@article {pmid42465057,
year = {2026},
author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, A and Taga, ME},
title = {Quenching corrinoid-based interactions in a model bacterial coculture.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag160},
pmid = {42465057},
issn = {2730-6151},
abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents an attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite "quenching" strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged in corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid, leading to inhibition of corrinoid-dependent growth. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity "molecular sponges" to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and potentiate precision microbiome manipulation strategies.},
}

@article {pmid42465603,
year = {2026},
author = {Yang, Y and Xia, Y and Li, Y and Li, W and Luo, J and Guo, C and Zhang, H and Jiang, B and Zhu, S and Li, J and Liu, Y and Wang, C},
title = {Relay maize after tobacco enhances rapeseed growth and nutrition by reshaping soil microbial communities in an annual triple cropping system.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1827060},
pmid = {42465603},
issn = {1664-462X},
abstract = {Multiple cropping systems are increasingly being adopted worldwide to improve land-use efficiency and promote sustainable agriculture. To optimize the traditional post-tobacco fallow period, we evaluated a novel tobacco-maize-rapeseed (T_M_R) triple-cropping system. Using field experiments and high-throughput amplicon sequencing, we investigated the effects of the preceding tobacco crop and the additional maize season on rapeseed performance and soil microbial ecology. The addition of a maize season enhanced early growth vigor of rapeseed and improved key yield components, resulting in a theoretical yield of 5388.48 kg/ha. Rapeseed nitrogen uptake significantly increased compared with the conventional rotation (P < 0.05), and was positively associated with soil alkali-hydrolyzable nitrogen and major yield components. Different cropping systems significantly reshaped the β-diversity of soil microbial communities in the root-zone soil of rapeseed. Under the maize addition treatment, bacterial co-occurrence networks exhibited greater connectivity and complexity. Chujaibacter, Sporosarcina, and Epicoccum were enriched and identified as discriminative taxa using random forest analysis. In conclusion, the tobacco-maize-rapeseed triple-cropping system enhances nitrogen nutrition and reshapes soil microbial communities, providing a sustainable strategy for improving crop performance and agroecosystem functioning.},
}

@article {pmid42459877,
year = {2026},
author = {Romero-Arguelles, R and Ruiz-Ayma, G and Rodriguez-Castro, VA and Gonzalez-Rojas, JI and Gomez-Govea, MA},
title = {Next-generation soil monitoring: linking metagenomics, biosensors, and ecological modeling for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1861333},
pmid = {42459877},
issn = {1664-302X},
abstract = {Soils represent one of the most complex and dynamic biological systems on Earth, where microbial communities play a central role in regulating ecosystem functions, including nutrient cycling, carbon sequestration, and plant productivity. However, increasing pressures from land-use intensification and climate change threaten soil health and biodiversity, highlighting the need for innovative monitoring and management approaches. In this review, we synthesize current advances in soil microbial ecology, sustainable soil management, environmental sensing technologies, and metagenomics to propose an integrative framework for soil monitoring and prediction. This review integrates environmental sensing, microbiome characterization, ecological modeling, and AI-based analytics into a unified framework for next-generation predictive soil monitoring systems. We discuss how high-resolution environmental sensors enable real-time characterization of soil physicochemical dynamics, while metagenomic approaches provide unprecedented insights into the taxonomic and functional diversity of soil microbiomes. Furthermore, we explore the role of microbial network analysis and ecological modeling in uncovering interaction patterns and predicting ecosystem responses to environmental change. The integration of these tools through machine learning and data-driven approaches is transforming soil science from a descriptive to a predictive discipline. We also address key challenges, including data standardization, scalability, and the interpretation of complex biological datasets. Finally, we highlight emerging directions such as microbiome-informed precision agriculture, microbiome engineering, and the development of soil digital twins. Together, these advances pave the way toward sustainable soil management strategies that enhance ecosystem resilience and agricultural productivity in the face of global change.},
}

@article {pmid42460974,
year = {2026},
author = {Gouka, L and Groen, E and Makowicz, E and Christensen, JH and Raaijmakers, JM and Cordovez, V},
title = {Yeast-Fusarium interactions and mycotoxin modulation in the phyllosphere.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag187},
pmid = {42460974},
issn = {1751-7370},
abstract = {Yeasts are prevalent members of the phyllosphere microbiome, but fundamental knowledge of the chemical basis of their interactions with other members of the phyllosphere microbiota remains largely elusive. Our previous study revealed that wheat flag leaves harbor taxonomically diverse populations of yeasts with various traits important for successful colonization and survival in the harsh phyllosphere environment. In this study, we investigated interactions between two specific yeast genera, Aureobasidium and Metschnikowia, and the mycotoxigenic fungus Fusarium graminearum, causal agent of Fusarium head blight (FHB). Using multiple experimental approaches, we demonstrate that phyllosphere yeasts effectively colonize wheat leaves and heads, markedly reducing FHB incidence when established before pathogen arrival. Based on metabolomic data, we further show that Aureobasidium and Metschnikowia isolates can degrade the Fusarium mycotoxin deoxynivalenol (DON) and DON-inducing plant compounds produced during or in response to FHB. Our findings highlight the ecology of phyllosphere yeasts and the chemical basis of their multipartite interactions with a mycotoxigenic fungus and the host plant.},
}

@article {pmid42461036,
year = {2026},
author = {Munford, KE and Grégoire, DS and Hug, LA},
title = {Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0031126},
doi = {10.1128/aem.00311-26},
pmid = {42461036},
issn = {1098-5336},
abstract = {Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership, and metal cycling across a landfill's lifespan has not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing Older (aged 31-39 years) and Newer (aged 3-20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals-all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemical data from the time of filling to the present and microbial membership data across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual model for understanding this critical, final stage in a landfill's life cycle.IMPORTANCEAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond ~20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership, and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension-a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer term.},
}

@article {pmid42461822,
year = {2026},
author = {Svendsen, CD and Nielsen, R and Larsen, TH and Kuiper, KKJ and Eagan, TM},
title = {The oral and lower airway microbiota and coronary heart disease in COPD patients and controls.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353738},
pmid = {42461822},
issn = {1932-6203},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/complications ; *Microbiota ; Male ; Female ; Middle Aged ; *Coronary Disease/microbiology/complications ; Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Mouth/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) and coronary heart disease (CHD) are major causes of morbidity and mortality, with shared risk factors and often co-occurring. This study investigated the association between both the oral and lower airway microbiome and CHD in healthy controls and COPD patients.

METHODS: 228 participants from the MicroCOPD study (101 controls and 127 COPD patients) underwent coronary CT angiography to assess calcium score (CaSc) and coronary stenosis. Oral wash (OW) and bronchoalveolar lavage (BAL) samples were collected. Microbial DNA was analyzed using 16S rRNA gene sequencing with the Illumina MiSeq platform. Microbiome composition and diversity were analysed using established pipelines in Quantitative Insights into Microbial Ecology 2 (QIIME 2) and R.

RESULTS: Alpha diversity (Shannon index) differed significantly between COPD patients and controls in OW (p < 0.01), but not BAL. No statistically significant alpha (Shannon or Faith's PD) diversity differences were found between CHD and non-CHD groups. Beta diversity analysis (Bray-Curtis dissimilarity) revealed no significant differences in microbial composition between CHD and non-CHD groups, both for COPD patients and controls (p > 0.05). Firmicutes dominated across all subgroups, followed by Bacteroidetes and Actinobacteria. Several taxa were found to be differentially abundant between CHD and non-CHD groups but comprised less than 1% of all taxa.

CONCLUSION: The microbiome differed between COPD patients and controls, but we could not find evidence that either the oral or lower airway microbiome differed between those with and without coronary heart disease.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/complications
*Microbiota
Male
Female
Middle Aged
*Coronary Disease/microbiology/complications
Aged
RNA, Ribosomal, 16S/genetics
Case-Control Studies
*Mouth/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid42462426,
year = {2026},
author = {Zhang, F and Zhang, X and Wang, Y and He, Y and Qiu, Z and Zhao, S and Gao, S and Zhu, M},
title = {A fungal CRY-DASH photoreceptor mediates light-dependent and-independent regulation of growth and conidiation in Trichothecium roseum.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111972},
doi = {10.1016/j.ijfoodmicro.2026.111972},
pmid = {42462426},
issn = {1879-3460},
abstract = {Light is a key environmental cue shaping fungal growth and development. Among the several photoreceptor families, cryptochrome-DASH (CRY-DASH) proteins are conserved blue-light receptors best known for photolyase/photoreactivation activity, but emerging evidence suggests broader regulatory roles in fungi. Here, we demonstrate that the CRY-DASH photoreceptor acts as a key regulator governing fungal development in the postharvest pathogen Trichothecium roseum under white light and dark conditions. We generated TrCRY-DASH knockout (ΔTrCRY-DASH) and complementation (ΔTrCRY-DASH-C) strains and integrated phenotyping with transcriptomic, metabolomic, and molecular analyses. Loss of TrCRY-DASH caused contrasting light-dependent phenotypes: under white light condition, ΔTrCRY-DASH displayed growth arrest and reduced conidiation, whereas in darkness it exhibited excessive hyphal expansion with minimal conidiation, indicating a critical role in light-dependent growth regulation. Stress assays further showed strong light-dependent sensitivity to osmotic, cell-wall, and oxidative stress that was mitigated in darkness. Multi-omics revealed a far larger transcriptional reprogramming in darkness than in light, with enrichment of pathways linked to cell-wall metabolism, signaling, Reactive Oxygen Species (ROS) homeostasis, and secondary metabolism. TrCKI was predicted as a putative candidate for TrCRY-DASH interaction based solely on bioinformatic analysis, providing a hypothesis for future experimental exploration. Together, our data indicate that TrCRY-DASH is an important regulator that modulates dark-associated growth to maintain growth-conidiation balance and thereby influencing the virulence of T. roseum toward fruits.},
}

@article {pmid42462719,
year = {2026},
author = {Michoud, G and Geers, A and Peter, H and Thorpe, AC and Zhong, ZP and Rich, V and Battin, TJ},
title = {Evolutionary radiation of Polaromonas from mountain glaciers downstream.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.06.070},
pmid = {42462719},
issn = {1879-0445},
abstract = {Habitat transitions are central to microbial ecology and evolution and have been extensively studied across vastly different environments, such as between saline and non-saline environments. However, microbial habitat transitions along other large-scale environmental gradients remain poorly studied. This is particularly true for transitions involving the cryosphere, despite building evidence suggesting the Cryogenian as important for evolutionary radiation. Here, we investigated ecosystem transitions and the related genomic adaptations of the cosmopolitan cryospheric Polaromonas bacterium. We constructed a pangenome from 282 high-quality genomes, sourced from glaciers, glacier-fed streams (GFSs), lakes, wetlands, groundwater, rivers, and soils. Phylogenetic reconciliation suggested that the ancestral Polaromonas genome radiated from glacier ecosystems into various downstream environments through multiple independent transitions. These transitions were likely marked by extensive horizontal gene transfer and gene loss, with mobile genetic elements such as plasmids and prophages playing key roles in genomic diversification. Predicted ancestral genomes encoded versatile metabolic and stress-response capacities, which support adaptation to fluctuating and extreme conditions in the various cryospheric habitats. Compared to the ancestral Polaromonas genome, distinct genomic signatures were associated with specific habitats: GFS lineages possess expanded stress-tolerance repertoires, glacier lineages gained chemolithotrophic and anaerobic pathways, lake and wetland genomes acquired phototrophic functions, and soil lineages expanded substrate transport and stress tolerance. Together, our findings highlight the role of genomic plasticity in the ecological success of Polaromonas and also underscore the cryosphere as a potential evolutionary cradle from which lineages dispersed and adapted to downstream aquatic and terrestrial environments.},
}

@article {pmid42464117,
year = {2026},
author = {Kazemifard, N and Shahrokh, S and Dimitrov, G and Totonchi, M and Dimitrov, S},
title = {From signals to systems: the epigenetic-microbiome-mitochondrial axis in IBD pathogenesis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2692755},
doi = {10.1080/19490976.2026.2692755},
pmid = {42464117},
issn = {1949-0984},
mesh = {Humans ; *Epigenesis, Genetic ; *Inflammatory Bowel Diseases/microbiology/genetics/metabolism ; *Mitochondria/metabolism/genetics ; Animals ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Intestinal Mucosa/microbiology ; },
abstract = {Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is increasingly recognized not merely as an immune-mediated disorder, but as a systems-level condition arising from dynamic interactions among host genetics, environmental exposures, the gut microbiome, and epigenetic regulation. While genetic susceptibility confers risk, accumulating evidence indicates that epigenetic mechanisms act as molecular integrators that translate environmental and microbial signals into sustained transcriptional programs governing immune tolerance, epithelial integrity and tissue repair. Concurrently, intestinal dysbiosis, characterized by loss of short-chain fatty acid-producing commensals and expansion of pro-inflammatory taxa, reshapes host metabolism and chromatin states through microbial-derived metabolites including short-chain fatty acids, secondary bile acids, and tryptophan catabolites. These metabolites affect epigenetic enzymes and modulate the epigenetic chromatin landscape as well as mitochondrial bioenergetics, linking microbial ecology to inflammatory gene regulation. In turn, epigenetic alterations in epithelial and immune compartments influence antimicrobial defense, barrier function, and cytokine networks, thereby sculpting microbial community organization. This bidirectional microbiome-epigenome dialogue creates self-reinforcing circuits that can either sustain mucosal homeostasis or drive chronic inflammation and colitis-associated tumorigenesis. In this review, we synthesize emerging insights into the microbiome-epigenome-mitochondrial axis in IBD and propose a conceptual framework in which metabolic, microbial, and genome-mediated signals converge to determine disease trajectory. We discuss how this integrative perspective may assist biomarker discovery and therapeutic innovation, including epigenetic modulators and microbiota-targeted interventions. Understanding IBD as a dynamically regulated host-microbe ecosystem may accelerate the development of precision strategies aimed at restoring resilient mucosal equilibrium.},
}

Humans
*Epigenesis, Genetic
*Inflammatory Bowel Diseases/microbiology/genetics/metabolism
*Mitochondria/metabolism/genetics
Animals
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Intestinal Mucosa/microbiology

@article {pmid42464327,
year = {2026},
author = {Dhiman, C and Kumar, A and Sonak, SS and Erukulla, P and Nimbarte, VD and Narayan, KP},
title = {Microbiota-derived metabolite landscapes modulate Fusobacterium fitness and colorectal cancer cell behaviour.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00859-9},
pmid = {42464327},
issn = {1757-4749},
abstract = {BACKGROUND: Gut microbiota dysbiosis is increasingly viewed as a disruption of microbial metabolic functions rather than only a shift in microbial composition. Microbiota-derived metabolites not only shape microbial ecology but also directly influence surrounding host tissues by modulating epithelial cell signaling, inflammation, and tumor-associated processes. Among dysbiosis-associated microbes, Fusobacterium is consistently enriched in colorectal cancer (CRC) and contributes to tumor progression, yet the ecological factors regulating its expansion and interaction with host tissues remain unclear. Here, we investigated how microbiome-derived metabolite environments associated with healthy and dysbiotic microbial communities influence Fusobacterium fitness and colorectal epithelial cell behavior.

METHODS: CRC-associated dysbiosis was generated using an orthotopic murine CRC model combined with antibiotic-induced microbiota perturbation. Gut microbial communities were profiled using 16 S rRNA gene sequencing. Metabolite-enriched supernatants derived from healthy gut microbiota, oral microbiota, dysbiotic microbiota and probiotic cultures were evaluated for their effects on CRC-associated bacteria and Fusobacterium sp. growth, adhesion and invasion. These metabolite supernatants were applied to colorectal cancer cells and their effects on viability (MTT assay), migration (scratch assay), apoptosis (Annexin V-FITC flow cytometry), and inflammatory signaling (Western blot analysis of inflammatory markers) were evaluated.

RESULTS: CRC-associated dysbiosis showed reduced microbial diversity with enrichment of opportunistic taxa including Fusobacterium and depletion of beneficial commensals such as Lactobacillus and Bifidobacterium. Metabolite-enriched supernatants from healthy gut and oral microbiota suppressed Fusobacterium growth by 55-65% and reduced bacterial adhesion and invasion in epithelial cells. In epithelial models, these metabolite environments reduced CRC viability to 60% of untreated control, with comparatively smaller effects observed in non-cancerous epithelial cells. They also inhibited cell migration, accompanied by suppression of inflammatory signaling pathways including IL-6, IL-1β, NF-κB, and HIF-1α. In contrast, conditioned media from dysbiotic cancer-microbiota interactions increased tumor cell viability to 120-140% of controls. These findings suggest an association between microbiota-derived metabolite landscapes, pathobiont fitness and epithelial responses under CRC-associated dysbiosis.},
}

@article {pmid42451600,
year = {2026},
author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I},
title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132229},
pmid = {42451600},
issn = {1420-3049},
mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; },
abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.},
}

Humans
*Wound Healing/drug effects
*Microbiota
Chronic Disease
*Host Microbial Interactions
Animals
Probiotics/therapeutic use
Skin Microbiome
Biofilms
Translational Research, Biomedical

@article {pmid42452138,
year = {2026},
author = {Bodur, S and Asiloglu, R and Yazici, K},
title = {Soil Acidification Reshapes Microbial Trophic Interactions, with Implications for Plant Responses and Ecosystem Functioning in Tea Plantation Systems.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/plants15131929},
pmid = {42452138},
issn = {2223-7747},
abstract = {Soil acidification is a widespread consequence of intensive agriculture and represents a major abiotic stress affecting plant performance, nutrient availability, and ecosystem functioning. Long-term tea (Camellia sinensis) plantations provide model systems of chronic acidification, where sustained low pH imposes strong environmental filtering on soil microbial communities. Although microbial responses to acidification have been extensively studied, research has focused predominantly on bacteria and fungi, leaving other key functional groups, particularly protists, largely overlooked. Here, we synthesize current knowledge on microbial communities in acidified soils and highlight trophic interactions, especially protist-mediated regulation, as a potentially critical but underexplored dimension linking abiotic stress to plant-soil processes. We propose that soil acidification may not only filter microbial community composition but also reshape trophic interactions. Based on evidence from other soil systems, protist-mediated trophic interactions could influence nutrient cycling, pathogen suppression, and ultimately plant responses under stress conditions. Integrating environmental filtering with trophic perspectives provides a conceptual framework for understanding microbiome dynamics in acidified soils. However, direct evidence linking protist-mediated trophic regulation to ecosystem functioning and plant performance in tea plantation soils remains limited and requires experimental validation. We further suggest that these systems provide unique opportunities to investigate how abiotic constraints and biotic interactions jointly shape plant performance. Addressing this gap is essential for advancing predictive understanding of plant-microbiome interactions under ongoing environmental change.},
}

@article {pmid42453107,
year = {2026},
author = {Rigerte, L and Sommer, A and Vlot, AC and Prada-Salcedo, LD and Reitz, T and Heintz-Buschart, A and Tarkka, MT},
title = {Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818676},
pmid = {42453107},
issn = {1664-302X},
abstract = {INTRODUCTION: Synthetic microbial communities (SynComs) could help plants withstand biotic stress and reduce the need for pesticides. However, it remains unclear whether SynComs composed of host- or non-host-associated rhizosphere bacteria can trigger induced systemic resistance (ISR) in barley without causing major shifts in the native rhizosphere bacterial community.

METHODS: Here, we constructed two SynComs with known strain composition, composed of bacterial strains isolated from the host-associated barley rhizosphere and non-host-associated wheat rhizosphere. Their ability to trigger induced systemic resistance (ISR) against the barley powdery mildew pathogen Blumeria graminis f. sp. hordei (Bgh) was tested. To investigate plant-microbe interactions from both plant and microbial perspectives, we quantified Bgh propagation in leaves by DAF staining, analysed leaf transcriptomes, and profiled the rhizosphere microbiome using 16S rRNA gene amplicon sequencing and metatranscriptomics.

RESULTS: Both SynComs reduced fungal growth in barley leaves to a similar extent as the positive control strain, Pseudomonas simiae WCS417r, suggesting that ISR-like protection can also be achieved by defined multi-strain communities. Although both SynComs provided similar overall protection, the barley SynCom exhibited the strongest numerical reduction in fungal growth. These findings build on previous single-strain ISR studies and suggest that community-mediated protection is not restricted to host-derived bacterial consortia. Inoculations with both SynComs and WCS417r were not associated with statistically significant changes in the rhizosphere bacterial community structure. All treatments induced only subtle pre-infection transcriptional responses in barley leaves that were consistent with ISR-mediated priming. However, treatment with WCS417r yielded a higher number of differentially expressed genes than either SynCom. Rhizosphere metatranscriptomics revealed treatment-specific functional shifts. The two features K05516 and PF02868 were affected by all three treatments, implying the existence of shared changes related to stress adaptation and microbial activity. OTUs matching the inoculated SynCom members were still present in the rhizosphere at harvest, suggesting the persistence of at least some of the introduced communities.

CONCLUSION: Together, these findings suggest that SynCom-based ISR is potentially a more ecologically relevant approach to microbiome-mediated disease protection in barley.},
}

@article {pmid42454909,
year = {2026},
author = {Götz, F},
title = {mSphere Legacy: Fritz about Fritz.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0036126},
doi = {10.1128/msphere.00361-26},
pmid = {42454909},
issn = {2379-5042},
abstract = {Looking back over the past 50 years, staphylococcal research has evolved from a relatively narrow niche into a broad, interdisciplinary field encompassing genetics, genomics, bioinformatics, host-bacterium interactions, immunity, microbial ecology, the microbiota, and commensalism. My career progressed in parallel with these research developments. Much of what contributed to my success was the ability to recognize emerging questions early on, to combine classical microbiology with new technologies as they emerged, and to collaborate with talented students and colleagues across disciplines. Despite the diversity of the topics I have explored, my work has consistently been driven by a central question: what do staphylococci do, and how do they manage to persist so tenaciously? A brief overview of my research interests may illustrate this trajectory.},
}

@article {pmid42455235,
year = {2026},
author = {Radaelli, E and Palladino, G and Leuzzi, D and Scicchitano, D and Rampelli, S and Turroni, S and Randhawa, HS and Candela, M},
title = {Unraveling the Influence of Behavioural Ecotypes on Fish Gut Microbiome: Focus on the Atlantic cod (Gadus morhua) in Icelandic Waters.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02832-0},
pmid = {42455235},
issn = {1432-184X},
abstract = {This study investigated the gut microbiome of Atlantic cod in northern Icelandic waters to assess how resident (coastal) and migratory (frontal) behavioural ecotypes influence gut microbial community composition, with a focus on the effects of ecological adaptation and the potential drivers of microbial shifts within this species. A total of 81 intestinal samples from coastal and frontal Atlantic cod collected in northern Iceland in December 2021 and January 2024 were analysed using 16S rRNA gene metabarcoding. Environmental datasets from the Copernicus Marine Service were used to assess the relationship between annual shifts in microbiome composition and changes in environmental conditions. Our results highlight that the Icelandic cod gut microbiome is a highly dynamic system primarily shaped by environmental shifts, such as warming trends and anthropogenic stressors. Because different behavioural ecotypes are inherently exposed to distinct environmental configurations, these distinct macro-scale exposures may indirectly translate into ecotype-specific microbial signatures that shape the differentiation between coastal and offshore habitats; the effects were particularly evident in the coastal populations, underscoring the greater vulnerability of nearshore habitats to environmental shifts and anthropogenic stressors. These findings suggest the role of the microbiome in ecological plasticity of Atlantic cod; concurrently, they reveal distinct ecotype-specific sensitivities to environmental shifts, particularly those of anthropogenic origin, providing a valuable framework that may support future marine conservation strategies.},
}

@article {pmid42455310,
year = {2026},
author = {Gopakumar, A and Billah, MM and Vezzi, A and De Pascale, F and De Battisti, D and Bonato, M and Dafforn, KA and Airoldi, L},
title = {Microbial Diversity, Structure and Predicted Carbon-cycling Pathways Show Partial Convergence in Restored and Natural Salt Marshes in Venice Lagoon.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02836-w},
pmid = {42455310},
issn = {1432-184X},
abstract = {Salt marshes are increasingly restored following widespread degradation, yet the responses of sediment microbial communities to restoration remain poorly understood, despite their central role in ecosystem functioning. We compared microbial diversity, composition, structure and predicted function between natural (N) and two types of restored salt marshes in Venice lagoon, Italy: marshes restored with tidal creeks (RC), favouring a more natural tidal exchange and creek formation at the low marsh, and marshes restored with barriers (RB), which constrain tidal flow. We analysed sediment microbial communities in the three dominant habitat types of each marsh (unvegetated low marsh, vegetated low marsh, vegetated mid marsh) by amplicon sequencing of the V4 and V5 hypervariable regions of the 16 S rRNA gene. Microbial diversity was similar across natural and restored salt marshes, but community composition and structure were different. Natural marshes were characterised by higher abundances of taxa associated with sulphate reduction and organic matter degradation (e.g. Syntrophobacterales, Bacteroidales and Desulfatiglandales), whereas restored marshes showed greater representation of Desulfobacterales, Desulfobulbales and Chromatiales. In vegetated habitats, microbial communities also differed between low- and mid-marsh elevations, with low marshes enriched in Syntrophobacterales and Desulfobulbales and mid marshes characterised by Ignavibacteriales and Defluviicoccales. Despite these taxonomic differences, predicted carbon-cycling pathways were remarkably similar across restoration types and elevations. This suggests that key microbial functions can recover even when community composition remains distinct, indicating rapid re-establishment of microbial functional potential following restoration.},
}

@article {pmid42458642,
year = {2026},
author = {Scheelings, TF and Beale, DJ and Van, TTH and Moore, RJ and Arnould, JPY},
title = {The faecal microbiota and its influence on fur seal (Arctocephalus sp.) physiology.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00603-3},
pmid = {42458642},
issn = {2524-4671},
abstract = {BACKGROUND: The gastrointestinal microbiota is a key determinant of vertebrate physiology, metabolism, and adaptation, forming a dynamic holobiont system that supports host health and resilience. However, while the gut microbiota of several fur seal species has been described, most studies have focused primarily on taxonomic composition, leaving a major gap in understanding how microbial communities influence host physiology in marine mammals. This study provides the first comprehensive comparison of the faecal microbiota and blood metabolomic profiles of Australian (Arctocephalus pusillus doriferus) and New Zealand fur seals (A. forsteri) across age classes (adult vs. pup), integrating 16S rRNA gene sequencing, and untargeted metabolomics and untargeted lipidomics to examine host-microbe interactions.

RESULTS: Adult fur seals exhibited a conserved microbial structure dominated by the phyla Bacillota, Fusobacteriota, and Bacteroidota, while pups displayed lower microbial diversity and higher relative abundances of Actinobacteriota and Campylobacterota, alongside enrichment of metabolites involved in DNA synthesis (2-deoxy-D-ribose, 2-deoxycytidine, and 2-deoxyuridine) and lipid metabolism. Correlations between bacterial taxa and metabolites implicated in growth, fat deposition, and hair development suggest that it is possible that early-life microbial communities may play an important role in supporting rapid development and thermoregulation.

CONCLUSIONS: Despite logistical constraints inherent to field-based sampling of wild marine mammals, our findings demonstrate consistent microbial patterns within the Arctocephalus genus and clear age-related differences in blood metabolic profiles. Together, these results enhance understanding of the complex interplay between host development, diet, and microbial ecology in fur seals, and establish a foundation for future research into the functional significance of microbiota in marine mammal health and adaptation.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42459125,
year = {2026},
author = {Chen, S and Nie, C and Wang, Y and Guo, Z and Zhao, K and Yu, Q and Xie, J and Chen, Y},
title = {The Ganoderma atrum Polysaccharide PSG-1 Attenuates Acrylamide-Induced Hepatotoxicity by Modulating the FXR-FGF15-Mediated Gut-Liver Axis.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {14},
pages = {e70543},
pmid = {42459125},
issn = {1613-4133},
support = {2024YFF1106100//National Key R&D Program of China/ ; 20242BAB20329//Natural Science Foundation of Jiangxi Province/ ; 20232BCD44004//Science and Technology Innovation Base Construction Project of Jiangxi Province/ ; },
mesh = {Animals ; Receptor, Farnesoid X-Activated ; *Receptors, Cytoplasmic and Nuclear/metabolism ; *Fibroblast Growth Factors/metabolism ; *Liver/drug effects/metabolism/pathology ; *Ganoderma/chemistry ; *Acrylamide/toxicity ; *Chemical and Drug Induced Liver Injury/prevention & control/drug therapy/metabolism ; Male ; Bile Acids and Salts/metabolism ; *Polysaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress/drug effects ; Antioxidants ; },
abstract = {Acrylamide (AA), a widespread food-processing contaminant, induces intestinal injury and hepatotoxicity by disrupting barrier function, redox balance, bile acid metabolism, and gut microbial ecology. This study examined the protective benefits of Ganoderma atrum polysaccharide (PSG-1), focusing on the gut-liver axis. PSG-1 reduced serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), and total bile acid (TBA) levels and improved liver histology. It also restored antioxidant defense by enhancing superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities while lowering malondialdehyde (MDA). At the intestinal level, PSG-1 alleviated barrier disruption and reversed gut dysbiosis, restoring Lactobacillus abundance. This microbial modulation coincided with reactivation of the farnesoid X receptor (FXR)/fibroblast growth factor 15 (FGF15) pathway, which normalized hepatic cholesterol 7α-hydroxylase (CYP7A1) expression and improved bile acid homeostasis. PSG-1 also corrected retinol metabolism disorders by reducing lecithin-retinol acyltransferase (LRAT) and restoring retinol-binding protein 4 (RBP4). These results demonstrate that PSG-1 protects against AA-induced intestinal and hepatic injury through coordinated regulation of oxidative stress, gut microbiota composition, and FXR-mediated bile acid signaling along the gut-liver axis.},
}

Animals
Receptor, Farnesoid X-Activated
*Receptors, Cytoplasmic and Nuclear/metabolism
*Fibroblast Growth Factors/metabolism
*Liver/drug effects/metabolism/pathology
*Ganoderma/chemistry
*Acrylamide/toxicity
*Chemical and Drug Induced Liver Injury/prevention & control/drug therapy/metabolism
Male
Bile Acids and Salts/metabolism
*Polysaccharides/pharmacology
Gastrointestinal Microbiome/drug effects
Oxidative Stress/drug effects
Antioxidants

@article {pmid42459365,
year = {2026},
author = {Xu, H and Chen, W and Xiao, Q and Ren, J and Yang, D and Li, S and Cai, Y and Tuerheng, J and Tang, R and He, K and Wu, D},
title = {Microbiota-gut-brain axis imbalance: a promising therapeutic target for preserving brain health in high-altitude environment.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1820153},
pmid = {42459365},
issn = {1662-4548},
abstract = {High-altitude hypobaric hypoxia poses a significant threat to brain function, yet effective neuroprotective strategies remain limited. Emerging evidence highlights the microbiota-gut-brain axis (MGBA) as a key mediator in high-altitude-induced cognitive impairment, positioning it as a potential therapeutic target. This review synthesizes current knowledge on how high-altitude exposure dynamically reshapes gut microbial ecology, characterized by reduced diversity, phylum-level instability, and functional metabolic shifts. Furthermore, we delineate how such altitude-induced dysbiosis has been associated with neural dysfunction through interconnected pathogenic mechanisms that are proposed to link gut ecology to brain outcomes: intestinal barrier disruption with metabolic dysregulation, LPS/TLR4-mediated neuroinflammation, vagal and enteric nervous system alterations, oxidative stress imbalance, and neuroendocrine dysregulation. Most current evidence is correlational, and further research is needed to establish causality. A critical unresolved question is whether short-term, transient gut dysbiosis at high altitude can instigate long-lasting neurological deficits independent of ongoing microbial perturbation. We further evaluate microbiota-targeted neuroprotective strategies, including probiotics, prebiotics, and fecal microbiota transplantation, highlighting their distinct mechanisms and summarizing the current evidence supporting MGBA-targeted interventions for high-altitude brain health. Preclinical studies suggest these approaches hold promise by restoring barrier integrity, attenuating inflammatory signaling, and rebalancing microbial metabolite profiles, while human intervention evidence remains scarce. Finally, we discuss critical challenges and future directions for translating these mechanistic insights into personalized interventions, emphasizing deeper mechanistic exploration and the synergistic interactions among microbial taxa. These insights may inform more effective therapeutic strategies for the growing populations residing in or traveling to high-altitude regions.},
}

@article {pmid42446838,
year = {2026},
author = {Dias-Souza, MV and Alves, AL and de Cássia Mourão Silva, U and Júlio, ADL and Veiga, A and Pagnin, S and Dos Santos, VL},
title = {Diversity, biofilm formation and antimicrobial susceptibility of aerobic heterotrophic bacteria isolated from cooling towers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42446838},
issn = {1573-0972},
mesh = {*Biofilms/growth & development ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Brazil ; *Bacteria, Aerobic/isolation & purification/classification/drug effects/genetics/physiology ; Phylogeny ; *Water Microbiology ; Drug Resistance, Bacterial ; Refrigeration ; Biodiversity ; *Bacteria/classification/isolation & purification/drug effects/genetics ; DNA, Bacterial/genetics ; },
abstract = {Cooling towers (CTw) are essential for industrial refrigeration but provide favourable conditions for microbial growth and biofilm formation, potentially facilitating the spread of antimicrobial-resistant bacteria (ARB). This study examines bacterial diversity, biofilm potential and antimicrobial susceptibility in two industrial CTw in Brazil using culture-based and metataxonomic (16 S rRNA gene amplicon sequencing) approaches. Fourteen bacterial genera and 22 species were identified, including Bacillus spp. (60% of isolates), Acinetobacter spp. (14%) and others like Pseudomonas, Serratia, and Ochrobactrum, many linked to biofilm formation and ARB. Metataxonomic analysis revealed a broader and more diverse microbial community, comprising families such as Burkholderiaceae, Comamonadaceae, and Sphingomonadaceae, which are known for their biofilm resilience. Pathogens including Legionella were also detected. Bacterial richness was higher in CTw 2, likely due to untreated industrial and domestic effluent inputs, whereas CTw 1, supplied with treated secondary industrial effluent, exhibited lower diversity. Functional predictions indicated genes associated with biofilm formation, quorum-sensing, motility and xenobiotic degradation. Antimicrobial susceptibility testing showed high resistance to β-lactams and nitrofurantoin, with meropenem being the most effective. Higher resistance rates in CTw 2 suggest selective pressure from industrial contaminants. These findings underscore the complex microbial ecology of CTw and the coexistence of cultivable and non-cultivable bacteria with biofilm-forming capacity and antimicrobial resistance traits in these systems.},
}

*Biofilms/growth & development
RNA, Ribosomal, 16S/genetics
Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
Brazil
*Bacteria, Aerobic/isolation & purification/classification/drug effects/genetics/physiology
Phylogeny
*Water Microbiology
Drug Resistance, Bacterial
Refrigeration
Biodiversity
*Bacteria/classification/isolation & purification/drug effects/genetics
DNA, Bacterial/genetics

@article {pmid42446994,
year = {2026},
author = {Cortés-Tapia, C and Cid-Rojas, F and Moya-Beltrán, A and García-Yunge, J and Castro, M and Rojas-Villalobos, C and Gil, F and Quatrini, R and Pizarro-Guajardo, M and Paredes-Sabja, D},
title = {Distinctive spore architecture and developmental biology of Turicibacter sanguinis reveal unexpected diversity among gut spore formers.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0002926},
doi = {10.1128/jb.00029-26},
pmid = {42446994},
issn = {1098-5530},
abstract = {Sporulation is a widespread but incompletely characterized trait among gut commensals, where it underpins microbial persistence, transmission, and ecological resilience. Most insights into spore biology derive from Bacilli and Clostridia; however, little is known about sporulation in phylogenetically distant gut-associated lineages. Turicibacter sanguinis, a strict anaerobe linked to host serotonin metabolism, lipid homeostasis, and neurodegenerative disease, represents one such understudied taxon. Here, we integrate ultrastructural, physiological, and comparative genomic analyses to define the sporulation and germination program of T. sanguinis. We show that T. sanguinis forms heat-resistant spores with a canonical core-cortex-coat architecture but displays previously undescribed features, including a dual-layered outer envelope and bimodal electron-dense coat morphotypes. Developmental stages of sporulation follow canonical stages of Bacillus- and Clostridium-like sporulation, while genomic analyses reveal a hybrid regulatory architecture combining Clostridial-type Spo0A initiation with Bacillus-like late-stage sigma factor control. Germination assays and genomic signatures further indicate a nutrient-responsive, Bacillus-like pathway involving Ger-family receptors, SpoVA-mediated Ca-DPA release, and CwlJ- and SleM-type cortex hydrolases. Together, these findings identify T. sanguinis as a distinct spore-forming lineage within the human gut microbiota and expand the known diversity of sporulation strategies across the Firmicutes.IMPORTANCEThe gut bacterium Turicibacter sanguinis is linked to critical host functions, including serotonin production and lipid homeostasis. In this work, we show that T. sanguinis forms spores as a potential mechanism to survive and transmit. Unlike well-studied bacteria, T. sanguinis encodes a unique, hybrid sporulation program that mixes regulatory and structural elements from distant bacterial species. These observations fill a significant gap in our understanding of gut microbial ecology. It suggests that T. sanguinis persists in the gut through a distinct, specialized survival program. The outlined mechanisms provide a roadmap to study how this bacterium persists in the gut and impacts host health.},
}

@article {pmid42447623,
year = {2026},
author = {Su, K and Tian, S and Xia, Y and Zhao, X and Huang, J and Hu, S and Ye, J},
title = {Species composition and functional characteristics of the human multi-organ microbiome: A metagenomic study.},
journal = {Journal of forensic and legal medicine},
volume = {122},
number = {},
pages = {103213},
doi = {10.1016/j.jflm.2026.103213},
pmid = {42447623},
issn = {1878-7487},
abstract = {Postmortem microbial communities may provide useful information for forensic microbiology, but species-level and functional profiles across multiple cadaveric anatomical sites remain poorly characterized. Here, shotgun metagenomic sequencing was performed on 144 samples from six anatomical sites, including the oral cavity, nasal cavity, trachea, lung, colon, and anus, collected from 24 human cadavers. A total of 15,301,799,968 raw reads were obtained, and 6565 species were identified, and KEGG pathways were annotated at the L1, L2, and L3 levels. Species-level microbial composition differed significantly among anatomical sites. PERMANOVA with permutations blocked by individual identity showed that anatomical site was the dominant factor explaining microbial community variation (R[2] = 0.3778, p = 0.001, q = 0.001), whereas postmortem interval did not show a significant independent effect within the 1-38-day interval. KEGG functional profiles also differed significantly among anatomical sites at the L2 and L3 levels, and 182 of 214 L3 pathways showed significant site-associated differences after false-discovery-rate correction. Pathway-level mixed-effect models further indicated that anatomical site remained significantly associated with most L3 pathways after accounting for postmortem interval, age, sex, cause of death, and repeated sampling from the same individual. Species-pathway correlation analysis identified significant taxon-function associations, but these were interpreted as correlative rather than direct evidence of species-specific functional contribution. Low-biomass sensitivity analyses indicated that respiratory-site results, especially lung and tracheal findings, should be interpreted cautiously because of high host DNA proportions and low non-host read counts. Inter-site shared occurrence and intra-site co-occurrence analyses further described distributional associations across anatomical sites. This study establishes a multi-site postmortem metagenomic reference framework for characterizing anatomical-site-specific microbial and functional patterns, offering insights into forensic microbiology and postmortem microbial ecology.},
}

@article {pmid42447669,
year = {2026},
author = {Kim, IT and Jeong, Y and Lee, YE and Ahn, KH and Jung, JH},
title = {Biogas-driven sidestream nitrogen removal: A perspective on replacing partial nitritation with aerobic methane oxidation-denitrification toward carbon-neutral wastewater treatment.},
journal = {Water research},
volume = {305},
number = {},
pages = {126456},
doi = {10.1016/j.watres.2026.126456},
pmid = {42447669},
issn = {1879-2448},
abstract = {Sidestream reject water from anaerobic digesters imposes a disproportionately high nitrogen load (typically ∼15-25% of the total plant nitrogen load despite comprising <5% of total influent volume) on wastewater treatment plants. However, existing biological removal technologies, including partial nitritation/anammox and anaerobic methane oxidation-based processes, are structurally disconnected from onsite biogas valorization. In this review, we evaluated the feasibility of replacing the conventional partial nitritation stage with aerobic methane oxidation coupled with denitrification (AME-D) in an integrated two-stage system toward carbon-neutral sidestream nitrogen removal. We synthesized the current knowledge on methane-oxidizing microbial ecology, interguild carbon transfer networks, and the enabling roles of reject water composition and biogas-derived CO2 in sustaining integrated process performance. The key findings indicate that AME-D can serve as a multifunctional upstream stage, concurrently supplying nitrite, reducing ammonium load, and providing carbon intermediates to the downstream nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) consortium. This enables biogas-driven complete nitrogen removal without external carbon input. The principal challenges involved in this process include greenhouse gas emission management, membrane fouling under high-strength sidestream conditions, and constraints on micronutrient bioavailability, which may compromise long-term microbial stability. This review proposes an integrated conceptual framework for AME-D/n-DAMO process design, identifies research priorities in pilot-scale validation and multi-guild community engineering, and articulates a pathway toward circular bioeconomy implementation in urban water resource recovery.},
}

@article {pmid42447682,
year = {2026},
author = {Löffler, T and Feckler, A and Roodt, AP and Schulz, R and Bundschuh, M},
title = {Holding poison: Retention and biodegradation of pesticides by freshwater biofilms.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120496},
doi = {10.1016/j.ecoenv.2026.120496},
pmid = {42447682},
issn = {1090-2414},
abstract = {Biofilms play a central role in the self-cleaning capacity of freshwater ecosystems and bioremediation of chemical contaminants. In this study, we evaluated the contribution of biofilms developing on organic and inorganic substrates to the retention and degradation of pesticides in freshwater streams under controlled laboratory conditions. Experiments were conducted at two temperatures (16 and 20°C) and using a mixture of ten pesticides at three concentrations (0, 2.5 and 35 µg/L). Our results confirmed a significant contribution of biofilms to pesticide retention, as evidenced by reduced concentrations in the water column being partially more than a factor of two higher than in absence of biofilms. This is supported by pesticide-specific sorption-factors to biofilms between 0.3 and 28734. Biofilm origin had a significant effect on microbial taxonomic composition and enzyme profiles (PERMANOVA, p < 0.001), which in turn influenced interaction mechanisms and the efficiency of pesticide removal. Biofilms associated with inorganic substrates primarily functioned as sinks, retaining pesticides, whereas those associated with organic substrates predominantly acted as bioremediators, promoting pesticide degradation. In contrast, temperature and pesticide concentration had no significant effects, indicating comparatively minor influence on the retention and degradation efficiency of pesticides by biofilms under the tested conditions. Therefore, this study highlights the important role of biofilms in reducing xenobiotic concentrations in aquatic environments, with this function being resilient to temperature and pesticide concentration. Moreover, we are - to the best of our knowledge - the first to document functional differences in pesticide retention and reduction between biofilms associated to organic and inorganic substrate, respectively.},
}

@article {pmid42449053,
year = {2026},
author = {Maurice, K and Baldovini, N and Zaremski, A and Damay, J and Lehnebach, R and Estevez, Y and Ducousso, M},
title = {The Microbial and Chemical Terroir of Agarwood in French Guiana.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02824-0},
pmid = {42449053},
issn = {1432-184X},
support = {Acquilascent//Agence Nationale de la Recherche/ ; },
abstract = {Agarwood is a highly valued aromatic resinous wood formed in Aquilaria species following stress or infection, yet the putative microbial drivers of its quality remain poorly understood, particularly outside its native range. In this study, we investigated the bacterial and fungal communities associated with agarwood produced from Aquilaria crassna Pierre ex Lecomte planted in French Guiana and examined their relationships with volatile chemical compounds relevant to agarwood fragrance. Using high‑throughput sequencing and comprehensive chemical profiling, we characterized microbial community composition and agarwood volatile profiles across multiple cultivation plots. Despite spatial variability in microbial assemblages, agarwood samples exhibited a conserved chemical signature dominated by chromone derivatives and sesquiterpenoids, indicating the presence of a stable chemical terroir under Guianese environmental conditions. Network analysis revealed numerous bacterial and fungal taxa significantly associated with key chemical classes, suggesting potential microbial contributions to agarwood chemical complexity through plant-microbe interactions or microbial metabolic activity, although causality remains to be established. Comparative analyses with commercial agarwood samples from South-East Asia and the Middle East revealed a distinct chemical profile for Guianese agarwood, highlighting the influence of geographic origin on agarwood quality and supporting an extension of the terroir concept to woody aromatic products. Overall, this study demonstrates that Aquilaria trees cultivated in French Guiana can produce high‑quality agarwood and provides new insights into the interplay between microbial communities and agarwood chemistry. These findings lay the groundwork for the development of locally adapted, microbiome‑informed strategies for sustainable agarwood production.},
}

@article {pmid42449225,
year = {2026},
author = {Maqbool, F and Naqvi, RZ and Rehman, R and Amin, I and Imran, I and Imran, A},
title = {PGPR-induced regulation of Zn and Fe transporters in wheat (Triticum aestivum L.) uncovered through integrated genome-wide analysis and functional validation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09415-8},
pmid = {42449225},
issn = {1471-2229},
abstract = {Zinc (Zn) and iron (Fe) deficiencies affect more than two billion people globally, particularly in cereal-dependent regions where wheat, despite its high consumption, provides inadequate micronutrient levels. Conventional interventions such as genetic modification and mineral supplementation remain costly, unevenly accessible, and insufficient for large-scale nutritional improvement. Agronomic biofortification using plant growth-promoting rhizobacteria (PGPR) offers a promising yet underexplored alternative, especially for regulating metal homeostasis genes in wheat. This research integrates multi-season field trials of Zn-biofortified Akbar-19 and the local cultivar Khaista-17, conducted under reduced fertilizer conditions with PGPR consortia. Afterwards, genome-wide analyses including phylogenetic relationships, promoter elements, gene interaction networks, expression profiles, and conserved domains/motifs of the TaNAS (19 genes), TaNAAT (6), TaDMAS (3), and TaVIT (31) gene families was performed. This was followed by transcriptional expression (qPCR) of six candidate genes in wheat grown under hydroponic Zn/Fe stress in the presence of PGPR. Field evaluation showed that PGPR inoculation boosted yield by 15-18% and increased grain Zn/Fe by 15-20% in Akbar-19 and 25-28% in Khaista-17, consistently outperforming fertilizer-only controls across both seasons. The genome-wide analyses exhibited the phylogenetic relationship of wheat TaDMAS, TaNAAT, and TaNAS genes with barley, while TaVIT and TaVTL genes with rice and maize. Promoter analyses of these genes showed an enrichment of stress-responsive cis-elements, such as IDE1/2, ZDRE1/2, IRO2-binding sites, and metal-responsive elements suggesting coordinated regulation of micronutrient chelation, uptake, and homeostasis. qPCR results confirmed PGPR-induced upregulation of NAS1, NAS6, NAS9, NAAT2, DMAS1, and VIT2 under Zn/Fe stress, with stronger induction in Khaista-17. Overall, the results show that PGPR modulate metal‑transporter gene networks and improve micronutrient biofortification in wheat, providing a genotype‑responsive and sustainable approach to address micronutrient deficiency.},
}

@article {pmid42449422,
year = {2026},
author = {Webster, SJ and Cock, IE and Matheson, C and Sweeney, EL},
title = {Vaginal microbiomes and their pertinent social context: a microbial ecological review proffering AMR-STI acquisition and emergence.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00953-2},
pmid = {42449422},
issn = {2042-6410},
support = {Research Training Program (RTP) Domestic Scholarship//Australian Government/ ; },
abstract = {BACKGROUND: In the landscape of sexual health, sex, gender, and sexuality are inextricably linked and highly relevant to sexually transmitted infections (STIs). Globally, key sexual and reproductive health concerns of women have been associated with the socioeconomic status of their country, indicating that social context bears influence over sexual health outcomes. Further, the increasing prevalence of antimicrobial resistant STIs (AMR-STIs) in the sexual networks of gay and bisexual men-who-have-sex-with-men (GBMSM) suggests an implicit connection between microbiological and social phenomena, although research to date is relatively limited and often fails to reflect the complexity and nuance of sexual networks. Vulval and vaginal microbiome composition may influence STI acquisition and transmission, yet the relationships between composition, microenvironment, and STIs remain largely overlooked, especially in the context of women and gender-diverse people. In this article, we explore the possibility that a combination of social, sexual, and behavioural factors, combined with biological features, shape the microbiological context of STIs within the vaginal microenvironment. MAIN: The human vaginal microbiome (VMB) forms an ecological niche home to a complex ecosystem of microorganisms. The microbial composition of the VMB is diverse between individuals, with variations observed across racial and ethnic groups, and intrapersonal fluctuations linked to a plethora of factors both within and outside of personal control. Importantly, VMB health is a crucial component of wellbeing for people assigned female at birth (AFAB), transgendered women with neovaginas, and their sexual partners. Clinical context also remains important; in Australia, doxycycline prophylaxis (Doxy-PEP) has recently become available to GBMSM networks aimed to protect against the acquisition of STIs. However, Doxy-PEP guidelines exclude AFAB people and fail to specify regarding use among gender diverse individuals. Given the high prevalence of AMR-STIs within GBMSM networks, the impact of this intervention on excluded partners should be thoroughly investigated. Factors in the VMB such as biofilm formation and necessary microbial balance with opportunistic pathogens renders this ecological microbial niche a hypothetically perfect platform for AMR development and emergence within the social context.

CONCLUSION: This review explores the social context of vaginal microbiomes, their potential influence on AMR-STI development, and highlight several important knowledge gaps to benefit from further research.},
}

@article {pmid42449926,
year = {2026},
author = {Mitova, N and Lazarova, Z},
title = {Microbial Composition of Carious Dentin and the Impact of Minimally Invasive Excavation Techniques: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135648},
pmid = {42449926},
issn = {1422-0067},
mesh = {Humans ; *Dental Caries/microbiology/therapy ; *Dentin/microbiology ; *Microbiota ; Biofilms/growth & development ; },
abstract = {Dental caries is a biofilm-mediated dysbiotic disease characterized by ecological shifts within the oral microbiome and progressive demineralization of dental hard tissues. The microbiological composition of carious dentin and the impact of minimally invasive excavation techniques on residual microbial communities remain subjects of ongoing investigation due to methodological heterogeneity and inconsistencies among published studies. This narrative review aimed to summarize current evidence regarding the microbial ecology of carious dentin, compare culture-based and molecular methods for microbiological assessment, and evaluate the microbiological outcomes associated with contemporary approaches to managing minimally invasive caries. The relevant literature on dentinal caries microbiology, microbial detection methods, and excavation techniques was analyzed. The available evidence indicates that carious dentin contains a highly diverse polymicrobial community composed of acidogenic, aciduric, anaerobic, and proteolytic microorganisms. Culture-based methods primarily detect viable and cultivable taxa, whereas molecular approaches reveal substantially greater microbial diversity, including uncultivable and low-abundance species. Comparative studies demonstrate that minimally invasive excavation techniques significantly reduce microbial load but rarely achieve complete microbial elimination. The available evidence suggests that successful caries management is associated with a reduction in and ecological modulation of the residual microbiota within a sealed environment. The integration of culture-based and molecular findings provides a more comprehensive understanding of the microbiology of carious dentin and supports biologically oriented, minimally invasive strategies for caries management.},
}

Humans
*Dental Caries/microbiology/therapy
*Dentin/microbiology
*Microbiota
Biofilms/growth & development

@article {pmid42450045,
year = {2026},
author = {Urbanowicz, T and Mattina, A and Cielecka-Piontek, J and Raffa, GM and Pisano, C and Grywalska, E and Hymos, A and Rahnama, M and Kowalewski, M and Suwalski, P and Jemielity, M and Krasiński, Z},
title = {Advanced Functional Wound Dressings in Precision Surgery: Immunometabolic Reprogramming, Bioadaptive Biomaterials, and Intelligent Regenerative Interfaces.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135772},
pmid = {42450045},
issn = {1422-0067},
support = {PNRR-POC-2023-12378186 CUP I73C24000330006//European Union/ ; },
mesh = {Humans ; *Biocompatible Materials ; *Wound Healing ; Animals ; *Bandages ; Metabolic Reprogramming ; Regenerative Medicine/methods ; *Precision Medicine/methods ; },
abstract = {Postoperative wound complications remain a major cause of morbidity, prolonged hospitalization, increased healthcare costs, and reduced quality of life. While traditional wound dressings functioned primarily as passive barriers against contamination and exudate, advances in wound biology have transformed surgical wound management. Tissue repair is now recognized as a dynamic immunometabolic process involving coordinated interactions among immune cells, stromal populations, extracellular matrix remodeling, mechanotransduction, mitochondrial function, redox balance, microbial ecology, and bioelectrical signaling. Consequently, modern wound dressings are increasingly designed as bioactive systems capable of actively modulating the wound microenvironment. Recent developments in biomaterials science, immunoengineering, nanotechnology, extracellular vesicle biology, bioelectronics, and artificial intelligence have enabled the creation of advanced wound platforms, including stimuli-responsive hydrogels, immunomodulatory biomaterials, nanozyme-based dressings, conductive scaffolds, oxygen-generating matrices, extracellular vesicle-loaded systems, and biosensor-integrated interfaces. Therapeutic strategies are progressively shifting from antimicrobial-focused approaches toward immune-regenerative modulation targeting chronic inflammation, mitochondrial dysfunction, ferroptosis, cellular senescence, and impaired mechanobiological signaling. This review examines emerging surgical wound dressings from mechanistic, translational, and biomaterial perspectives, highlighting current innovations, translational challenges, and future directions. Collectively, these technologies may enable intelligent therapeutic systems capable of sensing and directing tissue regeneration in real time.},
}

Humans
*Biocompatible Materials
*Wound Healing
Animals
*Bandages
Metabolic Reprogramming
Regenerative Medicine/methods
*Precision Medicine/methods

@article {pmid42450455,
year = {2026},
author = {Zhao, D and Zhang, J},
title = {From Molecular Flavor Signatures to Mechanism-Oriented Food Quality: Advances in Flavoromics, Fermentation Ecology, Functionality, and Safety.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/foods15132337},
pmid = {42450455},
issn = {2304-8158},
abstract = {Food quality is now understood less as a single attribute than as an integrated system of flavor perception, nutritional value, microbial ecology, processing history, and safety assurance [...].},
}

@article {pmid42450684,
year = {2026},
author = {Cheng, S and Wang, HH and Chi, ML and Jiang, WP and Liu, SL and Zou, WW and Chen, ZL and Li, F},
title = {Time-Dependent Polystyrene Nanoplastic Toxicity in Cherax quadricarinatus: Oxidative Stress, Gut Dysbiosis, and Hepatopancreatic Bioaccumulation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16131977},
pmid = {42450684},
issn = {2076-2615},
support = {2025SNJF010//Zhejiang Province Agriculture, Rural Areas, and Nine Directions Project/ ; 2026YSZX01-5//Zhejiang Provincial Research Institute Special Project/ ; 2023NKY05//The Seed Capital for Innovation and Entrepreneurship of Wencheng County/ ; Zdwc2401//Research and Demonstration of Localized Artficial Seeding Cultivation of Australian Blue Shrimp/ ; 2025RAC//Research and Application of Characteristic Breeding Technology for Rice Fields in Wencheng Mountain Creek and Model Breeding Equipmengt in Hilly and Mountainous Areas/ ; },
abstract = {Polystyrene nanoplastic (PS-NP) contamination poses an emerging threat to aquaculture species, yet time-resolved assessments integrating host physiology, gut microbial ecology, and tissue bioaccumulation remain limited. Here, we evaluated the temporal effects of 100 mg/L PS-NPs (100 nm) on Cherax quadricarinatus (Von Martens, 1868) over a 3-week exposure period. Crayfish were assigned to a control group (Group A) and three treatment groups exposed for 1 (Group B), 2 (Group C), or 3 (Group D) weeks. No mortality occurred. Hepatopancreatic antioxidant enzyme activities (superoxide dismutase and glutathione peroxidase) displayed a hormetic response (upregulation at weeks 1-2 followed by depletion at week 3), indicating oxidative stress overload. Alkaline phosphatase activity declined progressively, reflecting cumulative immunosuppression. Histological examination revealed time-dependent structural damage in the hepatopancreas: hepatic tubule enlargement, increased vacuolation, B cell hypertrophy, and cellular disorganization/lysis after three weeks. 16S rRNA sequencing revealed that PS-NPs induced time-dependent gut dysbiosis, characterized by depletion of beneficial taxa and enrichment of opportunistic pathogens. Alpha-diversity metrics (ACE, Chao1, Shannon) were significantly reduced in Group D compared to controls, confirming loss of microbial evenness and richness. Pyrolysis gas chromatography-mass spectrometry quantification demonstrated marked PS-NP bioaccumulation in the hepatopancreas, with concentrations rising from 6.94 μg/g in controls to 65.38 μg/g in Group D, a 9.4-fold increase. Collectively, prolonged PS-NP exposure is associated with oxidative stress, immune dysfunction, progressive gut dysbiosis, and substantial hepatopancreatic nanoplastic burden in C. quadricarinatus. These findings carry implications for ecological risk assessment and highlight the need for further investigation into food safety risks associated with human consumption of crayfish from PS-NP-contaminated environments.},
}

@article {pmid42451154,
year = {2026},
author = {Biagioli, V and Matera, M and Imola, I and Mela, F and Lemmi, D and Verrotti, A and Striano, P},
title = {Beyond Ketosis: Dietary Therapies and the Microbiota-Gut-Brain Axis in Epilepsy.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132151},
pmid = {42451154},
issn = {2072-6643},
mesh = {Humans ; *Epilepsy/diet therapy/microbiology ; Diet, Ketogenic ; Probiotics/administration & dosage ; *Gastrointestinal Microbiome/physiology ; Prebiotics/administration & dosage ; *Ketosis ; *Brain ; *Brain-Gut Axis/physiology ; Animals ; Diet, Carbohydrate-Restricted ; Diet, Mediterranean ; Diet, High-Protein Low-Carbohydrate ; },
abstract = {Background: Epilepsy is a complex neurological disorder in which growing evidence supports a significant role for the microbiota-gut-brain axis (MGBA) in modulating neuroinflammation, neuronal excitability, and treatment responsiveness. Beyond their traditional role in inducing ketosis, dietary therapies may influence epilepsy by modulating gut microbial ecology, intestinal barrier integrity, immune signaling, and microbiota-derived metabolites. Methods: This narrative review critically examines current clinical and experimental evidence regarding the relationship between epilepsy, gut microbiota, and dietary interventions. Particular attention was given to ketogenic dietary therapies, the Modified Atkins Diet (MAD), low-glycemic-index treatment (LGIT), Mediterranean dietary patterns, restrictive diets, and microbiota-targeted supplementation, including probiotics, prebiotics, and postbiotics. Results: Available evidence suggests that patients with epilepsy exhibit alterations in gut microbial composition associated with impaired short-chain fatty acid production, intestinal inflammation, and altered neuroimmune regulation. Ketogenic and microbiota-supportive dietary approaches may modulate these pathways beyond ketosis alone, potentially contributing to seizure reduction through integrated metabolic, inflammatory, and microbial mechanisms. Emerging evidence also supports a role for probiotics, prebiotics, and postbiotics in modulating gut-brain communication and neuroinflammatory signaling, although current clinical data remain limited. Conclusions: Dietary therapies in epilepsy should no longer be viewed exclusively as metabolic interventions aimed at inducing ketosis, but rather as potential modulators of the microbiota-gut-brain axis and neuroimmune homeostasis. While further mechanistic and clinical studies are needed, microbiota-targeted nutritional approaches may represent valuable complementary strategies to be integrated alongside conventional antiseizure therapies within more personalized models of epilepsy management.},
}

Humans
*Epilepsy/diet therapy/microbiology
Diet, Ketogenic
Probiotics/administration & dosage
*Gastrointestinal Microbiome/physiology
Prebiotics/administration & dosage
*Ketosis
*Brain
*Brain-Gut Axis/physiology
Animals
Diet, Carbohydrate-Restricted
Diet, Mediterranean
Diet, High-Protein Low-Carbohydrate

@article {pmid42440521,
year = {2026},
author = {Lv, M and Xu, W and Wang, T and Mou, K and Ni, Z and Tu, Q and Zhang, J and Wu, X and Song, S and Cheng, G},
title = {Host-microbiome-immune disequilibrium in oral disease: mechanisms, dysbiosis, and precision therapeutics.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1854213},
pmid = {42440521},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology ; *Microbiota/immunology ; Animals ; Immunity, Mucosal ; *Mouth Diseases/immunology/microbiology/therapy ; Precision Medicine ; *Host Microbial Interactions/immunology ; Mouth/microbiology/immunology ; },
abstract = {BACKGROUND: The oral cavity harbors a dynamic microbial ecosystem that interacts with epithelial barriers, host immunity, and local tissue environments. Disruption of this balance is increasingly recognized as a key driver of major oral diseases, including periodontitis, dental caries, and oral squamous cell carcinoma (OSCC). However, the biological links between microbial ecology, immune regulation, and disease progression are insufficiently integrated, limiting mechanistic understanding and translational progress.

METHODS: This structured narrative review searched PubMed/MEDLINE, Web of Science, Embase, and Scopus for relevant studies on oral microbiome ecology, mucosal immunity, dysbiosis, oral diseases, and emerging therapies. Evidence was narratively synthesized across microbiome ecology, mucosal immunology, disease pathogenesis, and translational research, with consideration of study type, mechanistic relevance, and translational significance.

RESULTS: Current evidence supports that oral homeostasis relies on coordinated interactions among commensal microbial communities (CMC), epithelial and salivary barriers, and immune surveillance. Dysbiosis disrupts this equilibrium by promoting the expansion of pathobionts, amplifying inflammatory responses, and contributing to tissue injury. This systems-level perspective helps explain the persistence and heterogeneity of oral diseases beyond pathogen-centered models. Emerging technologies are reshaping this field. These include microbiome-modulating therapies, host-directed interventions, multi-omics approaches, and artificial intelligence (AI). These approaches are advancing disease stratification, biomarker discovery, and precision therapeutic development.

CONCLUSION: Oral diseases should be understood as disorders of host-microbiome-immune disequilibrium rather than as isolated infections. This perspective highlights the need for integrated strategies that consider microbial ecology, immune regulation, epithelial barrier function, and clinical context to improve prevention, diagnosis, and treatment in precision oral medicine.},
}

Humans
*Dysbiosis/immunology
*Microbiota/immunology
Animals
Immunity, Mucosal
*Mouth Diseases/immunology/microbiology/therapy
Precision Medicine
*Host Microbial Interactions/immunology
Mouth/microbiology/immunology

@article {pmid42440971,
year = {2026},
author = {Gahlot, KD},
title = {Dietary modulation of the gut resistome: ecological and metabolic pathways driving antimicrobial resistance.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1868638},
pmid = {42440971},
issn = {2296-861X},
abstract = {Antimicrobial resistance (AMR) is traditionally viewed as a consequence of antibiotic exposure and genetic adaptation; however, resistance also emerges from the ecological and metabolic context of microbial communities. The human gut microbiome represents a major reservoir of antibiotic resistance genes (ARGs), and diet is increasingly recognised as a dominant regulator of its structure and function. Here, I synthesise current evidence and propose a conceptual framework in which diet shapes resistome dynamics through three interrelated pathways: ecological selection, metabolic regulation, and physicochemical modulation of horizontal gene transfer. Dietary components influence microbial composition, metabolic activity, and the spatial organisation of fermentation along the colon. Diverse fibre types differentially regulate short-chain fatty acid production and microbial competition, whereas high-fat, low-diversity diets destabilise communities and favour opportunistic taxa. Beyond macronutrients, food additives and the physical structure of food alter gut barrier function, microbial stress responses, and spatial ecology, thereby influencing resistome stability. Diet-induced metabolic states further determine antibiotic susceptibility, including transitions between tolerance and resistance. Taken together, this integrated ecological perspective positions diet as a modifiable driver of AMR and highlights nutritional strategies as complementary approaches to mitigating resistome expansion.},
}

@article {pmid42441583,
year = {2026},
author = {Luo, H and Zhang, H and Xu, L and Hong, L and Tang, H and Wang, C},
title = {Application of Acupuncture in the Management of Skin Diseases: A Review from the Perspective of the Microbiome.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {232},
pages = {},
doi = {10.3791/71199},
pmid = {42441583},
issn = {1940-087X},
mesh = {Humans ; *Acupuncture Therapy/methods ; *Microbiota ; *Skin Diseases/therapy/microbiology/immunology ; Skin Microbiome ; },
abstract = {Inflammatory skin diseases (e.g., atopic dermatitis, psoriasis, acne vulgaris, and chronic urticaria) are increasingly recognized as systems-level disorders arising from the interplay among immune dysregulation, barrier impairment, neuroendocrine imbalance, and microbial dysbiosis. High-resolution microbiome studies have moved the field beyond species-level associations to strain-level and functional insights, highlighting pathogenic Staphylococcus aureus lineages in atopic dermatitis (AD), disease-relevant Cutibacterium acnes phylotypes in acne, and gut microbial signatures that may prime type 17 helper T cell/regulatory T cell (Th17/Treg) imbalance and systemic inflammation across multiple dermatoses. Acupuncture is widely applied in dermatology to alleviate pruritus and reduce disease burden, with emerging sham-controlled trials and high-quality randomized evidence in chronic spontaneous urticaria (CSU) suggesting clinically meaningful symptomatic improvement. Mechanistically, acupuncture can engage neuro-immune circuits (including vagal anti-inflammatory pathways), modulate cytokine networks, and improve epithelial barrier integrity-host processes that strongly shape microbial ecology and metabolite production. Meanwhile, accumulating microbiome-focused studies in non-dermatologic conditions indicate that acupuncture can alter gut microbiota composition and diversity, as well as microbial metabolites (e.g., short-chain fatty acids), providing a plausible biological bridge to the gut-skin axis. In this narrative review, we synthesize evidence linking (i) skin/gut microbiome dysbiosis with inflammatory skin pathogenesis, (ii) acupuncture-mediated neuro-endocrine-immune modulation, and (iii) microbiome remodeling as a potential mediator of systemic and cutaneous immune modulation. We propose an integrative mechanistic framework and discuss methodological pitfalls (heterogeneous acupuncture protocols, challenges with sham designs, limited dermatology-specific microbiome endpoints, and gaps in causal inference), providing actionable directions for multi-omics longitudinal trials and mechanistic validation.},
}

Humans
*Acupuncture Therapy/methods
*Microbiota
*Skin Diseases/therapy/microbiology/immunology
Skin Microbiome

@article {pmid42441839,
year = {2026},
author = {Deng, S and Yang, Y and Guo, X and Yuan, MM and Zhang, Y and Wu, L and Shi, W and Zhou, X and Cornell, CR and Bates, CT and Liu, XA and Zhang, Q and Tian, R and Jian, S and Liu, S and Liang, Z and Lei, J and Gao, Q and Shi, Z and Wu, L and Liu, X and Luo, Y and Ning, D and Tiedje, JM and Zhou, J},
title = {Experimental drought drives divergent succession of soil microbiota.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {29},
pages = {e2537753123},
doi = {10.1073/pnas.2537753123},
pmid = {42441839},
issn = {1091-6490},
support = {32161123002//MOST | National Natural Science Foundation of China (NSFC)/ ; DE-SC0004601//U.S. Department of Energy (DOE)/ ; DE-SC0010715//U.S. Department of Energy (DOE)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Droughts ; *Microbiota/physiology ; Bacteria/genetics/classification ; Biodiversity ; Ecosystem ; Fungi/genetics/classification ; Soil/chemistry ; Biomass ; },
abstract = {As droughts become increasingly severe and prolonged worldwide, understanding how belowground biodiversity changes over time under water limitation is critical for assessing ecosystem resilience. However, long-term and continuous observations of soil microbial responses to drought remain rare. Here, using a 6-y experimental drought in a tallgrass prairie ecosystem, we showed that experimental drought reshaped the community compositions of soil bacteria, fungi, and protists, accompanied by progressive declines in microbial diversity and biomass. Analyses of time-decay relationships and paired community differences between drought and ambient conditions revealed increasingly divergent successional trajectories of soil microbiota under drought. Although stochastic processes dominated community assembly overall, their relative importance declined over time, particularly for bacteria in drought-treated soils, suggesting increasingly strong deterministic environmental filtering imposed by drought. In addition, drought reduced microbial network size but increased the complexity and stability of bacterial networks by favoring drought-tolerant taxa. Furthermore, drought-driven shifts in microbial community compositions significantly altered functional genes and associated ecosystem functioning. These findings suggest that microbial communities may become less variable but more vulnerable, and the detrimental effects of biodiversity loss on ecosystems could be more severe in an increasingly drought-prone world.},
}

*Soil Microbiology
*Droughts
*Microbiota/physiology
Bacteria/genetics/classification
Biodiversity
Ecosystem
Fungi/genetics/classification
Soil/chemistry
Biomass

@article {pmid42441851,
year = {2026},
author = {Landry, ZC and Foffi, R and Anelli, V and Arosio, P and Gil-Garcia, M and Henshaw, RJ and Müller, O and Paccagnan, G and Schneider, TN and Schubert, CJ and Słomka, J and Lee, KS and Zambelli, T and T Zweifel, S and Stocker, R},
title = {Raman imaging of the phycosphere reveals sharp gradients of organic matter exuded by single phytoplankton cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {29},
pages = {e2535317123},
doi = {10.1073/pnas.2535317123},
pmid = {42441851},
issn = {1091-6490},
support = {955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; PZ00P2_202188//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; ETH-07 24-2//Eidgenössische Technische Hochschule Zürich (ETH)/ ; LT000192/2018//Human Frontier Science Program (HFSP)/ ; BPN/PPO/2024/1/00008//Narodowa Agencja Wymiany Akademickiej (NAWA)/ ; RS2025-00554860//Korea Basic Science Institute (KBSI)/ ; 1.260002.01//Ulsan National Institute of Science and Technology (UNIST)/ ; },
mesh = {*Phytoplankton/metabolism/chemistry ; *Spectrum Analysis, Raman/methods ; *Xanthophylls/metabolism ; Diffusion ; },
abstract = {Phytoplankton cells exude a wide array of chemicals in the water column, generating a localized microenvironment known as the phycosphere. Although it is now well accepted that the phycosphere mediates interactions between phytoplankton and bacteria, the chemical gradients around individual phytoplankton cells have never been explicitly measured, and their shape has been classically assumed to be set by ideal diffusion. Here we used Raman microspectroscopy to obtain micrometer-scale measurements of the concentration profile of a phytoplankton metabolite (fucoxanthin) around individual phytoplankton cells of different species, having radii between [Formula: see text] and 60 [Formula: see text]m. We found that fucoxanthin concentration decreases more rapidly with distance from the cell than predicted by ideal diffusion, showing that the phycosphere includes compounds whose diffusion is characterized by nonideal effects. We explain this observation using a space-dependent diffusivity model where nonideality arises from viscosity and solubility gradients in the extracellular environment. Our results suggest an onion-structured model of the phycosphere, in which small hydrophilic solutes that obey ideal diffusion generate broad but weak gradients, whereas insoluble compounds are retained within [Formula: see text] to [Formula: see text] from the phytoplankton cell surface and yield steep gradients of organic matter. These observations, supported by evidence that fucoxanthin can act as an effective chemoattractant for marine bacteria, show the existence of strong and highly localized chemical cues with potentially far-reaching impacts on microbial interactions in aquatic environments. These findings highlight the importance of directly measuring the microscale chemical landscape experienced by marine microbes.},
}

*Phytoplankton/metabolism/chemistry
*Spectrum Analysis, Raman/methods
*Xanthophylls/metabolism
Diffusion

@article {pmid42443490,
year = {2026},
author = {Zhang, Y and Ma, K and Hu, T and Ma, Y and Zhao, H and Peng, X and Yin, G and Zhang, H and Lin, F and Pan, Y and Zhang, T and Ban, H and Zhu, Y and Gao, T and Qiu, L},
title = {Vegetation structure shapes behavioral, neuroimmune and gut microbial recovery after chronic stress in mice.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10628-8},
pmid = {42443490},
issn = {2399-3642},
support = {32572139//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32572141//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Chronic stress impairs behavior, neuroimmune regulation and gut microbial ecology, but whether natural-environment structure shapes recovery remains unclear. Here, we tested whether landscape design, beyond greenness alone, promotes recovery in chronically stressed male mice. During a 28-day recovery phase, mice were exposed to five parameterized vegetated landscapes differing in openness, canopy density and visual complexity, a matched urban-gray setting, or standard housing. Vegetated exposure improved anxiety-like behavior, behavioral despair and anhedonia, whereas the gray setting showed little benefit. Recovery was design-dependent: multistrata, color-rich landscapes produced the fastest and most sustained behavioral improvement, while open lawn-dominant layouts showed weaker, partly transient effects. These gains were accompanied by lower interleukin-1β and interleukin-6, normalized hippocampal Iba-1, preserved brain-derived neurotrophic factor, and restored gut microbial diversity. Predicted microbial functions linked butyrate-related pathways with neuroimmune-behavioral indices. These findings support vegetation structure as a tunable environmental variable for coordinated recovery after chronic stress.},
}

@article {pmid42444003,
year = {2026},
author = {Taylor, T and Benti, G and F A Leite, M and Arias-Giraldo, LM and Etalo, DW and Abera, S and Lombard, L and Maciá-Vicente, JG and Sanow, S and Rybka, D and Mostert, T and Martinez de la Parte, E and Legesse, D and Tulu, UT and Daksa, J and van Doorn, R and Rosa Leite, R and Tessema, T and Crous, PW and Kawa, D and Kuramae, EE and Raaijmakers, JM and Brady, SM},
title = {Disentangling the importance of microbiological and physico-chemical properties of Ethiopian field soils for the Striga seed bank and sorghum infestation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00926-3},
pmid = {42444003},
issn = {2524-6372},
abstract = {BACKGROUND: Striga hermonthica (Striga) is a parasitic weed that severely affects sorghum yield in sub-Saharan Africa. Recent studies highlighted the soil microbiome's potential to suppress Striga through interference with specific stages in its life cycle.

RESULTS: Statistical analyses of data collected from 48 Ethiopian sorghum field soils sampled across a > 1000-km-transect revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga occurrence in the field. Striga infestation of sorghum and seedbank levels were negatively correlated with potassium and sulfur soil content and positively correlated with calcium and magnesium nutrient profile proportions. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial composition even in soils where Striga was not detected. Specific fungal and bacterial genera showed both positive and negative correlations with Striga measures, but patterns rarely held across taxonomic levels. To begin to validate these correlations, we tested an isolate from the fungal genus Neocosmospora, which negatively correlated with the Striga seedbank, and showed that this isolate promotes Striga seed germination in vitro. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil-Striga interactions.

CONCLUSIONS: This study highlights the complexity of soil-microbiome-Striga interactions and the potential for observational studies to reveal candidates for biological control of Striga.},
}

@article {pmid42444523,
year = {2026},
author = {Santucci, NR and Dike, CR and Hellmann, J and Ollberding, NJ and Duan, Q and Minar, P and Denson, LA and Haslam, DB and Castillo, D and Abu-El-Haija, M},
title = {Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70504},
pmid = {42444523},
issn = {1536-4801},
support = {K23DK135797//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; 23DK118190//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; R03 DK131156/DK/NIDDK NIH HHS/United States ; P30 DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati/ ; NCT04131504//Leona M. and Harry B. Helmsley Charitable Trust for the ENvISION study/ ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP), Crohn's disease (CD), and irritable bowel syndrome (IBS) are associated with gut dysbiosis, but differences and similarities between conditions are unknown. We hypothesized that gut microbial ecology would differ across these disorders.

METHODS: Stool was collected from 120 subjects (AP [n = 30], CD [n = 29], IBS Rome IV [n = 27], and healthy controls [HC, n = 34]). Shotgun metagenomic sequencing was performed on extracted DNA and taxonomic and functional profiles obtained using sylph and HUMAnN3 with default parameters.

RESULTS: Age interquartile range for all participants was 8.1-17.7 years. Shannon diversity was decreased in AP compared to IBS or HC (p < 0.0001) and similar to CD (p = 0.97). CD differed from IBS (p = 0.001) and HC (p < 0.0001) while IBS and HC were similar (p = 0.61). Ordination of the first two principal coordinate analyses axes showed sample clustering by condition (R[2] = 0.12, p < 0.001), and differences between all conditions in pairwise comparisons (p < 0.001). Escherichia coli, Ruminococcus gnavus, Staphylococcus aureus, and Thomasciavelia ramosa remained enriched when all conditions (AP, CD, and IBS) were compared as a single group to HC. Using a random forest machine learning algorithm for species relative abundance, the ability to classify a sample to each condition versus all others was highest for CD (area under the receiver operative characteristic curve, AUC = 0.97), followed by AP (AUC = 0.92), HC (AUC = 0.88), and IBS (AUC = 0.83).

CONCLUSION: Organic disorders (AP and CD) are associated with significant gut dysbiosis than IBS which appears more like HC. Interventions targeting shifts in commensals in AP and CD may be helpful in improving outcomes in both disorders.},
}

@article {pmid42445284,
year = {2026},
author = {Xi, M and Li, S and Tang, Y and Zhu, J and Deng, S},
title = {Interactions between taste and oral microbiome: mechanisms and implications for oral and systemic diseases.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2699527},
pmid = {42445284},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome is a complex microbial ecosystem that contributes to oral and systemic health. Emerging evidence suggests a bidirectional interaction between oral microbiota and taste, although its underlying mechanisms and disease implications remain incompletely understood.

OBJECTIVE: This review aims to summarize current knowledge regarding the interactions between the oral microbiome and taste, elucidate the potential mechanisms involved, and discuss their relevance to human diseases.

DESIGN: Recent advances in clinical and experimental studies were reviewed, focusing on microbial metabolism, immunoinflammatory regulation, taste receptor modulation, and microbial-host interactions.

RESULTS: Oral microorganisms may influence taste perception through metabolite production, inflammatory pathways, alteration of taste receptor expression, and other mechanisms such as physical barriers. Conversely, taste perception and taste receptors can regulate microbial colonization by shaping dietary behaviors and local immune responses. These interactions may contribute to the development and progression of oral diseases, extraoral inflammatory diseases, cardiometabolic disorders, cancer, and neurodegenerative conditions.

CONCLUSIONS: The taste-oral microbiome axis represents an emerging regulatory network linking microbial ecology, sensory function, and disease pathogenesis. Further longitudinal and mechanistic studies are required to clarify causal relationships and explore microbiome-targeted therapeutic strategies.},
}

@article {pmid42445494,
year = {2026},
author = {Zhang, H and Xu, J and Zhou, X and Han, R and Li, H and Li, J and Zuo, J and Bai, Y and Wang, W and Li, B and Hu, R and Zhang, J},
title = {Effects of lubabegron fumarate on ruminal fermentation and microbial community in a rumen simulation system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1863733},
pmid = {42445494},
issn = {1664-302X},
abstract = {INTRODUCTION: The expansion of the global beef industry intensifies concerns regarding ammonia emissions, posing a significant challenge to environmental sustainability and production efficiency. Lubabegron fumarate (LBF), a novel β-adrenergic receptor modulator approved to mitigate these emissions, lacks a defined ruminal mode of action. This study aimed to characterise the effects of LBF on in vitro rumen fermentation, microbial ecology, and nitrogen metabolism.

METHODS: Using a rumen simulation system, we evaluated the effects of LBF on fermentation parameters, nutrient digestibility, and urease activity. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed to characterise shifts in microbial community structure, functional potential, and metabolic output, with a specific focus on nitrogen-cycling microbiota.

RESULTS: LBF did not directly inhibit urease. Instead, it optimised the rumen microenvironment by increasing total volatile fatty acids and pH, while reducing ammonia nitrogen (NH₃-N) and enhancing starch digestibility. Crucially, LBF orchestrated a selective enrichment of key taxa (e.g., Ruminococcus_E, specific Prevotella spp.) and promoted pivotal pathways (e.g., starch metabolism and amino acid biosynthesis) without eroding microbial diversity. Metabolomics revealed a redirected carbon flux towards propionic acid production, facilitating efficient microbial nitrogen assimilation and redirecting nitrogen from ammonia into microbial protein (MCP).

DISCUSSION: LBF reshaped the rumen microecosystem to synchronise carbohydrate fermentation and nitrogen assimilation, thereby optimising nutrient capture and reducing nitrogen waste. These findings provide a mechanistic basis for the strategic application of LBF as a pharmaceutical intervention to improve nitrogen efficiency and mitigate ammonia emissions in cattle production.},
}

@article {pmid42434299,
year = {2026},
author = {Shen, Q and Bian, C and Zhou, M and Shen, X and Jin, X and Li, B},
title = {Microbiota-mediated mechanisms of natural products in atherosclerosis: focus on metabolic and inflammatory pathways.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1818349},
pmid = {42434299},
issn = {1664-2392},
mesh = {Humans ; *Atherosclerosis/metabolism/microbiology/drug therapy ; *Biological Products/pharmacology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/metabolism/microbiology ; Signal Transduction ; },
abstract = {BACKGROUND: Atherosclerosis (AS) is a chronic inflammatory vascular disease characterized by lipid accumulation, endothelial dysfunction, immune dysregulation, and plaque formation. Beyond conventional lipid-related mechanisms, gut microbiota dysbiosis and microbiota-derived metabolites have emerged as important regulators of atherogenesis. Natural products, including polyphenols, flavonoids, alkaloids, fatty acids, polysaccharides, saponins, and terpenoids, may modulate AS by reshaping gut microbial ecology and metabolic outputs.

METHODS: This narrative review qualitatively synthesized English-language studies published from 2016 to 2026, with emphasis on recent preclinical and emerging clinical evidence. Literature was retrieved from PubMed and Google Scholar using terms related to natural products, gut microbiota, and atherosclerosis. Evidence was integrated across natural product categories, microbial metabolites, host signaling pathways, preclinical models, clinical observations, and translational limitations.

RESULTS: Natural products consistently acted on convergent microbiota-dependent pathways rather than isolated mechanisms. They reduced trimethylamine/trimethylamine N-oxide production, promoted short-chain fatty acid generation, remodeled bile acid metabolism, and modulated microbial tryptophan-derived metabolites. These metabolic changes were associated with improved intestinal barrier integrity, suppression of TLR4/NF-κB and NLRP3-mediated inflammation, immune rebalancing, reduced oxidative stress, enhanced cholesterol efflux, and attenuation of plaque-related phenotypes. Polyphenols and berberine showed relatively stronger mechanistic support, whereas polysaccharides, saponins, terpenoids, and complex formulas remain mainly exploratory. Most evidence derives from animal and in vitro studies, while clinical studies remain limited by small samples, short follow-up, heterogeneous interventions, surrogate endpoints, and insufficient causal validation.

CONCLUSIONS: Natural products provide an integrated framework for targeting the gut microbiota-metabolite-vascular pathology axis in AS. Although current evidence supports their biological plausibility and adjunctive therapeutic potential, standardized preparations, causal microbiome validation, multi-omics-based biomarkers, and well-designed clinical trials with vascular or cardiovascular endpoints are required before clinical translation.},
}

Humans
*Atherosclerosis/metabolism/microbiology/drug therapy
*Biological Products/pharmacology
Animals
*Gastrointestinal Microbiome/physiology
*Inflammation/metabolism/microbiology
Signal Transduction

@article {pmid42434559,
year = {2026},
author = {Saraiva, M and Gerilovych, A and Ay, H},
title = {Editorial: Harnessing aquatic microbial symbioses for sustainable aquaculture: unveiling biodiversity and ecosystem dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1897215},
doi = {10.3389/fmicb.2026.1897215},
pmid = {42434559},
issn = {1664-302X},
}

@article {pmid42434790,
year = {2026},
author = {Afeeza, K and Priya Dharshini, B and Vasugi, S and Dilipan, E},
title = {Comparative microbial ecology of seagrass and coral reef sediments in the Lakshadweep archipelago using high-throughput 16S rRNA sequencing.},
journal = {3 Biotech},
volume = {16},
number = {8},
pages = {319},
pmid = {42434790},
issn = {2190-572X},
abstract = {Seagrass and coral reef sediments from Minicoy Island were investigated to compare bacterial community composition and predicted functional potential using 16S rRNA gene (V3-V4) amplicon sequencing. Sequence data were processed in QIIME2 with Deblur-generated amplicon sequence variants and taxonomic classification against the SILVA database. Alpha and beta diversity analyses revealed high similarity in microbial community composition between seagrass and coral reef sediments, indicating strong ecological connectivity within the atoll environment. Proteobacteria, Bacteroidota, and Desulfobacterota were dominant across both habitats, while sulfate-reducing families such as Desulfobulbaceae and Desulfobacteraceae were relatively enriched in seagrass sediments. Correlation analysis showed that microbial diversity was positively associated with nutrient concentrations and turbidity, and negatively associated with temperature and particulate organic carbon. Functional prediction using PICRUSt2 and KEGG pathway annotation identified habitat-associated trends in transport- and signalling-related pathways, although these functional differences were interpreted cautiously due to the limitations of predictive approaches. Henceforth, the study provides a baseline assessment of benthic microbial communities in Lakshadweep ecosystems and highlights the need for geographically independent sampling and multi-omics approaches to validate functional and ecological inferences.},
}

@article {pmid42435155,
year = {2026},
author = {Kim, H and Park, D and Kwon, YJ and Imm, JY},
title = {Dietary milk polar lipids ameliorate hepatic lipid accumulation through coordinated regulation of Wnt-PPARγ signaling and remodeling of the gut microbiota.},
journal = {Food science of animal resources},
volume = {46},
number = {1},
pages = {},
pmid = {42435155},
issn = {2636-0780},
support = {RS-2020-NR048142//Ministry of Science, ICT and Future Planning/ ; },
abstract = {This study investigated the protective effects of milk polar lipids (MPL) against non-alcoholic fatty liver disease (NAFLD) and explored the underlying mechanisms using a high-fat high-sucrose (HFHS) diet-induced mouse model. MPL diet significantly reduced body weight gain, adiposity, and hepatic lipid accumulation, in addition to decreasing serum levels of liver injury markers. Mechanistically, MPL diet activated hepatic Wnt/β-catenin signaling, as evidenced by increased expression of low-density lipoprotein receptor-related protein 6 (LRP6), Wnt family member 3 A (Wnt3a), and β-catenin. Concurrently, MPL treatment suppressed peroxisome proliferator-activated receptor gamma (PPARγ) and downstream lipogenic proteins involved in triglyceride synthesis and de novo lipogenesis. In addition, MPL diet markedly reshaped the gut microbiota composition disrupted by HFHS feeding. Notably, MPL group showed a significant increased the abundance of Akkermansia muciniphila and short-chain fatty acid-producing bacteria, including members of Romboutsia and Christensenellaceae. These findings demonstrate that dietary MPL effectively attenuates HFHS diet-induced NAFLD through coordinated regulation of hepatic Wnt-PPARγ signaling and gut microbial ecology.},
}

@article {pmid42435199,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Correction to: Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
doi = {10.1007/s00248-026-02821-3},
pmid = {42435199},
issn = {1432-184X},
}

@article {pmid42436636,
year = {2026},
author = {Deng, S and Shi, W and Tian, R and Guo, X and Ning, D and Zhou, X and Yuan, M and Feng, J and Zhou, A and Fu, Y and Xu, G and Mu, D and Shi, P and Fan, X and Teng, Y and Zhao, X and Li, Z and Liu, J and Liu, X and Wu, L and He, Z and Liu, X and Luo, Y and Tiedje, JM and Yang, Y and Zhou, J},
title = {Increased precipitation decelerates temporal succession of grassland soil microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag176},
pmid = {42436636},
issn = {1751-7370},
abstract = {Global precipitation regimes have been shifted in recent decades, imposing significant consequences in water-limited grassland ecosystems. However, the effects of increased precipitation on the succession of soil microbial communities remain unclear, mainly due to the scarcity of long-term experiments with time-series data. Here, we examined temporal succession of grassland soil microbial communities in a long-term increased precipitation experiment. Both soil microbial taxonomic and functional structures were significantly altered by increased precipitation. Increased precipitation significantly decelerated the succession rates of soil microbial functional structure (ie, time-decay relationships). Consistent with the increased microbial decomposition and heterotrophic respiration, the abundances of soil microbial carbon decomposition genes were markedly enhanced by increased precipitation. Furthermore, increased precipitation stimulated genes involved in nutrient cycling processes, potentially promoting plant growth. Collectively, the contributions of stochastic processes in shaping microbial communities were increased under increased precipitation, suggesting that microbial successional trajectories may shift toward multiple alternative states characterized by greater stochasticity under future altered precipitation regimes.},
}

@article {pmid42439608,
year = {2026},
author = {Huo, W and Qiao, Y and Wang, C and Li, R and Li, E},
title = {Mycotoxins as silent modulators of enteric viral susceptibility and vaccine responsiveness.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/10408398.2026.2700434},
pmid = {42439608},
issn = {1549-7852},
abstract = {Enteric viral infections remain a major cause of morbidity and mortality worldwide, particularly in children and intensively raised livestock. Although live oral vaccines have reduced disease burden, vaccine efficacy varies greatly across regions. Factors such as host genetics, microbiota, maternal antibodies, and nutrition have been widely studied, whereas chronic exposure to dietary toxicants has received less attention. Mycotoxins, fungal metabolites contaminating staple crops including maize, wheat, and peanuts, are commonly consumed at low but persistent levels in regions heavily affected by enteric viral diseases. Increasing evidence shows that mycotoxins disrupt intestinal barrier integrity, alter innate and adaptive immune responses, and reshape gut microbial ecology even without overt toxicity. These effects target pathways essential for antiviral defense and oral vaccine efficacy. This review proposes a mechanistic framework in which chronic mycotoxin exposure alters epithelial-immune-microbiota interactions, thereby increasing susceptibility to enteric viral infection and reducing vaccine-induced protection. We summarize evidence linking mycotoxins to barrier dysfunction, interferon dysregulation, antigen-presenting cell impairment, IgA suppression, intestinal stem cell injury, and microbiota-mediated changes in viral infectivity. Recognizing mycotoxins as covert regulators of mucosal antiviral immunity may provide new strategies to improve oral vaccine performance and reduce global enteric viral disease burden.},
}

@article {pmid42433682,
year = {2026},
author = {Wan, R and Nong, S and Zhang, C and Wang, Z and Wang, K and Zou, Z},
title = {Effects of fermented mulberry leaves on growth performance, nutrient digestibility, diarrhea, and intestinal microecology in weaned piglets: a preliminary study.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1874983},
pmid = {42433682},
issn = {2297-1769},
abstract = {This study investigated the effects of dietary fermented mulberry leaves (FML) on growth metrics, nutrient digestibility, diarrhea incidence, and gut microbial ecology in weaned piglets. A total of 200 piglets (28 days old) were randomly allocated into five groups: a basal diet control group and four treatment groups receiving the basal diet supplemented with 5%, 10%, 15%, or 20% FML (co-fermented with Lactobacillus and cellulase) over a 28-day period. Growth performance, apparent nutrient digestibility, diarrhea rate, intestinal pH, short-chain fatty acid (SCFA) concentrations, and cecal microbiota (via 16S rRNA sequencing) were evaluated. No notable differences in growth performance were detected across groups (P > 0.05); however, the feed-to-gain ratio was significantly lower in the 5% and 20% FML groups (P < 0.05). Diarrhea incidence declined across all FML-supplemented groups, with the greatest reduction (52.46%) in the 15% group during days 28-42. Duodenal pH decreased significantly in all treatment groups (P < 0.05). Cecal acetate and propionate levels rose markedly in the 10%, 15%, and 20% groups (P < 0.05), with the 15% group showing a 47.05% increase in acetate. FML supplementation also altered cecal microbial diversity and community composition. At the genus level, the 15% group had the highest relative abundance of Prevotella (22.46%), while Lactobacillus and Bifidobacterium tended to increase in FML groups. Overall, dietary inclusion of 5-20% FML did not significantly enhance growth performance but effectively reduced diarrhea, optimized intestinal pH, increased cecal acetate and propionate production, and modulated cecal microbiota composition, with 15% FML identified as the optimal level.},
}

@article {pmid42429666,
year = {2026},
author = {Zhao, Y and Chen, L and Li, C and Xu, Y and Huang, J and Chen, S and Yu, Z and Liu, X},
title = {Sialidase inhibitor modulates gut microbiota and enhances mucosal protection in the treatment of ulcerative colitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019426},
doi = {10.1128/msystems.00194-26},
pmid = {42429666},
issn = {2379-5077},
abstract = {Ulcerative colitis (UC) is characterized by mucosal barrier erosion, a process exacerbated by bacterial sialidases. We investigated the therapeutic efficacy of the sialidase inhibitor (SI) in UC. In a pilot randomized clinical trial, SI intervention significantly improved clinical symptoms and endoscopic outcomes in mild-to-moderate UC patients. This improvement correlated with an enrichment of butyrate-producing taxa and beneficial metabolic pathways. In a dextran sulfate sodium-induced colitis mouse model, SI attenuated inflammation and restored mucus layer integrity, accompanied by increased expression of Muc2 and Tff3. Crucially, unlike broad-spectrum antibiotics, SI preserved microbial community resilience while specifically enriching beneficial mucolytic commensals, Akkermansia muciniphila and Bacteroides acidifaciens. These findings identify SI as a promising therapeutic strategy that targets sialidase activity to reinforce the mucosal barrier and restore gut homeostasis.IMPORTANCEThe gut microbiota plays a pivotal role in maintaining mucosal integrity and intestinal homeostasis; however, dysbiosis-driven mucus layer degradation remains a hallmark of ulcerative colitis (UC). Current interventions like antibiotics often disrupt microbial diversity, exacerbating dysbiosis and failing to address mucosal thinning, which is a critical factor in UC progression. Developing strategies to reinforce the mucus barrier without compromising microbial balance is urgently needed, but such approaches remain underexplored. Our study demonstrates that sialidase inhibitors (SIs) uniquely preserve mucosal thickness by curbing microbial mucin degradation while selectively enriching beneficial taxa and butyrate-producing bacteria. Unlike antibiotics, SIs enhance mucosal protection without destabilizing microbial communities, offering a dual-action therapeutic strategy. This work bridges a critical knowledge gap, providing evidence for microbiota-targeted therapies that synergistically restore mucosal health and microbial ecology in UC.CLINICAL TRIALSThis study was registered with the Chinese Clinial Trial Registry as ChiCTR2000028767.},
}

@article {pmid42429763,
year = {2026},
author = {Tribbia, DZ and Lebre, PH and Vázquez-Campos, X and Ray, AE and Laird, T and Machado de Lima, N and Maggs-Kölling, G and Cowan, DA and Ferrari, BC},
title = {Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0026526},
doi = {10.1128/aem.00265-26},
pmid = {42429763},
issn = {1098-5336},
abstract = {UNLABELLED: Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earth's terrestrial surface by the end of the 21st century. In these environments, harsh conditions, including nutrient and water limitations, restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterized by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly (P < 0.005) reduced in hyperarid soils compared to their arid counterparts. In contrast, hyperarid fog-dominated soils exhibited significantly (P < 0.0005) elevated rates of atmospheric hydrogen oxidation, even in the absence of water inputs. We propose that sustained high-affinity hydrogen oxidation, coupled with rapid microbial resuscitation following wetting events, supports shallow sub-surface microbial communities in the Namib Desert, particularly in the coastal hyperarid zone. Together, these findings challenge current understanding of the lower limits of microbial activity and reveal alternative metabolic pathways that enable microbial persistence in hyperarid hot desert soils.

IMPORTANCE: Drylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry, hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.},
}

@article {pmid42429816,
year = {2026},
author = {Basu, DN and Khangar, P and Joshi, K and Krishna, S and Khan, I},
title = {Tracking Microbiome Composition and Stability Across Indian Social Honeybees Foraging in a Homogeneous Mustard Crop Landscape.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02828-w},
pmid = {42429816},
issn = {1432-184X},
abstract = {Microbial communities are essential for host health and ecosystem stability. However, whether host identity or shared foraging resources shapes microbiome structure among co-occurring species remains poorly understood. We studied bacterial and fungal communities of four Indian honeybee species in a mustard monoculture resource condition, integrating behavioural observation-based pollinator data with microbial co-occurrence networks derived from metabarcoding. Microbiome composition was more strongly associated with host identity rather than with foraging behaviour, bee abundance, or landscape use. This has strong implications for how microbial sharing among co-occurring social honeybee species can be limited, thereby preventing them from influencing each other's microbiomes through shared foraging and driving variable pollinator health within a shared ecosystem. While core bacterial taxa were shared, relationships among bacterial cobionts, unlike those among fungal genera, remained species-specific. Microbial diversity, along with community structure and function, influenced network stability, with a highly modular microbial network of Apis cerana exhibiting more predicted network robustness to simulated perturbations. In summary, host-specific filtering shaped the microbiome more than resource homogenisation, with closely related species facing unique risks of disruption of microbial co-occurrence, with broader implications for vulnerability to microbiome imbalance, environmental stress, and emerging infections.},
}

@article {pmid42429927,
year = {2026},
author = {Lirio, CPT and Albino, EED and Nisnisan, KKS and Castro, AE},
title = {Gut bacterial community profile of the endemic catfish Arius manillensis from Pasig River, Philippines.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037026},
doi = {10.1128/mra.00370-26},
pmid = {42429927},
issn = {2576-098X},
abstract = {The Pasig River is a highly urbanized waterway, yet the microbial ecology of its native fauna remains poorly understood. This study provides the first report of the gut bacterial community of the catfish Arius manillensis, revealing bacterial taxa and underscoring the need to study host-associated microbiomes in urban aquatic ecosystems.},
}

@article {pmid42429961,
year = {2026},
author = {Jordan, S and Pothier, JF and de Maayer, P and Kvitko, BH and Coutinho, TA and Smits, THM},
title = {Genome sequences of 71 ecologically and geographically diverse Enterobacter strains.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0033426},
doi = {10.1128/mra.00334-26},
pmid = {42429961},
issn = {2576-098X},
abstract = {We sequenced the genomes of 77 bacterial strains, tentatively identified as Enterobacter. Of these, 71 were identified as Enterobacter based on genomic analysis. These strains span 11 species of diverse ecological and geographical origin.},
}

@article {pmid42430702,
year = {2026},
author = {Bermúdez-Monsalve, JR and Berger, SA and Yalçın, G and Nejstgaard, JC},
title = {Correspondence on "Long-Term Changes in the Abundance, Size, and Morphotype of Marine Plastics in the North Pacific".},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02999},
pmid = {42430702},
issn = {1520-5851},
}

@article {pmid42430909,
year = {2026},
author = {Maranho, LT and Geraldo, MR and Nogueira, KDS and Gomes, MP},
title = {Associations between rhizosphere microbial community structure and antibiotic attenuation in a pilot-scale hybrid constructed wetland.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142886},
doi = {10.1016/j.jhazmat.2026.142886},
pmid = {42430909},
issn = {1873-3336},
abstract = {Constructed wetlands are widely used as nature-based solutions for wastewater treatment; however, the role of rhizosphere-associated microbial communities in the attenuation of emerging contaminants remains unclear. In this study, we evaluated the antibiotic removal and microbial community structure in a pilot-scale hybrid constructed wetland treating municipal wastewater by integrating vertical upflow (Sagittaria montevidensis), floating (Salvinia molesta + Lemna gibba), and horizontal subsurface flow (Canna indica) units. Antibiotics from different therapeutic classes were quantified using LC-MS/MS across the treatment compartments. The system achieved high attenuation efficiencies, with removal efficiencies exceeding 98% for the target compounds. The floating macrophyte unit showed the greatest reduction in concentrations relative to the upstream compartments. Microbial community analyses based on 16S rRNA gene sequencing revealed marked shifts in the community structure along the treatment gradient. Alpha diversity indices varied (Shannon index: 1.066-4.954), with higher diversity observed in rhizospheric communities associated with Sagittaria and Canna than in influent wastewater and pre-exposure samples. Beta diversity analysis (Bray-Curtis dissimilarity) showed a clear separation between the wastewater and rhizospheric communities (PERMANOVA, p = 0.001; R[2] = 0.66). Redundancy analysis and correlation-based approaches indicated that variations in dominant groups were statistically associated with antibiotic attenuation patterns across treatment compartments. These relationships represent ecological covariation patterns and should not be interpreted as direct evidence of microbial biodegradation activity. Overall, the results indicate that hybrid CW promote structured rhizosphere microbial communities that co-vary with antibiotic attenuation, supporting the future integration of microbial ecology into nature-based wastewater treatment optimization.},
}

@article {pmid42432346,
year = {2026},
author = {Muñoz-Laiton, P and Hernandez-Valencia, JC and Isaza, JP and Araújo, MDS and Salles, JF and Correa, MM},
title = {Bacterial and Fungal Microbiota in Anopheles darlingi Exhibit Differences in Diversity Across Three Main Colombian Malaria-endemic Regions.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02829-9},
pmid = {42432346},
issn = {1432-184X},
abstract = {Anopheles darlingi is the main malaria vector in the Neotropics. Despite their importance, little is known about the microbiota composition in areas where these vectors are found. Since the microbiota may influence host biology and vector competence, it is essential to understand these microbial communities in endemic regions. This study explores the bacterial and fungal communities in An. darlingi from three malaria-endemic areas in Colombia and examined how geography influences microbial composition. Mosquitoes were collected from the Bajo Cauca, Pacific and Amazonas regions, and their microbiota was characterized by amplifying and sequencing the 16 S rRNA V3-V4 region for bacteria and the ITS2 region for fungi. Analysis indicated greater alpha diversity in An. darlingi mosquitoes from the Amazonas region. Beta diversity findings demonstrated differences in bacterial and fungal community compositions across regions, especially between Amazonas and the other two regions. Additionally, the similarity of microbial communities declined slightly with increasing geographic distance. This study significantly advances our understanding of the microbiota associated with An. darlingi in endemic regions of Colombia, by revealing notable differences in bacterial and fungal community composition and abundance across diverse geographical populations. Importantly, these new insights extend beyond species and geographic boundaries by providing evidence of specific fungal communities linked to the vector, paving the way for innovative microbiota-based vector control strategies in malaria vector research.},
}

@article {pmid42432352,
year = {2026},
author = {Wang, X and Chen, J and Tang, Y and Liu, H},
title = {Insights into the Mechanism Underlying the Symbiosis between Seagrass and a Lulworthiaceae Fungus.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02808-0},
pmid = {42432352},
issn = {1432-184X},
support = {AoE/P-601/23N//Hong Kong Research Grants Council/ ; MCEF23SC02//Hong Kong Offshore Liquefied Natural Gas Terminal/ ; },
abstract = {Various fungi have been identified in seagrass compartments; however, the exact nature of their interactions with these marine flowering plants remains largely uncharacterized. The partnership between seagrasses and Lulworthiaceae fungi represents a typical and compelling example of such an underwater association. Here, we combine UHPLC-MS/MS, transcriptomics, and plant growth assays to validate the putative symbiosis between the seagrass Halophila ovalis and the Lulworthiaceae fungus Halophilomyces hongkongensis, and elucidate the underlying mechanism of this relationship. We confirmed that H. hongkongensis produces the phytohormone indole-3-acetic acid (IAA). Through transcriptomic analysis, we proposed its IAA biosynthesis pathways. All identified IAA biosynthesis genes were upregulated in seagrass roots/rhizomes compared to rhizosphere sediments, with the tryptophan aminotransferase gene (indole-3-pyruvic acid pathway) exhibiting a significant increase. Furthermore, H. hongkongensis was confirmed as a plant growth-promoting fungus; its culture filtrates promoted Arabidopsis thaliana shoot and lateral root/root hair growth, an effect strongly correlated with IAA production and highly likely in seagrass. Beyond IAA-specific analyses, its upregulated genes were significantly enriched in pathways such as tryptophan metabolism, starch/sucrose metabolism, and DNA replication. Collectively, these results indicate that H. hongkongensis establishes a growth-promoting symbiosis with H. ovalis by upregulating its IAA biosynthesis genes and secreting IAA; in return, the host provides carbohydrates that sustain fungal metabolism and support active DNA replication. This study provides the first mechanistic verification of a seagrass-Lulworthiaceae symbiosis, significantly advancing our understanding of marine plant-fungal interactions. It also demonstrates the first IAA-linked plant growth-promoting capacity of a member from the cryptic marine fungal family Lulworthiaceae.},
}

@article {pmid42432384,
year = {2026},
author = {Alías-Segura, S and Patiño, B and Gil-Serna, J},
title = {Metabarcoding Characterization of Fungal Communities in Spanish Cereals with a Special Focus on Fusarium Species.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02833-z},
pmid = {42432384},
issn = {1432-184X},
support = {PID2022-136803OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; PID2022-136803OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; PID2022-136803OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; CT25/24//Complutense University of Madrid and Banco Santander/ ; },
abstract = {Cereal safety is a critical public health concern, as crops are frequently compromised by mycotoxin-producing fungi, particularly those from the genus Fusarium. Although metabarcoding is a powerful tool for characterizing these fungal communities, the universal internal transcribed spacer 2 (ITS2) marker lacks the resolution required to distinguish closely related species with distinct toxigenic profiles. The objective of this work was to accurately characterize the mycobiota and specific Fusarium community structure in Spanish cereal field samples. We propose a high-resolution metabarcoding workflow within the QIIME 2 environment to optimize Fusarium identification using the translation elongation factor 1-α (TEF1) gene. We developed a TEF1 Naive Bayes classifier trained on a curated database derived from FUSARIUM-ID v.3.0, expanded with eukaryotic sequences to prevent false-positive assignments. This approach was validated through direct comparison with ITS2 in the same samples. As expected, ITS2 significantly underestimates Fusarium diversity, whereas TEF1 enables precise species-level resolution within this genus. General mycobiota analysis performed using ITS2 revealed that fungal communities are shaped primarily by geographical location rather than host cereal species. Crucially, our approach confirmed the persistence of key toxigenic species, such as F. langsethiae and F. graminearum, and revealed broader diversity through the consistent detection of species often overlooked by traditional methods, including F. equiseti, F. acuminatum, and F. culmorum. We conclude that our metabarcoding framework reveals a high Fusarium diversity in Spanish cereal grains, and this knowledge is essential for designing targeted strategies to predict and mitigate mycotoxin contamination in these crops.},
}

@article {pmid42433202,
year = {2026},
author = {Buessecker, S and Klos, AS and Quan, ME and Finch, AH and Sobol, MS and Evans, GN and Anbar, AD and Kaçar, B and Dekas, AE},
title = {Microbial N2O Reduction in Sulfidic Waters: Implications for Proterozoic Oceans.},
journal = {Geobiology},
volume = {24},
number = {4},
pages = {e70056},
doi = {10.1111/gbi.70056},
pmid = {42433202},
issn = {1472-4669},
support = {80NSSC17K0296/NASA/NASA/United States ; },
mesh = {*Nitrous Oxide/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; *Sulfides/metabolism ; *Rhodopseudomonas/metabolism ; Oceans and Seas ; Oxidoreductases/metabolism/genetics ; Copper/metabolism ; },
abstract = {Throughout Earth's history, shifts in ocean redox influenced the bioavailability of trace metals, shaping the activity of microorganisms. In Proterozoic oceans, the precipitation of copper (Cu) with sulfide was hypothesized to limit the bioavailability of Cu. This limitation may have suppressed microbial reduction of nitrous oxide (N2O), due to the Cu dependency of nitrous oxide reductase (Nos). It is thought that without this critical microbial sink, Proterozoic oceans were a significant net source of N2O. Here, we revisit this paradigm in light of recently derived ~20-fold lower estimates for sulfide in Proterozoic seawater and an empirical evaluation of the potential for microbial N2O reduction under sulfidic conditions. Leveraging publicly available environmental metatranscriptomes, we infer active N2O reduction from the detection of nosZ transcripts in multiple marine and lacustrine systems in which sulfide and Cu concentrations are analogous to those of the Proterozoic. In controlled culture experiments, we demonstrate that the purple non-sulfur bacterium Rhodopseudomonas palustris can reduce N2O at sulfide concentrations up to 50 μM, well above levels predicted for Proterozoic oceans. Based on trace metal speciation modeling, we suggest that Cu remains bioavailable under Proterozoic-like conditions as a dissolved CuHS[0] complex. Collectively, these observations suggest microbial N2O reduction occurs under euxinic conditions, implying that Proterozoic marine N2O emissions were lower than previously proposed. Our conclusions inform our understanding of the microbial ecology in sulfidic waters, the early climate, and the search for extraterrestrial life.},
}

*Nitrous Oxide/metabolism
Oxidation-Reduction
*Seawater/microbiology/chemistry
*Sulfides/metabolism
*Rhodopseudomonas/metabolism
Oceans and Seas
Oxidoreductases/metabolism/genetics
Copper/metabolism

@article {pmid42420641,
year = {2026},
author = {Kittredge, HA and Dougherty, KM and Glanville, K and Evans, SE},
title = {Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02827-x},
pmid = {42420641},
issn = {1432-184X},
support = {DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DEB 2224712//Directorate for Biological Sciences/ ; DEB 2224712//Directorate for Biological Sciences/ ; DEB 2224712//Directorate for Biological Sciences/ ; DEB 2224712//Directorate for Biological Sciences/ ; },
abstract = {Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying-rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying-rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (- exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.},
}

@article {pmid42421214,
year = {2026},
author = {Raya Tonetti, F and Han, H and Fondevila, MF and Wei, W and Özdirik, B and Bajaj, JS and Schubert, ML and Sikaroodi, M and Gillevet, PM and Lang, S and Demir, M and Rahman, IR and van der Donk, WA and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Stärkel, P and Bataller, R and Hsu, CL and Llorente, C},
title = {Non-absorbable antibiotics worsen alcohol-associated liver disease in gastric acid-suppressed mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694797},
doi = {10.1080/19490976.2026.2694797},
pmid = {42421214},
issn = {1949-0984},
mesh = {Animals ; *Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use ; *Proton Pump Inhibitors/adverse effects/administration & dosage ; Mice ; *Gastric Acid/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Liver Diseases, Alcoholic/microbiology/pathology ; Dysbiosis/chemically induced ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Liver/pathology/drug effects ; },
abstract = {Gastric acid-suppressive medications, particularly proton pump inhibitors (PPIs), are commonly used in patients with alcohol-associated liver disease (ALD) to prevent and manage upper gastrointestinal bleeding, gastroesophageal reflux disease, and non-steroidal anti-inflammatory/aspirin-induced gastroesophageal damage. By inhibiting the gastric H[+]/K[+]-ATPase, PPIs suppress acid secretion and impair bacterial killing, thereby promoting gut dysbiosis that disrupts barrier integrity and enhances bacterial translocation, ultimately exacerbating liver injury. PPIs are frequently co-administered with antibiotics for indications such as gastrointestinal bleeding, Spontaneous Bacterial Peritonitis (SBP), other infections, or hepatic encephalopathy prophylaxis, but the consequences of this combined therapy on gut microbial ecology and disease outcomes remain unclear. Our study addresses this gap by showing how PPI use, alone or with antibiotics, reshapes the gut microbiome and aggravates liver disease progression. In previous studies, we showed that PPIs promote dysbiosis and ALD progression in mice and humans by facilitating intestinal expansion and hepatic translocation of Gram-positive Enterococcus. Fecal cytolysin, an Enterococcus faecalis exotoxin that induces hepatocyte death, predicts mortality in patients with alcohol-associated hepatitis (AH). In this study, we have examined the mechanism by which PPIs alone and in combination with non-absorbable antibiotics targeting Gram-positive bacteria influence ALD, as well as the disease mechanisms associated with cytolytic Enterococcus faecalis and the development of therapeutic strategies. In mice, alcohol administration during gastric acid suppression promoted expansion of Gram-positive taxa, including cytolysin-producing Enterococcus. Similarly, PPI use in patients with AH was associated with increased fecal Enterococcus and higher 30-d mortality, underscoring the translational relevance of our findings. Unexpectedly, treatment of acid-suppressed mice with non-absorbable antibiotics designed to suppress Gram-positive bacteria worsened ethanol-induced steatohepatitis: while Enterococcus abundance decreased, Streptococcus and other potentially pathogenic taxa expanded, leading to increased bacterial translocation and aggravated liver injury. In patients with cirrhosis or metabolic dysfunction-associated steatotic liver disease (MASLD), PPIs did not promote Enterococcus expansion, indicating etiology-dependent microbiome responses. Finally, we identified dipalmitoylphosphatidylcholine and Caspase-1 inhibitor as in vitro and in vivo modulators of cytolysin activity, highlighting potential therapeutic avenues. Collectively, our study demonstrates how PPIs and non-absorbable antibiotics targeting Gram-positive bacteria interact with the gut microbiome to drive ALD, underscoring the need for careful therapeutic management.},
}

Animals
*Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use
*Proton Pump Inhibitors/adverse effects/administration & dosage
Mice
*Gastric Acid/metabolism
Male
*Gastrointestinal Microbiome/drug effects
*Liver Diseases, Alcoholic/microbiology/pathology
Dysbiosis/chemically induced
Humans
Mice, Inbred C57BL
Disease Models, Animal
Liver/pathology/drug effects

@article {pmid42421228,
year = {2026},
author = {Serrano-García, L and Martínez-Salvador, E and Belda-Marco, A and Herrero-Oliva, C and Cortés, J and Llombart-Cussac, A and Fernández-Murga, L},
title = {Modulation of the response to immunotherapy in triple-negative breast cancer: the role of the microbiota and microbial metabolites in the tumor microenvironment.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2697600},
doi = {10.1080/19490976.2026.2697600},
pmid = {42421228},
issn = {1949-0984},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Triple Negative Breast Neoplasms/therapy/immunology/microbiology ; Female ; *Immunotherapy ; *Gastrointestinal Microbiome/immunology ; Animals ; },
abstract = {Triple-negative breast cancer is an aggressive and heterogeneous breast cancer subtype for which immune checkpoint inhibitors combined with chemotherapy have improved outcomes in selected patients. However, primary and acquired resistance remain common, underscoring the need to identify extrinsic, modifiable determinants of antitumor immunity. Increasing evidence indicates that the gut and tumor-associated microbiota shape systemic and intratumoral immune tone and influence the efficacy of cancer therapies. Beyond microbial composition, microbiota-derived metabolites-including short-chain fatty acids, indole-tryptophan derivatives, bile acids, polyamines, and other small molecules-can act as functional mediators linking microbial ecology to immune-cell programming and tumor biology. These metabolites modulate dendritic cell function, T-cell priming and fitness, myeloid polarization, inflammatory set points, and metabolic pathways within the tumor microenvironment, thereby potentially enhancing or constraining responses to chemoimmunotherapy. Importantly, while some studies propose intratumoral microbial effects, most clinically actionable evidence currently supports systemic gut-derived metabolites and immune tone modulation that secondarily shapes the TNBC tumor microenvironment. In this review, we synthesize current knowledge on (i) the immunobiology of triple-negative breast cancer (TNBC) relevant to microbiota-driven modulation, (ii) mammary and gut microbiome features reported in TNBC, and (iii) mechanistic pathways through which microbial metabolites may regulate antitumor immunity and immune checkpoint inhibitors (ICI) sensitivity. We also discuss methodological considerations for integrating microbiome profiling with metabolomics and immune phenotyping and evaluate emerging opportunities to leverage microbiota-derived metabolites as biomarkers and therapeutic targets. Finally, we highlight translational strategies-including diet, pre/probiotics, antibiotic stewardship, fecal microbiota transplantation, and metabolite-centric ("postbiotic") approaches-and outline priorities for TNBC-focused, prospective multi-omics studies to move from associative signatures toward actionable interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Triple Negative Breast Neoplasms/therapy/immunology/microbiology
Female
*Immunotherapy
*Gastrointestinal Microbiome/immunology
Animals

@article {pmid42423764,
year = {2026},
author = {Righetti, D and Soliman Tamayo, BK and Lampis, S and Lens, PNL},
title = {Effects of Per- and Polyfluoroalkyl Compounds (PFASs) on Anaerobic Granular Sludge: Methane Production and Microbial Community Composition.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02793-4},
pmid = {42423764},
issn = {1432-184X},
abstract = {PFASs are a group of pollutants ubiquitous in the environment, for which their effects on the microbial community composition and activity of anaerobic granular sludge are still poorly understood. With our study, we aimed to provide insight into the impact of four PFASs on the methane yield of anaerobic granular sludge (AGS) using acetate as the substrate. Anaerobic granular sludge was exposed to different concentrations of 1H,1H,2H,2H-Tridecafluorooctan-1-ol (6:2FTOH), 1H,1H,2H,2H-Perfluoro-1-decanol (8:2FTOH), Tridecafluorohexane-1-sulfonic acid (PFHxS) and Perfluorooctanoic acid (PFOA). While the two fluorotelomers caused marginal changes in methane production, PFHxS and PFOA greatly inhibited acetoclastic methanogenesis. Depending on the concentration, the AGS could recover its activity after a certain number of hours when incubated with PFASs. The 50% Inhibitory Concentration (IC50) of the methane production was estimated to be 278.98 (± 3.2) mg/L for PFOA and 1,091.9 (± 26.78) mg/L for PFHxS. PFASs exposure also influenced the archaeal and eubacterial communities. The most significant change was observed with the eubacterial community, which showed an increase in the relative abundance of the genus Sulfurospirillum in the samples treated with 2,000 mg/L of 8:2FTOH and 600 mg/L of PFOA, whose presence grew to represent 16.65% and 45.4% of all reads in those samples. These findings provide insight into the differential impact of PFASs on methanogenic processes and highlight their potential to disrupt key microbial functions in anaerobic systems.},
}

@article {pmid42424815,
year = {2026},
author = {Tang, Q and Zhang, Y and Garza, DR and Ruan, C and Liu, B and Rocha, U and Shen, P and Wei, Y and Deng, Y and Zhang, J and Richnow, HH},
title = {Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion.},
journal = {Water research},
volume = {305},
number = {},
pages = {126401},
doi = {10.1016/j.watres.2026.126401},
pmid = {42424815},
issn = {1879-2448},
abstract = {Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.668 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.},
}

@article {pmid42425005,
year = {2026},
author = {Murugan, SG and Lee, CW and Wong, WACY and Wong, YY and Liu, B and Narayanan, K and Sim, EUH and Bong, CW and Wang, A},
title = {Growth Dynamics of selected Vibrio spp. in mono-, co-culture and multi-bacterial microcosms: Investigating the prevalence of Vibrio parahaemolyticus in seawater.},
journal = {Marine environmental research},
volume = {221},
number = {},
pages = {108257},
doi = {10.1016/j.marenvres.2026.108257},
pmid = {42425005},
issn = {1879-0291},
abstract = {We examined the growth dynamics and interspecific competition of six environmental Vibrio isolates (V. parahaemolyticus, V. vulnificus, V. cholerae, V. mimicus, V. cincinnatiensis, and V. zhanjiangensis) recovered from Malaysian seawater. Monoculture assays were conducted across temperature (25-37°C), salinity (0.3-40 ppt), and nutrient (0.001X-0.05X Marine Broth or MB equivalent strength) gradients, followed by co-culture and multi-bacterial microcosm experiments (at 31°C, 26 ppt, 0.01X MB). Regression analyses showed no significant positive response to increasing temperature, whereas tested species responded positively to increasing salinity. Responses to nutrient enrichment suggested that V. parahaemolyticus, V. mimicus and V. vulnificus exhibited r-strategy framework, whereas V. zhanjiangensis represented K-strategy. In contrast, V. cholerae and V. cincinnatiensis could not be clearly classified. In co-culture and multi-bacterial microcosms, V. parahaemolyticus consistently outcompeted both Vibrio and non-Vibrio competitors, even when introduced at lower initial abundance. Therefore, the ecological success of V. parahaemolyticus in these systems was not solely determined by intrinsic growth capacity or environmental suitability, but also by interspecific dynamics. The frequent involvement of V. parahaemolyticus in aquaculture disease outbreaks may be driven by previously underappreciated interspecific competitive advantages that enable it to outcompete other microbes.},
}

@article {pmid42427432,
year = {2026},
author = {Davar, D and Zarour, HM and Trinchieri, G},
title = {Toward a Dual-Axis Model of Microbiome Modulation in Cancer Immunotherapy: Pathobiont Elimination and Functional Ecosystem Restoration.},
journal = {Cellular and molecular bioengineering},
volume = {},
number = {},
pages = {},
pmid = {42427432},
issn = {1865-5025},
abstract = {PURPOSE: The gut microbiome is increasingly recognized as a modulator of cancer immunotherapy efficacy, including responses to immune checkpoint inhibitors (ICIs) and chimeric antigen receptor T-cell (CAR-T) therapy. Recent clinical trials of microbiome-targeted interventions such as fecal microbiome transplantation (FMT) and live biotherapeutic products (LBPs) suggest the potential to enhance antitumor immunity and improve clinical outcomes. Yet responses remain heterogeneous and are not fully explained by engraftment of donor taxa alone.

METHODS: We integrate evidence from interventional trials, observational cohort studies, and principles from gut microbial ecology to develop a model hypothesis on how microbiome-targeted therapies may shape response to immunotherapy, with potential to inform future trial design, analyses, and interpretation.

RESULTS: Drawing on the available evidence, we propose that therapeutic perturbation of the gut microbiome may augment immunotherapy efficacy through two parallel axes: (1) elimination of immunosuppressive pathobionts that restrain CD8+ T-cell activation and promote myeloid-mediated immunosuppression, and (2) functional restoration of the gut ecosystem through engraftment of taxa that provide metabolites, structural cues, and immunoregulatory signals required for effective antitumor immunity. The success of both axes appears to depend on ecological processes governed by predator-prey dynamics, including colonization resistance, resilience of the resident microbiota, and the ability of administered organisms to displace entrenched dysbiotic communities. This ecological lens may help to explain discrepancies across trial designs, donor types, and intervention modalities, and suggests that complete donor engraftment is neither necessary nor sufficient for clinical benefit.

CONCLUSIONS: A dual-mechanism model of pathobiont elimination and functional microbial restoration may help explain microbiome-mediated enhancement of cancer immunotherapy, highlighting a balanced immune permissive gut ecosystem as a key determinant of therapeutic success.},
}

@article {pmid42429144,
year = {2026},
author = {Wei, L and Kong, X and Li, Y and Wu, H and Gan, Y and Sun, F},
title = {Gut dysbiosis‑derived butyrate loss predicts feeding intolerance: Multiomics evidence guiding nurse‑driven microbiota‑supportive interventions (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {3},
pages = {},
doi = {10.3892/mmr.2026.13958},
pmid = {42429144},
issn = {1791-3004},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; Multiomics ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Critical Illness ; },
abstract = {Feeding intolerance (FI) is a common and debilitating challenge among critically ill patients that is linked to a pathway involving the collapse of the gut microbial ecology. The present review synthesizes multiomics evidence supporting a framework whereby critical illness‑associated gut dysbiosis results in a functional deficit of a microbially derived short‑chain fatty acid butyrate, a pivotal metabolite involved in maintaining intestinal barrier integrity, immuneoregulation and gastrointestinal motility. The loss of butyrate‑producing bacteria and their genetic pathways is strongly correlated with FI and may represent a contributory pathogenic mechanism. Key butyrate‑producing organisms diminished during this process include Faecalibacterium prausnitzii and Roseburia spp. Building upon this mechanistic framework, a pragmatic, nurse‑driven intervention model aimed at preserving and restoring microbial health in critically ill patients was proposed. This model is founded on four principal strategies: Minimizing iatrogenic harm (such as antibiotic/proton pump inhibitor stewardship), targeted microbiota nourishment (pre/synbiotics), cautious microbial restoration (probiotics/fecal microbiota transplantation) and innovative monitoring approaches. By integrating principles of microbial ecology with clinical nursing science, the present review provides a framework for developing nurse‑driven protocols designed to address the underlying pathophysiology of FI and improve patient outcomes.},
}

Humans
*Dysbiosis/microbiology/metabolism
Multiomics
*Gastrointestinal Microbiome
*Butyrates/metabolism
Critical Illness

@article {pmid42429610,
year = {2026},
author = {Yu, C and Ao, J and Long, M and Xu, Z and You, S and Jiao, Y and Zhu, S and Liu, S-L and Wang, S and Bao, H},
title = {Deciphering the in vitro mucin-driven interaction dynamics of a synthetic gut bacterial community.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0028926},
doi = {10.1128/msphere.00289-26},
pmid = {42429610},
issn = {2379-5042},
abstract = {The gut microbiota is a complex microbial community that plays a crucial role in host health. Environmental and biological factors within the ecosystem influence the dynamic interactions among its members. Although dietary and host-derived nutrient availability play a key role in shaping microbial ecology and interaction patterns, the dynamics of these interactions within the mucus layer remain poorly understood. In this study, we analyzed a synthetic community comprised of six species with variable abilities to utilize mucin. We performed in vitro growth analyses and monitored the interactions among community members in monoculture, co-culture, and community batch culture under different nutrient conditions. Our results showed that positive interactions were prevalent among bacteria when mucin served as the sole carbon source. In contrast, the addition of glucose or high nutrient availability significantly increased inter-bacterial competition. These findings suggest that mucin mitigates competitive antagonism and potentially promotes community diversity. Further in vivo studies supported the role of mucin in increasing community diversity and modulating bacterial metabolic patterns. Deciphering these intricate relationships is essential for understanding how gut microbiota stability is maintained, and what factors might disrupt this delicate balance.IMPORTANCEThe gut microbiota is essential for host health, yet microbial interactions within the intestinal mucus layer remain poorly understood. Current understanding of gut microbial ecology is largely based on nutrient-rich media that do not accurately reflect the mucosal environment. Here, we demonstrate that when bacteria rely solely on mucin as a carbon source, cooperative interactions predominate. In contrast, the introduction of simple sugars shifts the balance toward intensified interbacterial competition. Mucin mitigates competitive antagonism, promotes resource utilization, and enhances community diversity. By demonstrating that mucus actively shapes microbial interaction patterns, this study provides a mechanistic framework for understanding gut ecosystem resilience. Furthermore, these findings support the development of more physiologically relevant in vitro models for predicting gut microbial dynamics and may guide microbiome-based therapies.},
}

@article {pmid42418012,
year = {2026},
author = {Hanström, N and Jan, KMG and Winder, M},
title = {Environmental Gradients Shape the Distribution of Free-Living and Host-Associated Syndiniales Life Stages.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42418012},
issn = {1432-184X},
mesh = {*Dinoflagellida/genetics/physiology/classification ; Animals ; *Seawater/parasitology/chemistry ; *Life Cycle Stages ; RNA, Ribosomal, 18S/genetics ; *Host-Parasite Interactions ; Salinity ; *Alveolata/genetics/physiology/classification ; Environment ; },
abstract = {Marine alveolate parasites, particularly early-branching dinoflagellates of the order Syndiniales, play critical yet often overlooked roles in shaping marine microbial communities. These parasitoids infect diverse hosts, including dinoflagellates, copepods, and fish eggs, and rely on short-lived, free-living dinospores for transmission. Despite their ecological significance, the distributions of Syndiniales dinospores and host-associated life stages across environmental gradients remain poorly understood. We used 18S rRNA gene region DNA metabarcoding combined with size-fractionated water filtration across vertical and horizontal gradients of salinity, oxygen, and nutrients in the Baltic Sea-Skagerrak system to characterize Syndiniales life-stage distributions and identify clades producing dinospores. This approach enables the differentiation of free-living dinospores and host-associated life stages. Most reads were assigned to Syndiniales groups I and II, indicating the presence of both host associations and dinospore presence. Dinospore communities were more diverse than host-associated life stages and showed variation in spatial distribution and community composition. The spatial variation was related to salinity, oxygen, and nitrogen concentrations, emphasizing the role of environmental conditions in shaping niches suitable for host-parasite associations and infection transmission. Our findings highlight the prevalence of Syndiniales communities across an environmental gradient and the influence of environmental conditions on their distribution patterns.},
}

*Dinoflagellida/genetics/physiology/classification
Animals
*Seawater/parasitology/chemistry
*Life Cycle Stages
RNA, Ribosomal, 18S/genetics
*Host-Parasite Interactions
Salinity
*Alveolata/genetics/physiology/classification
Environment

@article {pmid42418271,
year = {2026},
author = {Touati, A},
title = {Beyond bacterial communication: host factors that modulate quorum sensing and virulence in human pathogens.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/17460913.2026.2700916},
pmid = {42418271},
issn = {1746-0921},
abstract = {Quorum sensing (QS) coordinates collective bacterial behavior, but during infection, its activity is also shaped by host biology. This review examines how host-derived factors modulate QS-linked virulence in enteric pathogens, Pseudomonas aeruginosa and Staphylococcus aureus. Across these systems, host control operates through three recurring modes: activation or signal mimicry, enzymatic signal degradation, and extracellular sequestration or receptor-level interference. Catecholamines and related metabolites can feed into bacterial sensory pathways and promote virulence signaling; PONs (paraoxonases) and other host enzymes can degrade autoinducers; and lipoproteins, immune mediators, and epithelial surveillance systems can intercept or reinterpret quorum signals. Together, these data support the view that the host is an active signal-processing environment that reshapes colonization, persistence, and tissue damage, and they point to host-inspired anti-virulence strategies that target signaling rather than viability.},
}

@article {pmid42419260,
year = {2026},
author = {Heredia, MY and Caballero-Flores, G},
title = {An acidic welcome: How microbial metabolites keep fungi in line.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1151-1153},
doi = {10.1016/j.chom.2026.06.011},
pmid = {42419260},
issn = {1934-6069},
mesh = {*Candida/growth & development/metabolism ; *Fungi ; Antifungal Agents/metabolism/pharmacology ; *Fatty Acids, Volatile/metabolism/pharmacology ; *Microbiota ; Humans ; },
abstract = {Microbiota-derived metabolites shape gut microbial ecology, but how they limit expansion of potentially pathogenic fungi remains elusive. In this Cell Host & Microbe issue, Mishra et al. and Yasuma-Mitobe et al. identify short-chain fatty acids as antifungal metabolites promoting colonization resistance against Candida species via intracellular acidification and metabolic stress.},
}

*Candida/growth & development/metabolism
*Fungi
Antifungal Agents/metabolism/pharmacology
*Fatty Acids, Volatile/metabolism/pharmacology
*Microbiota
Humans

@article {pmid42419828,
year = {2026},
author = {Ekanayaka, R and Chaurasia, A},
title = {Factors influencing the head and neck microbiome.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {111-126},
doi = {10.1016/bs.ai.2026.03.009},
pmid = {42419828},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Neck/microbiology ; *Head/microbiology ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Animals ; Bacteria ; Host Microbial Interactions ; },
abstract = {The head and neck microbiome comprises a diverse and complex community of microorganisms, including bacteria, archaea, fungi, and viruses. It contributes to oral homeostasis by maintaining a harmonious balance within the oral environment. Disruptions in the balance of the oral microbiota, known as dysbiosis, can lead to the development of various oral health conditions and may extend their effect beyond the oral cavity and influence the initiation or worsening of systemic diseases. Changes in the head and neck microbiome are attributed to interactions between the host, the environment, and the resident microbial ecology. Host-related factors, including genetic background, immune competence, age and physiological status interact closely to mould the microbial colonization across different anatomical sites within the head and neck region. Anatomical and local environmental factors create discrete ecological niches that further support site-specific microbial populations. Microbial communities interact with one another through cooperative and competitive mechanisms. In healthy conditions, the oral microbiome maintains a favorable commensal relationship with its environment. However, in certain circumstances, opportunistic microorganisms within the oral microbiome may undergo a shift and become pathogenic, thereby influencing the stability, resilience, and pathogenic potential of microbiome. Microbial changes within the head and neck region are highly dynamic and respond to both short term, transient influences such as dietary intake and oral hygiene practices, as well as long term, chronic exposures, systemic disease, and sustained immune dysregulation Host related, environmental, and microbial influencing factors therefore exhibit a complex interplay in both health and disease, such that alterations in one component are capable of inducing shifts across the entire microbial ecosystem.},
}

Humans
*Microbiota/immunology
*Neck/microbiology
*Head/microbiology
*Dysbiosis/microbiology/immunology
*Mouth/microbiology
Animals
Bacteria
Host Microbial Interactions

@article {pmid42419832,
year = {2026},
author = {Chaurasia, A and Ponangi, K},
title = {The microbiome of the head and neck region.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {25-51},
doi = {10.1016/bs.ai.2026.03.002},
pmid = {42419832},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Dysbiosis/immunology/microbiology ; *Head and Neck Neoplasms/microbiology/immunology ; Animals ; *Head/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology ; },
abstract = {The head and neck region is a host to a diverse and complex microbiome, comprising of very specific microbial communities across different anatomical niches such as the oral cavity, nasal sinuses, pharynx, larynx, salivary glands, and middle ear. The existence of these communities is determined by various factors such as physicochemical conditions, local environment and host genetics playing a critical role in maintaining mucosal integrity, immune modulation, colonization resistance, and thereby achieving metabolic homeostasis. As the human ages, the microbiome constantly evolves, influenced by diet, hormonal changes, and lifestyle even causing disruptions such as dysbiosis linked to diseases like head and neck squamous cell carcinoma (HNSCC). This chapter attempts to explore the anatomical and ecological diversity, site-specific microbial compositions, functional roles, developmental trajectories, and the challenges in understanding these microbial communities. Even though there were significant advances in sequencing technologies helping in identifying the microbial protective and pathogenic potential, hurdles like sampling difficulties and low biomass contamination tend to complicate the research process. Therefore it is of utmost importance to understand the baseline microbiome thereby helping in laying a foundation for studying its role in HNSCC, creating a pathway for microbial diagnostics and curative therapies.},
}

Humans
*Microbiota/immunology
*Dysbiosis/immunology/microbiology
*Head and Neck Neoplasms/microbiology/immunology
Animals
*Head/microbiology
*Squamous Cell Carcinoma of Head and Neck/microbiology/immunology

@article {pmid42410982,
year = {2026},
author = {Alanazi, A},
title = {Organ-Specific Human Microbiomes and Dysbiosis: Mechanistic Links to Disease and Emerging Therapeutic Strategies.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70307},
doi = {10.1002/jcla.70307},
pmid = {42410982},
issn = {1098-2825},
abstract = {BACKGROUND: The human microbiome is a dynamic and diverse community of microorganisms that affects susceptibility to illness and promotes wellness. Dysbiosis, or disruption of this delicately regulated microbial ecology, has been identified as a major factor in the emergence and development of systemic and organ-specific disorders.

OBJECTIVE: With an emphasis on dysbiosis-driven illness processes and therapeutic intervention implications, this study attempts to critically analyze host-microbiome interactions across key human organ systems.

METHODS: Using predetermined microbiome-related keywords, a systematic literature search (2001-2025) was carried out in PubMed, Scopus, Web of Science, and Google Scholar. To assess microbiome formation, organ-specific distribution, disease correlations, and therapeutic implications, English-language peer-reviewed original papers, meta-analyses, and clinical or validated animal studies were chosen and methodically compiled.

RESULTS: Microbiome dysbiosis is linked to cardiovascular, metabolic, inflammatory, neurological, hepatic, renal, and cancer-related illnesses by interfering with immune modulation, metabolic balance, and epithelial barrier integrity, according to evidence from human and verified animal research. Modified production of short-chain fatty acids, immunological signaling imbalance, chronic inflammation, and communication between the gut-organ axis are examples of mechanistic linkages. Immune and metabolic indicators improved condition-specifically with interventions such as probiotics, fecal microbiota transplantation, and diet-based regulation.

CONCLUSION: Collectively, current evidence supports the microbiome as a modifiable determinant of disease risk and therapeutic response, underscoring its translational potential for precision medicine.},
}

@article {pmid42413662,
year = {2026},
author = {Petrosino, S and Escobar, JVF and Di Marzo, V and Iannotti, FA},
title = {Diet, microbiota, and lipidomics: How fatty acids shape the endocannabinoidome and host metabolism.},
journal = {Progress in lipid research},
volume = {},
number = {},
pages = {101396},
doi = {10.1016/j.plipres.2026.101396},
pmid = {42413662},
issn = {1873-2194},
abstract = {The endocannabinoidome (eCBome) is a complex lipid signaling network that integrates metabolic, immune, and neurobehavioral processes in response to environmental cues. Dietary lipids and gut microbiota have emerged as major modulators of its activity and signaling tone. Intake of specific fatty acids, including the monounsaturated oleic acid, the omega-6 polyunsaturated linoleic acid, and omega-3 polyunsaturated fatty acids, influences the eCBome not only by serving as structural precursors of bioactive lipid mediators, but also by altering the relative abundance of these mediators through changes in substrate availability, enzymatic competition, and receptor-mediated feedback loops. Concurrently, the gut microbiota shapes host eCBome signaling by regulating lipid metabolism, inflammatory tone, and intestinal barrier integrity, while eCBome mediators reciprocally modulate microbial composition and function. Dysregulation of this complex diet-microbiota-eCBome interplay has been implicated in the pathogenesis of metabolic disorders, chronic inflammation, and neuropsychiatric conditions. In this review, we critically examine the molecular mechanisms underlying the interactions between dietary lipid composition, gut microbial ecology, and eCBome signaling. We discuss the implications for human health and highlight emerging diet-based therapeutic strategies targeting this axis.},
}

@article {pmid42414614,
year = {2026},
author = {Suárez, JP and Cevallos, S and Herrera, P},
title = {Multiscale Structuring of Mycorrhizal Fungal Communities of Tropical Epiphytic Orchids.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02830-2},
pmid = {42414614},
issn = {1432-184X},
support = {PIC-13-ETAPA-003//Secretaría de Educación Superior, Ciencia, Tecnología e Innovación/ ; },
abstract = {Symbiotic interactions with root-associated fungi are essential for orchid germination, nutrient acquisition and survival, yet the factors structuring these symbioses in tropical epiphytic orchids remain poorly understood. Tropical montane forests provide an ideal system for examining these interactions because steep environmental gradients occur over short geographic distances. We investigated how elevation, variation among populations within elevational belts and host identity shape root-associated fungal communities in the southern Ecuadorian Andes, a region of exceptional epiphytic orchid diversity. Root samples from 699 individuals representing 11 orchid species were analyzed using ITS2 amplicon sequencing. A total of 4,697 operational taxonomic units (OTUs) were recovered, including 271 putative orchid mycorrhizal fungi. Fungal richness peaked at mid elevation and declined at higher elevations. Community composition varied significantly among elevational belts, sites and host species, with differences among elevations driven primarily by species turnover rather than nestedness. Despite this turnover, mycorrhizal assemblages maintained a persistent core across elevations, while site-level heterogeneity contributed to fine-scale differentiation. These results indicate that fungal community assembly in epiphytic orchids is structured across multiple spatial scales by elevational gradients, local environmental conditions and host identity. The mid-elevation diversity peak and stronger filtering at higher elevations indicate that orchid-fungus symbioses are highly sensitive to environmental gradients, with potential consequences for their stability under ongoing environmental change in tropical montane forests.},
}

@article {pmid42414880,
year = {2026},
author = {Shen, N and Shan, X and Zheng, L and Qiao, J and Jiang, Y and Wu, R and Ning, T and Liu, S and Dong, C and Yan, J and Lu, T and Zhu, S},
title = {Oral microbiota characteristics in children younger than 3 years with febrile seizures: a prospective observational study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05375-z},
pmid = {42414880},
issn = {1471-2180},
support = {Z2025119//Suqian Sci & Tech Program/ ; XZSYSKF2024040//Jiangsu Key Laboratory of Immunity and Metabolism Project/ ; },
abstract = {This study investigated the oral microbiota of children younger than 3 years with febrile seizures (FS). Oral swab samples were collected from 48 children with FS and 47 healthy controls, and the V4 region of the bacterial 16 S rRNA gene was sequenced. The Shannon index did not differ significantly between groups, whereas the ACE index was significantly lower in the FS group. Although beta-diversity analysis based on weighted and unweighted UniFrac distances showed no significant between-group differences, partial least squares discriminant analysis provided an exploratory supervised visualization showing apparent separation between the FS and control groups. Among the key genera, Streptococcus, Prevotella, and Granulicatella were significantly enriched in the FS group, whereas Neisseria, Haemophilus, Porphyromonas, and Capnocytophaga were significantly depleted. Predicted functional analysis showed increased relative abundances of pathways related to translation, replication and repair, nucleotide metabolism, cell growth and death, and bacterial infectious diseases, whereas pathways related to energy metabolism, cell motility, signaling molecules and interaction, and transport and catabolism were reduced. These findings suggest that FS is associated with selective ecological reconfiguration of the early-life oral microbiota, mainly reflected by altered proportions of key resident genera.},
}

@article {pmid42415201,
year = {2026},
author = {Srithanasuwan, A and Zou, Y and Zadoks, RN and Suriyasathaporn, W and Schukken, YH},
title = {Recombination, mobile genetic elements, and genetic transfer contribute to the adaptation of Streptococcus uberis causing mastitis.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42415201},
issn = {1297-9716},
mesh = {Animals ; *Streptococcus/genetics/physiology ; *Mastitis, Bovine/microbiology ; *Interspersed Repetitive Sequences ; *Streptococcal Infections/veterinary/microbiology ; *Recombination, Genetic ; Cattle ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Female ; Thailand ; Adaptation, Physiological/genetics ; },
abstract = {Streptococcus uberis is a major cause of bovine mastitis. However, the genomic mechanisms that facilitate adaptation of the pathogen within different host-associated environment or selection pressures remain poorly understood. This study analyzed whole-genome sequence data from three Thai dairy herds to investigate the contributions of recombination and mobile genetic elements (MGEs) to S. uberis evolution and adaptation. Among the 138 S. uberis genomes, 42 core genome sequence types (cgSTs) were identified, along with frequent detection of MGEs such as plasmid-associated genes (81.1% of isolates), prophages (67.4% of isolates), and insertion sequences (26.1% of isolates). The isolates from farm A exhibited the longest recombined fragment size, but with extremely low recombination frequency and recombination-to-mutation ratio. By contrast, the isolates from farm B, which had the highest prevalence of antimicrobial resistance (AMR) gene, showed a high recombination-to-mutation ratio (R/θ = 4.42) and more frequently contained MGEs associated with AMR genes. Finally, isolates from farm C shared a single core genome and AMR profile but harbored diverse prophages. Several prophages shared high sequence similarity (>99%) with phages infecting other bacterial genera, suggesting that ecological overlap between bacterial species may facilitate cross-genus genetic exchange, highlighting the influence of microbial ecology on the evolution of S. uberis. Collectively, our results illustrate the variety of mechanisms and genetic elements that contribute to the adaptive evolution of S. uberis in dairy farming environments.},
}

Animals
*Streptococcus/genetics/physiology
*Mastitis, Bovine/microbiology
*Interspersed Repetitive Sequences
*Streptococcal Infections/veterinary/microbiology
*Recombination, Genetic
Cattle
*Gene Transfer, Horizontal
Genome, Bacterial
Female
Thailand
Adaptation, Physiological/genetics

@article {pmid42415234,
year = {2026},
author = {Shahin, K and Wang, L and He, Z and Lv, B and Van Alin, A and Lo-Man, R and Wu, H and Sansonetti, P and Collard, JM},
title = {A metabolite-dependent mechanism by which Bifidobacterium animalis subsp. lactis promotes Bacteroides colonization.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2696647},
doi = {10.1080/19490976.2026.2696647},
pmid = {42415234},
issn = {1949-0984},
mesh = {Animals ; *Bacteroides/growth & development/metabolism ; Humans ; Mice ; Feces/microbiology ; *Bifidobacterium animalis/metabolism/growth & development ; *Gastrointestinal Microbiome ; Symbiosis ; Bifidobacterium/metabolism ; Metabolome ; Coculture Techniques ; Bacteroides fragilis/growth & development/metabolism ; },
abstract = {Prokaryote-prokaryote symbiotic relationships influence interactions within microbial communities, affecting colonization, survival, and organization. Unlike competition, consortium species facilitate growth via metabolite cross-feeding. This study explored interactions between two early human gut colonizers: partially aerotolerant Bifidobacterium spp. and strict anaerobic Bacteroides spp., using omics techniques. Promotion of Bacteroides spp. growth by Bifidobacterium animalis subsp. lactis was demonstrated through co-culture experiments in anaerobic conditions. Metabolomic analysis revealed over 150 unique metabolites present in B. animalis subsp. lactis supernatants are absent in other Bifidobacterium species, including 3-hydroxycapric acid, D-alanyl-D-alanine, 2-isopropylmalic acid, and D-glucose 2-phosphate. These compounds served as nutritional substrates, including carbon and nitrogen sources, significantly enhancing Bacteroides spp. growth. In murine models, early colonization by B. animalis subsp. lactis consolidated Bacteroides fragilis colonization (1.7 × 10[4] to 9.7 × 10[6] copy number/g fecal sample) by providing these metabolites as a niche. These findings highlight B. animalis subsp. lactis plays a critical role in gut colonization of Bacteroides spp. via its exclusive metabolic profile, offering insights into partitioned metabolic activity within gut communities and emphasizing the importance of specific metabolites in early microbial establishment.},
}

Animals
*Bacteroides/growth & development/metabolism
Humans
Mice
Feces/microbiology
*Bifidobacterium animalis/metabolism/growth & development
*Gastrointestinal Microbiome
Symbiosis
Bifidobacterium/metabolism
Metabolome
Coculture Techniques
Bacteroides fragilis/growth & development/metabolism

@article {pmid42405327,
year = {2026},
author = {Kusuma, SAF},
title = {Selective Modulation of Cutibacterium acnes Biofilms in Acne: Limitations of Conventional Therapies and Emerging Anti-Virulence Strategies.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {621646},
pmid = {42405327},
issn = {1178-7015},
abstract = {Acne vulgaris is a multifactorial inflammatory skin disorder in which Cutibacterium acnes biofilm formation contributes to disease persistence, antimicrobial tolerance, and treatment failure. Conventional therapies primarily target bacterial viability but often fail to address biofilm-associated resilience and strain-specific virulence. Emerging strategies have therefore shifted toward the selective modulation of bacterial behavior rather than broad-spectrum eradication, with the aim of attenuating pathogenicity while minimizing disruption of the skin microbiome. This review critically evaluates selective modulation approaches targeting biofilm integrity, virulence pathways, and microbial ecology, including anti-virulence therapy, quorum-sensing inhibition, biofilm disruption, nanocarrier-based delivery systems, and microbiome-informed interventions. Preclinical studies suggest that these strategies may disrupt biofilm architecture, attenuate virulence factor expression, and potentially reduce selective pressure associated with conventional antimicrobial therapies. Approaches such as antimicrobial peptides, quorum-sensing inhibitors, and advanced delivery systems have demonstrated promising in vitro, ex vivo, and early preclinical outcomes; however, clinical evidence remains limited. Significant challenges remain, including insufficient in vivo validation, formulation instability, biofilm-associated delivery barriers, regulatory considerations, and limited long-term safety data. Overall, selective modulation represents a promising emerging framework for acne management, although its successful clinical translation will require robust clinical validation, improved disease-relevant models, and the integration of personalized strategies based on microbiome profiling and advanced delivery technologies.},
}

@article {pmid42405599,
year = {2026},
author = {O'Keefe, KP and Boice, MN and Samuel, AM and Andrade, CC},
title = {Detection of Ehrlichia, Francisella, and Rickettsia in Dermacentor Ticks in Eastern Washington.},
journal = {Journal of vector ecology : journal of the Society for Vector Ecology},
volume = {51},
number = {1},
pages = {27-38},
doi = {10.52707/1081-1710-51.1-27},
pmid = {42405599},
issn = {1948-7134},
mesh = {Animals ; *Dermacentor/microbiology ; *Francisella/isolation & purification/genetics ; *Rickettsia/isolation & purification/genetics ; *Ehrlichia/isolation & purification/genetics ; Washington ; Polymerase Chain Reaction ; },
abstract = {Dermacentor ticks are widespread in eastern Washington and are known vectors of bacterial pathogens and harborers of endosymbionts belonging to the genera Francisella and Rickettsia. Some Dermacentor species can become infected with Ehrlichia chaffeensis Anderson et al. (Rickettsiales: Ehrlichiaceae); it remains unclear if any are competent vectors for this bacterial pathogen. This study reports the abundance of Dermacentor species and prevalence of select tick-borne bacterial pathogens collected from two conservation areas popular among hikers in Spokane County, Washington. In total, DNA from 599 adult ticks was analyzed using PCR; 87.8% (526/599) were identified as Dermacentor andersoni Stiles and 12.2% (73/599) as D. similis Lado, Glon and Klompen (Ixodida: Ixodidae). Ticks were also screened for the presence of bacterial DNA using genus- or species-specific primers targeting Rickettsia spp., Francisella spp., and E. chaffeensis. Rickettsia endosymbionts, R. peacockii Niebylski et al. or R. rhipicephali (Burgdorfer et al.) Weiss and Moulder (Rickettsiales: Rickettsiaceae), were found in 4.0% (21/526) of D. andersoni. Francisella-like endosymbionts were detected in 65.9% (395/599) of all ticks. No species known to be pathogenic belonging to either Rickettsia or Francisella were detected. However, E. chaffeensis was detected in 15.3% (12/73) of D. similis, which to our knowledge is the first report of ticks harboring this species of bacteria in Washington state. These findings contribute to understanding the microbial ecology of ticks in the Inland Northwest.},
}

Animals
*Dermacentor/microbiology
*Francisella/isolation & purification/genetics
*Rickettsia/isolation & purification/genetics
*Ehrlichia/isolation & purification/genetics
Washington
Polymerase Chain Reaction

@article {pmid42405791,
year = {2026},
author = {Alexander, AM and Loo, HQ and Askew, L and Raghuram, V and Satola, SW and Read, TD and Goldberg, JB},
title = {Intraspecific diversity of Staphylococcus aureus populations isolated from cystic fibrosis respiratory infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0036726},
doi = {10.1128/spectrum.00367-26},
pmid = {42405791},
issn = {2165-0497},
abstract = {UNLABELLED: Long-term associations within an individual host allow bacterial populations to diversify over time, sometimes resulting in the coexistence of multiple species or variants of the same species. Traditional methods for identifying infective agents generally involve isolating a single pathogen and potentially even a single colony from a given sample. While screening samples for virulent or difficult-to-treat pathogens is an important part of informing clinical treatment and correlative research, these reductive methods alone do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population. In this study, we begin to address this limitation by comparing the phenotypic and genotypic diversity of single colonies and pooled isolates of Staphylococcus aureus taken from fresh sputum samples from three patients with cystic fibrosis. Additionally, we compare the results collected in our research laboratory to those processed by the Emory Clinical Microbiology Laboratory with the identical sputum samples. We identified unrelated coexisting lineages in two out of three sputum samples, as well as clinically relevant population structures that were not apparent from studying single-colony isolates alone. Altogether, our observations presented here demonstrate that the true nature and phenotype of a clinically isolated pathogen can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.

IMPORTANCE: When obtaining bacterial isolates from infections, it is important to consider the ecological biases introduced by methods used for collection and processing. In this study, we demonstrate how reductive sampling and processing methods traditionally used by clinical microbiology labs often do not adequately capture complex and clinically relevant traits present in diverse pathogen populations. When treating or studying bacteria like Staphylococcus aureus that can maintain multiple variants within a population over a long period of time, it may be more effective and informative to employ sampling methods that account for the potential diversity within a population, as outlined in our approach presented here.},
}

@article {pmid42406122,
year = {2026},
author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B},
title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02817-z},
pmid = {42406122},
issn = {1432-184X},
support = {REIG-FPS-2025/038//UCSI University/ ; },
abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.},
}

@article {pmid42406144,
year = {2026},
author = {Garrigós, M and Veiga, J and Garrido, M and García-López, MJ and Morales-Yuste, M and Marín, C and Recuero, J and Rosales, MJ and Moreno-Indias, I and Martínez-de la Puente, J},
title = {Drivers of Mosquito Microbiome Composition: Effects of Species, Locality, Season, and Plasmodium Infection.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02801-7},
pmid = {42406144},
issn = {1432-184X},
abstract = {Mosquito microbiota influences mosquito physiology and pathogen development, finally affecting their vectorial capacity. Identifying the factors that affect the composition of mosquito microbial communities in nature is essential for designing effective strategies to control vector-borne pathogens. Here, we used a 16 S rRNA metabarcoding approach to analyse the microbiome of 196 mosquito pools (four females per pool) of three common species: Culex pipiens, Aedes albopictus, and Culiseta longiareolata. Mosquitoes were collected from spring to autumn 2022 in five sampling localities of southern Spain. Mosquito bacterial alpha diversity was higher in Cs. longiareolata compared to Cx. pipiens and Ae. albopictus. In addition, beta diversity and the relative abundance of different bacterial taxa differed among mosquito species. Wolbachia dominated the bacterial community of Cx. pipiens and Ae. albopictus, but were virtually absent in Cs. longiareolata. Furthermore, using Cx. pipiens -the most extensively sampled species here- we further investigated differences in the microbiome composition according to sampling localities, seasons, and avian Plasmodium infection status. Locality and season affected the bacterial alpha and beta diversity, with mosquitoes collected in autumn from the Fuengirola locality showing a higher observed richness. Differences in beta diversity among localities and seasons could be, at least in part, influenced by differences in beta dispersion. The relative abundance of different taxa in Cx. pipiens varied by locality, season, and avian Plasmodium infection status. In sum, both intrinsic and environmental factors influence mosquito microbiome, yet the potential consequences for pathogen transmission should be further addressed. This study provides a comprehensive framework to understand the ecological drivers of wild mosquito microbiome, a key step for predicting vector-pathogen interactions and improving strategies for vector-borne disease control.},
}

@article {pmid42410155,
year = {2026},
author = {Ali, H and Khaleque, A and Sadia, T and Azmuda, N and Parvez, MAK and Adnan, N and Akter, S and Ahmed, MF},
title = {Cross-domain microbial differences across freshwater and marine habitats in a tropical delta.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61157-7},
pmid = {42410155},
issn = {2045-2322},
abstract = {Microbial communities are central to aquatic ecosystem functioning, yet integrated cross-domain comparisons of prokaryotic and microeukaryotic microbiomes remain underexplored in tropical regions, particularly in Bangladesh. Here, we investigated habitat-associated differences in microbial community structure across freshwater and marine ecosystems of the Bangladesh tropical delta using 16S and 18S rRNA gene amplicon sequencing and assessed inferred functional potential for prokaryotic communities. Six freshwater and ten seawater samples were analyzed, comprising eight newly generated datasets (six freshwater and two seawater) and eight previously published seawater datasets. Prokaryotic communities exhibited significantly higher alpha diversity in freshwater, whereas microeukaryotic diversity showed no significant habitat-associated differences after correction, despite a weak freshwater enrichment trend. Beta diversity revealed clear compositional separation between habitats for both domains, with prokaryotes exhibiting centroid shifts and microeukaryotes showing greater within-group dispersion. Taxonomic profiles showed seawater dominance by Gammaproteobacteria and Alphaproteobacteria, whereas freshwater communities were more evenly distributed across Bacteroidota, Actinomycetota, and Verrucomicrobiota. Microeukaryotic assemblages also displayed pronounced habitat-associated restructuring. Functional inference of prokaryotic communities indicated conservation of core pathways across habitats despite taxonomic turnover. Exploratory cross-domain correlation analysis identified mixed positive and negative associations, although none remained significant after multiple-testing correction. Collectively, these findings reveal consistent habitat-associated microbial differentiation across tropical freshwater and marine ecosystems and provide a comparative baseline for understanding cross-domain microbial biogeography in climate-sensitive aquatic environments.},
}

@article {pmid42410848,
year = {2026},
author = {Huang, X and Gao, Y and Sun, J and Shi, L},
title = {Association between oral microbiome diversity and cardiovascular-kidney-metabolic syndrome in US adults: Analysis of NHANES 2009 to 2012.},
journal = {Medicine},
volume = {105},
number = {27},
pages = {e49530},
doi = {10.1097/MD.0000000000049530},
pmid = {42410848},
issn = {1536-5964},
mesh = {Humans ; *Microbiota/genetics ; *Metabolic Syndrome/epidemiology/microbiology ; United States/epidemiology ; Nutrition Surveys ; Female ; Cross-Sectional Studies ; Male ; Adult ; *Cardiovascular Diseases/epidemiology/microbiology ; *Mouth/microbiology ; Middle Aged ; *Kidney Diseases/epidemiology/microbiology ; },
abstract = {The present study aimed to examine the association between oral microbiome alpha diversity and the severity of cardiovascular-kidney-metabolic (CKM) syndrome among US adults. Emerging evidence suggests that the oral microbiome may influence systemic cardiometabolic health; however, its relationship with integrated CKM syndrome remains unclear. We conducted a cross-sectional analysis of adults aged ≥20 years from the 2009 to 2012 National Health and Nutrition Examination Survey, a nationally representative survey of the US population, including participants with available oral microbiome data (n = 4834). Alpha diversity was assessed using observed amplicon sequence variants richness, Faith's phylogenetic diversity Shannon index, and Simpson index. CKM syndrome was classified into 5 stages (0-4), with advanced CKM defined as stages 3-4, representing subclinical or clinical cardiovascular disease and/or significant kidney involvement. Weighted multivariable logistic regression models were used to estimate odds ratios and 95% confidence intervals. Higher oral microbiome diversity was consistently associated with lower odds of advanced CKM. In fully adjusted models, each unit increase in observed amplicon sequence variants was associated with a 2% lower odds of advanced CKM (odds ratio = 0.98, 95% confidence interval = 0.97-1.00). Participants in the highest tertile of diversity had 10% to 12% lower odds of advanced CKM compared with the lowest tertile across diversity indices, with significant trends. Associations were consistent across demographic and clinical subgroups. Greater oral microbial diversity was inversely associated with advanced CKM syndrome in US adults. These findings support a potential association between oral microbial ecology and integrated cardiometabolic-renal health, although longitudinal and mechanistic studies are required to clarify temporality and causality.},
}

Humans
*Microbiota/genetics
*Metabolic Syndrome/epidemiology/microbiology
United States/epidemiology
Nutrition Surveys
Female
Cross-Sectional Studies
Male
Adult
*Cardiovascular Diseases/epidemiology/microbiology
*Mouth/microbiology
Middle Aged
*Kidney Diseases/epidemiology/microbiology

@article {pmid42399628,
year = {2026},
author = {Yuan, J and Zhang, XY and Yang, S and Luo, CL and Wang, ZH and Wang, QQ and Hao, YY and He, Y and Wang, S and Kong, FL and Zhao, M and Cao, ZJ and Li, SL and Wang, W},
title = {Peripartum hypophosphatemia is associated with a hindgut-centered microbiota-metabolite-host axis in transition dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01078-5},
pmid = {42399628},
issn = {2055-5008},
support = {32202713//National Natural Science Foundation of China/ ; },
abstract = {The transition period in dairy cows is accompanied by profound shifts in mineral homeostasis and gut microbial ecology. While endocrine regulation of hypocalcemia has been extensively characterized, adaptive responses to hypophosphatemia-and the potential involvement of the gut microbiota-have received far less attention. Twenty-four Holstein dairy cows were randomly assigned to control or low-phosphorus groups. Hypophosphatemia was induced by dietary supplementation with 300 g/d synthetic zeolite from 21 days prepartum to 3 days postpartum. Blood and feces samples were collected at -21, -7, 0, 1, and 3 d relative to calving for longitudinal analysis of physiology, hindgut microbiome and plasma metabolomics to investigate host-microbiome adaptation to peripartum hypophosphatemia in dairy cows. Cows with hypophosphatemia exhibited pronounced compositional remodeling of their hindgut microbiota and extensive, persistent alterations in their plasma metabolome, with glycerophospholipid metabolism being a consistently affected pathway. Integrated correlation and mediation analyses revealed close associations between hindgut microbial variation, host metabolic reprogramming, and circulating phosphorus dynamics. In addition, a plasma feature putatively annotated as α-methyl-m-tyrosine (AMT) was identified as a candidate statistical mediator associated with the observed relationships between Lachnospiraceae_NK3A20_group abundance with systematic phosphorus concentrations. Collectively, these findings indicate that peripartum hypophosphatemia in dairy cows is accompanied by coordinated host metabolic and hindgut microbial remodeling, supporting a hindgut-centered host-metabolite-microbiome framework for understanding phosphorus adaptation during early lactation.},
}

@article {pmid42399737,
year = {2026},
author = {Steele, S and Mazengenya, P and Chambuso, R},
title = {Pathology-derived clinical micro-architectural diagnostics of tumour-microbiome interactions in colorectal cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42399737},
issn = {1479-5876},
abstract = {BACKGROUND: Classical tumour pathology reports contain a largely untapped layer of information that may indicate tumour-microbial interactions. However, routine colorectal cancer pathology staging does not take into account microbiome-associated tumour micro-architecture signatures, thus limiting insights into intratumoral microbial ecology, prognostic stratification and treatment-relevant microbial information. In this study, we analysed scanned USA pathology reports to quantify likely intratumoral microbiome-associated micro-architectural signatures.

METHODS: We studied 1,978 TCGA colorectal cancer pathology reports from 1,249 colon adenocarcinomas, 559 rectal adenocarcinomas and 170 reports without a definitive anatomic site using rule-based natural language processing to extract microbiome-linked micro-architectural features. Barrier-disruption and invasion-access signatures were identified from the reports as microbiome-associated pathology micro-architecture signatures that occur with microbial-related necrosis, hypoxia, toxins, colonisation, persistence, metabolic activity and/or tumour interaction. We developed a z-scored composite index called Report-based Microbial Ecology Likelihood Score (RMELS) and used Kaplan-Meier log-rank analyses, multivariable Cox regression, Kruskal-Wallis tests and receiver operation characteristic curves with bootstrap confidence intervals. Proportional hazards assumptions were tested for statistical significance at two-sided p < 0.05.

RESULTS: Microbiome-associated pathology micro-architectural signatures were highly prevalent in the pathology reports. Barrier-disruption features, including ulceration (41.1%) and mucin alteration (16.7%), were common and increased with tumour stage (Kruskal-Wallis p < 0.0001). Prominent invasion-access features included infiltrative growth (59.4%, 95% CI 57.2-61.5), lymphovascular invasion (18.6%, 95% CI 17.0-20.4) and perineural invasion (22.9%, 95% CI 21.1-24.8). All showed heterogeneous, non-monotonic distributions across pathologic stages, indicating activation of microbial injury and invasion programmes. Integration of these features into our signature score, ordered tumours along a continuous microbiome-permissiveness gradient independent of pathological stage. With limited information, our signature score discriminated early (T1) from advanced (T4) disease more effectively than barrier or invasion features alone (AUC = 0.66, 95% CI 0.58-0.74, p < 0.0001). Right-sided colonic tumours exhibited significantly higher scores than left-sided colonic and rectal tumours (FDR q < 0.001), aligning with known microbial biogeography. In multivariable Cox models adjusted for pathological stage, our signature score RMELS showed modest but directionally consistent association with overall and progression-free survival, capturing microbiology-relevant risk not resolved by pathological staging.

CONCLUSIONS: Routine classical colorectal cancer pathology reports contain intratumoral microbiome-associated pathology micro-architectural signatures. Quantifying these exploratory tumour-microbial signatures using digital pathology will enable scalable, microbiology-informed risk stratification and prognostic modelling to complement the current pathological staging.},
}

@article {pmid42401776,
year = {2026},
author = {Zapata-Peñasco, I and Herrera-Díaz, J},
title = {Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.},
journal = {Advances in experimental medicine and biology},
volume = {1510},
number = {},
pages = {121-145},
pmid = {42401776},
issn = {0065-2598},
mesh = {*Proteomics/methods ; *Petroleum/microbiology ; Corrosion ; *Oil and Gas Industry ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacterial Proteins/metabolism ; Sewage/microbiology ; *Bacteria/metabolism/genetics ; },
abstract = {Petroleum-associated environments are among the most chemically complex and biologically extreme systems encountered in the field of industrial biotechnology. Here, microbial activity plays a pivotal role in hydrocarbon biodegradation, reservoir souring, and microbiologically influenced corrosion (MIC). In these systems, proteins constitute the functional interface between microbial metabolism and physicochemical processes affecting infrastructure integrity and environmental impact. This chapter presents an integrated proteomics-based workflow for the characterization of microbial communities inhabiting oil pipeline sludges, with particular emphasis on sample preparation strategies tailored to hydrocarbon-rich, metal-laden, and saline matrices. Optimized phenol-based extraction, electrochemical in vitro corrosion assays, two-dimensional gel electrophoresis, and high-resolution mass spectrometry are combined with metagenomic information to enable robust identification and functional interpretation of proteins involved in redox metabolism, biofilm formation, extracellular electron transfer, sulfur and nitrogen cycling, and stress adaptation. The approach is illustrated through a biocorrosion case study of marine pipeline sludge, revealing key enzymatic systems, including oxidoreductases, hydrolases, cytochromes, ABC transporters, and biofilm-associated structural proteins that mediate metal dissolution and microbial energy conservation. By integrating proteomics with electrochemical measurements and systems-level analysis, this chapter highlights how tailored sample preparation and functional protein profiling can overcome the limitations of culture-dependent methods, providing mechanistic insight into complex petroleum microbiomes. These advances establish proteomics as a critical tool for monitoring, predicting, and ultimately mitigating biocorrosion, as well as for guiding the development of biotechnology-based strategies in the oil and gas industry.},
}

*Proteomics/methods
*Petroleum/microbiology
Corrosion
*Oil and Gas Industry
Biodegradation, Environmental
Biofilms/growth & development
*Bacterial Proteins/metabolism
Sewage/microbiology
*Bacteria/metabolism/genetics

@article {pmid42402041,
year = {2026},
author = {Gao, Z and Pang, M and Li, M and Ming, Y and Liu, H and Yin, K},
title = {Assessing the effects of ocean alkalinity enhancement on marine protozoa: physiological dynamics and transcriptomic responses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0029826},
doi = {10.1128/aem.00298-26},
pmid = {42402041},
issn = {1098-5336},
abstract = {Ocean alkalinity enhancement (OAE) is proposed as a potential tool to remove atmospheric CO2 and mitigate climate change. However, the effects of OAE on marine protozoa remain poorly understood. In this study, we conducted acute and acclimated experiments on two heterotrophic nanoflagellates, i.e., Cafeteria burkhardae and Paraphysomonas longispina, to investigate their responses to two substances (NaHCO3 and NaOH) at low (set ~2,600 µmol L[-1]) and high (set ~4,000 µmol L[-1]) levels, respectively. Our results showed that the two species had similar negative reactions under acute exposure. However, the two species showed different tolerances after acclimation. The growth rates of C. burkhardae decreased under all OAE treatments, while its reactive oxygen species accumulated only at the high OAE level. The low-level OAE treatments had no significant effects, but high-level OAE was more adverse for P. longispina, which grew more slowly and grazed more, indicating lower growth efficiency. Underlying transcriptomic mechanisms were only analyzed for low-level OAE, which were consistent with the physiological responses. Replication and repair and metabolism-related pathways were significantly inhibited, with translation-related pathways stimulated in C. burkhardae. For P. longispina, in addition to translation-related pathways, replication and repair, and metabolism pathways were significantly upregulated. Overall, our findings suggest the potential negative effects of OAE on marine protozoa, and the effects can vary depending on the species, level, and substances. Given the critical role of protists in marine ecosystems, these adverse effects raise important concerns about the broader implications of OAE for marine biodiversity and ecosystem stability.IMPORTANCEOcean alkalinity enhancement (OAE) represents a novel approach to mitigate climate change by increasing the ocean's CO2 sequestration capacity. However, the potential ecological and environmental impacts of OAE on marine microorganisms, particularly protozoa, remain poorly understood. This study investigates the responses of two heterotrophic nanoflagellates, Cafeteria burkhardae and Paraphysomonas longispina, to varying levels of OAE treatments using NaHCO3 and NaOH. Our findings reveal significant species-specific differences in tolerance and physiological responses, with implications for microbial community dynamics in marine ecosystems. By employing transcriptomic analysis, we uncover the underlying molecular mechanisms. Ultimately, our study informs the development of sustainable ocean-based climate solutions, emphasizing the importance of considering microbial ecology in environmental management and policy.},
}

@article {pmid42402236,
year = {2026},
author = {Na, M and Xiang, M and Wu, Y and Wu, D and Xu, S and Wang, L and Zhou, J and Rousk, J},
title = {Cadmium pollution alters the priming effect of biochar application on soil organic carbon mineralization.},
journal = {Journal of environmental management},
volume = {413},
number = {},
pages = {130426},
doi = {10.1016/j.jenvman.2026.130426},
pmid = {42402236},
issn = {1095-8630},
abstract = {Biochar has high potential to reduce cadmium (Cd) bioavailability in polluted soils. While effective in Cd remediation, biochar amendment can stimulate native soil organic carbon (SOC) mineralization via the priming effect, resulting in soil C release. However, it remains unclear whether Cd pollution alters the impact of biochar application on SOC mineralization, and how microbes modulate biochar-induced priming effect in Cd-polluted soils. To address these questions, a 120-day laboratory experiment was conducted by applying two types of biochar derived from C4 crop residues to C3 paddy soils under Cd pollution (0, 4 and 8 mg kg[-1]). In unpolluted soils, sorghum biochar, with higher C availability and C:nitrogen (N) ratios, triggered stronger positive priming of SOC mineralization than sugarcane biochar. This process was mediated by bacterial groups, where higher N-degrading gene abundances and associated enzyme activities promoted N-mining from soil organic matter (SOM). Low Cd pollution reduced priming responses, resulting in an overall negative priming. This result coincided with increased DOC and mineral N, which mitigated microbial resource demand from SOM. Under high Cd, sorghum biochar induced a positive cumulative priming at the late stage, whereas sugarcane biochar triggered an overall negative priming. This could be because higher labile C in sorghum biochar sufficiently activated microbes to produce enzymes which co-metabolized SOM, a process driven by fungal groups and persistent C-degrading genes. These findings highlight a double-edged sword effect that biochar remediation of highly Cd-polluted soils has the potential to trigger soil C emissions.},
}

@article {pmid42402256,
year = {2026},
author = {Ferreira, J and Rediers, H},
title = {Phytophthora cactorum: From Pathogen Biology to Disease Management.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-04-26-0120-RVW},
pmid = {42402256},
issn = {0031-949X},
abstract = {Phytophthora cactorum is a versatile plant pathogen with a wide host spectrum causing substantial yield losses in various forest and agricultural systems, the most affected being apple, ginseng, and strawberry. This review synthesizes the current knowledge on the biology and epidemiology of P. cactorum and presents an extensive overview of the available management strategies, including preventive measures, cultural practices, detection tools, chemical and biological control. Beyond compiling existing data, this review also highlights emerging conceptual shifts in our understanding of P. cactorum, particularly the transition from viewing it as a single broadly infective generalist to recognizing the presence of partially specialized lineages with host- and organ-specific adaptations. We further link advances in molecular biology, including effector repertoire characterization, with practical implications for disease management in agricultural and nursery systems. By integrating insights across disciplines, we aim to establish a strong foundation for deciphering the mechanisms underlying pathogenicity and to support the development of more effective and sustainable management strategies.},
}

@article {pmid42403403,
year = {2026},
author = {Zhou, J and Zhang, K and Shah, F and Lam, SS and Xie, Z},
title = {Biochar and milk vetch synergistically enhance rice yield and soil fertility via regulating N-cycling in reddish paddy fields.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1839609},
pmid = {42403403},
issn = {1664-462X},
abstract = {INTRODUCTION: Biochar and milk vetch (MV) are known to improve soil fertility and crop yield. However, the effects of the combined application of rice straw biochar (RSB) and MV over multiple years on nitrogen (N) dynamics, microbial ecology, and rice yield remain unclear. This study is to evaluate the synergistic effects of RSB and MV over multiple growing seasons.

METHODS: A three-year field experiment was conducted with four treatments, N fertilizer alone (CK), N+RSB (B), N+MV (M), and N+RSB+MV (BM), and measured various indicators of soil health and rice yield.

RESULTS: Soil organic C, total N, inorganic N (NH4 [+] and NO3 [-]), microbial biomass C/N, and enzyme activities (urease, nitrate, and nitrite reductase) were 14%-30%, 12%-25%, 18%-40%, 20%-45%, and 15%-50% higher in the B and M treatments than in the CK; the greatest increases in these parameters (by 14%-89%) were observed in the BM treatment. Microbial diversity (α-diversity of soil microbes) was increased and the expression of N-cycling functional genes (nifH, amoA, narG, nirS/nirK, nosZ) was 9.1%-400% higher in the BM treatment than in the CK. High gene abundances (AOA amoA, AOB amoA, narG, nirS, nirK, and nosZ) were associated with increased N uptake and grain yield. Microbial biomass C and N were key drivers of shifts in microbial communities influencing N-cycling genes. Increased soil C and N availability in the BM treatment stemmed from changes in the expression of microbial genes and enzyme activities enhancing N assimilation and rice yield.

DISCUSSION: Hence, combining RSB with MV can promote soil fertility, rice productivity and ecological benefits.},
}

@article {pmid42396672,
year = {2026},
author = {Flint, HJ},
title = {Combining sequence-based approaches with anaerobic microbiology and modelling to understand gut microbial communities.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-29},
doi = {10.1017/S0029665126105072},
pmid = {42396672},
issn = {1475-2719},
abstract = {Gut micro-organisms possess biochemical capabilities that far exceed those of their mammalian hosts, particularly in the ability to gain energy from the breakdown of diet-derived plant material (fibre). This article reviews investigations into gut microbial communities conducted by Harry Flint and his research group. First, extracellular cellulosome and amylosome enzyme complexes were found to mediate the breakdown of plant cell walls and resistant starch by specialised Firmicutes bacteria, both in the human colon and in the rumen. In contrast, Bacteroidetes (Bacteroides, Prevotella spp.) rely on their ability to capture soluble carbohydrates. Human dietary studies examining the impact of fibre sources upon microbiota composition and metabolism identified 'diet-responsive' species. In addition, dominant species of butyrate-producing bacteria, including a subset able to convert lactate to butyrate, were isolated from healthy human volunteers. Most produce butyrate from carbohydrates via butyryl-CoA:acetate CoA-transferase, with uptake of external acetate, while lactate conversion is associated with a highly inducible gene cluster (lct). In pH-controlled chemostat studies, mildly acid pH depressed growth of propionate-producing Bacteroidetes, but favoured butyrate production by Firmicutes. This may explain why % butyrate among SCFA increases with total faecal SCFA concentration in human studies. Although lactate is normally consumed by lactate-utilising bacteria, destabilisation of the microbial community associated with lactate accumulation can result in radically altered microbiota and metabolite profiles. A theoretical model based on microbial functional groups (MFG) was developed to better understand community dynamics. Consequences for nutritional research of our expanding knowledge of the microbial ecology of the human gut are considered.},
}

@article {pmid42397708,
year = {2026},
author = {Marinos, G and Moors, KA and Schlicht, K and Rühlemann, M and Waschina, S and Lieb, W and Franke, A and Laudes, M and Groussin, M and Poyet, M and Kaleta, C and Kadibalban, AS},
title = {Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694811},
doi = {10.1080/19490976.2026.2694811},
pmid = {42397708},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet ; *Life Style ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Microbial Interactions ; Models, Biological ; },
abstract = {Microbiomes and their host environments form complex, interconnected ecosystems. The microbial species within a microbiome, on the one hand, compete for resources, while on the other hand, they exchange vital metabolites to support their survival. These interactions are influenced by the microbial genetic repertoire, environmental conditions, and availability of nutrients. We developed EcoGS (http://www.github.com/KaletaLab/EcoGS), a metabolic modeling tool designed to predict the ecological interactions between pairs of microbes. Applying EcoGS to the microbiomes of two distinct human cohorts revealed a shift from collaborative to exploitative ecological interactions associated with increased dietary intake of simple sugars (glucose and fructose) in diabetic individuals and those living industrialized lifestyles. On the other hand, the consumption of cobalamin (vitamin B12), phylloquinone (vitamin K1), and biotin (vitamin B7), among other compounds, was associated with increased collaboration in the gut microbiome. We conclude that the abundance of simple sugars as an energy source reduces the necessity for microbes to cooperate, thereby increasing competition and hostility among microbiome members. Moreover, our study proposes multiple compounds, such as urate, deoxyadenosine, deoxyguanosine, and hypoxanthine, for in vitro validation tests as dietary interventions that have the potential to restore the ecological balance within the community. EcoGS serves as a valuable tool for exploring microbiome dynamics and their connections to environmental changes and disease.},
}

Humans
*Gastrointestinal Microbiome
*Diet
*Life Style
*Bacteria/metabolism/genetics/classification/isolation & purification
*Microbial Interactions
Models, Biological

@article {pmid42397960,
year = {2026},
author = {J Bruggeman, F and Paez-Watson, T and Teusink, B and Kleerebezem, R},
title = {Stoichiometric analysis of microbial communities links function, structure, and biomass carrying capacity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag133},
pmid = {42397960},
issn = {1751-7370},
abstract = {Microbial communities carry out important ecological functions. Their activities emerge from interactions between species, often potentiated by metabolic traits. We lack a quantitative understanding of how these traits shape community properties. Here, we present theory for microbial communities, leveraging concepts from quantitative microbial physiology. We focus on how steady-state metabolic exchanges between species determine their fractional abundances, given their biomass and byproduct yields on nutrients. We start by deriving formal conditions for the steady states of communities of microbes that grow, die and cross-feed metabolites. We describe the metabolic stoichiometry of nutrient uptake and the formation of biomass and byproducts for each species in terms of charge- and chemical-element balanced reactions (macrochemical reactions). Byproducts function as nutrients for other species. Next, we express the relative abundances of species (living and dead), the net metabolic conversion of a community, and the biomass carrying capacity in terms of the metabolic stoichiometry, growth rates and death rates of the species. We show how niche creation can emerge from stoichiometric imbalances in cross-feeding communities. Finally, we discuss how relative species abundances depend on the ATP stoichiometries of intracellular metabolism.},
}

@article {pmid42396632,
year = {2026},
author = {Gandhi, RR and Khandeparker, RDS and Nikhita, PR and Chudasama, K},
title = {Mangrove health shapes lignocellulolytic bacterial communities.},
journal = {Letters in applied microbiology},
volume = {79},
number = {7},
pages = {},
doi = {10.1093/lambio/ovag049},
pmid = {42396632},
issn = {1472-765X},
support = {//Council for Scientific and Industrial Research (CSIR)/ ; },
mesh = {*Lignin/metabolism ; *Bacteria/enzymology/classification/isolation & purification/genetics/metabolism ; India ; *Wetlands ; Temperature ; *Geologic Sediments/microbiology ; Hydrogen-Ion Concentration ; },
abstract = {The process of lignocellulosic biofuel production needs enzymes that are resistant to high temperatures and low pH. The mangrove sediments, which are typified by variable conditions, can contain bacteria that synthesize intrinsically steady enzymes. We selected 193 bacterial isolates of 12 mangrove sites in Goa, India and tested them to produce lignocellulolytic enzymes (cellulase, laccase, xylanase, xylose isomerase) under the conditions of neutral (37°C, pH 7), acidic (37°C, pH 5), thermophilic (50°C, pH 7), and combined stress (50°C, pH 5). Bacillus and Vibrio dominated, with 22 genera identified. There were no significant differences in alpha diversity following Benjamini-Hochberg FDR correction (all P_adj = 1.00, Cohen d < 0.5) but significant compositional differentiation in beta diversity (PERMANOVA: R[2] = 0.243, P = 0.017). Salinity (R[2] = 0.903, P_adj = 0.003) and temperature (R[2] = 0.722, P_adj = 0.006) were major structuring factors. Site-type differentiation was the most significant factor in xylanase-producing communities (R[2] = 0.272, P = 0.013). Although there was limited replication of dead sites (n = 3), the results confirmed that candidates undergo biochemical characterization and that ecosystem degradation does not decrease diversity but alters community composition.},
}

*Lignin/metabolism
*Bacteria/enzymology/classification/isolation & purification/genetics/metabolism
India
*Wetlands
Temperature
*Geologic Sediments/microbiology
Hydrogen-Ion Concentration

@article {pmid42389176,
year = {2026},
author = {Ubani, O and Ngole-Jeme, VM},
title = {Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112987},
pmid = {42389176},
issn = {2352-3409},
abstract = {This article describes a long-read whole-genome shotgun sequencing dataset generated from microbial communities inhabiting industrially and municipally impacted freshwater wetlands in South Africa. Surface water samples were collected from five strategically selected sites exposed to distinct anthropogenic pressures, including industrial effluent discharge, sewage overflow, greywater inputs, informal settlement runoff, and landfill leachate to generate a unique microbial genomic data. Environmental DNA was extracted and sequenced using the PacBio Sequel IIe platform, producing high-fidelity long reads suitable for improved assembly contiguity and functional reconstruction. Post-quality control processing yielded 4.9 × 10[4] to 1.6 × 10[5] HiFi reads per sample, corresponding to 0.34-1.02 Gb of high-accuracy sequence data per site. Long-read assemblies generated between 16,080 and 54,670 predicted protein-coding genes per sample. Taxonomic classification using Kaiju assigned 94.1-99.8% of assembled sequences to reference taxa. Domain-level profiles were exclusively bacterial dominated, with few rare or undetected (0.000-0.001%) archaeal, eukaryotic, or viral representation. Phylum-level composition was strongly dominated by Pseudomonadota (83-95%), followed by Bacillota (3-10%) and Bacteroidota (1-14%), with Actinomycetota consistently below 1%. Functional annotation using the DRAM pipeline identified 9390-31,251 KEGG orthologs, 969-3039 MEROPS peptidases, 13,454-45,103 Pfam domains, and 202-776 carbohydrate-active enzyme (CAZy) genes across assemblies. Distilled metabolic modules indicated the presence of near‑complete electron transport chain complexes (I-V), denitrification-associated pathways, sulfur oxidation and dissimilatory reduction genes, and diverse carbohydrate degradation functions; methanogenesis‑associated modules were not detected among the annotated metabolic pathways recovered in this dataset. The dataset provides genomic coverage of urban wetland microbiomes shaped by mixed industrial and municipal stressors and represents one of the few long-read metagenomic resources available for southern African freshwater wetlands. The availability of assembled contigs, gene annotations, metabolic reconstructions, enables reuse for comparative environmental genomics, biogeochemical modelling, bioremediation gene discovery, resistome screening, and microbial ecology investigations. This high-fidelity long-read sequencing resource expands opportunities for structural and functional analyses of anthropogenically influenced wetland ecosystems and supports future research in environmental biotechnology, bioinformatics-driven ecosystem monitoring, and microbial adaptation to urban pollution gradients.},
}