@article {pmid41938779,
year = {2026},
author = {Luttenschlager, H and Noel, G and Alabi, T and Carpentier, J and Francis, F and Megido, RC},
title = {Microbial drivers of Black Soldier Fly biowaste valorization: from microbiome functions to scalable insect-microbe systems.},
journal = {AIMS microbiology},
volume = {12},
number = {1},
pages = {126-149},
pmid = {41938779},
issn = {2471-1888},
abstract = {Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect-microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.},
}

@article {pmid41938782,
year = {2026},
author = {Mataragka, A and Ringø, E and Papastathis, AK},
title = {Climate-driven restructuring of sediment microbiomes and ecosystem functions in aquaculture systems.},
journal = {AIMS microbiology},
volume = {12},
number = {1},
pages = {150-172},
pmid = {41938782},
issn = {2471-1888},
abstract = {Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.},
}

@article {pmid41938867,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R},
title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779554},
pmid = {41938867},
issn = {2235-2988},
mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.

METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.

RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.

DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.},
}

Female
Humans
Phylogeny
*Candidiasis, Vulvovaginal/virology/microbiology
Genome, Viral
Vagina/virology/microbiology
Metagenomics
Capsid Proteins/genetics
RNA, Viral/genetics
RNA-Dependent RNA Polymerase/genetics
Adult
*Double Stranded RNA Viruses/genetics/isolation & purification/classification

@article {pmid41939093,
year = {2026},
author = {},
title = {Gut microbiome metaproteomics for colorectal cancer risk stratification: moving from taxonomic signatures to functional protein biomarkers: Retraction.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {4},
pages = {2724},
pmid = {41939093},
issn = {2049-0801},
abstract = {[This retracts the article DOI: 10.1097/MS9.0000000000004567.].},
}

@article {pmid41939102,
year = {2026},
author = {Mohan, A and Sultany, A and Fatima, SB and Hasan, ZW and Butt, MD and Alkhazender, AHJ and Lal, PM and Aminpoor, H and Karimi, H and Kumar, V and Tejwaney, U and Kumar, S},
title = {Association between atrial fibrillation and gastrointestinal bleeding: pathophysiology, risk stratification, and management - a narrative review.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {4},
pages = {2566-2573},
pmid = {41939102},
issn = {2049-0801},
abstract = {Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, significantly increasing the risk of thromboembolic events, necessitating anticoagulation therapy. However, anticoagulation, particularly with novel oral anticoagulants, elevates the risk of gastrointestinal bleeding (GIB), creating a clinical dilemma in managing AF patients. This narrative review explores the pathophysiology linking AF and GIB, emphasizing the hypercoagulable state in AF and the mucosal damage caused by anticoagulants. Epidemiological data reveal that GIB incidence in AF patients ranges from 1.32% to 5.4% annually, with risk factors including older age, prior GIB, and concomitant antiplatelet use. Risk stratification tools such as CHA2DS2-VASc and HAS-BLED aid in balancing thromboembolic and bleeding risks, though their predictive performance remains modest. Comparative studies highlight that rivaroxaban carries a higher GIB risk, while apixaban offers a safer profile. Management strategies include proton pump inhibitors for prophylaxis, endoscopic interventions for acute bleeding, and individualized decisions on resuming anticoagulation post-GIB, typically within 7-30 days. Emerging research on the gut microbiome's role in AF pathogenesis suggests potential novel therapeutic avenues. A multidisciplinary approach involving cardiologists, gastroenterologists, and hematologists is essential to optimize outcomes. Future directions include developing safer anticoagulants, refining risk prediction models, and exploring microbiome-targeted therapies.},
}

@article {pmid41939187,
year = {2026},
author = {Zhang, H and Wu, ZH and Sun, XM and Sun, C and Chang, J and Yuan, L},
title = {Gender-specific and dose-dependent responses to L-se-methylselenocysteine are mediated by the gut microbiota-metabolite axis: implications for intestinal homeostasis and safe clinical application.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1803630},
pmid = {41939187},
issn = {2296-861X},
abstract = {INTRODUCTION: L-Se-methylselenocysteine is a prominent naturally occurring organic selenium compound with notable health benefits and validated efficacy in managing various diseases. However, its impacts on intestinal microecology and the role of the gut microbiota-metabolite axis in mediating host health outcomes remain unclear.

METHODS: Sprague-Dawley rats were subjected to a 90-day chronic toxicity study, combined with integrated intestinal microbiome and metabolome analysis, to explore L-Se-methylselenocysteine's effects and underlying mechanisms.

RESULTS: L-Se-methylselenocysteine at doses of 0.25-0.75 mg/kg bw/ day enhanced gut microbiota biodiversity, enriched probiotic abundance, ameliorated hematological and serum biochemical indices, and promoted synthesis of beneficial metabolites via modulating the gut microbiota-metabolite axis. Notably, high-dose L-Se-methylselenocysteine (2.25 mg/kg bw/day) induced irreversible hepatosplenic injury in female rats but not males, with gender-specific responses mediated by the axis.

DISCUSSION: L-Se-methylselenocysteine confers intestinal health benefits through the gut microbiota-metabolite axis, while defining a safe dosage range. This study provides a solid scientific basis for the rational application of L-Se-methylselenocysteine as a selenium supplement.},
}

@article {pmid41939240,
year = {2026},
author = {Barrera-Suarez, MA and Zhao, CY and Karnatovskaia, LV and Sung, J},
title = {Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2650247},
pmid = {41939240},
issn = {2993-3935},
abstract = {Diet-gut microbiome interactions drive substantial inter-individual variability in metabolic responses to food, a fact that challenges the efficacy of uniform dietary recommendations. To address this complexity, advances in multi-omics profiling, dietary assessment technologies, and host clinical phenotyping now generate high-resolution multimodal datasets. However, managing these vast amounts of data necessitates the integration of artificial intelligence (AI) and machine learning (ML) approaches. In this review, we first delineate the multimodal data landscape and its associated computational workflows. These range from the initial preprocessing of heterogeneous inputs (filtering, normalization, dimensionality reduction) to ML modeling strategies designed to address high dimensionality, sparsity, and compositionality through feature engineering and regularization. We then summarize core ML applications, including the classification of habitual dietary patterns from microbiome signatures, prediction of postprandial metabolic responses, responder stratification, and in silico simulation of dietary perturbations. Furthermore, recent randomized controlled trials demonstrate the tangible clinical potential of AI-guided personalization. Next, we highlight composite microbiome health metrics and diet-specific indices, such as GMWI2 and DI-GM. These tools are essential because they condense high-dimensional taxonomic profiles into interpretable wellness scores for monitoring diet-induced shifts. We subsequently examine genome-scale metabolic models and microbiome "digital twins" that mechanistically link dietary substrates to community metabolism and host-relevant metabolites. We also discuss emerging hybrid AI-mechanistic frameworks that enhance interpretability, biological plausibility, and scalability. Finally, we outline translational priorities-including the development of diverse longitudinal cohorts, standardized benchmarking, and clinically trustworthy AI-that are required to realize equitable, microbiome-informed precision nutrition.},
}

@article {pmid41939241,
year = {2026},
author = {Pereira, FC and El Aidy, S},
title = {Drug-microbiome interactions: What we know and why predictive translation remains elusive.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2649166},
pmid = {41939241},
issn = {2993-3935},
abstract = {Medication-induced alterations of the gut microbiome influence drug efficacy, toxicity, and long-term outcomes. Despite extensive evidence for drug-microbe interactions, predictive translation into clinical practice remains limited. Generalization from shifts in taxonomic profiles, mechanistic studies or isolated enzymatic assays is challenging because microbial activity is highly context-dependent. Drug-microbiome interactions are shaped by host factors including pH, transit time, nutrient and cofactor availability, and spatial organization along the gastrointestinal tract. Here, we argue that predictive translation requires measuring functional outputs, site-specific activity, ecological interactions, and host-contextual modulation, rather than static microbial properties.},
}

@article {pmid41939697,
year = {2026},
author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M},
title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786817},
pmid = {41939697},
issn = {1664-302X},
abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.},
}

@article {pmid41939699,
year = {2026},
author = {Zeng, H and Gao, Z and Wang, Z and Li, K and Xu, B and Yan, Z and Gu, Y and Du, W and Ding, H and Wang, J},
title = {Temporal succession and assembly of marine bacterial communities in Maxwell Bay, Antarctica during summer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1748960},
pmid = {41939699},
issn = {1664-302X},
abstract = {INTRODUCTION: In recent years, ecological feedbacks driven by climate change have become increasingly prominent. The polar amplification effect has made Antarctic ecosystems pivotal indicators for reflecting global climatic impacts. As core drivers of biogeochemical cycling, marine microbes play a central role. Therefore, deciphering their temporal dynamics and assembly mechanisms is crucial for projecting the trajectories of polar ecosystems. However, the intrinsic ecological processes regulating microbial summer succession, particularly the relative contribution of deterministic processes, remain insufficiently quantified.

METHODS: In the present study, Maxwell Bay, Antarctica-a coastal marine region heavily influenced by glacial melt-was selected as the model system. Surface seawater samples were collected sequentially during the 2022 austral summer, followed by 16S rRNA gene amplicon sequencing and phylogenetic null model analysis.

RESULTS: Our results revealed a distinct shift in the assembly mechanisms of bacterial communities. In January, community structure was shaped jointly by stochastic and deterministic processes, with stochastic processes contributing a greater proportion to assembly. This state transitioned to the predominance of deterministic homogeneous selection (84.68%) in February. Mantel tests, followed by linear regression analyses, confirmed that this phylogenetic transition was driven by shifting environmental factors. Specifically, water temperature served as the primary influencing factor in January, whereas silicate and nitrate concentrations emerged as the key factors in February. Subsequent partial least squares path modeling (PLS-PM) and redundancy analysis (RDA) further validated these findings, demonstrating that the identified environmental variables collectively explained more than 50% of the observed variation in community structure. Notably, nitrate drawdown was significantly correlated with the increased relative abundances of dominant bacterial genera in February.

DISCUSSION: By quantifying the relative roles of deterministic and stochastic processes in microbial community assembly, this study demonstrates that environmental selection is the dominant factor mediating microbial responses to polar warming. These findings provide a mechanistic foundation for the development of predictive models for future marine biogeochemical cycles in polar regions.},
}

@article {pmid41939702,
year = {2026},
author = {Shi, Y and Chu, H and He, R and Ma, W and Liang, Q and Li, Z and Gao, Y and Luo, C},
title = {Harnessing rhizosphere microbes: the synergistic roles of PGPR and AMF in sustainable tomato production under stress.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746930},
pmid = {41939702},
issn = {1664-302X},
abstract = {Tomato (Lycopersicon esculentum L.) is among the most economically important vegetable crops worldwide, yet its production is severely constrained by multiple biotic and abiotic stresses, including pathogens, pests, drought, salinity, and heavy metal toxicity. Amid intensifying climate change and increasing demands for sustainable agriculture, plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) have emerged as key beneficial rhizospheric microorganisms with significant potential for enhancing plant stress tolerance and promoting growth. PGPR directly promote the growth of tomato plants through biological nitrogen fixation, solubilization of phosphate and potassium, siderophore-mediated iron uptake, and the production of phytohormones. Indirectly, PGPR suppress pathogens, activate induced systemic resistance (ISR), reinforce cell walls, enhance the activities of antioxidant enzymes, and regulate the accumulation of osmolytes. AMF form symbiotic associations with the roots of tomato plants, enhancing nutrient and water absorption via extraradical mycelial networks, improving phosphorus and nitrogen uptake, modulating abscisic acid (ABA), jasmonic acid (JA), and strigolactone signaling pathways, activating mycorrhiza-induced resistance (MIR), and enhancing photosynthetic efficiency and water-use efficiency under stress. The co-inoculation of PGPR and AMF yields synergistic effects by facilitating mutual colonization, optimizing nutrient bioavailability, coordinately strengthening antioxidant and osmotic regulation systems, and reinforcing systemic defense responses, thereby conferring more robust and efficient stress tolerance than single inoculations. Despite significant advances, key challenges persist in elucidating tripartite molecular crosstalk, maintaining stability during field applications, and developing tailored microbial consortia. This review synthesizes the individual and synergistic mechanisms through which PGPR and AMF enhance the resilience of tomato plants to biotic and abiotic stresses, offering valuable insights for engineering microbial communities to enhance stress resistance in crops.},
}

@article {pmid41939703,
year = {2026},
author = {Liao, HY and Ren, YS and Li, J and Huang, HT and Li, ZL and Zeng, Y and Zhu, DH},
title = {Geographical variation of Ceracris kiangsu gut microbiota and its association with environmental factors.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752887},
pmid = {41939703},
issn = {1664-302X},
abstract = {The yellow-spined bamboo locust (Ceracris kiangsu) is one of the most destructive forest pests in China, causing severe damage to bamboo forests across multiple provinces. Understanding the relationship between its gut microbiota and environmental factors is crucial for revealing its ecological adaptability and migration potential. This study used 16S rRNA high-throughput sequencing to analyze gut bacterial communities of C. kiangsu from six geographically distinct populations in China. The results showed that Firmicutes and Proteobacteria were the dominant phyla, while bacterial diversity and composition varied significantly among populations. Precipitation and sunshine duration were identified as the main environmental factors most strongly associated with microbial community structure. These findings suggest that environmental conditions are strongly associated with variation in the gut microbiota of C. kiangsu, potentially affecting its adaptability and outbreak dynamics. This research provides new insights into the ecological mechanisms underlying pest distribution and offers a microbiome-based foundation for developing sustainable control strategies to reduce the agricultural and forestry losses caused by this species.},
}

@article {pmid41939705,
year = {2026},
author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP},
title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768977},
pmid = {41939705},
issn = {1664-302X},
abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.},
}

@article {pmid41939710,
year = {2026},
author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J},
title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741638},
pmid = {41939710},
issn = {1664-302X},
abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.},
}

@article {pmid41939716,
year = {2026},
author = {Zhang, B and Zhao, J and Zhuang, L and Liu, Y and Meng, P and Wang, S and Liu, Y and Zhang, T and Xu, J and Qin, W},
title = {Peat promotes production of the edible mushroom Oudemansiella raphanipes by regulating casing soil microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1774800},
pmid = {41939716},
issn = {1664-302X},
abstract = {INTRODUCTION: As an exotic edible mushroom, Oudemansiella raphanipes has attracted extensive attention for efficient cultivation. Peat-amended casing soil is known to increase its productivity, while the underlying mechanisms remain unclear.

METHODS: In this study, high-throughput 16S rRNA gene sequencing was performed to characterize bacterial communities in casing soils with five peat proportions.

RESULTS: Results showed that peat proportion had a significant effect on O. raphanipes yield, with the 70% peat treatment achieving the maximum yield of 279.21 g per cultivation bag, 38.12% higher than the control without peat. Casing soil with 70% peat harbored higher bacterial richness, enriched beneficial taxa such as Paenisporosarcina, enhanced chemoheterotrophy and nitrogen fixation functions, and more deterministic community assembly compared with other treatments. The bacterial ecological network in casing soil with 70% peat also showed the highest average connectivity, shortest average path length, and strongest robustness. Further, soil physical properties had a greater influence on bacterial community structure in the casing soil than chemical properties. Soil density, available phosphorus and potassium significantly influenced the bacterial community in the 70% peat group.

CONCLUSION: Together, this study suggested that peat promoted O. raphanipes production by regulating the casing soil microbiome, providing a theoretical basis for optimizing practical cultivation strategies.},
}

@article {pmid41939722,
year = {2026},
author = {Ryan, SM and Brayden, DJ},
title = {Food-derived molecules as regulators of intestinal tight junctions and barrier function: mechanisms and implications.},
journal = {Frontiers in drug delivery},
volume = {6},
number = {},
pages = {1692219},
pmid = {41939722},
issn = {2674-0850},
abstract = {Controlling TJ permeability in the small intestine facilitates nutrient absorption, maintains luminal osmotic balance, and prevents the paracellular entry of pathogens. The pharmaceutical industry has leveraged the capacity of medium-chain fatty acids and their derivatives to transiently and reversibly open epithelial TJs in formulations to enable oral administration of therapeutic peptides, some of which have received regulatory approval or are progressing in advanced clinical trials. Other food-derived agent including chitosan and its analogues enhance mucoadhesion and also modulate TJ permeability in the intestine. Recently, pelargonidin, a polyphenolic pigment isolated from strawberries, has emerged as a promising food-derived TJ opener, facilitating oral insulin delivery in rat models. Conversely, other food or food-derived molecules reinforce TJ integrity while exerting antioxidant effects, thereby offering potential therapeutic benefits for conditions characterized by increased intestinal permeability including inflammatory bowel disease, sepsis, and coeliac disease. Examples of such agents include the short-chain fatty acid (SCFA), sodium butyrate, various essential and non-essential amino acids, fermented food, the trace element, zinc, and anthocyanins. The exploration of food-derived substances as modulators of intestinal epithelial TJ dynamics is still in its early stages but holds significant promise for future health applications.},
}

@article {pmid41939734,
year = {2026},
author = {Puppo, F and Carbone, RG},
title = {Microbiome in connective tissue diseases associated interstitial lung disease.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1738689},
pmid = {41939734},
issn = {2296-858X},
abstract = {Microbiome consists of a large community of bacteria, yeast, protozoa, and viruses that co-exist in symbiosis with human hosts. Changes in microbiome, named "dysbiosis," alter the interplay between microbiome and immune system triggering inflammation and contributing to the pathogenesis of connective tissue diseases (CTD). Interstitial lung diseases (ILD) are a group of pulmonary disorders characterized by lung tissue fibrosis and impaired lung function. The existence of a gut-lung axis is well demonstrated; however, it is not established whether gastrointestinal dysbiosis contributes to ILD development. ILD represent a major cause of morbidity and mortality in CTD patients. Lung microbiome changes and high microbial load are associated with worse prognosis and acute exacerbations in patients with CTD-ILD and especially in those affected by rheumatoid arthritis, systemic sclerosis and dermatomyositis. Probiotics are active microorganisms that normalize the intestinal flora and their use has been proposed as potential supportive treatment of CTD-ILD. Present knowledge of the relationships between dysbiosis and CTD-ILD development is largely incomplete and further studies are needed to validate this issue. Aim of this concise review is to report current knowledge on microbiome in CTD-ILD focusing on clinical lung aspects and therapeutic options.},
}

@article {pmid41939772,
year = {2026},
author = {Zheng, B and Shen, X and Han, N and Guo, X and Wan, S},
title = {The microbiota-gut-brain-epigenome axis as a novel therapeutic target for decoding postpartum depression.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1778348},
pmid = {41939772},
issn = {2296-858X},
abstract = {BACKGROUND: Postpartum depression (PPD) is a psychological disorder affecting approximately 10-15% of women following childbirth, with significant implications for maternal and infant well-being. While hormonal fluctuations and psychosocial factors have long been considered primary contributors, recent reports demonstrated that gut microbiome is implicated in modulating maternal mood and behavior. The bidirectional communication between the gut and brain, mediated by microbiota-gut-brain axis, along with genetic and epigenetic modifications, has gained increasing attention as a potential mechanistic pathway in PPD. However, the precise genetic and epigenetic underpinnings of this interaction remain to be elucidated.

OBJECTIVE: This review aims to explore the genetic and epigenetic landscape of postpartum depression, with a significant focus pertinent to gut microbiota role in shaping neurobiological outcomes. By integrating recent findings from genomic, epigenomic, and microbiome research, we seek to elucidate novel mechanistic insights and potential therapeutic avenues.

METHODS: A comprehensive literature search was conducted using public databases, including PubMed, Google Scholar, and NCBI, to identify relevant studies on PPD, gut microbiota, genetics, and epigenetics.

RESULTS: Gut microbiota and neuroimmune modulation: peripartum changes in gut microbiota composition have been linked to immune dysregulation, inflammation, and neurotransmitter imbalances, all of which are implicated in PPD pathophysiology. Genetics and epigenetics of PPD: Genome-wide association studies (GWAS) revealed a profound genetic risk loci associated with PPD. Additionally, DNA methylation, histone modifications, and non-coding RNAs have profound functional implications in gene expression regulation, influencing PPD susceptibility. Epigenetic influence of the gut microbiome: The gut microbiome affects epigenetic modifications, such as DNA methylation and histone acetylation, which may lead to fetal programming and maternal mental health disorders. Choline metabolism and maternal mental health: Choline, an essential nutrient involved in epigenetic regulation, influences gut microbiota composition and brain function. Dysregulation in choline metabolism is associated with higher risk of PPD. Clinical and therapeutic implications: Understanding the genetic and epigenetic mechanisms underlying PPD offers new avenues for personalized therapeutic interventions, including probiotic and prebiotic strategies, microbiome-based treatments, and targeted epigenetic therapies.

CONCLUSION: The interplay between genetics, epigenetics, and gut microbiota represents a novel and promising area of research in understanding postpartum depression. The microbiota-gut-brain axis serves as a crucial mediator in this relationship, influencing neuroimmune regulation, neurotransmitter synthesis, and epigenetic modifications. Future studies should focus on integrating multi-omics approaches to unravel the molecular complexity of PPD and develop targeted interventions aimed at restoring microbiome and epigenetic homeostasis.},
}

@article {pmid41939831,
year = {2026},
author = {Omolo, CA and Yata, VK and Janapati, YK and Dachani, SR},
title = {Editorial: Innovative therapeutic strategies for managing diabetic foot ulcers and mitigating associated complications.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1788742},
pmid = {41939831},
issn = {1663-9812},
}

@article {pmid41939871,
year = {2026},
author = {Tonk-Rügen, M and Schilling, T and Cabezas-Cruz, A and Hoelzle, LE},
title = {Microbiota-immune crosstalk in livestock: implications for tick-borne disease control.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1731518},
pmid = {41939871},
issn = {1664-3224},
mesh = {Animals ; *Livestock/immunology/microbiology ; *Tick-Borne Diseases/immunology/prevention & control/veterinary/microbiology ; *Microbiota/immunology ; Ticks/microbiology/immunology ; },
abstract = {Globally, livestock health, which impacts animal welfare and agricultural productivity, is continuously threatened by tick-borne diseases (TBDs). The growing issues of acaricide overuse in livestock, emerging resistance, and vector adaptation to climate change require novel and sustainable intervention strategies. Recent advances in microbiome research reveal how host and vector microbiota influence immune responses, particularly through natural antibodies (nAbs) that modulate vector competence and pathogen transmission. In livestock, nAbs targeting microbial glycans are heritable, measurable, and linked to health outcomes. In cattle, nAb titers to bacterial antigens are associated with mastitis risk and longevity, while in pigs, early-life nAb levels are proposed as resilience markers. Studies in poultry further demonstrate the importance of high nAb phenotypes for health and production. These findings highlight nAbs as both immunological markers and potential targets for genetic selection to improve disease resistance. Emerging interventions, such as anti-microbiota vaccines and immunobiotics, aim to modulate nAb repertoires, disrupt pathogen colonization, and enhance disease resilience. Additionally, microbial glycans serve as key targets for inducing cross-reactive immunity against TBDs. Manipulation of the livestock microbiota through diet, probiotics, and prebiotics shows promise in diversifying nAb profiles and improving robustness against infection. Despite these advances, research gaps remain, particularly in establishing causality and practical feasibility in livestock systems. This review emphasizes the need for integrative research across immunology, microbiology, and veterinary sciences to leverage microbiota-immune interactions in enhancing livestock resilience against TBDs, exploring how nAbs shaped by the gut microbiota can modulate tick microbiomes and impact pathogen transmission.},
}

Animals
*Livestock/immunology/microbiology
*Tick-Borne Diseases/immunology/prevention & control/veterinary/microbiology
*Microbiota/immunology
Ticks/microbiology/immunology

@article {pmid41939876,
year = {2026},
author = {Li, L and Zhu, G and Chen, M and Qiu, B and Li, Y and Liu, S and Gu, W and Liu, L},
title = {ARG1-polyamine axis: cell-type-specific functions in disease pathogenesis and therapeutic targeting.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1744890},
pmid = {41939876},
issn = {1664-3224},
mesh = {Humans ; *Polyamines/metabolism ; *Arginase/metabolism/antagonists & inhibitors ; Animals ; Neoplasms/metabolism ; },
abstract = {ARG1 catalyzes the conversion of L-arginine to L-ornithine, urea, polyamines, and L-proline, thereby balancing nitrogen detoxification with tissue-specific roles in proliferation and immunity. This review delineates the context-dependent functions of ARG1 across diverse cell types-including tumor cells, immune cells, endothelial cells, keratinocytes, and stem cells. In tumors, ARG1 drives immunosuppression and metabolic reprogramming but can paradoxically suppress tumorigenesis. Immune modulation via ARG1-polyamine crosstalk regulates T cell differentiation, macrophage polarization, and microbiota interactions, influencing infection and autoimmunity. Endothelial ARG1 exacerbates obesity-related vascular dysfunction, while keratinocyte ARG1 impacts wound healing and psoriasis. Emerging therapies-such as ARG1 inhibitors, engineered extracellular vesicles, and microbiome interventions-show preclinical promise in cancer, cardiovascular, and neurodegenerative diseases. By mapping ARG1's spatiotemporal metabolic networks, this work highlights its dual roles and positions ARG1 as a central player for precision medicine in complex pathologies.},
}

Humans
*Polyamines/metabolism
*Arginase/metabolism/antagonists & inhibitors
Animals
Neoplasms/metabolism

@article {pmid41939907,
year = {2026},
author = {Jayaraman, S and Mahalingam, SS and Zhu, Z and Faddoul, F and Paes da Silva, A and Asaad, R and Bhaskaran, N and Schneider, E and Taylor, T and Horne, S and Yoo, A and Zhang, L and Burgener, A and Pandiyan, P},
title = {Enrichment of Candida associated with dysbiosis contributes to mucosal CD4[+]FOXP3[+] regulatory T cell accrual and their dysfunction in aging.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1714595},
pmid = {41939907},
issn = {1664-3224},
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Dysbiosis/immunology/microbiology ; Middle Aged ; *Aging/immunology ; *Mouth Mucosa/immunology/microbiology ; Male ; Female ; Aged ; *Candida/immunology ; Adult ; Forkhead Transcription Factors/metabolism/immunology ; },
abstract = {Age-associated T cell dysfunction is a defining feature of inflammaging and immunosenescence, the progressive decline in immune competence observed with advancing age. Here we identified the association between aging (defined as age >60) and fungal dysbiosis, notably characterized by increased colonization of Candida species in the oral mucosa. There is also a notable enrichment of other taxa related to the order Saccharomycetales in older individuals. In contrast, younger individuals exhibit a greater abundance of Cryptococcus, Yarrowia, Kluyveromyces, and various Incertae sedis lineages. Further analysis, stratified by HIV status, shows that older individuals in both healthy and HIV+ groups display significantly higher levels of Candida. Gingival tissues reveal that both healthy older group and HIV-positive group exhibit elevated levels of CD4[+]FOXP3[+] regulatory T cells (Tregs) along with increased salivary concentrations of soluble TLR-2 and IL-6 compared to younger healthy group. Importantly, the abundance of Candida is positively correlated with elevated levels of mucosal Tregs, dysfunctional Tregs (TregDys), and hyperactivated CD4[+] T cells. In vitro experiments provided mechanistic insights by further demonstrating that Candida can induce both proliferation and dysfunction of Tregs in an IL-6 dependent manner, supporting the notion that Candida plays a role in oral T cell senescence and inflammaging. Collectively, these findings underscore a direct relationship between the commensal mycobiome and Treg population, which normally promotes mucosal homeostasis but becomes susceptible to dysfunction with aging.},
}

Humans
*T-Lymphocytes, Regulatory/immunology/metabolism
*Dysbiosis/immunology/microbiology
Middle Aged
*Aging/immunology
*Mouth Mucosa/immunology/microbiology
Male
Female
Aged
*Candida/immunology
Adult
Forkhead Transcription Factors/metabolism/immunology

@article {pmid41939911,
year = {2026},
author = {Zhao, WY and Zhao, JW},
title = {Pancreatic cancer immunotherapy biomarkers: from traditional markers to multimodal integration and dynamic monitoring.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1686658},
pmid = {41939911},
issn = {1664-3224},
mesh = {Humans ; *Pancreatic Neoplasms/therapy/diagnosis/immunology ; *Biomarkers, Tumor ; *Immunotherapy/methods ; *Carcinoma, Pancreatic Ductal/therapy/immunology/diagnosis ; Animals ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains an intractable cancer marked by delayed diagnosis, rapid progression, and significant resistance to current treatments. Conventional biomarkers, such as CA19-9, have insufficient sensitivity and specificity. Meanwhile, the practical use of newer markers such as the tumor mutational burden and microsatellite instability is limited by the absence of standardized testing protocols and definitive threshold values. Circulating tumor DNA and exosomal miRNA hold promise for continuously tracking tumor dynamics and effectiveness of immunotherapy, but additional validation is necessary before their routine clinical application. Recent advancements in multiomics, nanotechnology, and artificial intelligence have opened new possibilities for more accurate and comprehensive biomarkers. For instance, Shah et al. developed shortwave-infrared-emitting nanoprobes to specifically target CD8[+] cytotoxic T cells, permitting high-sensitivity in vivo imaging in breast cancer models. Batool et al. utilized nanoplasmonic sensors to detect changes in serum programmed death-ligand 1 and cytokine levels within 1-2 weeks post-treatment, achieving picomolar sensitivity. Chang et al. combined fluorescence and photoacoustic imaging in the NanoTrackThera platform, facilitating the real-time monitoring of immunotherapy efficacy. This review highlights the evolution of PDAC biomarkers from traditional markers to multimodal integration and dynamic monitoring. The limitations of current markers and potential of emerging technologies, including metabolic reprogramming markers, epigenetic regulators, and AI-driven predictive models, are discussed. Future directions include multicenter prospective trials to validate multimodal models, standardize detection methods, and increase interdisciplinary collaboration. By integrating genomic, epigenetic, metabolic, and microbiome data, these models can better capture the complexity of PDAC, thereby improving patient outcomes through precision immunotherapy.},
}

Humans
*Pancreatic Neoplasms/therapy/diagnosis/immunology
*Biomarkers, Tumor
*Immunotherapy/methods
*Carcinoma, Pancreatic Ductal/therapy/immunology/diagnosis
Animals

@article {pmid41939913,
year = {2026},
author = {Van Doorn, J and Brooks, SR and LiCausi, F and Zhou, K and Betrapally, NS and Gubitz-Hess, E and Cougnoux, A and Dell'Orso, S and Islam, S and Colbert, RA and Navid, F},
title = {Rapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1755132},
pmid = {41939913},
issn = {1664-3224},
mesh = {Animals ; *HLA-B27 Antigen/genetics/immunology ; *Sirolimus/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Transgenic ; Disease Models, Animal ; Cytokines/metabolism/genetics ; *Spondylarthritis/drug therapy/immunology/microbiology ; Humans ; Male ; Inflammation/drug therapy ; Colon/drug effects/immunology/microbiology/pathology ; },
abstract = {OBJECTIVE: To determine whether rapamycin affects HLA-B27-mediated gut inflammation in experimental spondyloarthritis (SpA).

METHODS: HLA-B27/human β2-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. Healthy age-matched wild type (WT) rats were treated in parallel. Gut inflammation was evaluated via stool scoring and histological assessment. Transcriptome and microbiome analyses were performed on colon tissue and cecal luminal contents, respectively. Bulk immune cells were isolated from the colonic lamina propria of B27-Tg and WT animals, treated with rapamycin ex vivo, and pro-inflammatory cytokine expression was measured using qPCR.

RESULTS: Rapamycin treatment reduced stool and colon histological scores in B27-Tg rats compared to vehicle-treated B27-Tg controls. Transcriptome analysis revealed that rapamycin reduced expression of key pro-inflammatory cytokines like Il17a, Il17f, Tnf, Il1a, IL1b, and Il22 in B27-Tg colon tissue compared to vehicle-treated B27-Tg controls. Ex vivo treatment of bulk immune cells isolated from B27-Tg rat colon with rapamycin reduced expression of Il17a, Il17f, Ifng, and Il22 compared to vehicle-treated cells. Rapamycin treatment decreased the abundance of cecum microbiota associated with inflammation in B27-Tg rats. Rapamycin also altered the gut microbiome in WT rats, without associated changes in the tissue transcriptome.

CONCLUSION: Our study demonstrates that rapamycin treatment substantially reduces HLA-B27-mediated gut inflammation in experimental SpA. Results from this pre-clinical model suggest further evaluation of rapamycin as a therapeutic strategy in HLA-B27 associated diseases is warranted.},
}

Animals
*HLA-B27 Antigen/genetics/immunology
*Sirolimus/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Rats
Rats, Transgenic
Disease Models, Animal
Cytokines/metabolism/genetics
*Spondylarthritis/drug therapy/immunology/microbiology
Humans
Male
Inflammation/drug therapy
Colon/drug effects/immunology/microbiology/pathology

@article {pmid41940020,
year = {2026},
author = {Usman, S and Yan, Q and Gao, L and Deng, S and Lu, L and Pang, T and Lai, D and Jones, CS and Yi, X and Zhang, J},
title = {Inclusion of different levels of fermented elephant grass in broiler chicken diet: effects on growth, physiology, carcass traits and gut microbial community.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1767570},
pmid = {41940020},
issn = {1664-042X},
abstract = {The physiological and microbiome-modulating benefits of dietary forage in monogastrics are impeded by recalcitrant fiber and anti-nutritional factors. However, fermentation and appropriate inclusion levels may overcome these limitations. This study evaluated the effects of two fermented cultivars of elephant grass (Cenchrus purpureus cv. Guiminyin and cv. Purple) incorporated into broiler diets at different inclusion levels, with emphasis on cultivar-specific responses, growth performance, physiological status, and gut microbial composition. A total of 240 male (30-days old) Jinling earth-neck chickens were housed in four replicate pens of 12 birds each, and randomly assigned to five dietary treatments (48 birds per treatment): a control diet with no inclusion (0%), CpGui5 (5% Guiminyin inclusion), CpGui10 (10% Guiminyin inclusion), CpPur5 (5% Purple inclusion), and CpPur10 (10% Purple inclusion). CpGui5 and Control diets had statistically similar and higher final weight, total weight gain, average daily gain and feed efficiency which were higher than the other treatments (P < 0.05). On the other hand, Control, CpGui5 and CpPur5 had higher daily feed intake compared to CpGui10 and CpPur10 which had the lower daily feed intake (P < 0.05). Slaughter performance revealed significant differences (P < 0.05), with the control, CpGui5, CpPur5 and CpPur10 groups maintaining higher live weight, dressed weight, half-bore, and breast muscle rate while CpGui10 recorded the lowest values. Blood biochemical indices, including total protein, albumin, liver enzymes, and renal function markers, were unaffected by dietary treatments (P > 0.05), indicating no adverse physiological effects. Gut microbiome analysis showed stable richness (Chao1, ACE) across treatments, while diversity (Shannon, Simpson) was reduced in CpPur5 relative to other groups (P < 0.05). A shared core microbiome of 202 OTUs was detected across all treatments, alongside treatment-specific enrichment of taxa. LEfSe (Linear Discriminant Analysis Effect Size) analysis identified treatment-specific enrichment of functionally relevant bacterial genera, including Megamonas in CpGui5 and Ruminococcaceae_UCG-014 and unclassified Lachnospiraceae at higher inclusion levels (CpGui10). Overall, moderate inclusion of fermented elephant grass, especially CpGui5 supports broiler performance while maintaining physiological health and gut microbial stability, highlighting its potential as a sustainable functional feed resource for poultry production.},
}

@article {pmid41940149,
year = {2026},
author = {Etesami, H and Yadegari, AH and Otabek, U and Zahro, B and Shavakatullo, N and Tolqinjon, A},
title = {The root's hidden ally: How the rhizosheath microbiome fortifies crops against drought.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100015},
pmid = {41940149},
issn = {2662-1738},
abstract = {Drought stress poses a significant threat to global agriculture, necessitating innovative strategies to enhance plant resilience. This review highlights the rhizosheath-the soil layer tightly bound to roots by mucilage and microbial biofilms-as a critical but underexplored microbial niche for sustainable drought mitigation. Unlike the vulnerable rhizosphere, the rhizosheath has a cohesive structure that acts as a protective "mini-oasis," preserving moisture and sustaining microbial activity when water is scarce. We synthesize evidence showing that resident rhizosheath bacteria, including genera such as Bacillus, Pseudomonas, and Azospirillum, enhance plant drought tolerance through multiple mechanisms: improving soil structure and water retention, modulating phytohormone levels, facilitating nutrient acquisition, and activating antioxidant and genetic defense pathways in the plant. Despite promising laboratory findings, there has been little field-scale validation of these effects. Here, we critically assess translational challenges and outline future research priorities, such as understanding plant-microbe specificity and optimizing synthetic microbial consortia. Addressing these questions will enable manipulation of the rhizosheath microbiome for development of climate-resilient crops and securing food production in water-limited environments.},
}

@article {pmid41940156,
year = {2026},
author = {Ma, J and Qiao, J and Cao, Y and Cheng, Z},
title = {Harnessing artificial intelligence to decode the rhizosphere microbiome.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100005},
pmid = {41940156},
issn = {2662-1738},
abstract = {The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its complexity, the rhizosphere microbiome is quite challenging to analyze using conventional approaches. Recent advances in artificial intelligence (AI) offer unprecedented opportunities to decipher intricate microbial interactions and leverage their potential for crop breeding. In this review, we assess AI methodologies derived from human microbiome studies that address foundational data challenges, including high dimensionality, compositionality, and sparsity. Next, we examine the uses of these methods for the functional prediction of microbial traits. We then shift our focus to the rhizosphere, exploring AI-driven approaches for predictive modeling of rhizosphere dynamics, integrating plant phenotypic and microbiome data, and designing synthetic microbial communities (SynComs). Finally, we discuss the major challenges and future prospects of using AI in rhizosphere microbiome research. Specifically, we propose an emerging AI paradigm that integrates complementary inside-out (hologenome-based genomic selection) and outside-in (SynCom design) strategies, powered by transformative technologies such as federated learning, large language models, digital twins, and autonomous AI agents. This review underscores the potential for AI to revolutionize microbiome science and crop improvement.},
}

@article {pmid41940273,
year = {2026},
author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X},
title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.},
journal = {Current zoology},
volume = {72},
number = {1},
pages = {14-29},
pmid = {41940273},
issn = {1674-5507},
abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.},
}

@article {pmid41940285,
year = {2025},
author = {Jeong, GH and Lim, KS},
title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.},
journal = {Journal of animal science and technology},
volume = {67},
number = {6},
pages = {1207-1214},
pmid = {41940285},
issn = {2055-0391},
abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.},
}

@article {pmid41940567,
year = {2026},
author = {De Zutter, N and Audenaert, K},
title = {Can We Breed Microbiomes to Sustain Plant Productivity?.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70351},
pmid = {41940567},
issn = {1751-7915},
mesh = {*Microbiota ; *Plant Breeding/methods ; *Crops, Agricultural/microbiology/genetics/growth & development ; Quantitative Trait Loci ; *Plants/microbiology/genetics ; },
abstract = {Global food systems face challenges from population growth, shifting diets and climate change. While decades of plant-centric breeding and high-input agriculture have generated high yielding crops, this strategy has unintentionally reshaped the plant associated microbiomes, often coinciding with a depletion of their functional diversity. We revisit these breeding strategies and propose extending breeding targets beyond the plant genome to include the plant microbiome. In this regard, resistance breeding shows, albeit unintended, that plant genetics shape the microbiome: by narrowing the genetic base, we have selected for highly specialised pathogenic microbiomes. This raises a key question: can we intentionally apply the same principle to select for beneficial microbiomes? To answer this question, a thorough insight into microbial community architecture, hubs and functional redundancy is key. We outline two complementary avenues: (i) rewilding to restore ancestral microbial partners and (ii) microbiome breeding guided by QTL/GWAS mapped host loci that gate microbial recruitment, immune filtering and exudate composition. This approach comprises the integration of trait-based phenotyping, multi-omics, network-informed SynCom design and field testing across environments to capture G × E × M (genotype × environment × microbiome) interactions. Treating the microbiome as a selectable, designable and heritable trait can convert small gains into durable long-lasting crop resilience.},
}

*Microbiota
*Plant Breeding/methods
*Crops, Agricultural/microbiology/genetics/growth & development
Quantitative Trait Loci
*Plants/microbiology/genetics

@article {pmid41940646,
year = {2026},
author = {Yin, X and Niu, Y and Chen, B and Zhang, H and Guo, R and Niu, C and Kang, J and Shi, H and Kong, X and Ma, W and Ma, Z and Wei, Y and Hua, Y},
title = {Screening and dynamic change study of microbial and metabolite markers for calf diarrhea based on multi-omics and machine learning.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000526},
doi = {10.1128/msystems.00005-26},
pmid = {41940646},
issn = {2379-5077},
abstract = {UNLABELLED: Neonatal calf diarrhea is a leading cause of calf mortality and substantial economic loss in the livestock industry, yet the dynamic microbial and metabolic signatures accompanying disease onset remain poorly defined. Here, we integrated 16S rRNA high-throughput sequencing, untargeted metabolomics, and machine learning approaches to longitudinally profile fecal samples from neonatal calves at 0, 5, 10, 15, and 20 days of age. Diarrheic calves exhibited significantly reduced gut microbial α-diversity, as indicated by lower Chao1 richness and Shannon index compared with healthy counterparts. At the genus level, Tyzzerella and Fusobacterium emerged as core differential taxa associated with diarrhea and were further validated as robust biomarkers using an XGBoost predictive model. Metabolomic analysis showed that differential metabolites were mainly enriched in pathways including the phosphotransferase system. Notably, dulcitol, N-acetylmuramate, and D-fructose were highlighted as potential contributors to diarrhea, possibly through modulating intestinal osmolality and inflammatory responses. Pearson correlation analysis revealed significant associations between Tyzzerella/Fusobacterium and key metabolites, suggesting coordinated microbe-metabolite interactions during disease progression. Temporal pattern analysis identified an early-life signal: a high abundance of Escherichia-Shigella at birth may act as an important trigger for subsequent diarrhea. In addition, several metabolites displayed distinct age-dependent trajectories, indicating their potential as time-resolved metabolic biomarkers. Collectively, this study delineates dynamic shifts in the gut microbiome and metabolome during neonatal calf diarrhea, identifies Tyzzerella and Fusobacterium, together with characteristic metabolites such as dulcitol and N-acetylmuramate, as candidate biomarkers, and provides a high-performance predictive framework to support early diagnosis and targeted microbiota-based interventions.

IMPORTANCE: Neonatal calf diarrhea causes substantial early-life mortality and economic losses, yet the dynamic microbiota-metabolite alterations and early-warning biomarkers during disease onset remain poorly defined. Here, we longitudinally profiled fecal microbiota and metabolites in calves from birth to day 20 and integrated machine learning approaches to systematically characterize diarrhea-associated signatures. Diarrheic calves showed reduced α-diversity, and Tyzzerella and Fusobacterium emerged as core differential genera with predictive value validated using an XGBoost model. Differential metabolites were mainly enriched in pathways such as the phosphotransferase system (PTS), and dulcitol and N-acetylmuramate may contribute to diarrhea by modulating intestinal osmolality or inflammatory responses. Notably, a higher abundance of Escherichia-Shigella at birth was potentially associated with subsequent diarrhea risk, while L-glutamic acid, choline, and LysoPC exhibited distinct temporal trajectories. Collectively, these findings provide translational candidate biomarkers to support early warning and microbiota-targeted precision interventions for neonatal calf diarrhea.},
}

@article {pmid41940665,
year = {2026},
author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X},
title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191125},
doi = {10.1128/spectrum.01911-25},
pmid = {41940665},
issn = {2165-0497},
abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.

IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.},
}

@article {pmid41940696,
year = {2026},
author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M},
title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0190325},
doi = {10.1128/aem.01903-25},
pmid = {41940696},
issn = {1098-5336},
abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.},
}

@article {pmid41940869,
year = {2026},
author = {Sharif-Askari, Z and Atoui, K and El Zein, W and Rizk, M and Sharif Askari, E},
title = {From periodontitis to neurodegeneration: Can probiotics modulate the P. gingivalis-amyloid pathway in Alzheimer's disease?.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261432686},
doi = {10.1177/13872877261432686},
pmid = {41940869},
issn = {1875-8908},
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the gradual destruction of cognitive and behavioral functions. Despite the continuous research efforts, there is still no cure for this disease. In recent years, researchers have investigated Porphyromonas gingivalis (P. gingivalis) as a potential cause of AD. P. gingivalis-lipopolysaccharides (LPS) and gingipains have been implicated in neuroinflammatory cascades relevant to AD. The gut-brain axis provides a pathway for microbial migration, immune activation, and regulation of the central nervous system function. Emerging evidence suggests that selected probiotics may modulate these pathways by restoring microbial balance, reinforcing epithelial barrier function, and regulating innate and adaptive immunity. Importantly, much of the evidence and mechanistic support for these effects derives from preclinical and animal studies, whereas human data remain limited to associative findings and early-stage clinical trials. Early clinical trials report modest improvements in cognitive scores and systemic inflammatory markers. Strain selection, dose, and treatment duration make direct comparisons challenging. This review integrates the literature on the links between P. gingivalis and AD, suggesting that probiotics may be used as neuroprotective agents. Taken together, current preclinical signals are consistent with the potential of probiotics as feasible adjuncts, pending confirmatory trials with standardized formulations.},
}

@article {pmid41941327,
year = {2026},
author = {Strope, TA and Easson, CG and Fiore, CL},
title = {Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis, Pre and Post Gemmulation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70331},
pmid = {41941327},
issn = {1758-2229},
support = {//Appalachian State University/ ; 1924540//National Science Foundation/ ; },
mesh = {*Symbiosis ; *Porifera/microbiology/growth & development/physiology ; Animals ; *Bacteria/classification/genetics/isolation & purification ; Fresh Water/microbiology ; *Microbiota ; Flavobacterium/genetics ; Phylogeny ; },
abstract = {Freshwater sponges, most of which have a dormant stage with gemmules, are well poised for microbiome focused experiments. Here, we leveraged field collections of freshwater sponges pre-gemmule (Pre) and post-gemmule (Post) formation to compare the microbial symbiont metatranscriptome at the two developmental stages. There were no broad changes to the microbiome in composition between the two stages; however, there were significant differences in the abundance of several bacterial taxa and functional genes between Pre and Post sponge samples. For example, many Polynucleobacter spp. increased from Pre to Post samples, but no putative symbiosis factors were associated with Polynucleobacter and these may be loosely associated with the sponges. In contrast, we hypothesise that Flavobacterium spp. are facultative symbionts of freshwater sponges that begin to leave when the sponge tissue degrades, or they may decrease their metabolic activity. Functions attributed to Flavobacterium spp. such as type IX secretion system (T9SS) component and ankyrin repeat domains, all decreased in the Post samples and suggests that this group can interact with the sponge host or be free-living. These results provide a foundation for future hypothesis testing and experimental work with the microbiomes of freshwater sponges.},
}

*Symbiosis
*Porifera/microbiology/growth & development/physiology
Animals
*Bacteria/classification/genetics/isolation & purification
Fresh Water/microbiology
*Microbiota
Flavobacterium/genetics
Phylogeny

@article {pmid41941330,
year = {2026},
author = {Dunn, ES and Spalding, HL and Hill-Spanik, KM and Fullerton, H},
title = {Examining Short Temporal Changes in Intertidal Macroalgal Microbiomes at 'Ewa Beach, O'Ahu, Hawai'i: Some Hosts Varied While Others Remained Stable.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70333},
pmid = {41941330},
issn = {1758-2229},
mesh = {Hawaii ; *Microbiota ; *Seaweed/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Climate Change ; Rhodophyta/microbiology ; Seawater/microbiology ; Phaeophyceae/microbiology ; },
abstract = {Understanding the temporal variability of microbiomes is crucial for predicting dynamics within macroalgal communities under future climate change scenarios, rising temperatures, and increased marine heatwave events. Short-term variation has been observed in human- and coral-associated microbes, but these dynamics are less understood in macroalgae. Intertidal macroalgal communities are ideal systems for investigating microbiome temporal variation due to their exposure to daily fluctuations in abiotic conditions. We characterised and examined the variability in the microbiota of seven macroalgal species, with representatives from three different phyla, across five sequential low tides in May 2021 at a single intertidal bench at 'Ewa Beach, O'ahu, Hawai'i, USA. Bacterial community compositions found in two red algae, Acanthophora spicifera and Laurencia dendroidea, and one brown alga, Dictyota sandvicensis, had variable abundances of several amplicon sequence variants contributing to significant dissimilarity through time. Two green macroalgae (Avrainvillea lacerata and Halimeda discoidea) were stable over time. Temporal stability of the macroalgal microbiotas, therefore, was variable amongst macroalgal species, but may be dependent on its horizontal or vertical positioning within the intertidal zone, which can vary the level of environmental stress (e.g., temperature, light, desiccation). Additional work exploring the drivers of the temporal variability observed herein is needed.},
}

Hawaii
*Microbiota
*Seaweed/microbiology
*Bacteria/classification/genetics/isolation & purification
Climate Change
Rhodophyta/microbiology
Seawater/microbiology
Phaeophyceae/microbiology

@article {pmid41941490,
year = {2026},
author = {Ventero, MP and Herrero, R and Tyshkovska, I and Valverde-Fredet, MD and Rodríguez, JC and Rodríguez-Fernández, M and González-De-La-Aleja, P and Trigo, M and Parra, M and Aller, AI and Otero, S and Espindola-Gomez, R and Ramos, JM and León, EM and García, M and Navarrete-Lorite, MN and Llenas-García, J and Portillo, I and Jover, F and Tasias, M and Caston, JJ and Gil, C and Vinuesa-Garcia, D and Gomez-Ayerbe, C and Martínez Marcos, FJ and Merchante, N and De Lucas, EM},
title = {Dynamics of the microbiota in patients with Clostridioides difficile: Recurrence, treatment, sex, and immunosuppression.},
journal = {PLoS pathogens},
volume = {22},
number = {4},
pages = {e1014063},
doi = {10.1371/journal.ppat.1014063},
pmid = {41941490},
issn = {1553-7374},
abstract = {BACKGROUND: Alterations in the gut microbiome are central to the pathogenesis and recurrence of Clostridioides difficile infection (CDI).

OBJECTIVE: To evaluate intestinal microbiome changes during CDI and their association with recurrence, sex, age, and immunosuppression.

METHODS: Patients from the CDI-ANCRAID-SEICV cohort were consecutively enrolled. Stool samples were obtained at diagnosis (Dx), end of treatment (ET), and eight weeks post-treatment (8W) or upon recurrence. Microbiota composition was analyzed by 16S rRNA sequencing using QIIME2 and R. Outcomes were compared by demographics, immunosuppression, and treatment (vancomycin [VNC], vancomycin-bezlotuzumab [VNC-BZL], fidaxomicin [FDX]).

RESULTS: Among 143 patients, non-recurrent cases showed higher biodiversity at 8W versus diagnosis (H p = 0.002, ASVs p < 0.001), unlike recurrent cases. Diversity decreased with VNC (H p > 0.001, ASVs p < 0.001) but was preserved with FDX (H p = 0.15). Recovery of Shannon diversity was limited in women (p = 0.50) and immunocompromised patients (p = 0.31). At ET, Fusobacteria and Verrucomicrobiota were less abundant in recurrent than non-recurrent cases (0.77%, 0.53% vs 3.43%, 3.50%). FDX-treated samples showed higher Bacteroidetes (31.33%) compared to VNC (5.23%) or VNC-BZL (3.12%). Women exhibited increased Firmicutes abundance (p = 0.034).

CONCLUSIONS: Restoration of microbial diversity correlates with CDI resolution. FDX preserves gut microbiota better than VNC or VNC-BZL. Women and immunocompromised patients demonstrate impaired microbiota recovery.},
}

@article {pmid41941984,
year = {2026},
author = {Margaux, E and Elise, T and Muriel, D and Matthijs, M and Jellina, P and Arnau, VV and Jean, S and Nicky, D and Bart, B and Jeroen, R and Kaat, A},
title = {A pilot study on the role of the oxytocinergic system in gut microbiome composition in children with autism: baseline associations and effects of intranasal oxytocin.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106579},
doi = {10.1016/j.bbi.2026.106579},
pmid = {41941984},
issn = {1090-2139},
abstract = {Autistic children often experience behavioral difficulties alongside nutritional and gastro-intestinal (GI) problems, including gut dysbiosis. Recent research has highlighted important interactions between the oxytocinergic system and gut microbiome compositions, however, insights into how exogenous administration of oxytocin may influence GI health remain largely unexplored. Here, we first examined whether nutrition, GI symptoms and microbiome compositions vary in autistic versus non-autistic children, and how alterations link to clinical-behavioral difficulties and oxytocinergic signaling. Next, we examined the effect of a four-week intranasal oxytocin administration regimen on GI health/dysbiosis in autistic children enrolled in a randomized placebo-controlled trial. Compared to non-autistic children, autistic children consumed more soft drinks, and fewer vegetables and experienced abdominal pain more frequently over the past three months. Notably, epigenetic variations in the oxytocin receptor gene (OXTR) were associated with stool consistency, indicating that children with looser stools exhibited lower OXTR methylation levels, indicative of increased receptor expression. Additionally, a higher abundance of Romboutsia was associated with OXTR hypo-methylation and more anxiety-like behavior. In autistic children, the four-week oxytocin regimen had no effect on bacterial diversity but did modify stool consistency, leading to less dense stools with an overall more normal stool consistency, and an increased abundance of the potentially anti-inflammatory genus Fusicatenibacter. To conclude, this study provides novel insights into the role of the oxytocinergic system in GI symptoms and gut microbiome compositions in autistic children, and preliminary evidence suggesting a modulatory effect of exogenously administered oxytocin on these parameters.},
}

@article {pmid41941985,
year = {2026},
author = {Bettio, MK and Vidal, T and Rose, JJ and Jois, M and Flavel, M and Petrovski, S},
title = {Polyphenol-Rich Feed Material increases Anaerostipes and reduces methanogenic archaea in the horse hindgut microbiome.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105885},
doi = {10.1016/j.jevs.2026.105885},
pmid = {41941985},
issn = {0737-0806},
abstract = {BACKGROUND: The gastrointestinal microbiota plays a critical role in horse health and performance. While sugarcane-derived polyphenols have shown microbiota-modulating properties in other species, their effects in horses remain unexplored.

AIMS/OBJECTIVES: This study investigated whether supplementation with a sugarcane-derived polyphenol feed material modulates the hindgut microbiota of healthy adult horses.

METHODS: An observational longitudinal study was conducted on six horses over 12 weeks. Faecal samples were collected at three time points: baseline (P1), during supplementation (P2), and post-supplementation (P3). Microbial composition was assessed by 16S rRNA gene sequencing targeting the V3-V4 region. Alpha and beta diversity, as well as differential abundance analyses, were performed.

RESULTS: Alpha diversity metrics (Chao1, Shannon, Simpson) showed no significant differences across time points. However, Anaerostipes increased by 105.3% during supplementation and 23.6% post-supplementation. Prevotella abundance also rose post-supplementation. Methanogenic Archaea, including Methanomassiliicoccus, decreased by 79.1% during supplementation, while members of Methanobacteriales were reduced by 61.8%. These changes partially reversed in the post-supplementation phase. Core microbiota genera remained stable throughout.

CONCLUSION: Supplementation with a sugarcane-derived polyphenol feed material modulated specific microbial taxa without disrupting overall microbial diversity. The intervention enhanced fermentative SCFA-producing bacteria and suppressed methanogenic Archaea, supporting the potential use of this feed material as a microbiome enhancer for improving hindgut health and reducing methanogenesis in horses.},
}

@article {pmid41942049,
year = {2026},
author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J},
title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.004},
pmid = {41942049},
issn = {2090-1224},
abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.

OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.

METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.

RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.

CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.},
}

@article {pmid41942109,
year = {2026},
author = {Alsarahead, RA and El-Shehabi, FS and Hijjawi, NS},
title = {Prevalence and subtype diversity of Blastocystis hominis among gastroenteritis patients in northern and central Jordan.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/trag033},
pmid = {41942109},
issn = {1878-3503},
support = {49//Deanship of Scientific Research at Hashemite University/ ; //Department of Graduate Studies/ ; },
abstract = {BACKGROUND: Blastocystis hominis is a common intestinal eukaryotic organism that infects both humans and animals. Although its pathogenicity remains debated, it has been associated with diarrhoea and gastroenteritis. This study aimed to determine its prevalence and characterize its genetic subtypes (STs) in symptomatic patients presenting with gastrointestinal complaints.

METHODS: DNA was extracted from 279 stool samples collected from patients in northern and central regions of Jordan. Nested polymerase chain reaction targeting the 18S rRNA gene locus and Sanger sequencing of positive samples were used for B. hominis detection and subtype identification. Phylogenetic relationships were analysed using Unipro UGENE and MEGA software. Statistical analyses, prevalence, Pearson's χ2 test (p<0.05) were conducted using SPSS.

RESULTS: The present study found a B. hominis prevalence of 7.2% (20/279). Three subtypes were identified: ST1 35% (7/20), ST2 10% (2/20) and ST3 55% (11/20). No mixed-subtype infections were detected. A statistically significant association was observed between B. hominis infection and patient age (p<0.05), with infection rates influenced by age and not by gender. The highest prevalence, based on sequencing, was observed in the 6- to <12-y age group. The association between B. hominis infection and gender was not statistically significant.

CONCLUSIONS: The relatively low prevalence of B. hominis among patients suggests it may function more as an indicator of gut health rather than as a primary pathogen. However, confirmation of this hypothesis requires additional microbiome and longitudinal studies. The frequent detection of ST1 and ST3 aligns with previous findings that link these subtypes to clinical symptoms. Broader epidemiological studies are needed to clarify the distribution patterns and clinical significance of B. hominis in human populations.},
}

@article {pmid41942178,
year = {2026},
author = {Opperman, C and Lloyd, C and Ratanpaul, V and Van, TTH and Brennan, C and Eri, R},
title = {Engineering SCFAs with dietary fibre combinations: insights from a kinetic-microbiome single-subject longitudinal study.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {118846},
doi = {10.1016/j.foodres.2026.118846},
pmid = {41942178},
issn = {1873-7145},
mesh = {*Dietary Fiber/metabolism/analysis ; Humans ; Fermentation ; Longitudinal Studies ; *Gastrointestinal Microbiome/physiology ; Male ; Manihot/chemistry ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Adult ; Saccharum ; Inulin/metabolism ; Female ; Starch/metabolism ; Kinetics ; Young Adult ; Musa ; Bifidobacterium/metabolism ; Psyllium ; },
abstract = {The human diet plays a pivotal role in health, yet many studies seeking to identify health-promoting foods rely on experimental designs that poorly reflect natural circumstances. The effects of dietary fibres on the microbiota are typically examined using pooled faecal material and isolated fibres, creating unrealistic environments. Additionally, little progress has been made in distinctly characterising the fermentation rates of dietary fibres. To evaluate the temporal dynamics of gut microbial composition and metabolite production, as well as to characterise the fermentation rates of dietary fibres at an individual level, we conducted an n-of-1 longitudinal study examining responses to eight distinct dietary fibres, fermented both individually and in combination. A blend of sugarcane fibre and cassava resistant starch produced significantly higher butyrate levels (p < 0.0001) than either fibre alone. Microbial profiling showed that inulin and pectin selectively enriched Bifidobacterium spp. Anaerobutyricum hallii was increased with psyllium husk, wheat dextrin, and banana resistant starch, but decreased with a mixture of sugarcane fibre and cassava resistant starch (p < 0.0001). Fermentation kinetics were distinctly categorised into "fast", "medium", "slow" and "poorly-fermentable". These findings indicate that combinations of dietary fibres can be used as a strategy to engineer synergistic health-promoting metabolite responses in an individual, while establishing a standardised framework for describing fermentation rates across studies.},
}

*Dietary Fiber/metabolism/analysis
Humans
Fermentation
Longitudinal Studies
*Gastrointestinal Microbiome/physiology
Male
Manihot/chemistry
*Fatty Acids, Volatile/metabolism
Feces/microbiology
Adult
Saccharum
Inulin/metabolism
Female
Starch/metabolism
Kinetics
Young Adult
Musa
Bifidobacterium/metabolism
Psyllium

@article {pmid41942241,
year = {2026},
author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X},
title = {Corrigendum to "Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu" [Food Res. Int. 223 (2026) 117868].},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {119013},
doi = {10.1016/j.foodres.2026.119013},
pmid = {41942241},
issn = {1873-7145},
}

@article {pmid41942569,
year = {2026},
author = {Connolly, JA and Del Carratore, F and Schmidt, K and Bisesi, AT and Martinson, JNV and Chua, J and Kuhs, M and Boneza, MM and Heinsch, SC and Kinkel, LL and Smanski, MJ and Harcombe, WR and Breitling, R and Takano, E},
title = {Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41942569},
issn = {2045-2322},
support = {NE/T010959/1//UK Research and Innovation/ ; 1935458//National Science Foundation/ ; },
mesh = {*Streptomyces/metabolism/genetics ; *Siderophores/metabolism ; *Soil Microbiology ; Metabolomics/methods ; Iron/metabolism ; *Microbiota ; Deferoxamine/metabolism ; Transcriptome ; Multigene Family ; Multiomics ; },
abstract = {Streptomyces are key contributors to soil microbiome function, known for their biosynthetic diversity. While advances in -omics technologies have improved our understanding of microbiome composition and metabolic potential, the mechanisms underpinning interspecies interactions remain poorly resolved. Here, we investigate the molecular basis of interactions among four sympatric Streptomyces soil microbiome isolates, focusing on phenotypic, metabolomic and transcriptomic responses. Co-culture experiments revealed that one isolate, strain A, exhibited pronounced phenotypic changes when grown alongside each of the other three strains. Untargeted metabolomics and RNA-seq analyses showed that strain A undergoes distinct metabolic and transcriptional shifts depending on its partner, with the strongest response elicited by strain C. Despite all four strains possessing a conserved desferrioxamine biosynthetic gene cluster, only strain C constitutively produced desferrioxamine B (DFO-B), a hydroxamate siderophore, indicating a role for iron bioavailability in the interaction. Supplementation with DFO-B or iron mimicked the growth stimulation of strain A observed in co-culture with strain C, and CRISPR base editing of desD in strain C abolished both DFO production and the phenotypic induction of strain A. However, transcriptomic profiles of strain A varied significantly depending on the partner strain, with distinct sets of biosynthetic gene clusters and metabolic pathways activated in response to strains B and C, suggesting additional cues beyond DFO-B. In contrast, strain D did not elicit growth stimulation in its partners, and itself showed downregulation of amino acid and carbon metabolism when co-cultured with strain C. These findings indicate that Streptomyces interactions are not only mediated by siderophore piracy but also involve complex, strain-specific molecular responses. Our findings demonstrate that Streptomyces interactions are highly strain-specific and only partly mediated by siderophore piracy, with DFO-B acting as a potent interspecies cue. The divergent molecular responses to different partners suggest nuanced mechanisms of microbial sensing and competition. These insights advance our understanding of microbial crosstalk and highlight the ecological and evolutionary complexity of siderophore-mediated interactions. By integrating transcriptomics, metabolomics, and biochemical assays, we present a robust framework for dissecting microbial interactions, with implications for microbiome engineering and synthetic community design.},
}

*Streptomyces/metabolism/genetics
*Siderophores/metabolism
*Soil Microbiology
Metabolomics/methods
Iron/metabolism
*Microbiota
Deferoxamine/metabolism
Transcriptome
Multigene Family
Multiomics

@article {pmid41942702,
year = {2026},
author = {Zhang, YK and Iskandar, MM and Kubow, S and Komarova, SV and Tauer, JT},
title = {Exploring the impact of collagen-I genetic variants on intestinal structure and gut microbiota in mouse models of osteogenesis imperfecta.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47221-2},
pmid = {41942702},
issn = {2045-2322},
support = {87500//Shriners of North America/ ; },
}

@article {pmid41942777,
year = {2026},
author = {Verdegaal, AA and Oh, J and Javdan, B and Wang, R and Wu, Q and Wang, TRW and González-Hernández, JA and Donia, MS and Crawford, JM and Goodman, AL},
title = {A drug-microbiome-drug interaction impacts co-prescribed medications for Parkinson's disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41942777},
issn = {2058-5276},
support = {R35GM118159//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AT010014//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; F31DK132941//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI172144//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; RM1GM141649//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Simultaneous prescription of multiple drugs is widespread in medicine. Although the gut microbiome is implicated in drug responses, its role in mediating drug-drug interactions is unexplored. Catechol-O-methyltransferase inhibitors (COMT-I), a class of drugs used alongside levodopa (L-DOPA) to treat Parkinson's disease symptoms, can alter microbiome composition in patients. Here we characterize the antibiotic properties of COMT-I drugs in vitro, ex vivo and in vivo and dissect how these interactions alter microbiome-mediated L-DOPA metabolism in vitro and ex vivo. Notably, in vitro iron availability determines COMT-I antibiotic activity at multiple levels: extracellular iron can drive non-enzymatic inactivation of COMT-I, rescuing COMT-I-mediated bacterial iron starvation responses. However, limitation of intracellular iron can protect sensitive bacteria from COMT-I antibiotic activity. Co-administration of COMT-I and L-DOPA to human faecal microbial communities ex vivo results in COMT-I-dependent alterations to L-DOPA metabolism in an individual-specific manner. These studies highlight a role for the gut microbiome in mediating drug-drug interactions and identify microbial features that could predict individual responses to co-prescribed drugs.},
}

@article {pmid41943076,
year = {2026},
author = {Ghathian, KSA and Halkjær, SI and Krogfelt, KA and Frimodt-Møller, N and Hansen, KH and Frederiksen, AKS and Holm, A and Petersen, AM},
title = {The effect of the probiotic supplement-ASTARTE™-on the reduction of recurrent urinary tract infection in women aged 18-40 years: protocol for a randomized, double-blind, placebo-controlled study.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-026-09679-3},
pmid = {41943076},
issn = {1745-6215},
abstract = {BACKGROUND: Urinary tract infection (UTI) is one of the most common bacterial infections, contributing to increased antibiotic consumption and high healthcare costs. Clinical studies suggest that probiotics can be effective dietary supplements reducing the risk factors for the development of infections in the intestine and vagina. In this study, we investigate the effect of the orally ingested probiotic combination ASTARTE™ on the composition of bacteria in vaginal and fecal samples, as well as on the occurrence of bacteriologically confirmed UTIs in women of reproductive age.

METHODS: A randomized, placebo-controlled, double-blind study evaluating the effect of the probiotic combination ASTARTE™ (Chr. Hansen A/S, Part of Novonesis Group, Denmark) on reducing the number of recurrent urinary tract infections (rUTIs) in women aged 18-40 years. Participants are randomized (1:1) to receive one daily probiotic capsule (5 × 10[9] CFU) containing Lactobacillus crispatus LBV 88™ (DSM22566), Lacticaseibacillus rhamnosus LBV 96™ (DSM22560), Lactobacillus jensenii LBV 116™ (DSM22567), and Lactobacillus gasseri LBV 150N™ (DSM22583), or placebo, for 6 months. Assessments, including symptom questionnaires, urine culturing and microbiome analysis of vaginal and rectal samples by shotgun sequencing, are conducted at baseline, 2, 4, and 6 months. Compliance is tracked by unused capsule counts. Follow-up visits occur at 8, 10, and 12 months. The primary outcome is the incidence of symptomatic bacteriologically confirmed UTIs during the 6 months intervention period. The secondary objective is the effect of ASTARTE™ on changes in vaginal and gut microbiome.

DISCUSSION: This randomized, placebo-controlled, double-blind study investigates the effectiveness of ASTARTE™ in restoring beneficial microbiomes and reducing UTI recurrence. The findings will provide valuable evidence on the effectiveness of a non-antibiotic strategy for the prevention of rUTI as well as insights into the complex interactions between the vaginal and gut microbiome and the risk of rUTI.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05553652. Registered 21 September 2022.},
}

@article {pmid41943109,
year = {2026},
author = {Crouzet, L and Kelly, W and Andrews, C and Soni, P and Tong, B and Tavendale, R and Rajasekaran, K and Wieliczko, K and Pilkington, K and Kaminsky, R and Matiya, F and Molano, G and Sandoval, E and Dobson-Hill, B and Reid, P and Muetzel, S and Khan, A and Maclean, P and Doohan, H and Burgess-Smith, T and Atkins, N and Bassett, S and Dekker, J and Hill, J and Bermingham, E and Attwood, G},
title = {Early life treatment with Lacticaseibacillus rhamnosus strains drives reduced enteric methane emissions in dairy heifers.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41943109},
issn = {1674-9782},
support = {PGGRC-Fonterra project contract 20-FONT- LAB AGR MET 5.4, Contract AgR: A27147.//This study was funded by the Pastoral Greenhouse Gas Research Consortium (PGgRc) and Fonterra Ltd./ ; },
abstract = {BACKGROUND: Methane emissions from enteric fermentation in ruminant livestock make up 27% of anthropogenic methane emissions.

RESULTS: Screening > 1,700 lactic acid bacteria identified Lacticaseibacillus rhamnosus FNZ118 (Kowbucha™ FNZ118) and L. rhamnosus FNZ142, (Kowbucha™ FNZ142) as capable of inhibiting rumen methanogens and methane production in vitro. FNZ118 or FNZ142 fed daily to Friesian heifer calves from birth to 14 weeks substantially lowered methane production through the first year of life compared to control animals. These strains also decreased feed intake and reduced ruminal metabolite concentrations without affecting animal live weight, suggesting an improvement in feed conversion efficiency. The observed effects did not cause major changes in the structure of the rumen microbiome.

CONCLUSIONS: These findings demonstrate that early life provision of specific L. rhamnosus strains lower CH4 production and have potential for the mitigation of enteric greenhouse gas emissions from growing dairy cattle.},
}

@article {pmid41943321,
year = {2026},
author = {Pu, D and Liang, T and Li, X and Xing, W and Luo, L and Ding, Y and Wan, C and Wu, M},
title = {Physicochemical properties and molecular weight-dependent gut microbiota modulation of inulin-type fructans from Codonopsis bulleynana.},
journal = {Carbohydrate polymers},
volume = {381},
number = {},
pages = {125217},
doi = {10.1016/j.carbpol.2026.125217},
pmid = {41943321},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Fructans/chemistry/pharmacology/isolation & purification ; *Codonopsis/chemistry ; *Inulin/chemistry/pharmacology ; Molecular Weight ; Mice ; Fermentation ; Molecular Dynamics Simulation ; },
abstract = {The therapeutic efficacy of dietary fibers is closely related to structural heterogeneity, yet the impact of chain length on physicochemical behavior and gut microbiota modulation remains unclear. Herein, three homologous linear β-(2 → 1)-linked inulin-type fructans with distinct molecular weights, hereafter referred to as CBP1-3, were isolated from Codonopsis bulleynana. All fractions spontaneously assembled into stable supramolecular nanoparticles/disks in water, a process thermodynamically driven by intermolecular hydrogen bonding according to molecular dynamics simulations. Biological evaluation revealed a striking divergence: while low-molecular-weight fractions showed superior efficacy in in vitro fermentation, the relatively high-molecular-weight CBP1 exhibited superior in vivo potency. Multi-omics analysis supports the hypothesis that this supramolecular structure, in synergy with extended chain length, may function as a structural barrier and confer sustained-release characteristics. This likely limits mucin-degrading Akkermansia proliferation via a nutrient-sparing effect, thereby maintaining metabolic homeostasis. These findings demonstrate that relatively high-molecular-weight polysaccharides possess unique ecological advantages in physiological contexts, challenging traditional in vitro screening paradigms and positioning CBP1 as a promising candidate for precision microbiome restoration.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Fructans/chemistry/pharmacology/isolation & purification
*Codonopsis/chemistry
*Inulin/chemistry/pharmacology
Molecular Weight
Mice
Fermentation
Molecular Dynamics Simulation

@article {pmid41936486,
year = {2026},
author = {Pasta, A and Formisano, E and Calabrese, F and Navazzotti, G and Giannini, EG and Savarino, V and Savarino, EV and Marabotto, E},
title = {Dietary and nutraceutical interventions for functional dyspepsia: A narrative review.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2026.03.010},
pmid = {41936486},
issn = {1878-3562},
abstract = {Functional dyspepsia (FD) is a prevalent disorder of gut-brain interaction. Commonly, meals may exacerbate FD symptoms like postprandial fullness, early satiation, epigastric pain, and nausea. We narratively synthesize meta-analyses, randomized trials, and observational evidence to outline mechanism-based dietary and nutraceutical options. Evidence favors small, regular, lower-fat meals and adjusting texture/osmolarity to minimize gastric distension. In selected phenotypes-particularly postprandial distress with bloating-a brief, dietitian-supervised low-FODMAP trial with staged reintroduction can define personal thresholds. Among nutraceuticals, peppermint-caraway, ginger, STW-5, curcumin, and selected probiotics show benefit, with melatonin and barrier-forming agents promising in subsets, while safety remains product-specific.},
}

@article {pmid41936491,
year = {2026},
author = {Burns, KF and Blair, RH and Mares, JA and LaMonte, MJ and Wactawski-Wende, J and McSkimming, D and Liu, Z and Millen, AE},
title = {Gut bacteria associated with an atherogenic TMAO-dietary pattern and choline-rich foods among aging women.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104635},
doi = {10.1016/j.numecd.2026.104635},
pmid = {41936491},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Choline can be metabolized by gut bacteria with a choline utilization gene, CutC, as identified through genome sequencing studies. This metabolism produces trimethylamine, the precursor to the atherosclerotic metabolite trimethylamine N-oxide (TMAO). Bacterial species involved in trimethylamine production in free-living humans have been under-investigated. We previously developed the TMAO dietary pattern (TMAO-DP), which is predictive of plasma TMAO and choline. We evaluated associations between the TMAO-DP, dietary choline, and choline-rich foods (fish, red meat, eggs) with the abundance of species with CutC. We also explored associations between the TMAO-DP and microbiome diversity.

METHODS AND RESULTS: This cross-sectional analysis included 287 women (mean age = 79.6 years) from the Women's Health Initiative. Diet was assessed using a food frequency questionnaire. Stool samples were collected and the V3-V4 regions of the 16S ribosomal RNA were sequenced. Adjusted linear regression models evaluated associations between the TMAO-DP with the CLR-transformed abundance of species with CutC and with alpha-diversity indices. For beta-diversity, PERMANOVA examined measures of Aitchison distance within and between quartiles of the TMAO-DP. Associations between dietary choline and choline-rich foods with the abundance of species were evaluated using linear regression. The TMAO-DP was associated with Acidaminococcus intestini [Beta (SE): 0.23 (0.09), p-value = 0.035] and Desulfovibrio desulfuricans [Beta (SE): 0.16 (0.6), p = 0.035]. The TMAO-DP was not associated with alpha- or beta-diversity.

CONCLUSION: This study provides evidence that Desulfovibrio desulfuricans and Acidaminococcus intestini, two species identified as having CutC by gene sequencing, may produce trimethylamine from diet in free-living women.},
}

@article {pmid41936687,
year = {2026},
author = {Viswan, A and Augustine, N},
title = {Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02726-1},
pmid = {41936687},
issn = {1432-184X},
}

@article {pmid41936794,
year = {2026},
author = {Evans, C and Petry, A and Johnson, T and Kogut, MH and Walk, CL and York, T},
title = {A NEW FOCUS ON FIBER.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106863},
doi = {10.1016/j.psj.2026.106863},
pmid = {41936794},
issn = {1525-3171},
abstract = {Dietary fiber (DF) in poultry nutrition was once viewed mainly as an anti-nutritional factor that reduced energy density and nutrient digestibility. Current research shows DF can play important functional roles in gut health, nutrient utilization, and overall performance when its type and inclusion level are carefully managed. Fiber fractions differ widely in chemical composition and physical properties such as solubility, water-holding capacity, and water-binding capacity. These factors influence digesta viscosity, passage rate, microbial fermentation, and satiety, making precise fiber characterization critical for effective diet formulation. Traditional methods like crude fiber analysis underestimate total fiber and miss key soluble fractions. Modern approaches, including total dietary fiber analysis and near-infrared spectroscopy allow for better quantification of both insoluble and soluble components and support incorporation into real-time feed formulation. By understanding and targeting specific non-starch polysaccharides or oligosaccharides, nutritionists can promote beneficial fermentation, encourage short-chain fatty acid (SCFA) production, and minimize undesirable protein fermentation or pathogen growth. Dietary fiber also supports intestinal barrier function by stimulating gut development, increasing villus height, and fueling epithelial cells through SCFAs. However, poorly balanced fiber can impair nutrient absorption, increase maintenance energy needs, or elevate digesta viscosity, particularly in young birds. Monitoring gut health is now possible by using biomarkers as tools to evaluate intestinal integrity, inflammation, and microbial balance as we investigate the impact of dietary fiber, but further work is needed to standardize these measures and account for flock variability When properly applied, DF can enhance feed efficiency, improve welfare by reducing hunger-driven behaviors, support reproductive performance, and strengthen disease resilience. A data-driven, precision approach combining accurate fiber analysis, enzyme supplementation, microbiome profiling, and non-invasive gut health biomarkers offers the greatest potential to optimize both productivity and sustainability in poultry systems. The purpose of this symposium was to stimulate discussion and enhance understanding of dietary fiber and its potential benefits in improving poultry production. This paper provides an overview of each contributing author's role in the symposium. Dr. Caitlin Evans addressed the challenges associated with current fiber nomenclature and emphasized the need to improve analytical methods and overall understanding of fiber. She brings strong credibility to this topic as a Technical Manager for Near-Infrared Spectroscopy and Feed Milling Engineer at AB Vista, and as a Ph.D. graduate of Kansas State University. Dr. Amy Petry shared her expertise on the impact of fiber in swine nutrition and how these findings can be applied to poultry. She is an Assistant Professor in the Division of Animal Sciences at the University of Missouri, where her research focuses on improving fiber utilization and its effects on energy efficiency and animal health. Dr. Tim Johnson, Professor in the Department of Veterinary and Biomedical Sciences at the University of Minnesota, highlighted the importance of understanding the poultry microbiome and its role in developing strategies to enhance bird performance. Dr. Mike Kogut contributed his expertise as a Research Microbiologist and Lead Scientist with the Food and Feed Safety Research Unit at the Southern Plains Agricultural Research Center. Finally, Dr. Carrie Walk, Head of Research at AB Vista, along with Dr. Tara York, AB Vista's Technical Director for North America, integrated the key themes of the symposium, connecting the presented research and practical applications.},
}

@article {pmid41936807,
year = {2026},
author = {Nualart C, D and Schwob, G and Orlando, J and Pashcke, K and Guerreiro, PM and McCormick, SD and Cheng, CC and Vargas-Chacoff, L},
title = {Microplastic pollution and thermal increase alter cellular stress responses and microbiomes in Antarctic and Sub-Antarctic fish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128039},
doi = {10.1016/j.envpol.2026.128039},
pmid = {41936807},
issn = {1873-6424},
abstract = {Antarctic and sub-Antarctic fishes of the genus Harpagifer inhabit extreme environments and face emerging anthropogenic stressors, including plastic pollution and warming. While each factor is known to affect fish physiology, their acute combined impacts on molecular responses and host-microbe interactions remain poorly understood. In this study, we investigated the immediate (24 h) transcriptional response of stress-related genes heat shock protein 70 (hsp70), S100 calcium binding protein (s100), High Mobility Group 1 box (hmg1b), E3 Ubiquitin Ligases (E3), and BCL2 Associated X (Bax) and gut microbiome diversity in H. antarcticus (King George Island, Antarctica) and H. bispinis (Punta Arenas, Chile) exposed to elevated temperature (TI), PVC microplastics (MP), or their combination (TI+MP). Both stressors altered gene transcription in a tissue- and species-specific manner, suggesting a synergistic stress response under combined treatment. Temperature rise consistently modulated stress markers, while acute PVC exposure intensified apoptotic signaling. Notably, species-specific patterns emerged: H. bispinis showed a more pronounced induction of pro-apoptotic pathways, whereas H. antarcticus maintained a higher induction of protective chaperones within this short temporal window. At the microbial level, while community-wide diversity metrics remained statistically stable, an exploratory analysis revealed increased inter-individual variability and the enrichment of specific stress-tolerant bacterial taxa. These results reveal that acute warming and microplastic exposure interactively disturb host, cellular homeostasis, with distinct transcriptional plasticity across closely related species. Our study provides mechanistic insights into the early physiological challenges faced by Notothenioids, highlighting the importance of coupling molecular biomarkers with microbiome analyses to assess the initial stages of response in cold-adapted fishes to environmental change.},
}

@article {pmid41936881,
year = {2026},
author = {Liang, L and Fu, Y and Guan, D and Zeng, H and Wang, H and Peng, J and Shao, Y and Zhang, S and Liu, L},
title = {Effects of 16S rRNA hypervariable region selection on respiratory Microbiome profiling in healthy adults.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107493},
doi = {10.1016/j.mimet.2026.107493},
pmid = {41936881},
issn = {1872-8359},
abstract = {Selection of the 16S rRNA gene target region can substantially influence inferred respiratory microbiome profiles, particularly in low-biomass samples. In this study, we compared full-length V1-V9 (Pacific Biosciences) and V3-V4 (Illumina) amplicon sequencing using exhaled breath condensate collected from 50 healthy adults. Samples that yielded successful amplification for both approaches were included in paired, within-subject comparisons of sequencing depth, alpha diversity, and taxonomic composition. Sequencing of the V3-V4 region yielded significantly higher read counts and greater alpha diversity (richness and Shannon index) than full-length V1-V9 sequencing (all p < 0.001). Both approaches consistently identified a shared set of dominant respiratory-associated genera, including Acinetobacter, Streptococcus, Psychrobacter, Gemella, Neisseria, and Granulicatella. However, relative abundance estimates differed by target region, with Acinetobacter enriched in V1-V9 profiles, whereas Streptococcus and Neisseria were more abundant in V3-V4 data. In contrast, several genera showed comparable abundances across regions. These findings indicate that while overall community membership is broadly conserved, quantitative diversity metrics and genus-level abundance estimates are strongly influenced by primer and target-region selection. Overall, these results provide methodological guidance for interpreting respiratory microbiome data derived from exhaled breath condensate and highlight the importance of aligning sequencing strategies with specific study objectives.},
}

@article {pmid41936917,
year = {2026},
author = {Zhang, S and Yue, T and Jin, P and Zhang, X and Huo, Q and Li, W and Tian, C and Dong, H and Dong, Y and Zhao, Y and Li, D},
title = {4-Octyl itaconate attenuates radiation-induced intestinal injury associated with ferroptosis inhibition and microbiota rebalance.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.04.006},
pmid = {41936917},
issn = {1873-4596},
abstract = {Radiation-induced intestinal injury (RIII) is a serious and common complication of radiotherapy, and there are currently no effective therapeutic strategies. This study investigates the protective role of 4-octyl itaconate (4-OI), a cell-permeable itaconate derivative, against RIII. In vitro, 4-OI pretreatment enhanced the viability of irradiated intestinal epithelial cells, reduced reactive oxygen species (ROS) accumulation, and alleviated DNA damage. In a murine model of total body irradiation, 4-OI administration mitigated intestinal structural disruption, promoted crypt stem cell regeneration, and suppressed epithelial apoptosis. Mechanistically, 4-OI exerted its cytoprotective effects by modulating the SLC7A11/GPX4 axis to inhibit ferroptosis and enhancing glutathione biosynthesis. Furthermore, 16S rRNA sequencing revealed that 4-OI treatment recalibrated radiation-induced gut microbiota dysbiosis, suggesting an additional microbiome-mediated protective pathway. To our knowledge, the results represent the first demonstration of 4-OI's protective effects in RIII pathogenesis, positioning it as a novel therapeutic candidate for clinical radioprotection through dual mechanism targeting.},
}

@article {pmid41936935,
year = {2026},
author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F},
title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134553},
doi = {10.1016/j.biortech.2026.134553},
pmid = {41936935},
issn = {1873-2976},
abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.},
}

@article {pmid41937023,
year = {2026},
author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H},
title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102978},
doi = {10.1016/j.tmaid.2026.102978},
pmid = {41937023},
issn = {1873-0442},
abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.

METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.

RESULTS: In total, 3,770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1,021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).

CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.},
}

@article {pmid41937169,
year = {2026},
author = {Mullin, CE and Louca, S},
title = {Effects of heat-assisted sample desiccation on microbiome surveys.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00889-5},
pmid = {41937169},
issn = {2524-6372},
abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.},
}

@article {pmid41937467,
year = {2026},
author = {Lee, HJ and Lee, JH and Kwak, YS},
title = {A Keystone-Taxa SynCom Reveals Chlorella-Microbiome-Plant Communication and Enhances Suppression of Fusarium oxysporum.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2601023},
doi = {10.4014/jmb.2601.01023},
pmid = {41937467},
issn = {1738-8872},
mesh = {*Chlorella/physiology ; *Fusarium/drug effects/growth & development ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; Solanum lycopersicum/microbiology/growth & development ; Antifungal Agents/pharmacology ; Mannitol/pharmacology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Chlorella, a microalga renowned for its high protein and lipid content, is extensively used as a biofertilizer due to its plant growth promotion and disease suppression capabilities. To reveal, Chlorella-microbiome-plant communication, in-depth microbiota structure and network analyses were conducted. As a result, keystone taxa, which are microbial element in interaction with Chlorella, keystone taxa (Psedomonas, Duganella, Brevibacterium) interaction with C. fusca CHK0059 within plant hosts were identified. Here, however, the mechanistic insights into these interactions remain limited. Therefore, we aimed to investigate the characteristics of keystone taxa to elucidate Chlorella effects on plants. By applying various substances, including Chlorella, Chlorella methanol extract (methanol extract), and D-mannitol, we observed changes in microbial distribution and diversity, with a notable increase in Pseudomonas abundance following 2% D-mannitol treatment. Additionally, we assessed the impact of Chlorella on plant growth and disease suppression, finding that a synthetic community (SynCom) of keystone taxa exhibited enhanced antifungal effects against Fusarium oxysporum in both strawberry and tomato, compared to individual strains. The findings in this study suggested the fundamental data that the SynCom can contribute to the mechanism of action of C. fusca CHK0059 and expect to maximize the effect of Chlorella when combined.},
}

*Chlorella/physiology
*Fusarium/drug effects/growth & development
*Plant Diseases/microbiology/prevention & control
*Microbiota
Solanum lycopersicum/microbiology/growth & development
Antifungal Agents/pharmacology
Mannitol/pharmacology
Bacteria/classification/genetics/isolation & purification

@article {pmid41937585,
year = {2026},
author = {Chen, X and Dong, T and Wu, D and Pan, Q and Wei, J and Liang, G and Lin, Z},
title = {Shifts in the Lung Microbiota and Antibiotic Resistance Genes Occur With Aging in Patients With Lower Respiratory Tract Infections.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e9038281},
pmid = {41937585},
issn = {2314-6141},
mesh = {Humans ; Adult ; Aged ; *Microbiota/genetics ; Middle Aged ; Adolescent ; Child ; *Aging/genetics ; Female ; *Respiratory Tract Infections/microbiology/drug therapy/genetics ; Male ; Aged, 80 and over ; *Lung/microbiology ; Child, Preschool ; Young Adult ; *Drug Resistance, Microbial/genetics ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Lower respiratory tract infections (LRTIs) are a leading cause of critical illness and mortality. The lung microbiome represents an important reservoir for the exchange of antibiotic resistance genes (ARGs). The pathogenic microbes remain poorly understood among different age groups, including children (0-17 years), youth (18-39 years), middle-aged adults (40-64 years), and older adults (65-99 years). We conducted a retrospective study of 699 bronchoalveolar lavage fluid (BALF) samples from LRTI patients aged 30 days to 99 years. The differences in the lung microbiome and ARG expression shift with age were evaluated based on targeted next-generation sequencing (tNGS) results. Correlation analysis revealed that age had a strongly positive correlation effect on the relative abundances of Candida albicans, Candida glabrata, Corynebacterium striatum, and Stenotrophomonas maltophilia. Meanwhile, age had a largely negative correlation effect on Enterococcus faecium and Mycoplasma pneumoniae. We found that ARG expression was significantly higher in adults compared with children. The beta-lactam ARG TEM was the most abundant, and the primary carrier of ARGs was Streptococcus in the LRTI microbiota. The proportion of adults expressing beta-lactams, aminoglycosides, and phenicol antibiotic types was higher compared to children. Our results indicated that ARGs in the human LRTI microbiota accumulate and become more complex with age, as older groups tend to harbor the highest abundance of these genes. Collectively, these results presented the respiratory tract core microbiota and ARGs in different age groups, supplying a foundation for microbiome-targeted interventions and emphasizing the potential of tNGS to improve clinical diagnosis.},
}

Humans
Adult
Aged
*Microbiota/genetics
Middle Aged
Adolescent
Child
*Aging/genetics
Female
*Respiratory Tract Infections/microbiology/drug therapy/genetics
Male
Aged, 80 and over
*Lung/microbiology
Child, Preschool
Young Adult
*Drug Resistance, Microbial/genetics
Infant
Bronchoalveolar Lavage Fluid/microbiology
Retrospective Studies
Infant, Newborn
Anti-Bacterial Agents/pharmacology

@article {pmid41937700,
year = {2026},
author = {Van Vu, S and Kundu, S and Woo, KH and Uttarotai, T and Van Doan, H},
title = {Impact of Body Weight on the Intestinal Microbiome of Cage-Cultured Oyster Pompano (Trachinotus anak).},
journal = {Animal genetics},
volume = {57},
number = {2},
pages = {e70092},
doi = {10.1002/age.70092},
pmid = {41937700},
issn = {1365-2052},
support = {106.05-2023.64//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; //Chey Institute for Advanced Studies' International Scholar Exchange Fellowship/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; *Body Weight ; Bacteria/classification/genetics ; *Ostreidae/microbiology ; },
abstract = {Oyster pompano (Trachinotus anak) is a commercially valuable marine species widely farmed in Southeast Asia, yet growth heterogeneity remains a persistent challenge in cage aquaculture. To investigate whether body weight influences the intestinal microbiota of this species, we compared the gut microbial communities of small and large T. anak using high-throughput 16S rRNA gene sequencing. The intestinal microbiota was dominated by Pseudomonadota (Proteobacteria) and Mycoplasmatota, together accounting for nearly 80% of total sequences, with additional contributions from minor phyla such as Spirochaetota, Thermodesulfo bacteriota, and Bacteroidota. While alpha- and beta-diversity analyses revealed no significant differences between groups, community composition and structure varied. Smaller fish harbored a more heterogeneous assemblage at the class level and a broader suite of core taxa, including Acinetobacter, Aeromonas, Bdellovibrio, and Comamonas. In contrast, larger fish were dominated by fewer classes, with Photobacterium and Brevinema emerging as distinctive core members. LEfSe analysis identified discriminant taxa between groups, although these trends were not statistically significant after multiple-testing correction. Network analysis highlighted striking differences in microbial interactions: smaller fish exhibited highly modular, densely connected networks with potential keystone taxa such as Paracidovorax and Ensifer, whereas larger fish displayed simpler, less structured networks indicative of reduced ecological stability. Together, these findings demonstrate that body weight is associated with subtle but ecologically meaningful shifts in microbiota composition, core membership, and interaction networks in cage-cultured T. anak. This work underscores the potential of microbiome-informed management strategies to mitigate growth variability and enhance the sustainability of marine aquaculture.},
}

Animals
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Aquaculture
*Body Weight
Bacteria/classification/genetics
*Ostreidae/microbiology

@article {pmid41937731,
year = {2026},
author = {Kong, JF and Phang, HC and Wan Kamal, WHB and Ng, Y and Mohamad, S and Kee, PE and Liew, KB},
title = {Role of Probiotics in Oral Health: A Review From Microbial Balance to Clinical Applications.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010421039251206192855},
pmid = {41937731},
issn = {1873-4316},
abstract = {A diverse microbial community exists within the human oral cavity that plays an essential role in maintaining health or inducing diseases such as dental caries, periodontal disease, and halitosis. Probiotics, live microorganisms that provide health benefits when consumed in adequate amounts, have been found to be promising as a means of modulating the oral microbiome and combating these diseases. This review incorporates present knowledge about the mechanism of probiotic action, including competitive exclusion of pathogens, antimicrobial metabolite production, biofilm disruption, and immune modulation. Efficacy against pathogenic bacteria like Streptococcus mutans and Porphyromonas gingivalis has been proven by prominent probiotic groups Lactobacillus, Bifidobacterium, and Streptococcus, resulting in oral microbial homeostasis. Clinical applications of probiotics include prevention of caries, plaque reduction, and management of gingivitis and periodontitis, with research focusing on strain-specific effects. Emerging trends include precision probiotics tailored to each oral condition, postbiotics as strong alternatives (formerly "strong contenders"), and innovative delivery systems to enhance viability and colonization. The hurdles of strain specificity, regulatory gaps, and inconsistencies of clinical outcome continue. Safety concerns, while rare, represent possible risks of horizontal gene transfer and opportunistic infections in immunocompromised hosts. Future directions lie in genetic modification, new delivery methods, and standard clinical protocols to enhance probiotic function. This review emphasizes the clinical potential of probiotics as adjunctive treatments in oral medicine, with the caveat that further work is needed to overcome current challenges and enhance their therapeutic efficacy.},
}

@article {pmid41937967,
year = {2026},
author = {Hiratsuka, D and Matsuo, M and Hirota, Y},
title = {Endometrial Microbiome and Implantation: From Basic Knowledge to Clinical Medicine.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70040},
pmid = {41937967},
issn = {1445-5781},
abstract = {BACKGROUND: Recurrent implantation failure (RIF) is an infertility condition in which uterine factors remain difficult to diagnose and treat. Recent studies implicate the endometrial microbiome in implantation.

METHODS: This clinically oriented narrative review summarizes female reproductive tract microbiota and evidence on endometrial microbiome testing and management in infertility.

MAIN FINDINGS RESULTS: Vaginal dysbiosis is linked to adverse reproductive outcomes and provides a reference for interpreting upper-tract findings. Endometrial microbial signals are detectable by sequencing, but interpretation is challenged by the low-biomass environment and vulnerability to carry-over, kitome effects, and contamination. Across ART studies, a Lactobacillus-enriched endometrial profile is more often associated with favorable pregnancy-related outcomes, whereas non-Lactobacillus-dominant patterns are more frequently reported in implantation failure, although effect sizes and statistical significance vary across cohorts and depend on sampling validity and cutoff definitions. Limited nonrandomized intervention studies suggest that testing-guided targeted management (typically antibiotics with or without vaginal Lactobacillus-containing probiotics) may benefit selected patients, but protocols are heterogeneous and results remain inconsistent.

CONCLUSION: Evidence is rapidly evolving, yet observational designs and methodological variability limit causal inference. Future progress will require standardized sampling and contamination controls, outcome-anchored threshold validation, and pragmatic real-world evaluations of protocolized test-and-treat pathways using clinically meaningful endpoints.},
}

@article {pmid41938040,
year = {2026},
author = {Khalil, A and Thayer, ZM and Rivera, LM},
title = {Preterm birth, airway microbiome, and the evolutionary origins of asthma.},
journal = {Evolution, medicine, and public health},
volume = {14},
number = {1},
pages = {1-2},
pmid = {41938040},
issn = {2050-6201},
}

@article {pmid41938156,
year = {2026},
author = {Liu, YH and Huang, JR and Tao, Y and Wang, CC and Gu, CQ and Zhang, YM and Li, WJ and Jiang, HC},
title = {Aridity gradient overrides degradation in shaping the topsoil microbiome of the Tianshan wild fruit forest.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100586},
pmid = {41938156},
issn = {2666-5174},
abstract = {The Tianshan wild fruit forest, a critical relict ecosystem and biodiversity hotspot, is experiencing severe degradation, a process widely assumed to be the primary driver of negative shifts in soil microbial communities. However, in arid regions, the overarching influence of climatic aridity may supersede localized degradation effects, creating a pivotal scientific question: which factor-aridity or degradation-dominantly regulates the soil microbiome in this unique habitat? To address this, we analyzed 360 topsoil samples across degradation and aridity gradients using high-throughput sequencing. The results demonstrate that the aridity index, not degradation level, is the paramount factor shaping microbial community structure, explaining the largest proportion of variation in both bacterial (∼43%) and fungal (∼30%) communities. The ecosystem harbors an exceptionally stable core microbiome, with community assembly predominantly governed by stochastic processes. Notably, alternating wet-dry (dry sub-humid) conditions significantly enhanced the complexity and stability of microbial co-occurrence networks compared to semi-arid or humid regions. Additionally, soil microbes mediated multiple core ecological processes, with nitrogen cycling as the most abundant-dominated by Rhodoplanes, Alcaligenes, and rhizobial taxa (Bradyrhizobium, Allorhizob), among others-wherein nitrate reduction was exceptionally active in the Tianshan wild fruit forest, particularly in humid and semi-arid habitats. These findings challenge the prevailing degradation-driven paradigm, highlighting aridity as the master regulator of microbial communities. This insight is crucial for guiding conservation strategies, emphasizing that managing water availability and protecting dry sub-humid habitats are essential for maintaining the microbial stability and functional resilience of this invaluable ecosystem under climate change.},
}

@article {pmid41938217,
year = {2026},
author = {Mphande-Nyasulu, FA and Meksang, S and Noranate, N and Kongpanyakul, S and Kulalert, P and Nilchan, P and Trivijitsilp, P},
title = {Investigating Candida species and associated bacteria from vaginal swabs and smears of symptomatic and asymptomatic adult women: A cross-sectional study.},
journal = {IJID regions},
volume = {19},
number = {},
pages = {100868},
pmid = {41938217},
issn = {2772-7076},
abstract = {OBJECTIVES: Vaginal Candida infections are common among women, affecting between 75% and 80% of women in their lifetime, with a higher prevalence in women of childbearing age. This study assessed vaginal carriage of Candida species and associated bacteria in adult women.

METHODS: A total of 101 vaginal swabs and smears from symptomatic and asymptomatic adult women were analyzed for the presence of Candida sp. using culture, Gram stain, and next-generation sequencing (NGS). Morphology of selected Candida sp. was examined using scanning electron microscopy.

RESULTS: Candida colonization was observed in 39.6% (40 of 101) of the women. Candida albicans was identified in 75.0% (30 of 40) of the women, whereas the non-albicans species Nakaseomyces glabrata was observed in 7.5% (three of 40), P. kudriavzevii in 5% (two of 40), and C. tropicalis in 2.5% (one of 40). Women aged 18-25 years had the highest prevalence of colonization among all age groups, 47.5% (19 of 40). A significant difference in vaginal bacterial composition was observed among age groups 18-25 and 26-35 years (α 0.05 <0.038*, 95% confidence interval [CI] -0.16 to 0.99); between women positive for Candida aged 26-35 years and those aged 46-55 years (α 0.05 <0.016*, 95% CI -0.28 to -0.03); and between women who were Candida-positive and those who were Candida-negative (α 0.05 <0.016*, 95% CI 0.17 to -0.40). Among the women positive for Candida, symptomatic individuals had predominantly Gram-positive bacterial species 92.6% (23 of 25) compared with 46% (19 of 42) in asymptomatic individuals. Five bacterial species were shared between the symptomatic and asymptomatic samples. Unique budding patterns, surface modifications, and phylogenetic clusters are reported.

CONCLUSION: Vaginal Candida colonization including differences in microbiome composition according to age, disease status, and colonizing Candida species are reported. This study opens new areas of study in vaginal Candida colonization, pathogen-pathogen interaction, and microbiome analysis in more specific age brackets, away from the traditional pre-menopausal and menopausal women.},
}

@article {pmid41938356,
year = {2026},
author = {Chen, Y and Zhao, S and Ma, X and Ling, L and Du, P and Liu, X and Yao, Y and Ma, Q and Cheng, Y and Wang, Y and Wei, J and Nian, H and Lian, T},
title = {Selenium nanoparticles and glutathione synergistically enhance salt tolerance in soybean via the jasmonic acid pathway and arbutin-regulated rhizosphere microbiota.},
journal = {aBIOTECH},
volume = {7},
number = {2},
pages = {100022},
pmid = {41938356},
issn = {2662-1738},
abstract = {Soil salinity threatens agriculture worldwide. Nano-fertilizers offer a promising strategy to enhance tolerance to salinity and other stresses in crops, but their field performance is sometimes unpredictable, potentially due to complex interactions within the plant-microbe holobiont. Here, we designed chitosan-stabilized selenium nanoparticles (SeNPs@CS) as a novel nano-fertilizer. SeNPs@CS exhibited a uniform size (∼109.8 nm) and a positively charged surface (+14.7 mV), which confers good adhesion to plant tissues. Due to their good biocompatibility and small size, SeNPs@CS can be readily absorbed and utilized by plant leaves. When SeNPs@CS were combined with glutathione (GSH) to form a nanocomposite (SeG), they significantly promoted plant growth and enhanced salt tolerance in soybean (Glycine max). Multi-omics analyses revealed that SeG activates jasmonic acid (JA) pathways in the plant and remodels the root metabolic profile, leading to the enrichment of arbutin, a key signaling molecule, in the rhizosphere. This metabolic shift recruits and enriches beneficial salt-tolerant microbes, including Bacillus and Streptomyces, thereby establishing a protective microbiome. Treatment of plants with a synthetic microbial community (SynCom) composed of these elite strains, in combination with arbutin, reproduced the salt tolerance phenotype conferred by SeG treatment. Therefore, SeG improves salt tolerance in soybean via activation of the JA defense pathway and arbutin-driven recruitment of salt-tolerant rhizosphere microorganisms. Together, these two mechanisms enhance plant resilience under salt stress. This multi-kingdom synergistic mechanism for alleviating stress provides a new paradigm for developing smart agricultural inputs that target the plant holobiont to improve crop resilience.},
}

@article {pmid41938562,
year = {2026},
author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F},
title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).},
journal = {Veterinary world},
volume = {19},
number = {2},
pages = {864-876},
pmid = {41938562},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.

MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), α- and β-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.

RESULTS: α-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, β-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.

CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.},
}

@article {pmid41938768,
year = {2026},
author = {Xue, Z and Han, Q and Han, H and Yan, L and Ma, X and Ji, P and Wang, B and Zhang, L and Wang, L and Liu, G},
title = {Mechanisms of fetal growth restriction in gestational cholestasis: role of gut microbiota and placental redox.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1815498},
pmid = {41938768},
issn = {2297-1769},
abstract = {INTRODUCTION: Intrahepatic cholestasis of pregnancy (ICP) is a cholestatic liver disorder associated with substantial fetal morbidity, including preterm birth, fetal distress, and even intrauterine demise. Although prior studies have documented structural and transcriptional alterations in the placenta during ICP, the mechanistic underpinnings linking maternal cholestasis to adverse fetal outcomes remain incompletely elucidated.

METHODS: In this study, a murine model of ICP was established by feeding pregnant C57BL/6 mice a 0.1% DDC (3,5-dicarboxylic acid-1,4-dihydrocollidine) diet from E0.5 to E18.5. We assessed fetal growth and employed multi-omics approaches, including placental transcriptome sequencing, maternal gut microbiome profiling, and serum/placental metabolome analysis.

RESULTS: Placental transcriptome sequencing revealed that ICP significantly downregulated the expression of antioxidant-related genes including Mgst1, Gstt1, Ggt1, Gpx8, Gstk1, and GSTA4 leading to reduced total antioxidant capacity in placental tissue and elevated levels of malondialdehyde (MDA), a marker of lipid peroxidation. Furthermore, ICP disrupted the maternal gut microbiota, resulting in decreased production of antioxidant microbial metabolites such as valeric acid and erythritol. This deficiency further aggravated oxidative damage in the placenta.

DISCUSSION: Collectively, our findings uncover a novel gut microbiota-placenta axis driven by cholestasis, which contributes to fetal IUGR. The maternal cholestasis induces gut dysbiosis, which diminishes the production of valeric acid and erythritol. The deficiency of these metabolites, coupled with a direct suppression of the placental Nrf2/Keap1 antioxidant signaling pathway by cholestasis, leads to placental oxidative stress. This oxidative damage impairs placental function, ultimately resulting in fetal growth restriction. Disrupting this pathogenic cycle may offer a promising therapeutic strategy for preventing or treating ICP-related reproductive disorders.},
}

@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.},
}