known to detect this molecule. These findings expand the functional scope of fungal quorum-sensing signals, uncover a previously unrecognized mechanism of interkingdom antagonism, and provide insights with potential applications in microbiome-based biocontrol.},
}

@article {pmid41930968,
year = {2026},
author = {Cheng, D and Luo, Z and Ning, W and Heath, SL and Gisslen, M and Price, RW and Adekunle, R and Salman, T and Johnson, D and McKinnon, JE and Ndhlovu, LC and Hossain, R and Hu, W and Jiang, W},
title = {Systemic translocation of Staphylococcus aureus promotes autoimmunity: implications in autoantibody-mediated poor immune reconstitution from antiretroviral therapy in HIV.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0196525},
doi = {10.1128/jvi.01965-25},
pmid = {41930968},
issn = {1098-5514},
abstract = {In 2017, our group first demonstrated that autoimmunity contributes to HIV pathogenesis, even without autoimmune disease. This concept is now broadly recognized, exemplified by the role of autoimmunity in severe COVID-19. In people with HIV (PWH) on suppressive antiretroviral therapy (ART), anti-CD4 autoantibodies may impair CD4+ T-cell recovery, though the mechanisms driving their production remain unclear. Building on evidence from our group and others that Staphylococcus aureus and its peptidoglycan (PGN) promote autoimmunity, we investigated their contribution to anti-CD4 IgG in HIV. Plasma from 32 ART-naive PWH, 53 ART-treated PWH, and 32 HIV-negative controls was analyzed for IgG autoantibodies and markers of S. aureus translocation using protein array and ELISA. EcoHIV mice were injected intraperitoneally with saline, S. aureus PGN, or Bacillus subtilis PGN. PGN structures were compared by mass spectrometry. Among 87 autoantibodies, 40% were elevated in ART-naive PWH and largely normalized by ART; however, anti-CD4 IgGs remained elevated in PWH on ART. Anti-CD4 IgG levels inversely correlated with CD4+ T-cell counts in ART-treated PWH and positively with markers of S. aureus translocation. In mice, S. aureus PGN induced anti-CD4 IgGs, reduced frequency of CD4+ T cells among total gut T cells, and promoted surface IgG binding and apoptosis in CD4+ T cells. S. aureus and its PGN translocation may drive anti-CD4 autoimmunity and hinder immune recovery in PWH on suppressive ART, highlighting S. aureus colonization as a therapeutic target and supporting the development of competitive probiotic interventions.IMPORTANCECurrently, no treatment is available for improving CD4+ T-cell recovery in people with HIV (PWH) on suppressive antiretroviral therapy (ART). Up to 20% of PWH on ART fail to restore peripheral CD4+ T-cell counts to levels observed in healthy individuals, a condition associated with increased morbidity and mortality and representing a major unmet challenge in HIV clinical care. Our study demonstrates that systemic Staphylococcus aureus translocation contributes to autoimmunity and impaired immune reconstitution in a subset of PWH on suppressive ART. These findings identify a previously unrecognized mechanism of immune failure and support a novel therapeutic strategy combining probiotics with ART to enhance immune recovery and reduce HIV-associated morbidity and mortality.},
}

@article {pmid41931049,
year = {2026},
author = {Rosen, CJ and Ingelfinger, JR},
title = {GLP-1 Receptor Agonists.},
journal = {The New England journal of medicine},
volume = {394},
number = {13},
pages = {1313-1324},
doi = {10.1056/NEJMra2500106},
pmid = {41931049},
issn = {1533-4406},
mesh = {Humans ; *Cardiovascular Diseases/etiology/metabolism/prevention & control ; *Diabetes Mellitus, Type 2/complications/drug therapy/metabolism ; Glucagon-Like Peptide 1/agonists/metabolism ; *Glucagon-Like Peptide-1 Receptor Agonists/adverse effects/pharmacology/therapeutic use ; Hypoglycemic Agents/adverse effects/pharmacology/therapeutic use ; Incretins/metabolism ; *Obesity/complications/drug therapy/metabolism ; *Renal Insufficiency/etiology/metabolism/prevention & control ; Anti-Obesity Agents/adverse effects/pharmacology/therapeutic use ; Disease Progression ; Gastric Emptying/drug effects ; Glucagon/metabolism ; Gastrointestinal Microbiome/drug effects ; Satiety Response/drug effects ; Randomized Controlled Trials as Topic ; Medication Adherence ; },
abstract = {Glucagon-like peptide-1 (GLP-1) receptor agonists are incretin analogues that promote glucose-mediated insulin release and are used to treat type 2 diabetes mellitus and obesity. GLP-1 receptor agonists and GLP-1 and glucose-dependent insulinotropic peptide agonists have several mechanisms of action, including reduction of gastric emptying, inhibition of glucagon secretion, beneficial changes in the intestinal microbiome, and direct effects on hypothalamic nuclei to enhance satiety (which promotes weight loss). Beyond the impressive effects of GLP-1 receptor agonists on blood glucose levels and body weight, large-scale randomized, controlled trials have shown that GLP-1 receptor agonists reduce cardiovascular risk and slow progression to renal failure in persons at high risk and those with type 2 diabetes. Adverse side effects from GLP-1 receptor agonists are mostly gastrointestinal but may also include loss of muscle and bone mass. Questions remain about long-term adherence, weight regain after discontinuation of treatment, and the functional implications of the loss of muscle and bone mass. Recent and ongoing targeted studies suggest the possibility of additional uses for GLP-1 receptor agonists.},
}

Humans
*Cardiovascular Diseases/etiology/metabolism/prevention & control
*Diabetes Mellitus, Type 2/complications/drug therapy/metabolism
Glucagon-Like Peptide 1/agonists/metabolism
*Glucagon-Like Peptide-1 Receptor Agonists/adverse effects/pharmacology/therapeutic use
Hypoglycemic Agents/adverse effects/pharmacology/therapeutic use
Incretins/metabolism
*Obesity/complications/drug therapy/metabolism
*Renal Insufficiency/etiology/metabolism/prevention & control
Anti-Obesity Agents/adverse effects/pharmacology/therapeutic use
Disease Progression
Gastric Emptying/drug effects
Glucagon/metabolism
Gastrointestinal Microbiome/drug effects
Satiety Response/drug effects
Randomized Controlled Trials as Topic
Medication Adherence

@article {pmid41931118,
year = {2026},
author = {Ansari, S and Purohit, KJ and Shelke, AB and Shah, M and Nkhoma, IA and Navale, AM and Wakchaure, R},
title = {Microbiota-driven mechanisms in multisystem diseases: integrative evidence across cardiovascular, metabolic, neurological and autoimmune disorders.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41931118},
issn = {1572-9699},
mesh = {Humans ; *Autoimmune Diseases/microbiology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; *Cardiovascular Diseases/microbiology ; *Nervous System Diseases/microbiology ; *Metabolic Diseases/microbiology ; *Microbiota ; Animals ; },
abstract = {The human microbiota represents one of the body's most influential biological systems, engaging in constant metabolic, immunological, and neuroendocrine communication with the host. Disruption of this intricate ecosystem, or dysbiosis, has emerged as a fundamental determinant in the onset and progression of numerous chronic diseases. This review consolidates contemporary evidence on how alterations in microbial composition, metabolite production, and barrier integrity contribute to pathophysiological changes across multiple organ systems. Gut-derived metabolites-including short-chain fatty acids, bile acid derivatives, trimethylamine-N-oxide, and lipopolysaccharide-serve as key mediators linking microbial imbalance to systemic inflammation, metabolic dysfunction, autoimmunity, and neurodegeneration. We outline the mechanistic pathways through which dysbiosis promotes hypertension, atherosclerosis, obesity, type 2 diabetes, Parkinson's disease, Alzheimer's disease, rheumatoid arthritis, inflammatory bowel disease, asthma, chronic obstructive pulmonary disease, urinary tract infections, and chronic kidney disease. Particular emphasis is placed on the gut-brain, gut-lung, and gut-kidney axes, which facilitate bidirectional immune and metabolic signalling between the intestine and distant tissues. Additionally, the review highlights emerging therapeutic interventions aimed at restoring microbial homeostasis, including targeted dietary strategies, probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and microbiome-directed pharmacological approaches. Collectively, the evidence positions the microbiota as a central regulator of human health and disease, offering a compelling platform for next-generation diagnostic and therapeutic innovation. Advancing mechanistic understanding of host-microbe interactions will be essential to developing personalized microbiome-based strategies capable of preventing, mitigating, or reversing disease across diverse clinical contexts.},
}

Humans
*Autoimmune Diseases/microbiology
*Gastrointestinal Microbiome
Dysbiosis/microbiology
*Cardiovascular Diseases/microbiology
*Nervous System Diseases/microbiology
*Metabolic Diseases/microbiology
*Microbiota
Animals

@article {pmid41931121,
year = {2026},
author = {Liu, B and Wan, SH and Zhang, YT and Lin, JH and Ke, XC and Lin, WH and Zhan, MX},
title = {Gut microbiome remodeling across hepatocellular carcinoma progression and transarterial chemoembolization is associated with therapeutic response and prognosis.},
journal = {Clinical and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10238-026-02137-z},
pmid = {41931121},
issn = {1591-9528},
support = {2023A1515012588 and 2022A1515220092//Guangdong Basic and Applied Basic Research Foundation/ ; 2022B1515020010//Guangdong Basic and Applied Basic Research Foundation/ ; 82472084//the National Natural Science Foundation of China/ ; 82272103//the National Natural Science Foundation of China/ ; 2021B1212040004//the Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment/ ; },
}

@article {pmid41931829,
year = {2026},
author = {Venkitaraman, AR},
title = {Proteostasis Deregulation by Metabolism Drives the Hallmarks of Cancer.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051424-052148},
pmid = {41931829},
issn = {1545-4509},
abstract = {Cancer cells acquire hallmark behaviors through adaptations that extend beyond genetic and epigenetic changes. Proteostasis-the biochemical network governing protein synthesis, folding, trafficking, and degradation-is a fundamental, yet underappreciated, mediator of these adaptations that merits consideration as a hallmark-enabling mechanism. Metabolic alterations impose proteotoxic stress, globally rewire protein homeostasis, and selectively modulate key oncogenic and tumor suppressive proteins. A unifying framework is proposed wherein metabolic deregulation of proteostasis operates throughout carcinogenesis: early, by enhancing accumulation of premalignant clones bearing cancer-driving somatic mutations in response to environmental and systemic metabolic stress, and later, by buffering proteotoxic stress to sustain malignant growth in hostile tissue environments. This perspective connects cancer risk with genetic background, diet, microbiome-derived metabolites, and metabolic disease, introduces metabolic bypass of tumor suppression as an alternative to classical genetic models, and highlights the metabolism-proteostasis interface as a promising target for cancer prevention and therapy.},
}

@article {pmid41931987,
year = {2026},
author = {Dang, W and Li, W and Dong, F and Huang, Y and He, S and Zhu, Y},
title = {Microbial metabolites: Bridging the gut-brain divide in ischemic stroke.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128510},
doi = {10.1016/j.micres.2026.128510},
pmid = {41931987},
issn = {1618-0623},
abstract = {The Microbiota-Gut-Brain Axis (MGBA) has recently crystallized into a focal frontier spanning neuroscience and microbiology, illuminating the intricate reciprocity between intestinal microbes and the central nervous system. Stroke, a devastating and life-threatening cerebrovascular disorder, is now recognized to have its onset, progression, and long-term outcome intimately entwined with MGBA dynamics. Accumulating empirical literature substantiates the existence of intimate bidirectional gut-brain signaling circuits, wherein the gut microbiome functions as a central modulator. This microbial consortium not only orchestrates neuroinflammatory cascades following cerebral insult, but also bio-transforms dietary and host-derived substrates into multifunctional metabolites that exert both local and systemic bioactivity. Emerging evidence suggests that individual microbial metabolites and their secondary derivatives may serve as candidate signaling intermediaries, mediating the transduction of microbial cues into neurovascular responses. Accordingly, the present review provides a forward synthesis of how the MGBA intersects with ischemic stroke pathobiology, focusing on elucidating the therapeutic potential and strategies of gut microbial metabolites in ischemic stroke. It provides theoretical insights and translational prospects for gut-derived metabolites as therapeutic targets.},
}

@article {pmid41932005,
year = {2026},
author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A},
title = {A survey of bacterial and fungal communities of table olives.},
journal = {International journal of food microbiology},
volume = {455},
number = {},
pages = {111759},
doi = {10.1016/j.ijfoodmicro.2026.111759},
pmid = {41932005},
issn = {1879-3460},
abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.},
}

@article {pmid41932098,
year = {2026},
author = {Zhang, M and Xiong, W and Shao, R and Wang, Z and Shen, Z and Zhou, Q and Du, G},
title = {Disrupted Salivary Fungal Community in Patients With Oral Lichen Planus.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109546},
doi = {10.1016/j.identj.2026.109546},
pmid = {41932098},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Oral lichen planus (OLP), a chronic inflammatory oral mucosal disorder with malignant potential, has been associated with oral microbial dysbiosis. While bacterial community alterations in OLP are well-documented, the fungal community architecture and ecological dynamics, particularly within salivary microbiota, remain poorly characterised.

METHODS: Saliva samples were collected from 30 participants and stratified into 3 cohorts: 10 healthy controls (HC), 10 reticular OLP (R-OLP) patients and 10 erosive OLP (E-OLP) patients. The fungal community profile was assessed using internal transcribed spacer (ITS) sequencing, complemented by multi-dimensional analytical approaches, including diversity metrics, co-occurrence network construction and functional prediction.

RESULTS: Significant diversity disparities distinguished fungal communities across groups. Taxonomically, Pseudozyma and Simplicillium demonstrated reduced abundance in OLP patients versus HC, while Pyronema was exclusive to OLP cohorts. Fungal ecological networks in OLP exhibited increased density compared to HC. Linear discriminant analysis effect size (LEfSe) analysis identified Pseudozyma as an HC-associated biomarker and Pyronema as an E-OLP discriminant, while predictive models highlighted Pseudozyma and Simplicillium as effective group stratifiers. FUNGuild profiling revealed predominant saprotrophic activity across all groups, with decreased pathotroph-symbiotroph guild representation in OLP patients.

CONCLUSIONS: Salivary fungal communities in OLP exhibit structural and compositional alterations. Through integrated analyses of relative abundance, random forest modelling and LEfSe, this study indicated that 3 fungal taxa may be as potential biomarkers for distinguishing OLP from HC. Among these, Pseudozyma and Simplicillium showed characteristics suggesting a possible probiotic role, while Pyronema, with its detection limited to OLP and absence in HC, may be associated with the disease.

CLINICAL RELEVANCE: The fungal profile observed in this study, comprising the potentially beneficial taxa Pseudozyma and Simplicillium as well as the OLP-linked Pyronema, offers new directions for developing noninvasive diagnostics and microbial-targeted therapies for OLP.},
}

@article {pmid41932183,
year = {2026},
author = {Liu, L and Liu, L and Li, A and Liu, Z and Xue, S and Li, J and Mao, Y},
title = {Robust gut microbiota as a key protective barrier for Ruditapes philippinarum survival following an extreme-rainfall disturbance.},
journal = {Marine environmental research},
volume = {218},
number = {},
pages = {108033},
doi = {10.1016/j.marenvres.2026.108033},
pmid = {41932183},
issn = {1879-0291},
abstract = {Gut microbiota is critical for host health, yet its role in buffering filter-feeding bivalves against acute habitat disturbance remains poorly understood. Here, the Manila clam Ruditapes philippinarum was used as a model to investigate how an extreme rainfall event reshaped microbial communities in the gut and surrounding habitat (water and sediment), with sampling conducted before and 10 and 30 days after the event. Extreme rainfall caused mass mortality and markedly disrupted host-associated microbiota. Surviving clams harbored gut microbiota with higher diversity and richness, enrichment of putatively beneficial taxa (e.g., Actinomycetota, Bacteroidota, Verrucomicrobiota, and Bacillus), reduced abundance of the opportunistic pathogen Vibrio, and increased network complexity and stability, accompanied by enrichment of functional potentials related to energy metabolism, signal transduction, and stress adaptation. Notably, gut community assembly shifted toward greater stochasticity, broader niche breadth, and reduced dispersal limitation during recovery, indicating a reassembly pattern that balances compositional stability with adaptive flexibility. Together, these results highlight gut microbiota robustness and assembly plasticity as key mechanisms linking extreme-rainfall disturbance to clam resilience, providing insights for microbiome-informed management to support sustainable bivalve aquaculture.},
}

@article {pmid41932251,
year = {2026},
author = {Huang, H and Yin, J and Xu, C and Gu, HY},
title = {The role of the gut-spinal axis in immune-metabolic coupling after spinal cord injury.},
journal = {International immunopharmacology},
volume = {178},
number = {},
pages = {116581},
doi = {10.1016/j.intimp.2026.116581},
pmid = {41932251},
issn = {1878-1705},
abstract = {Spinal cord injury (SCI), representing a devastating trauma to the central nervous system (CNS), is often accompanied by complex immune responses and metabolic dysregulation, significantly affecting patients' functional recovery and quality of life. In recent years, the gut-spinal axis, as an important pathway connecting the gut microbiome and the CNS, has emerged as a pivotal area of investigation regarding the pathological mechanisms of SCI. Changes in the gut microbiome modulate inflammatory responses and tissue repair processes after SCI by regulating immune system activation and metabolic pathways. However, the specific mechanisms by which the gut-spinal axis mediates the interplay between immune and metabolic processes after SCI have not been fully elucidated. This article summarizes the structural and functional characteristics of the gut-spinal axis, as well as the gut microbial imbalance, immune activation, and metabolic regulation induced by SCI. It focuses on how the gut-spinal axis mediates the interaction between immunity and metabolism, thereby influencing the pathological progression and repair potential of SCI. By integrating basic and clinical research findings, it aims to offer a theoretical framework for the comprehensive regulatory mechanisms of immunity and metabolism in SCI and to explore innovative therapeutic strategies targeting the gut-spinal axis.},
}

@article {pmid41932357,
year = {2026},
author = {Winston, JA and Jennings, R and Randolph, NK and Welton, M and Partridge, E and Schreeg, M and Yaxley, PE and Rudinsky, AJ},
title = {Fecal microbiota transplantation dosing regimen accelerates clinical resolution in canine parvovirus infection: a novel spectrum-of-care approach.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/javma.25.11.0764},
pmid = {41932357},
issn = {1943-569X},
abstract = {OBJECTIVE: To evaluate the efficacy of a novel spectrum-of-care fecal microbiota transplant (FMT) dosing regimen as an adjunctive therapy for canine parvovirus (CPV).

METHODS: 27 client-owned dogs naturally infected with CPV were enrolled from March to November 2023 in a prospective, double-blinded, placebo-controlled clinical trial. Patients were randomized into FMT-treated (n = 19) or placebo-treated (8) groups. Along with conventional treatments, CPV-infected dogs were administered FMT (single FMT enema, then 14 days of oral lyophilized FMT capsules) or placebo (single saline enema, then 14 days of oral placebo capsules) at admission. During hospitalization, dogs were monitored daily including fecal, clinical severity, and medication scores. Feces and serum were collected at admission, day 4, day 7, day 14, and day 21 for quantification of CPV viral shedding and immune response (bead-based multiplex of cytokines/chemokines). The primary outcome variable was length of hospitalization.

RESULTS: Interim analysis revealed that placebo-treated dogs had excessive study withdrawals due to worsening clinical status when compared to FMT-treated dogs (37.5% compared to 0%, respectively), leading to ethical discontinuation of the placebo arm. Fecal microbiota transplant-treated dogs had significantly reduced hospitalization length and medications required for treatment (maximum medication score) compared to placebo-treated dogs. Fecal microbiota transplant did not reduce fecal viral shedding or elicit a host immune response.

CONCLUSIONS: This novel FMT dosing regimen (single enema FMT followed by oral capsular FMT), designed to be feasible for inpatients or outpatients, accelerated clinical recovery from CPV.

CLINICAL RELEVANCE: In-house and commercially available FMT products were effective in CPV-infected dogs, thus broadening the spectrum of care available to these patients.},
}

@article {pmid41932913,
year = {2026},
author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M},
title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00976-y},
pmid = {41932913},
issn = {2055-5008},
abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.},
}

@article {pmid41933092,
year = {2026},
author = {Han, M and Liu, X and Li, G and Li, P},
title = {Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70335},
doi = {10.1111/1758-2229.70335},
pmid = {41933092},
issn = {1758-2229},
support = {32260652//The National Natural Science Foundation of China/ ; },
mesh = {*Ralstonia solanacearum/physiology/genetics/pathogenicity ; *Plant Diseases/microbiology/prevention & control ; *Adaptation, Physiological ; Quorum Sensing ; Virulence ; Soil Microbiology ; },
abstract = {The Ralstonia solanacearum species complex (RSSC) ranks among the most destructive plant pathogens worldwide, due to its broad host range, extensive geographic distribution and remarkable environmental adaptability. Its persistence in soil and colonization of plant vascular tissues severely limits the effectiveness of conventional chemical control, posing significant challenges for disease management. This review highlights recent advances in understanding the environmental adaptation mechanisms of RSSC. Key topics include the dynamic evolution of pathogenicity, niche-specific survival strategies and virulence regulation mediated by quorum sensing, and complex interactions with surrounding microbial communities that shape its behaviour and fitness. We further provide a comprehensive assessment of current control strategies from an ecological perspective, encompassing physical, chemical, genetic, agronomic and microbial approaches, with critical evaluation of their mechanisms, potential and limitations. Meanwhile, we discuss the major challenges in bacterial wilt management and outline future directions, with an emphasis on multi-omics-informed precision breeding, microbiome engineering and intelligent integrated disease management (IDM). These emerging strategies hold promise for the sustainable and effective long-term control of bacterial wilt disease caused by RSSC.},
}

*Ralstonia solanacearum/physiology/genetics/pathogenicity
*Plant Diseases/microbiology/prevention & control
*Adaptation, Physiological
Quorum Sensing
Virulence
Soil Microbiology

@article {pmid41933095,
year = {2026},
author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W},
title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44972-w},
pmid = {41933095},
issn = {2045-2322},
abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.},
}

@article {pmid41933198,
year = {2026},
author = {Ondreičková, K and Böhmer, M and Rusňáková, D and Kubáňová, M and Szemes, T and Pániková, L and Oxikbayev, BK and Mukasheva, D and Janiga, M},
title = {Microbial community structure across freshwater ecosystem types in a high-altitude region, Zhongar Alatau, Kazakhstan.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41933198},
issn = {1573-0972},
support = {101160008//European Union's Horizon Europe research and innovation programme/ ; AP26102759//Ministry of Education and Science of the Republic of Kazakhstan/ ; },
}

@article {pmid41933201,
year = {2026},
author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB},
title = {Unbinned contigs expand known diversity in the global microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41933201},
issn = {2058-5276},
support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.},
}

@article {pmid41933264,
year = {2026},
author = {Ma, Y and Li, X and Luo, Y},
title = {Microbiome-driven innovations for climate-resilient crop production.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {41933264},
issn = {2662-1355},
support = {41991335//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
}

@article {pmid41933289,
year = {2026},
author = {Lawther, K and Tapio, I and Vera-Ponce de León, A and Aho, VTE and Huws, SA and Dimonaco, NJ},
title = {A curated database of rumen ciliate protozoal 18S rRNA gene sequences for metataxonomic applications.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01420-y},
pmid = {41933289},
issn = {2730-6844},
abstract = {OBJECTIVES: Protozoa are key members of the rumen microbiome playing significant roles in nutrient cycling and methane production, yet are understudied. As rumen metataxonomic studies increasingly incorporate protozoal primers, the lack of curated dedicated reference databases limits accurate classification. This dataset was developed to address that gap and support future protozoa-focused rumen microbial analyses.

DATA DESCRIPTION: The curated dataset comprises 228 rumen ciliate protozoal 18S rRNA gene sequences sourced from publicly available datasets. Sequences were processed to remove redundancy and standardise naming. The final database spans 23 families, 53 genera, and 100 species, and is suitable for use in metataxonomic pipelines, including QIIME2. It provides a valuable resource for researchers aiming to improve taxonomic resolution of protozoal communities in rumen environments.},
}

@article {pmid41933306,
year = {2026},
author = {Adamczak, M and Pokora, P and Kaczmarczyk, M and Gojowy, D and Wierzbicka-Woś, A and Cembrowska-Lech, D and Kolonko, A and Łoniewski, I and Więcek, A},
title = {Intestinal microbiome and acute transplanted kidney rejection - results of a single-center, case-control study.},
journal = {BMC nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12882-026-04951-9},
pmid = {41933306},
issn = {1471-2369},
}

@article {pmid41933371,
year = {2026},
author = {Yao, T and Fan, M and Hao, Z and Jiang, Z and Li, X and Wang, S and Xu, Z},
title = {Gordonibacter-associated regulatory T cell dysfunction and S100A11-mediated neural impairment in Hirschsprung's disease: a microbiota-immune-neural axis.},
journal = {Cell & bioscience},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13578-026-01562-7},
pmid = {41933371},
issn = {2045-3701},
support = {PL2024H140//Natural Science Foundation of Heilongjiang Province/ ; 24ZX008//Pediatric Special Project of the Sixth Affiliated Hospital of Harbin Medical University/ ; ZL2024H001//Key Project of the Joint Fund of the Natural Science Foundation of Heilongjiang Province/ ; },
abstract = {BACKGROUND: Hirschsprung's disease (HSCR) is a congenital disorder characterized by intestinal aganglionosis. Despite evidence linking gut microbiota and immune cells to various gastrointestinal diseases, their role in HSCR pathogenesis remains poorly understood. We investigated associations between gut microbiota composition, immune cell phenotypes, and neural impairment in HSCR patients.

RESULTS: Mendelian randomization analysis identified associations between Gordonibacter species and elevated HSCR risk (OR = 2.74, 95% CI 1.42-5.28), potentially mediated through CD28⁺CD39⁺ regulatory T cells. Multi-omics profiling revealed notable S100A11 upregulation in HSCR tissues. CD28⁺CD39⁺ Tregs from HSCR patients exhibited functional alterations, including reduced suppressive capacity alongside elevated S100A11 production. Both CD4⁺ T cells and CD68⁺ macrophages expressed S100A11 by immunohistochemistry. S100A11 treatment activated RAGE-NF-κB signaling in vitro, accompanied by suppression of neural developmental markers (SOX10, RET, PHOX2B) and impaired neuronal migration. Serum S100A11 showed diagnostic potential (AUC = 0.947). Microbiome profiling demonstrated differential bacterial enrichment, while antibiotic depletion experiments indicated microbiota-dependent modulation of immune-neural interactions.

CONCLUSION: Our findings link gut microbiota alterations, immune dysregulation, and neural developmental impairment in HSCR, implicating S100A11-RAGE-NF-κB signaling as a pathway deserving mechanistic investigation.},
}

@article {pmid41933391,
year = {2026},
author = {Liu, Y and Liu, J and Niu, D and Hu, L and Kou, F and Jiao, Y and Cao, W and Liu, Q and Fu, X and Hu, C and Tong, J and Xiong, H and Wang, Y},
title = {16S rRNA gene sequencing reveals distinct intratumoral bacterial microbiome signatures between CT indeterminate benign and early-stage malignant pulmonary lesions.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08078-1},
pmid = {41933391},
issn = {1479-5876},
}

@article {pmid41933403,
year = {2026},
author = {Dugény, E and Ceolotto, L and Franch, R and Pesce, G and Alvarez, E and Esposti, E and Mazzariol, S and Centelleghe, C},
title = {Optimizing cetacean blow collection methods under controlled conditions: implications for further non-invasive UAV-based sampling of the cetacean respiratory microbiome in the wild.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00555-8},
pmid = {41933403},
issn = {2524-4671},
support = {CN_00000033//NextGenerationEU/ ; ECS00000043//NextGenerationEU/ ; },
}

@article {pmid41933494,
year = {2026},
author = {Yang, X and Gao, S and Kong, X and Gao, F and Xu, Q},
title = {Host Filtering Overrides Environmental Heterogeneity in Shaping Sea Cucumber Gut Microbiomes.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70294},
doi = {10.1111/1462-2920.70294},
pmid = {41933494},
issn = {1462-2920},
support = {2025FY101004//Science and Technology Fundamental Resources Investigation Program/ ; 2022YFD2401305//National Key Research and Development Program of China/ ; 2025-73//Hainan Postdoctoral Scientific Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Sea Cucumbers/microbiology ; Ecosystem ; Phylogeny ; },
abstract = {Gut microbiomes play critical roles in host physiology and ecological contributions of sea cucumbers in tropical coral reefs. However, the relative importance of host filtering versus environmental factors in gut microbiome assembly remains poorly quantified in natural populations. Using 16S rRNA gene amplicon sequencing and sediment physicochemical analyses, this study characterized gut microbiomes of three co-occurring sea cucumber species (Holothuria atra, Holothuria edulis and Stichopus chloronotus) across heterogeneous habitats. Despite significant spatial variation in sediment properties and microbial communities, all three sea cucumber species maintained species-specific and stable gut microbiomes across sites. Although source tracking identified sediment as the primary microbial reservoir, variation partitioning revealed that host filtering far overrode environmental heterogeneity, with sediment physicochemical properties explaining a negligible fraction (< 1%) of community variation. Each host harboured distinct functional taxa, and most dominant genera showed no significant correlations with sediment properties. These results support a 'host as filter and sediment as source' pattern, indicating that host-mediated selection can filter microbes from distinct source pools to establish a conserved gut microbiome largely independent of environmental variation. By retaining microbial taxa with functional potentials, sea cucumbers may ensure consistent contributions to organic matter degradation and nutrient cycling regardless of environmental fluctuations.},
}

Animals
*Gastrointestinal Microbiome
Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Sea Cucumbers/microbiology
Ecosystem
Phylogeny

@article {pmid41933499,
year = {2026},
author = {Tonanzi, B and Massimi, A and Di Pippo, F and Petruccioli, M and Rossetti, S and Crognale, S},
title = {Unveiling Microbial Communities: Methodological Biases in DNA Extraction and 16S rRNA Sequencing Skew Microbial Profiles in Anaerobic Fermentation.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70297},
doi = {10.1111/1462-2920.70297},
pmid = {41933499},
issn = {1462-2920},
mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics/isolation & purification ; Anaerobiosis ; Fermentation ; *Bacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Modern molecular analyses have revolutionized the study of microbial communities, yet DNA extraction and sequencing remain critical sources of bias. This study investigated the impact of seven different DNA extraction protocols and two 16S rRNA hypervariable regions (V1-V3 and V3-V4) on the profiling of a complex anaerobic fermentative biomass selected for medium-chain fatty acids production. Microscopic analysis established a baseline community dominated by Actinobacteria (53% ± 2%) and Firmicutes (47% ± 3%). The results demonstrate that Kit1 and Kit5 provided the highest DNA yields (up to 603 ng/μL) and the most effective recovery of these hard-to-lyse phyla, although they introduced a slight taxonomic bias toward Actinobacteria. In contrast, protocols relying on intensive chemical lysis without robust mechanical disruption (Kit4) significantly underestimated total bacterial abundance and showed the lowest purity. 16S rRNA gene sequencing revealed that the V3-V4 region provided higher alpha-diversity and a more balanced representation of the community core compared to V1-V3, which was more susceptible to extraction-related variability and overrepresented the genus Olsenella. Our multi methodological approach reveals significant biases introduced by both extraction technique and 16S rRNA gene region. This evidence highlights that protocol optimization is mandatory for achieving an accurate and comprehensive characterization of microbial ecosystems.},
}

*RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/genetics/isolation & purification
Anaerobiosis
Fermentation
*Bacteria/genetics/classification/isolation & purification
Sequence Analysis, DNA/methods
*Microbiota/genetics
Phylogeny

@article {pmid41933506,
year = {2026},
author = {Qiu, CW and Zhang, S and Gao, ZF and Chen, ZH and Zhang, C and Ali, MA and Wu, F},
title = {First Tetraploa Genome and Multi-Omics Analysis Reveal Key Plant-Microbe-Soil Interactions for Salt Tolerance and Yield Improvement of Wheat.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70663},
pmid = {41933506},
issn = {1467-7652},
support = {32161143035//National Natural Science Foundation of China/ ; BP0618021//the 111 Project of China/ ; FT210100366//Australian Research Council/ ; WSU2303-001RTX//Grains Research and Development Corporation/ ; },
abstract = {Salinity is a major threat to global agricultural productivity of staple crops such as wheat. Although microbial-based solutions hold promise for alleviating salinity stress, practical implementation is hindered by insufficient mechanistic characterization of bioinoculants and their interactions with plants. Here, we assembled the first complete reference genome of a halotolerant strain within the genus Tetraploa-the endophytic fungus Tetraploa sp. E00680. This novel genomic resource serves as a foundation for exploring previously uncharacterised salt tolerance mechanisms in this potential fungal inoculant. Our research demonstrates that E00680 enhances wheat yield under both controlled and field saline conditions. We found that E00680 systematically modulates the plant-microbe-soil interactions by optimizing rhizosphere microbial communities, increasing nutrient bioavailability, and triggering coordinated transcriptional and metabolic reprogramming in wheat. Notably, E00680 expands tryptophan metabolism to synergistically boost auxin biosynthesis in wheat by supplying precursors and activating relevant metabolic pathways. This cross-kingdom metabolic coupling facilitates better growth and salt tolerance in wheat plants. Our findings offer multi-omics and rhizosphere-level insights that can guide the development of microbial inoculants to enhance climate-resilient and sustainable crop production.},
}

@article {pmid41933614,
year = {2026},
author = {Abdollahi, S and Vajhadin, F and Rafiei, A and Tamrin, SH and Daniel, SD and Banoei, MM and Zarin, B and Sen, A and Kim, K and Sanati-Nezhad, A},
title = {On-Chip modeling of drug-gut interactions in Oral drug delivery.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115864},
doi = {10.1016/j.addr.2026.115864},
pmid = {41933614},
issn = {1872-8294},
abstract = {The gastrointestinal tract is a dynamic ecosystem where biophysical forces, enzymatic gradients, and microbial metabolism converge to govern the fate of orally administered therapeutics. These multifactorial interactions-spanning shear stress, mucus transport, and microbial metabolism-collectively shape absorption, transformation, and therapeutic response. Such complexity drives the wide interindividual variability in oral pharmacokinetics and pharmacodynamics, challenging predictive modeling and formulation design. Capturing these intertwined processes requires experimental systems that bridge the physiological fidelity of human tissue with the analytical control of engineered models. Microphysiological Gut-on-a-Chip (GoC) platforms have emerged as promising tools that reconstruct human intestinal architecture and function with high precision. These devices integrate living epithelia, peristaltic motion, oxygen and nutrient gradients, immune and microbial co-cultures, and on-chip sensing within precisely engineered microenvironments. They enable direct observation and quantification of luminal-mesenchymal communication, barrier regulation, and metabolite exchange under physiologically relevant flow. This review delineates how GoC technology is advancing oral drug delivery by bridging biology, microengineering, and pharmacology. We summarize advances across three therapeutic domains-small-molecule drugs, macromolecular and biopharmaceutical agents, and microbiome-interacting therapeutics-highlighting how GoCs now recapitulate absorption, enzymatic metabolism, immune modulation, and microbial transformation in human-relevant contexts. By merging organ-level physiology with analytical precision, GoCs establish a unified platform for predicting oral bioavailability and systemic exposure. As these systems evolve toward sensor-integrated, multi-omics, and AI-enabled designs, they are poised to become the mechanistic backbone of next-generation preclinical drug discovery and personalized oral therapeutics.},
}

@article {pmid41933765,
year = {2026},
author = {He, Y and Wang, Z and Xu, Z and Wang, H and Yuan, L and Xu, X and Deng, W},
title = {Regulatory effects of natural polysaccharides on skin wound repair through modulation of immune-microbiome interactions.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {151732},
doi = {10.1016/j.ijbiomac.2026.151732},
pmid = {41933765},
issn = {1879-0003},
abstract = {Chronic non-healing wounds pose a significant clinical challenge, driven by dysregulation of the "inflammation-immune-microbiome" triad. Traditional "debridement-anti-infection-coverage" approaches fail to break the vicious cycle of dysbiosis and immune dysfunction. Leveraging structural diversity and bioactivity, natural polysaccharides provide a versatile platform for multi-targeted intervention. This review systematically explores the mechanisms through which polysaccharides modulate the wound immune microenvironment, restructure microbial communities, and facilitate barrier repair. This interaction enables precise regulation of macrophage polarization, particularly the promotion of the M2 phenotype, as well as neutrophil function and adaptive immunity, thereby alleviating chronic inflammation. Moreover, polysaccharides utilize a variety of mechanisms to impact the microbiome, including direct antimicrobial effects through electrostatic interactions and prebiotic support that promotes the colonization and metabolism of beneficial bacteria. This review also explores advancements in intelligent delivery systems, such as microenvironment-responsive hydrogels, discusses challenges in clinical translation, and considers future directions that incorporate single-cell multi-omics, microbiota-based personalization, organ-on-a-chip models, and phage-polysaccharide synergistic therapies. This work offers a theoretical foundation and translational perspective for the development of next-generation polysaccharide-based strategies for chronic wound management.},
}

@article {pmid41933826,
year = {2026},
author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D},
title = {The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128041},
doi = {10.1016/j.envpol.2026.128041},
pmid = {41933826},
issn = {1873-6424},
abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.},
}

@article {pmid41933853,
year = {2026},
author = {Rao, X and Zhou, R and Li, W and Chai, X and Zhang, H},
title = {Pulmonary Microbiota is a Hidden Link between Lung Cancer Development and Microenvironment: Potential for Future Immune Therapeutic Strategies.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105308},
doi = {10.1016/j.critrevonc.2026.105308},
pmid = {41933853},
issn = {1879-0461},
abstract = {Lung, as a vital interface with the external environment, hosts a diverse microbiota that plays a significant role in lung cancer development. The dual role of pulmonary microbiota is characterized by its potential to trigger chronic inflammation(precursor of cancer), and its ability to stimulate anti-tumor immune responses. In lung cancer patients, the pulmonary microbiota often exhibits reduced bacterial diversity and over representation of pathogenic bacteria. Distinct pathological types of lung cancer, and clinical stage of lung cancer were correlates with variations in microbial diversity. Particular focus on its influence on the immune microenvironment have also been delved. Including immune cells, inflammatory signaling pathways, microbiota-metabolic interactions, and modulation of the programmed cell death protein 1(PD-1)/ programmed death-ligand 1 (PD-L1) checkpoint, which is crucial for tumor immune evasion. Understanding these interactions is essential for optimizing lung cancer immunotherapy strategies. For instance, antibiotics may reduce the efficacy of immune checkpoint inhibitors (ICIs), especially in lung cancer patients with high PD-L1 expression or EGFR-mutant NSCLC. Additionally, new therapeutic interventions, such as microbiome-targeted therapies or probiotics, are suggested to enhance the efficacy of ICIs. By uniquely integrating clinical correlations with mechanistic insights on immune microenvironment, this may render pulmonary microbiota to be potential therapeutic strategies for future immunotherapy treatments.},
}

@article {pmid41934012,
year = {2026},
author = {Moraïs, S and Mizrahi, I},
title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.005},
pmid = {41934012},
issn = {1878-4380},
abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.},
}

@article {pmid41934098,
year = {2026},
author = {Sweeney, CJ and Bottoms, M and Hutcheson, K and Schulz, L},
title = {Dose response OECD 216 studies for agrochemicals.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag057},
pmid = {41934098},
issn = {1551-3793},
abstract = {The nitrogen transformation test, as described by Organisation for Economic Co-operation and Development (OECD) test guideline 216, forms the basis of the current European risk assessment to assess the impacts of pesticides on the soil microbiome. This guideline contains both a two-dose threshold approach and a dose response study design, for use with agrochemicals and non-agrochemicals respectively. Recent proposals have suggested the use of a dose response study design for agrochemical risk assessment. However, differences in the principles underpinning the threshold and dose response study protocols including the method of endpoint calculation, study length and interpretation of stimulatory versus inhibitory responses, necessitate careful consideration of how to appropriately perform and interpret dose response OECD 216 studies for pesticides. Our study explores these considerations, through the conduct of dose response OECD 216 nitrogen transformation tests on four agrochemicals (dicyandiamide, nitrapyrin, dinoseb acetate and a fludioxonil metabolite). A comparison of four potential methods for endpoint calculation revealed this has little impact on the ecotoxicological inference derived from dose response OECD 216 studies. Hormetic responses were present for two of the four compounds tested, and for these compounds, the system had not reached a steady state over the 28-day study period. Test extensions beyond the 28-day test period defined in the dose response study may therefore need to be considered, as is currently implemented in the two-dose threshold approach. Furthermore, as dose response studies allow for consideration of the full ecotoxicological response over a range of concentrations, we suggest that dose response OECD 216 studies for agrochemicals should focus on inhibitory and not stimulatory responses. Finally, our work has shown that dose response OECD 216 studies are possible for agrochemicals, and their use offers a sensible approach to improving the European soil microbial risk assessment.},
}

@article {pmid41934196,
year = {2026},
author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ},
title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {7},
pages = {e70450},
pmid = {41934196},
issn = {1613-4133},
support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; },
mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; },
abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.},
}

Humans
*Diet, Mediterranean
Male
Female
Adult
Bacteria/genetics/classification
*Microbiota
Metagenomics
Middle Aged
Olive Oil
*Gastrointestinal Microbiome
Feces/microbiology
Fruit
Vegetables
Multiomics

@article {pmid41934308,
year = {2026},
author = {He, L and Zhong, Q and Zhang, X and Li, T},
title = {The effects of cetylpyridinium chloride mouthwash combined with triamcinolone acetonide on oral microbiota and the Th17/Treg balance in patients with oral lichen planus.},
journal = {Pakistan journal of pharmaceutical sciences},
volume = {39},
number = {6},
pages = {1708-1720},
doi = {10.36721/PJPS.2026.39.6.162.1},
pmid = {41934308},
issn = {1011-601X},
mesh = {Humans ; *Lichen Planus, Oral/drug therapy/immunology/microbiology ; *Mouthwashes/administration & dosage/therapeutic use/adverse effects ; Female ; Male ; *T-Lymphocytes, Regulatory/drug effects/immunology ; Middle Aged ; *Th17 Cells/drug effects/immunology ; *Triamcinolone Acetonide/administration & dosage/therapeutic use/adverse effects ; Adult ; *Cetylpyridinium/administration & dosage/adverse effects/therapeutic use ; *Microbiota/drug effects ; Treatment Outcome ; Drug Therapy, Combination ; *Mouth/microbiology/drug effects ; *Anti-Inflammatory Agents/administration & dosage ; Cytokines ; },
abstract = {BACKGROUND: Oral lichen planus (OLP) is a chronic inflammatory disease associated with oral microbiome imbalance and immune dysregulation.

OBJECTIVES: To evaluate the effects of CPC mouthwash combined with triamcinolone acetonide on oral microbiota and Th17/Treg balance in erosive OLP patients.

METHODS: This study involved 80 patients with erosive OLP from January 2023 to January 2025. They were divided into: A control group treated with triamcinolone acetonide and a combination group treated with triamcinolone acetonide plus cetylpyridinium chloride mouthwash. After 4 weeks, primary outcomes included clinical efficacy, visual analog scale (VAS) pain scores, changes in signs and erosive area, oral salivary bacteria detection rate, Th17/Treg ratio, serum adipokine chemerin and cytokine levels (IL-17, TNF-α, IL-10) and OHIP-14 scores. Secondary outcomes were adverse reaction incidence and recurrence rates during follow-up.

RESULTS: The combination group showed better outcomes after 4 weeks of treatment. The total effective rate was 95%, higher than the control group's 80% (P=0.022). The combination group had superior pain relief (P=0.024), better mucosal repair (P=0.002) and a significant decrease in erosive area (P=0.021). It also had lower oral detection rates of Staphylococcus and Candida albicans (P<0.05). Immunologically, the combination therapy significantly reduced serum levels of chemerin, Th17 cells, Th17/Treg ratio, IL-17 and TNF-α (P<0.001), while increasing Treg cells and IL-10 levels (P=0.003), indicating stronger anti-inflammatory and immune-balancing effects. The combination group showed a greater reduction in the OHIP-14 score (P < 0.001), indicating improved oral health-related quality of life. No significant difference in adverse reactions was observed (P>0.05) and all were mild. The combination group had a lower recurrence rate within 3 months post-treatment, although the difference was not statistically significant (P=0.521).

CONCLUSION: The combination of cetylpyridinium chloride mouthwash with triamcinolone acetonide effectively regulates the oral microbiota structure and restores the Th17/Treg immune balance in OLP patients.},
}

Humans
*Lichen Planus, Oral/drug therapy/immunology/microbiology
*Mouthwashes/administration & dosage/therapeutic use/adverse effects
Female
Male
*T-Lymphocytes, Regulatory/drug effects/immunology
Middle Aged
*Th17 Cells/drug effects/immunology
*Triamcinolone Acetonide/administration & dosage/therapeutic use/adverse effects
Adult
*Cetylpyridinium/administration & dosage/adverse effects/therapeutic use
*Microbiota/drug effects
Treatment Outcome
Drug Therapy, Combination
*Mouth/microbiology/drug effects
*Anti-Inflammatory Agents/administration & dosage
Cytokines

@article {pmid41934511,
year = {2026},
author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM},
title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41934511},
issn = {1572-9699},
mesh = {*Chitosan/administration & dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; },
abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.},
}

*Chitosan/administration & dosage/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Animal Feed/analysis
*Bacteria/classification/genetics/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Diet
Dietary Supplements
*Fishes/microbiology
Biodiversity
Aquaculture

@article {pmid41934548,
year = {2026},
author = {Cui, K and Chen, J and Kuang, M and Yang, H and Bu, Z and Xiong, X and Liu, X and Hu, Y and Wang, R and Chen, Y and Xu, T and Zhu, Y},
title = {Integrated Physiological and Omics Analyses Reveal Endophytic Streptomyces Regulates N and P Uptake, Utilization, and Crop Productivity Enhancement.},
journal = {Physiologia plantarum},
volume = {178},
number = {2},
pages = {e70858},
doi = {10.1111/ppl.70858},
pmid = {41934548},
issn = {1399-3054},
support = {ZR2024QD159//Natural Science Foundation of Shandong Province/ ; 32172497//National Natural Science Foundation of China/ ; 32400100//National Natural Science Foundation of China/ ; CSTB2023NSCQ-MSX0852//Natural Science Foundation of Chongqing City/ ; 502251012//Yuelushan Laboratory Breeding Program/ ; },
mesh = {*Streptomyces/physiology/metabolism ; *Nitrogen/metabolism ; *Phosphorus/metabolism ; Plant Roots/microbiology/metabolism ; *Endophytes/physiology/metabolism ; Rhizosphere ; *Crops, Agricultural/growth & development ; Soil Microbiology ; },
abstract = {The inherent deficiency of available nitrogen (N) and phosphorus (P) in acidic soils severely limits productivity in agriculture and forestry. While plant-beneficial microorganisms offer a sustainable solution, the mechanisms by which endophytic actinobacteria regulate N and P absorption and utilization remain largely unexplored. In this study, we characterize Streptomyces sp. CoH27, an endophyte isolated from Camellia oleifera, which exhibits pronounced abilities in N fixation and insoluble P solubilization. Inoculation with CoH27 significantly promoted the growth of C. oleifera across different ages and propagation types, as evidenced by enhanced root architecture, improved photosynthetic parameters, and increased N and P absorption and utilization efficiencies. Physiological analyses revealed that CoH27 colonization upregulated the activity of key enzymes involved in organic acid synthesis and N assimilation in roots, thereby enhancing rhizosphere P mobilization and plant N utilization. Furthermore, CoH27 reshaped the rhizosphere microbiome, increasing bacterial diversity and the abundance of beneficial taxa, while reinforcing microbial networks. The driving effect of nutrient cycling was evidenced with enriched abundance of microbial genes involved in P solubilization (phnA, ppa) and N metabolism (nasA, narB, amoA, nxrA). Concurrently, transcriptomics identified the upregulation of critical transporter genes (CoPHT1;4, CoNRT2.5) and transcription factors in CoH27-inoculated roots, orchestrating improved N and P uptake and assimilation. The efficacy of CoH27 was further validated in Brassica napus L. and Capsicum annuum L., underscoring its potential as a versatile microbial inoculant to enhance sustainable crop production in acidic soils.},
}

*Streptomyces/physiology/metabolism
*Nitrogen/metabolism
*Phosphorus/metabolism
Plant Roots/microbiology/metabolism
*Endophytes/physiology/metabolism
Rhizosphere
*Crops, Agricultural/growth & development
Soil Microbiology

@article {pmid41934839,
year = {2026},
author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B},
title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141959},
doi = {10.1016/j.jhazmat.2026.141959},
pmid = {41934839},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.},
}

@article {pmid41934858,
year = {2026},
author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F},
title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141965},
doi = {10.1016/j.jhazmat.2026.141965},
pmid = {41934858},
issn = {1873-3336},
abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.},
}

@article {pmid41934884,
year = {2026},
author = {Macpherson, CV and Daisley, BA and Drosdowech, SM and Meers, JA and Raine, NE and Allen-Vercoe, E},
title = {Anthropogenic stressors drive microbiome assembly: A global meta-analysis of bumble bees.},
journal = {The Science of the total environment},
volume = {1029},
number = {},
pages = {181748},
doi = {10.1016/j.scitotenv.2026.181748},
pmid = {41934884},
issn = {1879-1026},
abstract = {Bumble bees (Bombus spp.) play a vital role in the provision of ecosystem services that benefit humans through crop pollination and supporting natural plant biodiversity. While their ecological function is well studied, the microbial communities within their gut are only beginning to be recognized for their contributions to bee health and resilience. To better understand these communities, we conducted a meta-analysis of 814 gut samples from 15 studies across 9 countries. This analysis confirmed Snodgrassella, Lactobacillus, Bifidobacterium, Bombilactobacillus, and Gilliamella as core gut taxa, and proposed the addition of Neisseriaceae_unclassified and Orbaceae_unclassified. Human-altered environments were identified as the most influential factor shaping microbiota composition, with indoor versus outdoor rearing showing the strongest effect. Outdoor bees collectively hosted 253% more genera and exhibited higher microbial richness, connectivity, and stability. In contrast, indoor bees showed reduced diversity and the loss of multiple environmentally-associated taxa. Based on these patterns, we propose a "captivity-sensitive core" of twelve taxa, including Frischella, Apilactobacillus, Staphylococcus, and Acinetobacter. These findings establish a robust reference for the bumble bee gut microbiome and highlight how anthropogenic environments alter microbial community structure, with implications for insect pollinator health, management, and conservation.},
}

@article {pmid41934901,
year = {2026},
author = {Usmani, A and Siddiqui, MA and Kumar, D and Gowri, S and Webster, TJ and Faiyazuddin, M},
title = {Next 5 years in autoimmunity: predictive diagnostics, immune signatures, and personalized immune therapy.},
journal = {International immunopharmacology},
volume = {179},
number = {},
pages = {116530},
doi = {10.1016/j.intimp.2026.116530},
pmid = {41934901},
issn = {1878-1705},
abstract = {Autoimmune diseases are experiencing a conceptual transformation in the traditional system of phenotypical classification to a more molecularly stratified system. The next five years suggest that immunological and metabolic signals, such as autoantibody patterns, epitope-spreading patterns, and inflammatory signals of microbiome interactions, will frequently predict clinical illness making the preclinical period a critical predictive and intervention time. Simultaneously, single-cell and multi-omic profiling are being used to discover molecular endotypes and pathogenic immune programs which can more effectively explain the heterogeneity of autoimmune diseases. Such insights are also incorporated more and more with computational methods, such as digital immune modeling, to allow for individual risk assessment and disease prediction. The combination of these advancements is hastening the shift toward precision immunology, where predictive diagnostics and targeted immune-modulating therapies can be implemented sooner and more successfully. This review synthesizes the major mechanistic innovations over the past few years and describes how predictive biomarkers, molecular endotyping, and novel treatment regimens in the coming years are likely to transform the diagnosis and treatment of autoimmune diseases.},
}

@article {pmid41935031,
year = {2026},
author = {Grassi, L and Heye, F and Proesmans, K and Abatih, E and Van Daele, A and Lahousse, L and Crabbé, A},
title = {Bacteria of the lung microbiome and health biomarkers in chronic airway disease: a systematic review and meta-analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00967-z},
pmid = {41935031},
issn = {2055-5008},
support = {12X6322N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {The lung microbiome is increasingly recognized as a key contributor to the development and progression of chronic airway diseases. While these conditions are typically associated with reduced microbial diversity and pathogen overgrowth, emerging evidence suggests that non-pathogenic bacteria may influence clinical outcomes. However, inconsistent findings across studies have made it difficult to determine their exact role in disease pathophysiology. To identify potentially beneficial members of the lung microbiome, we conducted a systematic review and meta-analysis of clinical studies investigating the association between non-pathogenic bacterial genera or species and clinico-pathological features in individuals with asthma, bronchiectasis, chronic obstructive pulmonary disease and cystic fibrosis. For the meta-analysis, data from different diseases were combined. Our analysis revealed that several bacteria in the lung microbiome were significantly associated with improved lung function and/or reduced airway inflammation across diseases. Although causal relationships cannot be established due to the absence of interventional studies, our findings highlight promising candidates for functional characterization and therapeutic exploration. Considerable heterogeneity in study design and reporting underscores the need for standardized methods and validation in relevant experimental models to advance our understanding of the lung microbiome in chronic airway diseases and inform the development of effective microbiome-based interventions.},
}

@article {pmid41935059,
year = {2026},
author = {Bodkhe, R and Sankaran, K and Shapira, M},
title = {Caenorhabditis elegans populations shape their microbial environment.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00975-z},
pmid = {41935059},
issn = {2055-5008},
abstract = {Nematodes represent one of the most abundant and ecologically significant taxonomic groups on earth, playing diverse roles in the cycling of organic matter. However, little is known about their effects on their microbial environment. To explore such effects, we took advantage of the bacteriovore free-living nematode Caenorhabditis elegans, which has been shown to assemble a characteristic gut microbiome from different microbial environments. Worm populations (initially germ-free) were raised in several microbially-distinct natural-like environments emulating the environment from which C. elegans are often isolated, allowing worms to go through four generations encompassing the typical boom-to-bust population growth cycle. Samples from worms, their environments, and from control environments without worms were analyzed using next-generation 16S rRNA gene sequencing. Data analysis showed that microbial diversity increased in the environment, either when worms were present or not, but that trajectories of change were different depending on the presence of worms. Importantly, the presence of worms led with time to convergence in the composition of their microbial environments, particularly affecting the abundance of members of bacterial families that are part of the C. elegans gut microbiome. Our findings reveal that C. elegans not only responds to environmental microbial changes but also shapes them, suggesting new roles for nematodes in modulating environmental microbial diversity and ecosystems.},
}

@article {pmid41935114,
year = {2026},
author = {Jia, Z and Meng, Y and Wang, W and Behm, J and Cai, FM and Mishra, S and Xia, S and Liu, S and Yang, X},
title = {Differential responses of termite gut bacterial and fungal community to tropical forest conversion.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09939-7},
pmid = {41935114},
issn = {2399-3642},
support = {41977057//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32201421//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Land-use change significantly impacts biodiversity, but its effects on the gut microbiomes of soil invertebrates remain poorly understood. We investigated how forest conversion to rubber plantations alters bacterial and fungal diversity, composition, and function in termite guts within a biodiversity hotspot Xishuangbanna, China. Our results showed that termites from natural forests harbored higher gut bacterial diversity than those from plantations, with effects varying across host species. Fungal diversity was shaped primarily by host species identity, with Odontotermes yunnanensis exhibiting the highest diversity index. While termite species solely governed bacterial community composition, both termite species and forest type shaped fungal composition. Fungal community variation correlated with local soil properties, whereas bacterial variation only associated with soil pH. Termites shared 17% of core gut bacteria (e.g., Bacillus, Pseudomonas, Mycobacterium) but 100% of fungi with the environment. Co-occurrence networks exhibited species-specific responses to forest conversion. Host species (Ancistrotermes and Odontotermes) predicted bacterial functional potential, but both forest type and host species influenced fungal functional potential. These findings demonstrate that termite gut microbiome responses to land-use change are multifaceted and taxon-specific, highlighting their role in ecosystem functional resilience under anthropogenic disturbance.},
}

@article {pmid41935132,
year = {2026},
author = {Łopucki, R and Stępień-Pyśniak, D and Wójciak, J and Pacan, M and Jurczyk, S and Kuźniar, A},
title = {Early-life gut microbiota differentiation in sympatric wild raptors.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47288-x},
pmid = {41935132},
issn = {2045-2322},
abstract = {The establishment of the gut microbiota during early life plays a crucial role in host physiology and development, yet remains poorly understood under natural conditions, particularly in wild raptors. Limited access to free-living nestlings constrains our understanding of how host species identity, parental trophic ecology (shaping dietary microbial input and nutrient availability), and environmental factors structure early-life microbiota. Here, we investigated the gut microbiota of nestlings of two sympatric raptor species, the white-tailed eagle (Haliaeetus albicilla) and the lesser spotted eagle (Clanga pomarina), which differ in parental foraging ecology (fish/waterbird vs. small mammal-based diet). Using non-invasive fecal sampling during routine ringing, we characterized gut microbiota composition and predicted functional potential, and tested the effects of host species, geographic distance between nests, and within-nest variability. Gut microbiota composition differed markedly between species, with clear separation of microbial communities and higher alpha diversity in white-tailed eagle nestlings. In contrast, geographic distance between nests had a limited influence on microbiome structure, while pronounced inter-individual and within-nest variability was observed, highlighting the importance of individual-specific and potentially stochastic processes during early microbiome assembly. Predicted functional profiles also differed between species, with enrichment of amino acid biosynthesis pathways in white-tailed eagles and carbohydrate-related pathways in lesser spotted eagles. No dysbiosis-like microbiome profiles were detected in either species, providing a baseline for future comparative studies. Overall, our findings demonstrate strong species-level differentiation in early-life gut microbiota in wild raptors, in the context of contrasting trophic ecology, while local environmental variation appears to be of secondary importance.},
}

@article {pmid41935154,
year = {2026},
author = {Pandey, K and Parmar, A and Vilas, S and Gosai, H and Mistry, H and Singh, KS and Roy, M and Dholpuria, S and Patel, RB},
title = {Weissella as a core member of the Gir cow milk microbiome: functional insights.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41935154},
issn = {1572-9699},
mesh = {Animals ; *Milk/microbiology ; Cattle ; *Weissella/genetics/isolation & purification/classification/physiology ; *Microbiota ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Female ; },
abstract = {Gir cow (Bos indicus) milk is widely valued for its nutritional quality, digestibility, and A2 β-casein content; however, the microbial determinants contributing to these attributes remain insufficiently characterized. In this study, dominant lactic acid bacteria (LAB) associated with Gir cow milk were isolated and evaluated using an integrated phenotypic and genome-based approach to elucidate their functional relevance. Raw milk samples were analyzed to isolate LAB, which were characterized through morphological, biochemical, and molecular analyses. Predominant isolates were identified as Weissella cibaria and Weissella confusa. Selected isolates exhibited strain-dependent tolerance to acidic pH, bile salts, and phenolic stress, along with auto-aggregation ability, cholesterol assimilation, and antagonistic activity against enteric pathogens. Survival under simulated gastrointestinal conditions was further validated by viable cell count analysis. Whole-genome sequencing of W. cibaria revealed a high-quality draft genome of approximately 2.43 Mb with a GC content of 44.97%, assembled into 21 contigs, encoding 2,282 protein-coding sequences, 11 rRNA genes, and 72 tRNA genes. Functional annotation indicated enrichment of genes associated with carbohydrate metabolism, stress adaptation, and membrane transport, while screening confirmed the absence of known virulence determinants and transferable antibiotic resistance genes, supporting its safety profile. The consistent predominance of Weissella spp. in Gir cow milk suggests a breed-associated microbial signature that may contribute to the functional characteristics of this indigenous dairy system. Collectively, these findings position Weissella as a promising functional component of the Gir cow milk microbiome and provide a genomic framework supporting its potential application in probiotic and functional dairy research.},
}

Animals
*Milk/microbiology
Cattle
*Weissella/genetics/isolation & purification/classification/physiology
*Microbiota
Genome, Bacterial
Phylogeny
RNA, Ribosomal, 16S/genetics
Female

@article {pmid41935253,
year = {2026},
author = {Liu, K and Zhang, Z and Su, Y and Ma, X and Wang, J and Yang, Q and Nie, Q and Mo, Z and Zhou, H and Zouboulis, CC and Guo, D and Liu, Z and Yang, X},
title = {Lactobacillus-derived extracellular vesicles provide multi-target acne treatment by enriched proteins and skin microbiota protection.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04291-8},
pmid = {41935253},
issn = {1477-3155},
support = {2024YFA0918500//National Key R&D Program/ ; },
abstract = {Numerous studies have highlighted the therapeutic potential of probiotics in acne. Given the complex and multifactorial nature of the disease, probiotic-based multi-target therapies may be promising. Additionally, due to their non-replicative and nanosized characteristics, probiotic-derived extracellular vesicles might provide a safer and more efficient alternative. Here, we selected three anti-acne targets-Propionibacterium acnes (P. acnes) inhibition, anti-inflammatory effects, and sebum suppression-for high-throughput screening, identifying Lactobacillus plantarum 5b4m2 with multi-target anti-acne potential. Next, we isolated 5b4m2-derived EVs (LP-EVs) and discovered that they retain the anti-acne potential of the parental bacteria while exhibiting superior skin permeability. Further studies in P. acnes-induced acne mice demonstrated that LP-EVs significantly alleviated inflammatory symptoms such as redness and swelling and effectively inhibited the colonization of P. acnes, leading to enhanced therapeutic efficacy. Then, proteomic analysis identified nine enriched proteins in LP-EVs directly associated with acne improvement, including mucus-binding protein, cell wall hydrolase, lipase, and thioredoxin. Correspondingly, pathway changes in the host were revealed by transcriptomic analysis, such as the chemokine signaling pathway, lipid metabolism, and tissue tight junctions. Moreover, LP-EVs effectively maintain the skin microbiota balance, which may also contribute to acne improvement. Collectively, our study offers a new perspective on probiotic-based multi-target strategies, which may facilitate the treatment of acne and other skin diseases in the future.},
}

@article {pmid41935274,
year = {2026},
author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S},
title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03152-y},
pmid = {41935274},
issn = {1743-422X},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.

METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.

RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.

CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.},
}

@article {pmid41935303,
year = {2026},
author = {He, W and Gao, M and Ren, Q and Wang, M and Zhou, S and Liu, Q and Chu, K and Qin, Y and Fan, Y and Zou, H and Cui, Y and Shu, Y and Wang, X},
title = {Causal relationship between GM, immune cells and esophageal adenocarcinoma: a mediation analysis based on MR.},
journal = {Journal of cardiothoracic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13019-026-03984-3},
pmid = {41935303},
issn = {1749-8090},
support = {LKZ2022019//Jiangsu Commission of Health/ ; LKZ2022019//Jiangsu Commission of Health/ ; LKZ2022019//Jiangsu Commission of Health/ ; 2025M782034//Supported by China Postdoctoral Science Foundation/ ; },
}

@article {pmid41935333,
year = {2026},
author = {Qi, X and Jin, D and Olimi, E and Chen, X and Cernava, T},
title = {What do we know about the seed microbiome?.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41935333},
issn = {2049-2618},
support = {2024YFD1501602//National Key Research and Development Program of China/ ; doi.org/10.55776/J4753//Austrian Science Fund/ ; CXTD[2025]041//Guizhou Provincial Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities (111 Program)/ ; },
mesh = {*Seeds/microbiology/growth & development ; *Microbiota ; Germination ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {The seed microbiome supports plant health and increases resilience under adverse environmental conditions. Seeds are also an important vector for transgenerational transfer of the plant microbiota. Even though research over the last decade has provided valuable insights into the functional roles of seed-associated microbes, these important members of the plant microbiome remain underexplored. This review systematically highlights recently discovered key functions of the seed microbiota. It covers taxonomic composition and diversity across plant species, transmission mechanisms, functional roles in germination and seedling establishment, growth promotion, and stress resistance. The review also addresses methodological challenges and highlights critical open questions regarding assembly, spatial compartmentalization, and translation into applications. Further research into seed microbiomes has the potential to not only increase the sustainability in plant production but also to increase food security in a changing climate. Reaching such outcomes will be facilitated by mechanistic studies that will disclose the remaining secrets of plant-microbe interplay at the very first developmental stage of most plants that nowadays inhabit Earth. Video Abstract.},
}

*Seeds/microbiology/growth & development
*Microbiota
Germination
*Plants/microbiology
*Bacteria/classification/genetics/isolation & purification

@article {pmid41935339,
year = {2026},
author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R},
title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00885-9},
pmid = {41935339},
issn = {2524-6372},
abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.

RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.

CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.},
}

@article {pmid41935342,
year = {2026},
author = {Herlemann, DPR and Riedinger, DJ and Fenández-Juárez, V and Delgado, LF and Andersson, AF and Pansch, C and Riemann, L and Bengtsson, MM and Gyraite, G and Reusch, TBH and Katarzyte, M and Kube, S and Martin, G and Rakowski, M and Labrenz, M},
title = {Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00881-z},
pmid = {41935342},
issn = {2524-6372},
abstract = {BACKGROUND: Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.

RESULT: As hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.

CONCLUSIONS: Our results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.},
}

@article {pmid41935395,
year = {2026},
author = {Theodosis-Nobelos, P and Papagiouvanni, I and Protopappas, AA and Papagiouvannis, G},
title = {Pathophysiology of CLD: Oxidative Stress and Antioxidant Mechanisms that may Limit its Progression.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303441513260220055400},
pmid = {41935395},
issn = {2212-3873},
abstract = {INTRODUCTION: Chronic liver disease (CLD) represents a progressive condition culminating in fibrosis and, ultimately, cirrhosis or hepatocellular carcinoma. A growing body of evidence implicates oxidative and nitrosative stress as key mediators in the pathogenesis of CLD.

OBJECTIVE: This review aims to summarize the role of oxidative stress in CLD progression and to highlight therapeutic strategies targeting redox imbalance and related signaling pathways.

METHODS: Relevant literature from preclinical and clinical studies was reviewed, with emphasis on mechanisms of oxidative and nitrosative stress, signaling pathways involved in fibrogenesis, and emerging therapeutic interventions targeting redox imbalance and the gut-liver axis.

RESULTS AND DISCUSSION: Reactive oxygen and nitrogen species contribute to hepatocyte damage, hepatic stellate cell activation, and extracellular matrix accumulation. Mitochondrial dysfunction, endoplasmic reticulum stress, and disrupted redox homeostasis induce tissue injury and fibrogenesis. Various signaling pathways, including Nrf2/Keap1, AMPK/SIRT1, JNK, PI3K/Akt/mTOR, and TGF-β/SMAD, serve as critical links between oxidative imbalance and fibrotic progression. The antifibrotic potential of antioxidants such as vitamin E, lipoic acid, berberine, and polyphenolic compounds is increasingly validated in preclinical and clinical studies. Additionally, modulation of NOX enzymes and support of endogenous defenses offer promising therapeutic avenues. The gut-liver axis and microbial dysbiosis further exacerbate redox disturbance, underscoring the systemic nature of liver injury. Probiotic and prebiotic therapies have shown hepatoprotective effects in NAFLD models.

CONCLUSION: In conclusion, targeting oxidative stress and its associated pathways represents a compelling strategy to attenuate or even reverse liver fibrosis, presenting a promising therapeutic strategy that could be integrated into clinical practice.},
}

@article {pmid41935448,
year = {2026},
author = {Hemati, S and Mohsenipour, Z},
title = {Immune exhaustion in bacterial infections: mechanisms, consequences, and therapeutic implications.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {30},
number = {3},
pages = {105809},
doi = {10.1016/j.bjid.2026.105809},
pmid = {41935448},
issn = {1678-4391},
abstract = {T-cell exhaustion, a well-characterized phenomenon, has historically been studied in the context of viral and oncological diseases. However, its relevance to chronic bacterial infections has only recently garnered attention. This review summarizes emerging evidence suggesting that bacterial pathogens can induce immune exhaustion through a variety of mechanisms. Additionally, we explore how bacterial biofilms, immune-privileged niches, and regulatory T-cell expansion contribute to persistent immune dysfunction. The article further examines the consequences of immune exhaustion, including secondary infections, antibiotic resistance, and microbiome dysbiosis, which are often underappreciated aspects of chronic immune impairment. Therapeutic strategies targeting these exhaustion pathways, such as immune checkpoint blockade, metabolic reprogramming, and microbiome modulation, are also discussed. We emphasize the need to consider chronic bacterial infections not as static conditions but as dynamic processes that interact with and suppress the immune system. Thus, understanding the mechanisms behind immune exhaustion highlights the importance of developing therapies that restore immune function, rather than solely relying on traditional antimicrobial treatments.},
}

@article {pmid41935631,
year = {2026},
author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , },
title = {Alcohol-Related Liver Disease Disrupts Bile Acid Homeostasis and Gut Microbial Bile Acid Metabolism.},
journal = {JHEP reports : innovation in hepatology},
volume = {},
number = {},
pages = {101848},
doi = {10.1016/j.jhepr.2026.101848},
pmid = {41935631},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.

METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n=462), alongside matched healthy controls (n=148), and validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.

RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F=69.9, p=8.6e-66) and feces (inprimis, cholic acid: F=5.5, p=1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multi-step dehydroxylation pathway (e.b. baiB) increased, whereas those in the reduction arm (baiN) were depleted. In ALD patients, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.

CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.

CLINICAL TRIAL NUMBER: GALAXY main cohort: Danish Data Protection Agency nos. 13/8204, 16/3492 and 18/22692; and Odense Patient Data Exploratory Network under study identification nos. OP_040 and OP_239 Validation cohort 1: EudraCT number 20214-001856-51 Validation cohort 2: ClinicalTrial.gov ID NCT03863730 IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive alcohol-related liver disease progression. Additionally, our study identifies specific bacterial species influencing bile acid concentrations in alcohol-related liver disease using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating alcohol-related liver disease.},
}

@article {pmid41935802,
year = {2026},
author = {Kwak, MJ and Park, B and Choi, H and Hong, W and Mun, D and Son, SH and Choi, YS and Pathiraja, D and Eor, JY and Ryu, S and Kim, JK and Whang, KY and Jeong, KC and Choi, IG and Kim, Y},
title = {Gut microbial extracellular vesicles modulate the development of metabolic dysfunction-associated steatohepatitis through the gut-liver axis.},
journal = {Pharmacological research},
volume = {227},
number = {},
pages = {108184},
doi = {10.1016/j.phrs.2026.108184},
pmid = {41935802},
issn = {1096-1186},
abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) represents a growing global health challenge due to its propensity to progress to irreversible hepatic disorders, including fibrosis, cirrhosis, and carcinoma. This study aimed to investigate the role of gut microbiota in the pathogenesis of MASH. We identified Romboutsia hominis as a key contributor to MASH progression, exacerbating hepatic lipid accumulation and inflammation via the tumor necrosis factor-α (TNF-α) signaling pathway. Conversely, Akkermansia muciniphila and its extracellular vesicles (EVs) mitigated MASH by reducing hepatic lipid deposition through lipid biosynthesis-related genes downregulation. Furthermore, by integrating gut microbiota profiles and serum biomarkers using a machine learning approach, we achieved over 90% accuracy in noninvasive MASH diagnosis. These findings elucidate critical mechanisms within the gut-liver axis and suggest novel therapeutic and diagnostic strategies targeting gut microbiota and their functional EVs for MASH.},
}

@article {pmid41935870,
year = {2026},
author = {Genkel, V and Zaripova, Y and Sluchanko, A and Lebedev, E and Kuznetsova, A and Saenko, A and Pykhova, L and Sumerkina, V and Nikushkina, K and Savochkina, A and Kupriyanov, S and Shaposhnik, I and Dolgushina, A},
title = {Ultrasound-measured visceral adipose tissue thickness and carotid atherosclerosis in patients with inflammatory bowel diseases.},
journal = {Obesity research & clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.orcp.2026.03.001},
pmid = {41935870},
issn = {1871-403X},
abstract = {BACKGROUND AND AIM: Visceral obesity plays a pivotal role in initiating and sustaining chronic systemic inflammation through complex interactions involving adipose tissue dysfunction, insulin resistance, immune system activation, and gut microbiome composition. Visceral obesity is also hypothesized to contribute to the development and progression of extraintestinal manifestations and complications in inflammatory bowel disease (IBD). The aim was to evaluate the interrelationships between ultrasound-measured visceral and subcutaneous adipose tissue thickness with carotid artery atherosclerosis indicators in IBD patients.

METHODS AND RESULTS: The study included 90 patients with IBD aged 40-64 years. All patients underwent duplex ultrasound scanning of the carotid arteries with measurement of carotid plaque burden indicators. Ultrasound measurements of subcutaneous and visceral adipose tissue thickness (ATT) were performed: minimal subcutaneous adipose tissue thickness (mSATT), maximal preperitoneal adipose tissue thickness (mPATT), periumbilical subcutaneous adipose tissue thickness (PSATT), visceral abdominal adipose tissue thickness, peri- and pararenal adipose tissue thickness. Ultrasound-derived indicators of visceral obesity (mPATT and abdominal ATT), but not BMI or WC, were associated with an increased odds ratio for the presence of carotid plaque after adjustment for sex and age. Both mPATT and abdominal ATT demonstrated positive correlations with apoB concentration, LDL-C, sdLDL, eLDL-TG, and inverse correlations with adiponectin concentration.

CONCLUSION: In patients with IBD aged 40-64 years, visceral adipose tissue thickness measured by ultrasound and WC were associated with the carotid plaque burdens. Ultrasound-measured mPATT and abdominal ATT, but not BMI and WC, were independently associated with carotid atherosclerosis in patients with IBD.},
}

@article {pmid41936070,
year = {2026},
author = {Duan, H and Ning, Z and Sun, Z and Guo, T and Sun, Y and Figeys, D},
title = {MetaDIA: A DDA-free Database Reduction Strategy for DIA Human Gut Metaproteomics.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzag029},
pmid = {41936070},
issn = {2210-3244},
abstract = {Microbiomes, especially within the gut, are complex and may comprise hundreds of species. The identification of peptides in metaproteomics presents a substantial challenge, as it involves matching peptides to mass spectra within an enormous search space for complex and unknown samples. This poses difficulties for both the accuracy and the speed of identification. Specifically, analysis of data-independent acquisition (DIA) datasets has relied on libraries constructed from prior data-dependent acquisition (DDA) results. However, this method is resource-intensive, consumes samples, and limits identification to peptides previously identified. These limitations restrict the application of DIA in metaproteomics research. We introduced a novel strategy to reduce the search space by utilizing species abundance and functional abundance information from the microbiome to score each peptide and prioritize those most likely to be detected. Using this strategy, we have developed and optimized a workflow called MetaDIA for the analysis of microbiome data generated by DIA, which operates independently of DDA assistance. Our approach successfully created a smaller, yet sufficient database for DIA data search in metaproteomics. The results demonstrated strong consistency with the traditional DDA-based library approach at both protein and functional levels. MetaDIA is readily accessible as an open-source project hosted on GitHub (https://github.com/northomics/MetaDIA).},
}

@article {pmid41936460,
year = {2026},
author = {Calbet, A},
title = {Gut Microbiomes of Marine Zooplankton: Consequences for Host Performance, the Biological Carbon Pump, and Prokaryote Biogeography.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70271},
doi = {10.1111/1462-2920.70271},
pmid = {41936460},
issn = {1462-2920},
support = {PID2023-150548NB-I00//MICIU/AEI/10.13039/5011 00011033/ ; //ERDF/EU/ ; //Consejo Superior de Investigaciones Científicas/ ; },
mesh = {Animals ; *Zooplankton/microbiology/physiology ; *Gastrointestinal Microbiome ; *Carbon/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {Marine zooplankton are a link between primary producers and higher trophic levels and play a pivotal role in organic matter export via diel vertical migration and faecal-pellet production. Molecular surveys have revealed each individual as a holobiont hosting dense, taxonomically structured microbiomes in the gut, on the cuticle, and within feeding structures. These microbial partners expand dietary breadth through carbohydrate-active enzymes, supply limiting vitamins, detoxify xenobiotics, and may buffer thermal and oxidative stress, thereby influencing host fitness and the fate of particulate organic carbon. Experimental studies show intact microbiomes often enhance growth or fecundity, with effects amplified under vitamin limitation or toxin exposure. In contrast, gut and pellet-associated respiration can substantially reduce the carbon content of pellets within hours to days, depending on temperature and microbial composition. Vertical migrators also transport live bacteria and viruses below the thermocline, potentially seeding mesopelagic niches and affecting remineralization patterns. Despite these influences, zooplankton holobionts remain largely absent from biogeochemical models. This minireview synthesises current understanding of microbiome assembly and plasticity, their contributions to host performance and carbon export, and their role in microbial dispersal, underscoring the need to integrate holobiont traits into Earth-system models to better predict ecosystem responses to warming and deoxygenation.},
}

Animals
*Zooplankton/microbiology/physiology
*Gastrointestinal Microbiome
*Carbon/metabolism
Bacteria/metabolism/classification/genetics

@article {pmid41929571,
year = {2026},
author = {Seenivasan, R and Pachiyappan, JK and Marimuthu, A and Halagali, P and Kuppusamy, G and Nayak, PG and Tippavajhala, VK},
title = {Gut microbiota shifts in spaceflight: a case study evidence and countermeasures for microbial homeostasis.},
journal = {3 Biotech},
volume = {16},
number = {4},
pages = {152},
pmid = {41929571},
issn = {2190-572X},
abstract = {The gut microbiota is a crucial component in maintaining overall human health since it has been found to influence not only metabolism but also neurobehavioral function and immunity. The extreme conditions of space, for example, cosmic radiation, microgravity, and confinement, can severely disrupt the functioning and alter the composition of gut microbiota. In fact, this will predispose the immune system to be dysfunctional, lead to psychological and metabolic disorders that are accompanied by a decrease in the diversity of beneficial microbes and change in the pattern of metabolite production. The spaceflight analog and ground, based studies have produced important findings concerning the mechanisms and reasons for gut microbial dysbiosis in extreme conditions. Different research works have been carried out, such as dietary intervention and high fiber to support the growth of healthy microbes. Further, advanced microbial monitoring using wearable sensors to identify the microbial and proinflammatory biomarkers will mitigate dysbiosis and safeguard the crew's health for longer-duration missions. This wearable sensor will not only help monitor astronauts' microbial status continuously, but it will also provide a significant feature for designing personalized dietary plans and probiotic supplements. This article provides a comprehensive understanding of astronaut health, including disturbances to the gut microbiome during space travel, space-analogue studies conducted by many researchers to unravel mechanisms, countermeasures to stabilize the gut microbiome, and its prospects.},
}

@article {pmid41929684,
year = {2026},
author = {Chen, C and Wang, P and Tong, G and Chen, R and Shen, Y and Wu, X and Liang, W and Pu, J},
title = {The structure of rhizosphere microbial and endophytic communities of Coptis chinensis var. brevisepala: variations across different ecological niches.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1785609},
pmid = {41929684},
issn = {1664-302X},
abstract = {Coptis chinensis var. brevisepala is a valuable traditional Chinese medicinal plant, whose resources are severely depleted due to long-term overexploitation. However, the associations between its rhizosphere microbiome and habitat soil properties, as well as the composition and functions of endophytes, remain unclear. This study employed high-throughput sequencing to characterize rhizosphere microbial communities of C. chinensis var. brevisepala from four distribution sites, analyze their correlations with soil chemical properties, and explore the differences and functional traits of endophytic communities in distinct tissues (leaves, rhizomes, fibrous roots). A total of 177 core bacterial genera and 146 core fungal genera were detected in rhizosphere soils of the four sites. The dominant bacterial phyla were Proteobacteria, Acidobacteriota, and Actinobacteriota, with norank_f_Xanthobacteraceae and Bradyrhizobium as the dominant genera. The dominant fungal phyla were Ascomycota and Basidiomycota, with Paraboeremia and Saitozyma as the dominant genera. Soil chemical properties exerted significant effects on both bacterial and fungal communities in the rhizosphere, among which soil pH and total nitrogen (TN) were the key drivers shaping rhizosphere microbial communities. For endophytes, 29 bacterial phyla (596 genera) and 12 fungal phyla (653 genera) were identified, with significant differences in diversity, richness, and dominant genera across tissues; leaves harbored the highest endophytic diversity. Functional prediction indicated that endophytic fungi were dominated by saprotrophy-related functional genes, and KEGG secondary functional annotation uncovered the presence of antimicrobial-related genes. This study clarifies the rhizosphere microbiome ecological traits and tissue-specific endophytic characteristics of C. chinensis var. brevisepala, providing a scientific basis for screening beneficial microorganisms to facilitate the restoration and reconstruction of this endangered medicinal plant.},
}

@article {pmid41929693,
year = {2026},
author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z},
title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1729476},
pmid = {41929693},
issn = {1664-302X},
abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.

METHODS: Vaginal swabs (sPTB, n = 37; term, n = 62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.

RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p < 0.05), and distinct community structure (PERMANOVA p < 0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC = 0.82), and a multi-metabolite model improved classification (AUROC = 0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.

CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.},
}

@article {pmid41929779,
year = {2026},
author = {Mishra, P and Prescott, SL and Logan, AC},
title = {The gut is guilty! Will legalomics transform forensic and legal psychology?.},
journal = {Frontiers in psychology},
volume = {17},
number = {},
pages = {1739593},
pmid = {41929779},
issn = {1664-1078},
abstract = {Multiple lines of converging research are supporting the idea that gut microbes play an outsized role in human cognition and behavior. Here in this perspective article, we argue that emergent gut-brain-microbiota research, and associated advances in multi-omics technologies, are destined to be of high-level relevance to forensic and legal psychology. After summarizing neural, immune, endocrine, and metabolic channels by which gut ecosystems can modulate behavior-relevant brain states, and discussing causal inferences from microbiota-transfer and adjacent human evidence, we present auto-brewery syndrome as a bounded legal precedent for microbiome-mediated impairment. The available evidence allows for a visualized future in which legalomics-the disciplined use of microbiome and omics evidence in prevention, treatment, competency, mitigation, risk assessments, reintegration care, correctional health, and professional wellness-is in the prevue of forensic and legal psychology. Framed by neurorights, we offer a series of ideas for future directions, with possible ways to strengthen research within ethical frameworks. Using auto-brewery syndrome as an example, we argue that the legalome offers forensic and legal psychology a way to calibrate, rather than replace, biopsychosocial judgement. Microbial signatures and legalomics-reliably obtained and narrowly construed-might one day help us judge more justly.},
}

@article {pmid41929949,
year = {2026},
author = {Zhang, Q and Almanie, L and Ouyang, Y and Cheng, Z and Zhang, H},
title = {From routine periodontal therapy to Alzheimer's disease early detection: A scoping review.},
journal = {Journal of Alzheimer's disease reports},
volume = {10},
number = {},
pages = {25424823261421629},
pmid = {41929949},
issn = {2542-4823},
abstract = {An epidemiological association has been observed between periodontitis and Alzheimer's disease (AD); however, salivary and blood assays often show low specificity. Periodontal tissues and fluids, which are routinely removed and discarded during periodontal treatment, may be collected to offer matrices useful for the early detection of AD. This study aimed to map current preclinical and clinical evidence on biomarkers measured in periodontal tissues and fluids for the early detection of AD and organize them within an AD-specificity pyramid anchored to brain-relevant endpoints. Following PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Extension for Scoping Reviews) guidance, we searched PubMed, Scopus, and Web of Science (January 1, 2015-August 31, 2025) for preclinical and clinical studies measuring AD-relevant biomarkers in periodontal matrices. The protocol was pre-registered (OSF DOI: 10.17605/OSF.IO/EDVU9; August 20, 2025). Two reviewers extracted the data, and other two independently verified them. The findings were organized using a four-tier AD-specificity pyramid. Results: Fourteen studies met the inclusion criteria. The biomarkers from the included studies were clustered into microbiome features, molecular signals, and genetic/transcriptomic findings. Evidence ranged from Tier-1 contextual inflammation/pathogens to Tier-4 core-pathology adjacency; five studies incorporated clinical/biological anchoring, with cerebrospinal fluid amyloid-β positivity providing the most brain-relevant anchor. Periodontal matrices are practicable, high-signal sources for AD-relevant biomarkers. However, translational validation linking periodontal biomarkers to brain endpoints is needed to assess the feasibility of multi-tier and chairside panels for early AD detection as part of routine periodontal care.},
}

@article {pmid41929953,
year = {2026},
author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE},
title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.},
journal = {Journal of Alzheimer's disease reports},
volume = {10},
number = {},
pages = {25424823261436287},
pmid = {41929953},
issn = {2542-4823},
abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.

OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.

METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.

RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (ε4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.

CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.},
}

@article {pmid41930197,
year = {2026},
author = {Wu, J and Jiang, C},
title = {The authors respond to feedback on Cancer Cell-Memory Macrophage Hybrid Theory for metastatic cancer cells.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1780597},
pmid = {41930197},
issn = {2234-943X},
abstract = {We have recently hypothesized that the hematogenous metastatic cancer cell of solid tumors is a hybrid between a primary cancer cell and a memory/trained macrophage (doi: 10.3389/fonc.2024.1412296). The hybrid cell respectively acquires mutator phenotype and overgrowth/hyperplasia property from the primary cancer cell and migratability/metastability from the memory/trained macrophage. We name this hypothesis Cancer Cell-Memory Macrophage Hybrid Theory. Since the publication of the article, a number of questions related to this Theory have been raised by colleagues in the oncology community, including intratumoral microbes and microbiomes/microbiotas, oncolytic viruses and bacteria, human papilloma virus vaccines, anti-cancer effects of γδ T-cells, and immune checkpoint inhibitors. The current article is prepared to address these issues. Additional to resolving questions like "Why metastatic cancer cells enter dormancy and can recur via stem-like self-renewal?", the Cancer Cell-Memory Macrophage Hybrid Theory distinguishes itself from other carcinogenesis and metastasis hypotheses/theories by offering answers to many puzzling clinical features including metastasis of seemingly malignant parasitic cells within the human body, intracellular microbes (including viruses, bacteria, fungi, and parasites) within cancer cells, paradoxal effects (recurrence vs. regression) of microbes on cancer, contradictory immune effects of human papilloma virus vaccines between young and adult/senior females, and immune context-dependent effects (stimulatory and inhibitory) of T-lymphocytes on cancer cells. The Theory also predicts that quantitatively and functionally dampening innate macrophages that have hybridized with cancer cells (i.e., cancer cell-memory macrophage hybrids), should be explored as a fundamental anti-cancer strategy. The Theory further forecasts how to prepare an organotropic/tumoritropic Coley's toxin-like anti-cancer microbe, which could potentially circumvent direct injection of microbial preparations into a tumor. A testable experiment that uses zebrafish larva models can potentially either validate or falsify the Theory.},
}

@article {pmid41930211,
year = {2026},
author = {Blagov, AV and Sazonova, MD and Ryzhkova, AI and Karagodin, VP and Popov, MA and Budnikov, EY and Ravani, AL and Orekhov, AN and Sazonova, MA and Arkhipenko, YV},
title = {Analysis of the use of monoclonal antibodies in the treatment of Crohn's disease.},
journal = {Antibody therapeutics},
volume = {9},
number = {2},
pages = {101-118},
pmid = {41930211},
issn = {2516-4236},
abstract = {Crohn's disease (CD) is a chronic inflammatory bowel disease with increasing global prevalence, significantly impacting patients' quality of life and healthcare costs. The introduction of monoclonal antibodies has revolutionized CD management, offering targeted therapy against specific inflammatory pathways. This review systematically analyzes the current state of monoclonal antibody therapy, including anti-TNF-α agents (infliximab, adalimumab, certolizumab pegol), anti-integrin antibodies (vedolizumab), and anti-cytokine therapies (ustekinumab, risankizumab). Despite remarkable therapeutic advances, significant limitations persist, including primary non-response (20%-40%), secondary loss of response (13%-20% annually), immunogenicity, safety concerns, and substantial economic burden. We propose evidence-based strategies to address these challenges, including therapeutic drug monitoring, combination therapy, and personalized medicine approaches. Furthermore, we identify promising novel therapeutic targets such as IL-36, IL-17C, SMAD7, TL1A, complement components, and microbiome-related factors. Targeting two or more specific targets simultaneously appears to be a promising direction of research for the development of bi- and polyspecific monoclonal antibodies capable of interfering with multiple pathological pathways in CD. The integration of advanced antibody engineering, personalized medicine, and innovative delivery systems represents the future direction for overcoming current limitations. Achieving sustained remission for all patients through safe, effective, and accessible therapeutic interventions remains the ultimate goal in CD management.},
}

@article {pmid41930263,
year = {2025},
author = {Du, YC and Wang, D and Song, YQ and Zheng, QS and Wang, L},
title = {Arbuscular mycorrhizal fungi regulate the peanut rhizosphere microbiome to alleviate salinity stress and enhance yield.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1739241},
pmid = {41930263},
issn = {1664-302X},
abstract = {Salt stress threatens peanut yield by impairing physiological performance and disrupting rhizosphere microbial community stability. To investigate how arbuscular mycorrhizal fungi (AMF) mediate plant-microbe interactions under salt stress, researchers conducted a controlled pot experiment with four treatments: non-salt control (CK), AMF inoculation (A), salt stress (S; 100 mM sodium chloride), and combined AMF inoculation under salt stress (SA), with five biological replicates in each group. Plant growth traits, yield, and rhizosphere bacterial community were assessed at different peanut growth stages. AMF inoculation significantly increased peanut biomass, chlorophyll content, and yield, both under salt and non-salt stress conditions. Salt stress significantly reduced bacterial richness and community evenness, while AMF partially restored α-diversity and reshaped bacterial community composition. Functional predictions indicated that AMF enriched nitrogen cycling pathways such as nitrate reduction and nitrogen fixation. Furthermore, AMF promoted a more complex and stable bacterial community under salt stress, characterized by enhanced synergistic effects among key taxa, including Actinobacteria, Firmicutes, and Proteobacteria. Overall, AMF inoculation enhanced plant performance and rhizosphere bacterial resistance, highlighting its potential as an effective ecological strategy for improving peanut yield in saline-alkali agricultural ecosystems.},
}

@article {pmid41930266,
year = {2026},
author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J},
title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag041},
pmid = {41930266},
issn = {2730-6151},
abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.},
}

@article {pmid41930333,
year = {2026},
author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T},
title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.},
journal = {MedComm},
volume = {7},
number = {4},
pages = {e70705},
pmid = {41930333},
issn = {2688-2663},
abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.},
}

@article {pmid41930403,
year = {2026},
author = {Ai, Y and Zhu, T and Gan, J},
title = {Parental autoimmune diseases and offspring's allergic disease: A systematic review and meta-analysis.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {4},
pages = {e70335},
pmid = {41930403},
issn = {1399-3038},
mesh = {Humans ; *Autoimmune Diseases/epidemiology ; Female ; *Hypersensitivity/epidemiology ; Asthma/epidemiology ; *Parents ; Male ; Child ; Rhinitis, Allergic/epidemiology ; },
abstract = {Epidemiological studies have reported an increased risk of allergic diseases in children born to parents with autoimmune diseases (AIDs); however, the mechanisms underlying this association remain unclear. We conducted a systematic review and meta-analysis to explore the relationship between parental AIDs and allergic diseases in offspring. EMBASE, Web of Science, and PubMed databases were searched for articles published up to December 1, 2025. AIDs in both mothers and fathers were included. Allergic outcomes included asthma, eczema, and allergic rhinitis. A random-effects model was used to synthesize the data. Twelve studies were included in the final analysis, and the methodological quality ranged from moderate to high. Maternal AIDs (of any type) were associated with an increased risk of asthma (odds ratio (OR) 1.25, 95% confidence interval (CI): 1.09-1.43), eczema (OR 1.30, 95% CI: 1.13-1.50), and allergic rhinitis (OR 1.04, 95% CI: 1.02-1.07) in offspring. Paternal AIDs were also associated with a higher risk of asthma (OR 1.16, 95% CI: 1.06-1.27) and eczema (OR 1.13, 95% CI: 1.02-1.26) in offspring. This systematic review and meta-analysis demonstrate that parental AIDs are associated with an increased risk of asthma and eczema in children. However, the available evidence is limited by potential bias in case ascertainment and inadequate adjustment for confounding factors. Larger high-quality studies are needed to confirm these findings and to elucidate the underlying genetic and microbiome-related mechanisms. Such evidence may facilitate early identification and targeted prevention or management of allergic diseases in children of parents with AIDs.},
}

Humans
*Autoimmune Diseases/epidemiology
Female
*Hypersensitivity/epidemiology
Asthma/epidemiology
*Parents
Male
Child
Rhinitis, Allergic/epidemiology

@article {pmid41930490,
year = {2026},
author = {Herrera, MJ and Khanna, A and Jones, JA and Betancur-R, R and Rohner, PT},
title = {Diet Outweighs Vertical Transmission in Shaping Dung Beetle Larval Gut Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {7},
pages = {e70336},
pmid = {41930490},
issn = {1365-294X},
support = {//University of California, San Diego/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Coleoptera/microbiology/growth & development ; Larva/microbiology ; *Diet ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Cattle ; },
abstract = {The microbiome is central to host development and adaptation, yet the balance between vertical and environmental acquisition, and how hosts shape surrounding microbial communities, remains poorly understood. Dung beetles rely on microbial symbionts to extract nutrients from vertebrate dung, with part of their microbiome vertically inherited via a maternal faecal pellet. However, the relative importance of vertical versus horizontal transmission is unclear. We examined this in the gazelle dung beetle (Digitonthophagus gazella), rearing larvae on brood balls made of dung from grass-(high-quality), hay-(low-quality) or silage-fed (a novel fermentable energy-rich diet) cattle, with or without maternal microbes. We integrated measures of gut morphology with 16S rRNA amplicon sequencing to assess host development and the gut microbiome. Diet significantly influenced overall size, hindgut area, and microbiome composition. Silage-dung fed larvae had more even and taxonomically rich microbiomes, with higher microbial diversity in individuals reared with maternal microbes. Diet explained ~26% of the variation in microbial composition, while the vertical transmission of microbes only explained 3%. Vertical transmission only slightly increases microbial species richness and relative hindgut area but did not influence overall microbial diversity. The larval brood ball contributed 40%-50% of the hindgut microbiome, while maternal microbes contributed < 0.05%. These findings demonstrate that horizontal acquisition through diet is the dominant force shaping larval gut microbiomes, while vertical inheritance plays a minor but detectable role in enhancing richness and gut development. More broadly, this work reinforces the importance of examining host-microbiome-environment interactions in ecological and evolutionary contexts.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Coleoptera/microbiology/growth & development
Larva/microbiology
*Diet
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Cattle

@article {pmid41930642,
year = {2026},
author = {Xu, S and Guo, G and Gao, J and Fang, Z and Chai, L and Gao, Y and Liu, J and Wang, J and Siqinbateer, and Zhang, L},
title = {Systematic Identification and Characterization of Causal Risk Genes Implicated in Colorectal Cancer by Integrating GWAS, eQTL, and mQTL Data.},
journal = {Current drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113894501444884260130225445},
pmid = {41930642},
issn = {1873-5592},
abstract = {INTRODUCTION: Knowledge of the mechanisms through which common single-nucleotide polymorphisms (SNPs) modulate colorectal cancer (CRC) susceptibility is central to elucidating the molecular basis of this disease. Genome-wide association studies (GWAS) reveal noncoding SNPs influencing CRC susceptibility, yet their functional mechanisms, particularly through gene expression dysregulation, DNA methylation alterations, and interactions with gut microbiota, remain uncharacterized. Through integrative analysis, systematically exploring the effects of genetic variations on gene expression heterogeneity, DNA methylation, and gut microbiome is expected to yield potential biomarkers for early diagnosis and intervention of CRC.

METHODS: An integrative framework is developed to prioritize causal risk genes at CRC-associated GWAS loci, applying the SMR&HEIDI (Summary-data-based Mendelian randomization and heterogeneity in dependent instruments) and TSMR (Two-sample Mendelian Randomisation) methods. The findings were validated via gene expression and TF binding affinity.

RESULTS: 10 tissue-specific gene-SNP pairs, 3 blood eQTL-gene pairs, 26 gene-CpG-SNP regulatory modules, and 39 microbiota-associated gene-SNP pairs are identified. A few potential regulatory influences on CRC development associated with genes and variants, such as POU5F1B and rs10797801, were identified. Moreover, the genetic variants disrupted TF binding affinity while only a few promoted the binding of transcription factors (TFs).

DISCUSSION: The data integration enabled us to prioritize genes according to different regulatory mechanisms, such as gene expression and DNA methylation, and bridge the gap between statistical associations and biological functionality.

CONCLUSION: Multi-omics integration reveals some causal risk genes and variants implicated in CRC. These findings offer novel insight into the molecular mechanisms underlying CRC susceptibility and provide valuable clues for diagnosis and therapeutic intervention strategies.},
}

@article {pmid41930694,
year = {2026},
author = {Yuhan, W and Zhiru, C and Yu, D and Ruiqing, Z and Guangtao, P and Jie, X},
title = {Research Progress on the Synergistic Role of Gut Microbiota and Exosomal miRNAs in the Treatment of Androgenetic Alopecia.},
journal = {Current topics in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115680266424195251211072643},
pmid = {41930694},
issn = {1873-4294},
abstract = {INTRODUCTION: Androgenetic alopecia (AGA), a widespread condition marked by the gradual shrinkage of hair follicles, involves complex pathogenic mechanisms. Recently, a growing body of research has begun to uncover the influence of gut microbial communities and exosomederived microRNAs (miRNAs) in hair follicle regulation. Although current findings remain preliminary, they point toward a potential interplay between intestinal microbiota and exosomal signaling pathways, which may offer novel therapeutic avenues. This review seeks to dissect the biological contributions of gut microbiota and exosomal miRNAs to the onset and progression of AGA, aiming to inform future clinical approaches through an integrative perspective.

METHODS: We performed a comprehensive literature search (2018-2025) in PubMed, Web of Science, and CNKI. Studies were selected based on predefined criteria focusing on gut microbiota, exosomal miRNAs, and their roles in AGA pathogenesis.

RESULTS: Gut microbiota contribute to hair follicle health by modulating host immune responses, metabolic pathways, and the skin microbiome, thereby enhancing follicular stem cell activity. Exosomes, as key mediators of intercellular communication, transport miRNAs that play essential roles in regulating the hair growth cycle. These miRNAs can counteract follicular miniaturization by targeting specific suppressor molecules.

DISCUSSION: The gut microbiota may influence the composition and functional properties of exosomes, thereby exerting indirect regulatory effects on hair follicle dynamics. These findings provide new insights into potential therapeutic strategies for AGA.

CONCLUSION: Gut microbiota and exosomal miRNAs may synergistically influence the progression of AGA through interconnected metabolic, immune, and microbial skin axes. Targeted modulation of the "microbiota-miRNA axis" could represent a novel, multidimensional approach for AGA treatment. Nevertheless, the precise molecular crosstalk and signaling cascades underlying these phenomena remain largely unresolved, warranting more targeted experimental investigations.},
}

@article {pmid41930951,
year = {2026},
author = {Everett, BA and Prindle, A},
title = {AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.},
journal = {mBio},
volume = {},
number = {},
pages = {e0023126},
doi = {10.1128/mbio.00231-26},
pmid = {41930951},
issn = {2150-7511},
abstract = {UNLABELLED: Aromatic amino acids-tryptophan, tyrosine, phenylalanine, and histidine-are essential for bacterial growth and are among the most energetically expensive metabolites to synthesize. Despite this cost, it has been recently shown that bacteria possess exporters for these amino acids. Here, we identify aexB (formerly yvjA) as a gene encoding a novel aromatic amino acid exporter in Bacillus subtilis. Using a transposon-based screen, we found that aexB overexpression confers resistance to the toxic tryptophan analog 5-fluorotryptophan. Additional analog screens revealed that AexB also promotes tolerance to toxic derivatives of tyrosine, phenylalanine, and histidine but not non-aromatic amino acids. LC-MS analysis showed that AexB specifically exports aromatic amino acids, and co-culture assays confirmed that overexpression of aexB can support the growth of aromatic amino acid auxotrophs. Furthermore, overexpression of aexB impaired growth when intracellular tryptophan was limiting. On the other hand, deletion of aexB exacerbated growth defects under excess tryptophan conditions, likely due to feedback inhibition of aromatic amino acid synthesis pathways. Our findings reveal that AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.

IMPORTANCE: Identification and characterization of amino acid exporters is a broadly relevant topic. Amino acid synthesis is energetically costly, and thus functional relevance for their export is unintuitive. Identification of the molecular components that allow export may offer new engineering opportunities to improve biomanufacturing and metabolic engineering. Characterization of these exporters may also provide a more complete understanding of the human microbiome where amino acids, especially tryptophan, have been established as nodes of crosstalk between host and microbiota.},
}

@article {pmid41930957,
year = {2026},
author = {Benucci, GMN and Garcia-Barreda, S and Sanchez, S and Marco, P and De Miguel, AM and Le Tacon, F and Marozzi, G and Baciarelli Failini, L and Eslick, H and Elliott, TF and Deveau, A and Murat, C and Donnini, D and Bonito, G},
title = {Mycorrhizal competition release and microbial dynamics in native and non-native Tuber melanosporum habitats.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0022526},
doi = {10.1128/aem.00225-26},
pmid = {41930957},
issn = {1098-5336},
abstract = {Truffles in the genus Tuber (Pezizales) are among the few ectomycorrhizal taxa successfully cultivated worldwide. Australia has recently become one of the top producers of Tuber melanosporum, a high-valued black truffle native to Europe. Truffle co-introductions in the Southern Hemisphere with their Northern Hemisphere plant symbionts are hypothesized to benefit from reduced ectomycorrhizal competition and natural enemies. In this study, we tested whether T. melanosporum in Australia experiences competition release by sampling soils and truffles across France, Spain, Italy, and Australia. Fungal and prokaryotic communities in truffle plantations were assessed in native (European) and non-native (Australian) habitats through ITS and 16S rDNA amplicon sequencing from soil and truffles. Community composition was primarily structured by site of origin and secondarily by presence of brûlé, vegetation-free area induced by truffle production of plant-growth inhibiting compounds, with significant interactions indicating site-dependent brûlé effects. European soils showed higher fungal richness outside the brûlé, with higher evenness overall and for ectomycorrhizal fungi only outside brûlé. T. melanosporum showed higher abundance in Australia, with significant differences restricted to outside the brûlé. Overall, ectomycorrhizal fungi in European soils had more than four times the taxa and higher diversity compared to Australian soils. Among the main competitors, Tomentella, Inocybe, and Trichophaea co-dominated in Europe, versus Scleroderma, Hebeloma, and Tarzetta in Australia. Despite differences in soil microbiomes, bacterial communities within T. melanosporum truffle ascocarps were strikingly similar across sites and continents and were dominated by Bradyrhizobium. Despite high site-level variation, our results support the competition release hypothesis, with reduced enemies benefiting T. melanosporum colonization outside the brûlé in Australia.IMPORTANCEThis study provides the first cross-hemisphere analysis of the truffle microbiome, comparing native and non-native soils and truffles from Europe and Australia. We demonstrate that the remarkable success of Tuber melanosporum cultivation in Australia is compatible with ecological release from competitors, which favors its development outside the brûlé. At the same time, we reveal striking cross-hemispheric similarities in truffle-associated bacterial communities, consistently dominated by Bradyrhizobium. These findings highlight both the novelty and transcontinental relevance of our work, offering new perspectives on fungal ecology and truffle cultivation.},
}

@article {pmid41927455,
year = {2026},
author = {Seo, JI and Koh, A and Lim, S and Yoo, HH},
title = {The 3M roles of the gut microbiome in pharmacotherapy for diabetes: mediator, modifier, and marker.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.12.006},
pmid = {41927455},
issn = {1879-3061},
abstract = {The rising global prevalence of type 2 diabetes mellitus (T2DM) presents major challenges to healthcare systems; thus, more effective treatment strategies are urgently needed. In this context, the growing recognition of the gut microbiome's role in T2DM pharmacotherapy has shifted attention toward integrating microbiome-derived mechanisms to optimize drug response. This review proposes a structured '3M' framework that classifies the gut microbiome's roles in T2DM pharmacotherapy into three translational categories: mediator of drug action, modifier of therapeutic response, and marker for predicting efficacy or intolerance, based on recent clinical and mechanistic insights. Together, these insights support a translational framework that may guide the integration of microbiome-informed strategies into future T2DM pharmacotherapy.},
}

@article {pmid41927536,
year = {2026},
author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J},
title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.},
journal = {Nutrition & diabetes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41387-026-00418-w},
pmid = {41927536},
issn = {2044-4052},
abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.

METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.

RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs > 0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.

CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.},
}

@article {pmid41927585,
year = {2026},
author = {Song, J and Tang, S and Guo, Y and Hong, C and Song, T},
title = {The gut-heart dialogue: an epigenetic perspective on myocardial infarction.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00974-0},
pmid = {41927585},
issn = {2055-5008},
support = {No. 20250602055RC//Jilin Province Science and Technology Department/ ; },
abstract = {Myocardial infarction (MI) remains a leading cause of global mortality, with adverse cardiac remodeling and heart failure presenting persistent metabolic and clinical challenges. While traditional pharmacotherapies have improved outcomes, there is an urgent need to elucidate how lifestyle and nutritional factors influence disease progression. Emerging evidence underscores the critical interplay between natural bioactive compounds (e.g., dietary fibers, polyphenols), the gut microbiota, and host metabolic regulation. This review systematically clarifies the "gut microbiota-epigenetic axis" as a pivotal mechanism linking nature-derived bioactives to cardiac repair. We delineate how the gut microbiota transforms specific bioactives into functional metabolites, such as short-chain fatty acids (SCFAs) from fibers and urolithin A from ellagitannins, which act as potent epigenetic modulators. These microbial metabolites remodel the epigenetic landscape of the host heart via histone modification and DNA methylation, thereby regulating gene networks governing inflammation, energy metabolism, and fibrosis. Synthesizing evidence from in vivo animal studies and clinical observations, we explore therapeutic strategies centered on natural bioactives, including high-fiber dietary interventions and polyphenol supplementation, alongside probiotics and postbiotics. By integrating the metabolic potential of the gut microbiome with epigenetic regulation, this review offers novel insights into how natural bioactive compounds can be leveraged for precision prevention and therapeutic strategies in myocardial infarction.},
}

@article {pmid41927589,
year = {2026},
author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, Č and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H},
title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71145-0},
pmid = {41927589},
issn = {2041-1723},
abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.},
}

@article {pmid41927609,
year = {2026},
author = {Duffy, EP and Sterrett, JD and Hale, LH and Ward, JO and Saba, LM and Frank, DN and Bachtell, RK and Ehringer, MA},
title = {Oxycodone self-administration and genetic background exert community-specific effects in the gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41666-1},
pmid = {41927609},
issn = {2045-2322},
}

@article {pmid41927721,
year = {2026},
author = {Nakamaru, K and Ito, T and Shimogama, T and Shijimaya, T and Tahara, T and Yamazaki, J and Orino, A and Masuda, M and Nakayama, S and Ikeura, T and Naganuma, M},
title = {Distinct difference of pancreatic tissue-specific microbiome in autoimmune pancreatitis and pancreatic ductal adenocarcinoma.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44821-w},
pmid = {41927721},
issn = {2045-2322},
support = {22K16032//JSPS KAKENHI Grant-in-Aid for Young Scientists/ ; },
abstract = {Autoimmune pancreatitis (AIP) is a form of chronic pancreatitis that may be difficult to distinguish from pancreatic ductal adenocarcinoma (PDAC). Emerging evidence suggests the substantial involvement of gut microbiome dysbiosis in various disorders, including pancreatic diseases. This study investigates the differences in pancreatic tissue-specific microbiomes between AIP and PDAC. Pancreatic tissues were obtained from patients with type 1 AIP (n = 17) or PDAC (n = 24) via ultrasound-guided tissue acquisition and subjected to 16S rRNA sequencing. The sequences were used to determine the bacterial alpha diversity and characterize the microbiome structures related to different sample groups. The pancreatic microbiome in PDAC exhibited increased bacterial alpha diversity compared to that in AIP. The abundances of 16 bacteria were significantly different between the AIP and PDAC groups, and most of them (15/16) were increased in PDAC relative to that in AIP. The bacterial index calculated using these bacteria had a favorable discriminative ability for these different groups, with an area under the curve value of 0.91. Functional analysis demonstrated that the pentose phosphate pathway, gondoate biosynthesis, and several pathways related to adenosine biosynthesis were positively associated with the bacterial index. The findings from this preliminary study indicate that pancreatic microbiome, as a new diagnostic alternative, may potentially help with the differential diagnosis of AIP and PDAC.},
}

@article {pmid41927746,
year = {2026},
author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA},
title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46933-9},
pmid = {41927746},
issn = {2045-2322},
support = {SRUG2204254606//National Research Foundation/ ; },
abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.},
}

@article {pmid41927935,
year = {2026},
author = {Gao, W and Wang, X and Shi, Y and Wu, G and Zhou, M and Lin, X},
title = {Retraction Note: Predictable regulation of gut microbiome in immunotherapeutic efficacy of gastric cancer.},
journal = {Genes and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41435-026-00397-z},
pmid = {41927935},
issn = {1476-5470},
}

@article {pmid41928235,
year = {2026},
author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE},
title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.},
journal = {BMC medical genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12920-026-02359-w},
pmid = {41928235},
issn = {1755-8794},
}

@article {pmid41928236,
year = {2026},
author = {Gschwendtner, S and Kovacevic, D and Gaede, KI and Herzmann, C and Overmann, J and Schloter, M and Krauss-Etschmann, S},
title = {Longitudinal dynamics and site-specific recovery of the human respiratory microbiome following smoking cessation.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03644-z},
pmid = {41928236},
issn = {1465-993X},
}

@article {pmid41928315,
year = {2026},
author = {Defazio, G and Lorusso, E and De Robertis, M and Mello, T and Galli, A and Pesole, G and Fosso, B},
title = {Machine learning-based assessment of the healthy human gut mycobiota landscape using ITS1 DNA metabarcoding data.},
journal = {BioData mining},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13040-026-00532-6},
pmid = {41928315},
issn = {1756-0381},
support = {H93C22000560003//Regione Puglia/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Università e della Ricerca/ ; },
abstract = {The human gut microbiome plays a critical role in maintaining host health and homeostasis, and current literature suggests a bidirectional relationship between microbiome ecology and host well-being. DNA metabarcoding has emerged as a powerful tool for investigating microbiome imbalances (i.e., dysbiosis). While the prokaryotic microbiome has been extensively studied, the fungal counterpart - or mycobiome - remains largely unexplored, despite its recognized role from the perinatal stage onward. Here, we present a comprehensive survey based on DNA metabarcoding analysis of approximately 1,500 publicly available ITS1 samples. This survey integrates conventional statistical approaches with Machine Learning (ML) methods coupled with explainable Artificial Intelligence (XAI). ML models successfully predicted host health status with accuracies exceeding 80%, and fungal genera such as Eurotium, Aureobasidium, Candida, and Cutaneotrichosporon emerged as key classification features. This study introduces a cutting-edge multiview analytical framework applied to publicly available mycobiome data, highlighting the potential of fungal community profiling as a non-invasive tool to support health diagnostics.},
}

@article {pmid41928361,
year = {2026},
author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S},
title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02392-y},
pmid = {41928361},
issn = {2049-2618},
support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; },
abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.

RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.

CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.},
}

@article {pmid41928384,
year = {2026},
author = {Valdez-Palomares, F and Noriega, LG and Reyes-Romo, D and Canizales-Quinteros, S and Nambo-Venegas, R and Salinas-Lara, C and Tovar-Palacio, A and Menjivar, M and Peña-Espinoza, B and Ortiz, G and Palacios-González, B},
title = {Human fecal transplantation from stunted children promotes metabolic dysfunction in mice fed with a high-fat and high-fructose corn syrup diet.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2651984},
doi = {10.1080/19490976.2026.2651984},
pmid = {41928384},
issn = {1949-0984},
mesh = {Animals ; Male ; *Fecal Microbiota Transplantation/adverse effects ; Mice ; Gastrointestinal Microbiome ; Humans ; Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Growth Disorders/microbiology/therapy/metabolism ; Child ; *High Fructose Corn Syrup/adverse effects/administration & dosage ; Bacteria/classification/isolation & purification/genetics ; Feces/microbiology ; Obesity/etiology/metabolism ; *Metabolic Diseases/etiology ; },
abstract = {Stunting, or impaired child growth due to poor nutrition and infections, is characterized by a low height-for-age and affects 48%-56% of school-aged children worldwide. It is associated with later weight gain and chronic diseases. The gut microbiome in undernourished children may increase obesity risk if they are exposed to high-calorie environments. To investigate this, we assessed whether the intestinal microbiome of stunted children elevates obesity risk upon exposure to an obesogenic environment. Fecal microbiota transplantation (FMT) was performed using pooled stools from healthy (n = 6) or stunted (n = 6) school-aged children from a low-income cohort in Mexico. Eight-week-old male C57BL/6 mice underwent bowel cleansing with polyethylene glycol (PEG), followed by weekly intragastric FMT for 4 weeks. The mice were subsequently fed either a control diet (CT) or a high-fat, high-fructose corn syrup diet (HFFr, including 15% HFCS-55) for 15 weeks. Metabolic outcomes were assessed through body composition, indirect calorimetry, oral glucose tolerance test, insulin tolerance test, and histological analysis of visceral adipose tissue. The microbiota composition was evaluated by 16S rRNA V3-V4 hypervariable region sequencing, and the predicted functional capacity was analyzed using PICRUSt2. FMT from stunted children increased susceptibility to diet-induced obesity, visceral adipose tissue hypertrophy, and insulin resistance. In contrast, FMT from healthy children promoted energy expenditure and visceral adipose tissue hyperplasia, conferring a protective effect against diet-induced obesity and insulin resistance in the mice. Healthy-FMT led to sustained enrichment of Akkermansia and Parabacteroides, whereas stunting-FMT increased Proteobacteria, Veillonella, Desulfovibrionaceae, and Bifidobacterium. Microbial‒phenotypic correlations showed that Akkermansia and Parabacteroides were negatively correlated with fasting glucose, body weight, and fat mass, and positively correlated with postprandial RER, VO2, and lean mass. In conclusion, stunting-FMT recipient mice showed a higher risk of obesity and metabolic issues in an obesogenic environment. Healthy-FMT confers metabolic resilience, characterized by increased abundance of taxa such as Akkermansia and Parabacteroides, which are linked to enhanced energy expenditure, improved glucose metabolism, and favorable adipose tissue structure.},
}

Animals
Male
*Fecal Microbiota Transplantation/adverse effects
Mice
Gastrointestinal Microbiome
Humans
Mice, Inbred C57BL
*Diet, High-Fat/adverse effects
*Growth Disorders/microbiology/therapy/metabolism
Child
*High Fructose Corn Syrup/adverse effects/administration & dosage
Bacteria/classification/isolation & purification/genetics
Feces/microbiology
Obesity/etiology/metabolism
*Metabolic Diseases/etiology

@article {pmid41928387,
year = {2026},
author = {Houshyar, Y and Zhang, F and Tavakoli, P and Grimm, MC and Hold, GL},
title = {Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2653288},
doi = {10.1080/19490976.2026.2653288},
pmid = {41928387},
issn = {1949-0984},
mesh = {Humans ; *Virome ; *Mycobiome ; *Inflammatory Bowel Diseases/microbiology/therapy/virology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology/virology ; *Fungi/classification/genetics/isolation & purification ; Animals ; Fecal Microbiota Transplantation ; *Viruses/classification/genetics/isolation & purification ; Bacteria/genetics ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing-remitting disorder of the gastrointestinal tract characterized by immune dysregulation, epithelial barrier dysfunction, and microbial imbalance. While bacterial dysbiosis, including depletion of short-chain fatty acid (SCFA) producers and enrichment of pathobionts, is well characterized, the gut virome and mycobiome remain comparatively neglected. Both exhibit high variability and are constrained by sequencing bias, contamination, and incomplete reference databases, leaving much of the viral and fungal diversity unresolved. Emerging evidence links fungal and viral dysbiosis to IBD pathogenesis, including Candida overgrowth, loss of Saccharomyces, expansion of Caudoviricetes phages, and detection of eukaryotic viruses such as Cytomegalovirus and Epstein-Barr virus in inflamed mucosa. These alterations disrupt barrier integrity, modulate immune signaling, and interact with bacteria and archaea in cross-kingdom networks that amplify inflammation. Translationally, the virome and mycobiome are now recognized as therapeutic targets, inspiring interventions from pre/probiotics and synbiotics to precision phage therapy and microbiota-based transplantation, including fecal virome transplantation (FVT) and fecal microbiota transplantation (FMT). This review recognizes the challenges and opportunities of studying these neglected kingdoms, reframes IBD dysbiosis and highlights new directions for biomarker discovery and multikingdom microbiota-directed therapies.},
}

Humans
*Virome
*Mycobiome
*Inflammatory Bowel Diseases/microbiology/therapy/virology
*Gastrointestinal Microbiome
Dysbiosis/microbiology/virology
*Fungi/classification/genetics/isolation & purification
Animals
Fecal Microbiota Transplantation
*Viruses/classification/genetics/isolation & purification
Bacteria/genetics

@article {pmid41928627,
year = {2026},
author = {Bong, SHS and Teh, KKJ and Wong, VW},
title = {Therapeutic Landscape Evolution: From Lifestyle Interventions to Precision Pharmacotherapy.},
journal = {Clinical and molecular hepatology},
volume = {},
number = {},
pages = {},
doi = {10.3350/cmh.2026.0125},
pmid = {41928627},
issn = {2287-285X},
abstract = {Steatotic liver disease (SLD) is a growing global epidemic, with metabolic dysfunction-associated steatotic liver disease (MASLD) now the most common chronic liver disease worldwide and closely linked to adverse cardiovascular outcomes. Lifestyle modification remains the cornerstone of management, with the Mediterranean diet as the preferred dietary intervention and emerging evidence supporting additional dietary and exercise strategies. Pharmacotherapy has advanced rapidly in recent years, with two U.S. Food and Drug Administration-approved options, resmetirom and semaglutide, for noncirrhotic metabolic dysfunction-associated steatohepatitis (MASH) with moderate-to-advanced fibrosis, alongside multiple agents in development targeting different disease mechanisms. In metabolic dysfunction- and alcohol-associated liver disease (MetALD), evidence remains limited, but management essentially focuses on alcohol cessation and optimization of cardiometabolic risk factors, with resmetirom, incretin-based therapies, and fibroblast growth factor (FGF)-21 analogues representing promising therapeutic agents that have yet to be fully evaluated in clinical trials. The field is increasingly moving toward a precision medicine paradigm integrating pharmacologic and lifestyle interventions, tailored to disease phenotype, genetic risk, and gut microbiome. Key challenges include heterogeneity in treatment response, assessment of alcohol intake, and real-world implementation barriers. This review summarizes current and emerging therapies and highlights the role of precision medicine in advancing individualized care across the SLD spectrum.},
}

@article {pmid41928791,
year = {2026},
author = {Bajaj, J and Sommer, A and Auch, B and Khoruts, A},
title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9142184/v1},
pmid = {41928791},
issn = {2693-5015},
abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.},
}

@article {pmid41928923,
year = {2026},
author = {Lesperance, DNA and Padhi, S and Macro, J and Olson, S and Stanwood, E and Kannan, K and Graveley, B and Rogina, B and Broderick, NA},
title = {Microbiome contribution to Indy longevity in Drosophila.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.714291},
pmid = {41928923},
issn = {2692-8205},
abstract = {UNLABELLED: Reduction in the Indy (I'm not dead yet) gene, a plasma membrane citrate transporter, in Drosophila and its homolog in worms extends lifespan by promoting metabolic homeostasis. Indy reduction delays the onset of aging-associated pathology in the fly midgut, including preservation of intestinal barrier integrity and intestinal stem cell homeostasis. Gut microbiota has broad impacts on host metabolism, health, and aging. Age-related dysbiosis impairs intestinal barrier function and drives mortality. However, the underlying mechanisms that link increased microbial load to frailty and negative effects on health remain mostly unclear. Here we show that Indy heterozygote flies have significantly lower bacterial load and increased diversity during aging compared to controls. However, the presence of the microbiome was not required for Indy lifespan extension, though removal of microbes did enhance the effects of Indy reduction on longevity, suggesting potential interactions between the microbiome and Indy . Indy down-regulation was linked to reduced expression of the JAK/STAT signaling ligands Upd3 and Upd2 in the midgut of young flies, which likely contributes to preserved intestinal stem cell homeostasis. Altogether, our results suggest that Indy reduction impacts microbiome load and composition, which preserves gut homeostasis and extends lifespan through impacts on JAK/STAT signaling pathway.

SIGNIFICANCE STATEMENT: Indy is a fly homologue of mammalian SLC13A5 (mSLC13A5) plasma membrane citrate transporter, a central metabolic regulator involved in health, longevity, and disease. Reduction of fly Indy gene activity preserves metabolic and intestinal stem cell homeostasis and extends longevity. Gut microbiota impacts host metabolism, health, and aging. Here we show that Indy reduction prevents age-associated increases in bacterial load and expression of the JAK/STAT signaling ligands Upd3, and Upd2, while maintaining microbiome diversity. These changes likely slow activation of epithelial cell turnover in the gut and contribute to downstream lifespan effects. As the role of INDY and microbiome are conserved across organisms, our study provides a framework to study underlying mechanisms of the effects of reduced Indy and the microbiome on health and longevity.},
}

@article {pmid41928970,
year = {2026},
author = {Rock, RR and Alexander, M and Noecker, C and Trepka, KR and Upadhyay, V and Ortega, EF and Ramirez, L and Siewert, L and Olson, CA and Halsey, T and Pröbstel, AK and Baranzini, SE and Turnbaugh, PJ},
title = {Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.16.711194},
pmid = {41928970},
issn = {2692-8205},
abstract = {UNLABELLED: Women are at increased risk of autoimmune diseases, including multiple sclerosis (MS); however, the degree to which sex differences in the gut microbiota impact autoimmunity remains largely unexplored. Our 27-cohort meta-analysis revealed 60 sex-associated gut bacterial species. Leveraging an independent clinical cohort, we demonstrate that female-enriched species significantly associate with MS status and clinical disability (EDSS). Top female-enriched species Eggerthella lenta drove disease in the experimental autoimmune encephalomyelitis (EAE) MS model, consistent with brain and gut lamina propria T cell infiltration and MS-associated T helper (Th) signatures. E. lenta induced intestinal Th1 and Th17 in healthy mice, independent of bacterial viability. Mechanistically, we demonstrate that TLR2 directly drives E. lenta -induced IFN-γ production in Th cells and is necessary for exacerbation of EAE. Together, we identify a causal host-microbe axis contributing to sex differences in autoimmunity and provide a framework for evaluating sex as a biological variable in human microbiome research.

HIGHLIGHTS: 27-cohort meta-analysis identifies a robust sex-signature in human gut microbiota.Female-enriched species are associated with MS risk and severity. Female-enriched Eggerthella lenta exacerbates the EAE model. E. lenta impacts neuroinflammation via toll-like receptor 2.},
}

@article {pmid41929040,
year = {2026},
author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ},
title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.714183},
pmid = {41929040},
issn = {2692-8205},
abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.

IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.},
}

@article {pmid41929113,
year = {2026},
author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R},
title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714056},
pmid = {41929113},
issn = {2692-8205},
abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.},
}

@article {pmid41929228,
year = {2026},
author = {Lester, BA and Kelly, C and Henry, SN and Elias, IP and Cevenini, SE and Hendrickson, MR and Park, T and Ashley, TD and Beltz, JM and Milner, JP and Pickrell, AM and Morton, PD},
title = {Germ-free piglets display variable neuroinflammatory-like perturbations in prefrontal cortical microglia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.22.713463},
pmid = {41929228},
issn = {2692-8205},
abstract = {UNLABELLED: Communication between gut microbiota and immune cells within the brain is essential for neurotypical development. Specifically, microglia are known to play a key role in regulating and supporting neural progenitor stem cell production during brain development, and are sensitive to changes in the maternal gut microbial composition during perinatal development. Here, we employed a germ-free (GF) porcine paradigm to examine how the absence of the microbiome affects microglial dynamics during a key epoch of brain development. We utilized automated software to evaluate microglial density and morphology across three developmentally significant regions: the ventricular/subventricular zone (VZ/SVZ), the prefrontal subcortical white matter (PFCSWM), and layers II/III of the prefrontal cortex (PFCII-III). We found no significant differences in microglial morphology or density in the VZ/SVZ or PFCSWM. In contrast, the PFCII-III of P16 piglets exhibited an increase in microglia density paired with morphologies indicative of an activated/reactive functional state. Notably, these effects were identified with no overall changes in microglial density in any of the regions assessed. Transcriptomics on RNA isolated from the PFCII-III revealed a significant upregulation of genes related to neuroinflammation, in agreement with a region-specific microglial and immune response in the absence of microbial colonization during postnatal development. Together, these findings build on the limited knowledge available on how microbiota influence brain development in large animal model organisms with high similarities to human brain anatomy and developmental trajectories.

SIGNIFICANCE STATEMENT: The prefrontal cortex of porcine display unique, ramified microglia which are sensitive to germ-free conditions whereby they display alterations in morphology with a more transcriptionally reactive signature. These findings indicate that microglia are regionally sensitive to stimuli in the periphery, and studies in lissencephalic mammalian models may not be directly correlative to other higher-order species. The neuroanatomical heterogeneity of microglia across species is informative and understudied, but necessary, to draw conclusions on the array of perturbations spanning neurodevelopmental trajectories in health and disease.},
}

@article {pmid41929259,
year = {2026},
author = {Baird, AW},
title = {Coordinated regulation of colonic fluid and mucus secretion.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1757501},
pmid = {41929259},
issn = {1663-9812},
abstract = {The human colon, unlike the small intestine which is relatively sterile, contains a diverse microbiome which contributes to host metabolism. The luminal environment is constantly changing and responds to epithelial absorption and secretion which occurs as motility is regulated by longitudinal and circular smooth muscle. Mucous gels are crucial to lubrication and maintenance of an unstirred layer which separate the epithelium from the lumen. Gel-forming mucins are produced and released by goblet cells and become hydrated, although the source of water is not definitively understood. The purpose of this review is to summarize regulation of water movements across the colonic epithelium, goblet cell secretion of mucus and to consider how these distinct processes are functionally coupled.},
}

@article {pmid41929306,
year = {2026},
author = {Kramer, M and Belleau, P and Tortora, SC and Deschenes, A and Founta, K and Gurjao, C and Yueh, B and Goodwin, S and Gee, D and Subhash, S and Barbi, M and Chung, C and Ozler, K and Eskiocak, O and Izar, B and Geiger, H and Chu, TR and Goldstein, Z and Winterkorn, L and Araneo, A and Whelan, RL and Rivadeneira, D and Fox, S and Kandel, A and Ozay, F and Talabong, DJA and Lanipekun, O and Talus, H and Zeng, J and Rishi, A and Chambwe, N and Robine, N and Boyd, J and Krasnitz, A and Beyaz, S and McCombie, WR and Martello, LA},
title = {Integrative Genomic, Transcriptomic, and Microbiome Profiles of Colon Cancer by Ancestry Provide Insights into Molecular Distinctions.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.25.26349226},
pmid = {41929306},
abstract = {Colorectal cancer (CRC) incidence, tumor biology, and clinical outcomes differ by patient ancestry, yet African ancestry (AFR) populations remain underrepresented in genomic and microbiome studies. Here, we comprehensively characterized genomic, transcriptomic and microbiome features of AFR and European ancestry (EUR) colon cancer patients residing in New York City and Long Island. While confirming known drivers from other large CRC studies, our AFR to EUR comparison of somatic variation also revealed a possible enrichment of functional KRAS variants in AFR tumors. Colon cancer genomes in patients in this study also exhibit distinct patterns of DNA copy number variation, correlating with consensus molecular subtypes. Fusobacterium nucleatum-positive tumors were enriched for co-occurring oral taxa, suggesting an organized oral microbial structure within the tumor microenvironment. Our findings highlight ancestry-associated differences in somatic mutation, copy number variation, and tumor microbiome composition, underscoring the urgent need to expand AFR representation in genomic studies to uncover population-specific determinants of CRC risk and to develop treatment strategies that reflect the full diversity of patients affected by this disease.},
}

@article {pmid41929401,
year = {2026},
author = {Bokemeyer, B and Plachta-Danielzik, S and Helwig, U and Beuchert, P and Schreiber, S},
title = {Competence network inflammatory bowel diseases in Germany: 25 years of interdisciplinary and cross-sectoral research and knowledge transfer across all levels of IBD care.},
journal = {Therapeutic advances in gastroenterology},
volume = {19},
number = {},
pages = {17562848261431187},
pmid = {41929401},
issn = {1756-283X},
abstract = {The Competence Network Inflammatory Bowel Diseases (Kompetenznetz Darmerkrankungen) was established in Germany in 1999 through a 10-year funding programme by the German Ministry of Education and Research. It was created to address the growing gap between the rising prevalence and therapeutic complexity of inflammatory bowel disease (IBD) and the fragmented care structures and isolated academic initiatives of the time. The network's continuing mission is to improve care for patients with Crohn's disease and ulcerative colitis by more closely integrating clinical practice, translational science and patient involvement. This review summarises the history, governance, registries, biobanking, clinical trials, educational programmes and collaborations of the Competence Network IBD. Over the past 25 years, the Competence Network IBD has established prospective national registries (e.g. RUN-CD, RUN-UC, VEDO-IBD and FilgoColitis), developed pragmatic real-world cohorts (TARGET and GeCer) and contributed to the UMBRELLA-IBD data warehouse of the Competence Network IBD in Germany. The network played a central role in creating the German IBD DNA collection and supported the Kiel University biobank, both of which link biospecimens with longitudinal clinical data to support genetic and microbiome research. It also conducts and coordinates multicentre clinical trials and has supported the development of the German evidence- and consensus-based IBD guidelines. With more than 800 members from university centres, community practices, nursing and patient organisations, it now provides a robust platform for research and knowledge transfer across all levels of IBD care. The Competence Network IBD demonstrates how long-term interdisciplinary and cross-sectoral collaboration can improve the management of chronic inflammatory diseases. By integrating research infrastructures with education and patient involvement, the network serves as a scalable and sustainable model for national and international collaboration in IBD.},
}