@article {pmid42320402,
year = {2026},
author = {Ortiz, C and Hatam, F and Quon, H and Hamilton, KA and Faucher, SP and Prévost, M},
title = {Meta-analysis of growth and inactivation kinetics of Legionella.},
journal = {Water research},
volume = {304},
number = {},
pages = {126280},
doi = {10.1016/j.watres.2026.126280},
pmid = {42320402},
issn = {1879-2448},
abstract = {Quantitative risk assessments intended to inform evidence-based water management plans and public health targets for Legionella in engineered water systems are constrained by fragmented and heterogeneous growth and inactivation kinetics. We conducted a meta-analysis of 25 growth and 39 thermal- and chemical-inactivation studies, fitting microbial persistence models to harmonize parameters. Nonlinear models outperformed first-order formulations, indicating that lag phases and resistant or protected subpopulations are central to Legionella persistence. Random forest analysis identified environmental and methodological drivers of variability based on 226 growth rates and reduction times for thermal (209) and chemical (135) inactivation. Growth was primarily governed by temperature, nutrient availability, and compatible Legionella-host pairings; thermal inactivation by quantification method, temperature, and turbidity; and chemical inactivation by inoculum size, disinfectant type, concentration, and host-associations. Accordingly, temperature-dependent growth parameters and exposure metrics for heat, free-chlorine, and monochloramine, expressed as TT (Temperature×time) and CT (Concentration×time), were derived as condition-specific inputs for predictive models. Growth optima around 37-40 °C, together with lag-time estimates, indicate that hot-water temperature setbacks and energy-saving practices may favor Legionella proliferation under repeated or prolonged lukewarm exposure. Culture- and viability-based TT differences highlight the need to consider viable‑but-non-culturable persistence in monitoring programs. CT comparisons suggest monochloramine may be advantageous because of its lower apparent sensitivity to host-associated protection. Although limited by restricted experimental conditions, the findings show that predictive models should account for microbial ecology, water matrix effects, and quantification endpoints. Future kinetic studies should prioritize realistic multi-host systems, strain pre-adaptation, complementary viability measurements, and standardized protocols and reporting to ensure reproducibility and enable robust system-level predictive modeling.},
}

@article {pmid42320622,
year = {2026},
author = {Hoebinger, C and Semmler, G and Petrenko, O and Rajcic, D and Hoffelner, DK and Duckova, T and Baranovskyi, T and Goederle, L and Khuu, MP and Reinhardt, C and Pjevac, P and Séneca, J and Mieczkowski, K and Burger, K and Bergheim, I and Gensluckner, S and Völkerer, A and Reiberger, T and Scheiner, B and Aigner, E and Wernly, B and Datz, C and Binder, CJ and Hendrikx, T},
title = {Alcohol intake reprograms hepatic immune-metabolic circuits to exacerbate murine atherosclerosis and human cardiovascular risk.},
journal = {JHEP reports : innovation in hepatology},
volume = {},
number = {},
pages = {101932},
doi = {10.1016/j.jhepr.2026.101932},
pmid = {42320622},
issn = {2589-5559},
abstract = {BACKGROUND AND AIMS: Recent reclassification of steatotic liver disease (SLD) distinguishes metabolic dysfunction-associated steatotic liver disease (MASLD) from MetALD, a newly defined entity combining MASLD with alcohol consumption. Since the mechanisms linking alcohol consumption in the context of SLD to cardiovascular disease (CVD), the leading cause of SLD mortality, remain elusive, we investigated how metabolic dysregulation and alcohol intake synergistically promote atherosclerosis.

METHODS: Low-density lipoprotein receptor-deficient (Ldlr[-/-]) mice were fed a high-fat, high-cholesterol (HFC) diet with regular or ethanol-containing drinking water (10-20% v/v). Germ-free and antibiotic-treated Ldlr[-/-] mice were used to assess the contribution of ethanol-induced dysbiosis. Associations between alcohol consumption and cardiometabolic risk were assessed in two human cohorts (N = 5115, N = 2515).

RESULTS: Ethanol intake in HFC diet-fed Ldlr[-/-] mice exacerbated hepatic steatosis and systemic dyslipidemia, despite only modest elevations in systemic ethanol levels (ps≤0.05). Liver transcriptomic profiling revealed ethanol-induced alterations in lipid metabolism and enhanced proinflammatory signatures, accompanied by increased recruitment of Ly6C[high] monocytes to the liver (p=0.0121) and elevated levels in circulation (p=0.0043). Correspondingly, ethanol-consuming HFC diet-fed Ldlr[-/-] mice developed enlarged aortic root lesions (p=0.0105). Neither germ-free conditions nor antibiotic treatment mitigated CVD progression. Metabolomic profiling revealed hyperuricemia in ethanol-exposed HFC diet-fed Ldlr[-/-] mice, which was associated with an upregulation of inflammasome-related genes in the liver, along with an increase in hepatic NLRP3 protein expression (ps≤0.05). Notably, human data mirrored these findings, demonstrating a dose-dependent association between alcohol intake, dyslipidemia, monocytosis, hyperuricemia, and increased cardiovascular risk (ps≤0.05).

CONCLUSION: Our findings identify alcohol as an important immune-modulatory lifestyle factor that contributes to elevated cardiovascular risk.

IMPACT AND IMPLICATIONS: Alcohol consumption, even at moderate levels, contributes to cardiovascular risk, particularly in individuals with SLD. Combining murine models with human cohort data, we show that alcohol intake in SLD is associated with coordinated immune-metabolic alterations, including dyslipidemia, monocytosis, hyperuricemia, and enhanced NLRP3 inflammasome signaling, collectively indicating an elevated cardiovascular risk profile. These findings are relevant to hepatology and cardiovascular medicine, linking alcohol consumption to measurable systemic pathways beyond liver injury. Clinically, systematic assessment of alcohol intake and incorporation into cardiovascular risk evaluation may improve risk stratification and support closer surveillance and preventive strategies in patients with SLD.},
}

@article {pmid42321844,
year = {2026},
author = {Li, Y and Chen, Q and Bin, X and Xu, S and Ma, H},
title = {Bronchoalveolar lavage microbiota signatures and stage-associated alterations in early-stage and advanced-stage non-small cell lung cancer: a pilot study.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08501-7},
pmid = {42321844},
issn = {1479-5876},
support = {2023YXZX17//Tianjin Municipal Education Commission/ ; TJYXZDXK-3-032C//National Key Clinical Specialty Discipline Construction Program of China/ ; },
abstract = {OBJECTIVES: The aims of this study were to characterize the microbial flora in the bronchoalveolar lavage fluid (BALF) of patients with early-stage (stage I, II, IIIA) and advanced-stage (stage IIIB, IIIC, IV) non-small cell lung cancer (NSCLC), and to explore the associations between microbial flora and lung cancer stage.

METHODS: We collected BALF from NSCLC patients (early-stage group 26 cases; advanced-stage group 31 cases). Absolute quantitative metagenomic sequencing was performed to identify differential taxa, genes, and enriched pathways. Flow cytometry was used to profile T cell subsets. We correlated the microbial species with immune cell and gene expression. Receiver operating characteristic (ROC) curve analysis was performed to assess the ability of differential taxa to distinguish advanced-stage from early-stage NSCLC.

RESULTS: Dokdonia (q = 0.040, LDA = 5.704) and Cocleimonas (q = 0.026, LDA = 5.329) were enriched in the early-stage group, whereas Barnesiella (q = 0.046, LDA = 4.784), Pedobacter (q = 0.040, LDA = 4.913) and unclassified Bacteroides (q = 0.046, LDA = 4.932) were significantly enriched in the advanced-stage group. The microbial genes gmhD (q < 0.001, LDA = 3.926), rfaD (q < 0.001, LDA = 3.918), nudF (q = 0.004, LDA = 4.283) and sfsA (q = 0.004, LDA = 3.915) were expressed remarkably in the advanced-stage group. The advanced-stage group exhibited altered T cell subset distributions, including a higher proportion of CD8⁺ T lymphocytes (q < 0.001), whereas it showed a lower proportion of CD4⁺ T cells and a decreased CD4/CD8 ratio (q < 0.001; q < 0.001). Bifidobacterium was negatively associated with the CD4/CD8 ratio (q = 0.015) and positively significant correlated with the genes which enriched in the advanced-stage group.

CONCLUSIONS: This study delineated the microbial structure and function of early-stage and advanced-stage of NSCLC. We identified discriminating taxa, genes, and pathways linked to cancer progression, characterized the T cell subset distributions in the advanced-stage of NSCLC. Bifidobacterium abundance was associated with altered T cell subset distributions and stage-related microbial genes, providing hypotheses for future mechanistic studies on microbiota-driven NSCLC progression.},
}

@article {pmid42322538,
year = {2026},
author = {Deore, P and Upadhyay, A and Thekkumpurath, AS and Devarumath, R and Saha, S},
title = {Amplicon sequencing reveals impact of imidacloprid residues on diversity profile of grape fructosphere microbiota.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42322538},
issn = {1573-0972},
mesh = {*Neonicotinoids/pharmacology/analysis ; *Bacteria/classification/genetics/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Vitis/microbiology ; *Nitro Compounds/pharmacology/analysis ; *Insecticides/pharmacology/analysis ; *Fungi/drug effects/classification/genetics/isolation & purification ; *Microbiota/drug effects/genetics ; *Pesticide Residues/analysis/pharmacology ; Fruit/microbiology ; Biodiversity ; Tandem Mass Spectrometry ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {In grape, fructosphere microbiota play an important role in nutrient cycling, pathogen suppression, berry quality, and fermentation processes. Insecticide imidacloprid (IM) is used to manage several insect pests of grape. However, the non-targeted effect of insecticide residues on grape-associated microbial communities is poorly understood. In the present study, the effect of IM applied at the recommended dose (RD) and ten times the recommended dose (10RD) on microbiota of grape berry surface was investigated under sub-tropical field conditions. Imidacloprid residues were quantified using LC-MS/MS, while bacterial and fungal community dynamics were analysed through 16S rRNA and ITS amplicon sequencing at three time points. Residue analysis revealed gradual dissipation of IM over time, although detectable residues persisted until harvest. Amplicon sequencing identified 1,556 bacterial and 1,348 fungal operational taxonomic units (OTUs). IM treatment significantly affected bacterial OTU abundance, whereas fungal OTUs were not significantly influenced. Beta diversity analysis demonstrated significant differences in bacterial community composition between control and IM-treated samples, while within-group dispersion remained non-significant. In contrast, fungal community composition did not differ significantly among treatments. Pseudomonadota (55-73%) was the dominant bacterial phylum across treatments, whereas Ascomycota (80-94%) predominated among fungal communities. IM exposure reduced the relative abundance of several ecologically important bacterial genera, including Pseudomonas, Sphingomonas, and Methylobacterium, at later sampling stages. Among fungal taxa, Lachnellula remained dominant across all treatments at day 30, whereas several low-abundance fungal genera showed reduced representation. Overall, the study indicated that persistent IM residues can restructure grape fructospheric microbial populations without causing much loss of microbial diversity. The findings suggested that pesticide residues may favour stress-tolerant microbial taxa, with potential implications for vineyard microbial ecology, vine health and berry quality.},
}

*Neonicotinoids/pharmacology/analysis
*Bacteria/classification/genetics/drug effects/isolation & purification
RNA, Ribosomal, 16S/genetics
*Vitis/microbiology
*Nitro Compounds/pharmacology/analysis
*Insecticides/pharmacology/analysis
*Fungi/drug effects/classification/genetics/isolation & purification
*Microbiota/drug effects/genetics
*Pesticide Residues/analysis/pharmacology
Fruit/microbiology
Biodiversity
Tandem Mass Spectrometry
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid42323440,
year = {2026},
author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD},
title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57628-6},
pmid = {42323440},
issn = {2045-2322},
support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; },
abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.},
}

@article {pmid42324861,
year = {2026},
author = {Lí, JT and Hicks, LC and Brangarí, AC and Rousk, J},
title = {Cross-stressor resilience of soil microbial growth and carbon metabolism under climate change.},
journal = {Ecology},
volume = {107},
number = {6},
pages = {e70439},
doi = {10.1002/ecy.70439},
pmid = {42324861},
issn = {1939-9170},
support = {2023-02438//Swedish research council Formas/ ; KAW 2022.0175//Knut and Alice Wallenberg Foundation/ ; KAW 2023.0384//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*Soil Microbiology ; *Climate Change ; *Carbon/metabolism ; *Bacteria/metabolism/growth & development ; *Stress, Physiological ; Droughts ; },
abstract = {The microbial ability to recover metabolism after perturbation events ensures ecosystem functional stability in a changing climate, where multiple climatic stressors increasingly occur in sequential and seasonally cyclic patterns. While prior exposure to a specific stress can enhance microbial resilience to that stress, whether this resilience extends to different stressors remains largely unexplored. Here, we investigated cross-stressor resilience of microbial communities by testing how prior exposure to one type of perturbation (frost or drought) affects microbial resilience to subsequent perturbations of either type in soil systems. We found that prior exposure to drought or frost enhanced the resilience of microbial growth to subsequent perturbations of either type and enabled the maintenance of higher microbial carbon use efficiency. It is likely that this cross-stressor resilience arose because frost and drought both can exert stress on microbes via effects on water potential. This suggests that induced microbial perturbation resilience can extend beyond the stressor they originally were exposed to, indicating that ecological memory transcends the original stressor. Repeated perturbation cycles did not confer additional resilience beyond a single event, indicating that a single perturbation could shape the microbial community's perturbation resilience. We also identified the lag phase as a critical period defining microbial perturbation resilience. Our findings demonstrate a broader adaptive capability within microbial communities under climate change so far overlooked, where winter frost could impact summer drought resilience and vice versa, creating a need to consider selective environmental drivers across seasons.},
}

*Soil Microbiology
*Climate Change
*Carbon/metabolism
*Bacteria/metabolism/growth & development
*Stress, Physiological
Droughts

@article {pmid42326782,
year = {2026},
author = {Fu, B and DeSchepper, LB and Sun, J and McKeithen-Mead, SA and Kapili, B and Ochoa-Andersen, P and Spencer, SP and Fardeen, T and Ricardo, M and El Kamari, V and Sinha, S and Relman, DA and Grembi, JA and Shalon, D and Estrela, S and Huang, KC},
title = {Multi-region sampling of the human small intestine using an ingestible device.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.09.26353912},
pmid = {42326782},
abstract = {The human small intestine (SI) plays a central role in nutrient processing, host-microbe interactions, and immune regulation, yet remains poorly characterized due to the lack of minimally disruptive sampling methods. Here, we present a protocol for deploying, recovering, and analyzing samples collected using an ingestible device that enables multi-region, lumen-targeted SI sampling during normal digestion. The device incorporates a ∼30-cm collapsible tube wound into pH- or time-responsive layers that sequentially unfurl in situ , typically capturing three spatially ordered samples with high yield and reliable retrieval. This protocol outlines study design, participant handling, device recovery, contamination control, and standardized workflows for analyses, including cell quantification, culturomics, sequencing, and metabolomics. We further describe benchmarking approaches for evaluating spatial resolution and strategies for assay prioritization when sample volume is limiting. By reducing participant burden and facilitating integration with stool, saliva, and clinical metadata, this approach enables longitudinal and large-cohort studies linking SI microbial ecology and host physiology to human health.},
}

@article {pmid42328308,
year = {2026},
author = {Sharma, N and Felsberger, M and Kurt, Z and Möst, M and Bayer, B},
title = {Seasonal differences and potential biological drivers of the methane paradox in two peri-Alpine lakes.},
journal = {Limnology and oceanography letters},
volume = {11},
number = {3},
pages = {},
pmid = {42328308},
issn = {2378-2242},
abstract = {Seasonal variations and the biological drivers underlying the methane paradox in freshwater lakes are poorly understood. Here, we investigated the relationship between subsurface methane inventories and phytoplankton in two peri-Alpine lakes across different seasons. Surface waters of both lakes were consistently saturated in methane, with maxima reaching 570 and 205 nmol L[-1] during summer in the metalimnion of lakes Mondsee and Attersee, respectively. Methane concentrations were positively correlated with phytoplankton abundance in meso-oligotrophic lake Mondsee but not in ultra-oligotrophic lake Attersee. However, although phytoplankton peaked in abundance at the methane maxima in Mondsee, incubation experiments with [13]C-labeled bicarbonate revealed negligible methane production from primary productivity. Instead, our results suggest that phytoplankton might only be indirectly involved in methane production through alternative pathways, or by providing precursor compounds to other members of the microbial community in these oligotrophic lakes.},
}

@article {pmid42319826,
year = {2026},
author = {Lin, SZ and Chen, Y and Wu, C and Sun, WH and Li, Z and Chen, HC and Wang, JY and Ji, CM and Li, SB and Wang, ZW and Tsai, WC and Ma, XQ and Lan, SR and Zhang, FP and Xie, YC and Yao, L and Zhang, Y and Lü, MM and Zhang, JJ and Zhang, DY and Ye, YQ and Yu, X and Xu, SS and Ma, ZH and Ding, GC and Cao, GQ and He, ZM and Wu, PF and Lin, KM and Liu, AQ and Lin, YQ and Ruan, SN and Liu, B and Cao, SJ and Zhou, LL and Li, M and Shuai, P and Hou, XL and Wu, YH and Li, N and Xiong, S and Hao, Y and Zhou, Z and Liu, XD and Zuo, DD and Li, J and Wang, P and Zhang, J and Liu, DK and Chen, GZ and Huang, J and Huang, MZ and Li, YY and Zheng, QY and Zhao, XW and Zhao, X and Zhong, WY and Zhang, XW and Xia, ZB and Yu, Y and Liu, ZW and Zheng, HK and Ming, R and Van de Peer, Y and Liu, ZJ},
title = {Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {117566},
doi = {10.1016/j.celrep.2026.117566},
pmid = {42319826},
issn = {2211-1247},
abstract = {Cupressaceae , a gymnosperm family, draws attention due to its controversial phylogenetic position. Here, we present a comprehensive genome analysis of Chinese fir (Cunninghamia lanceolata), a Cupressaceae species, to enhance our understanding of gymnosperm evolution. The 11.24 Gb assembled genome, shaped by inefficient long terminal repeat removal, offers insights into its phylogenetic position. Phylogenetic analysis refines gymnosperm relationships between Cycads-Ginkgo and their relation to Gnetales-Pinaceae. Whole-genome duplication (WGD) analysis reveals no evidence for an ancient polyploidization event in the lineage of C. lanceolata, and confirms a seed-plant-shared WGD event. We also explore genomic evidence to explain the population history and adaptability of C. lanceolata, including potential glacial refugia, dispersal centers, and unique sterility. Furthermore, the refined (A)B(C) model for reproductive organ development in C. lanceolata has broader applications across gymnosperms. This study provides a valuable genome sequence and contributes to the understanding of gymnosperm evolution.},
}

@article {pmid42320159,
year = {2026},
author = {Jo, YH and Kim, WS and Kim, YR and Ju, MS and Ghassemi Nejad, J and Kim, KH and Lee, HG},
title = {Seasonal heat stress alters rumen fermentation, microbial community, and microbial amino acid composition in cattle.},
journal = {Journal of thermal biology},
volume = {139},
number = {},
pages = {104509},
doi = {10.1016/j.jtherbio.2026.104509},
pmid = {42320159},
issn = {0306-4565},
abstract = {In this study, we investigated the effects of seasonal changes on ruminal temperature, pH, fermentation characteristics, microbial composition, and microbial amino acids (AAs) in cattle. The experiment was conducted using six fistulated Holstein steers in two separate 9-d trials conducted in spring and summer (3 d adaptation and 6 d sampling). The average ambient temperature and relative humidity were 10.7 °C and 58% in spring and 24.5 °C and 83.5% in summer, respectively. Ruminal temperature was approximately 0.9 °C higher in summer than in spring, whereas ruminal pH was 0.15 units lower in summer. Among rumen fermentation parameters, butyrate concentration increased during summer, while the concentrations of acetate, propionate, branched-chain fatty acids, total volatile fatty acids, and NH3-N decreased (p < 0.05). Despite identical feed intake, ruminal degradation rates increased after 24 h in summer, with significant increases in the degradation of dry matter, crude protein, and neutral detergent fiber (p < 0.05). Microbial community analysis revealed that at the phylum level, Spirochaetota decreased, whereas Planctomycetota and Chloroflexi increased during summer (p < 0.05). At the genus level, Succiniclasticum and Treponema decreased, while Eubacterium coprostanoligenes and Oscillospiraceae increased compared with spring (p < 0.05). Changes in microbial composition were accompanied by alterations in microbial AA profiles, characterized by increases in alanine, glutamate, histidine, and non-essential AAs, and decreases in glycine, serine, methionine, threonine, and essential AAs during summer (p < 0.05). Notably, methionine content decreased by 13% in summer relative to spring. Overall, these findings demonstrate that seasonal thermal conditions directly alter rumen fermentation, microbial ecology, and microbial AA composition, even under identical feeding conditions. This study provides foundational evidence for developing nutritional and management strategies to optimize rumen function under heat stress conditions.},
}

@article {pmid42313156,
year = {2026},
author = {Quintanilla, E and Salazar, J and van de Water, J and Madurell, T},
title = {Bacterial Microbiota Signatures Suggest Acclimation of the Gorgonian Leptogorgia sarmentosa to Highly Impacted Environments in the Mediterranean Sea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02809-z},
pmid = {42313156},
issn = {1432-184X},
abstract = {Anthropogenic disturbances increasingly compromise marine environments, with severe consequences for vulnerable coral ecosystems. While global stressor impacts on stony corals are well-documented, the mechanisms by which local perturbations influence gorgonians remain poorly characterized. This limits our ability to predict the tolerance of temperate octocorals in human-dominated coastal landscapes. The Mediterranean gorgonian Leptogorgia sarmentosa is remarkably resilient, thriving in both marine protected areas (MPAs) and highly impacted urban habitats. To investigate the microbiota's role in this adaptability, we characterized the bacterial communities of L. sarmentosa from a protected site (Western Mediterranean) and an impacted seaport (Barcelona). For broader regional context, results were compared in parallel with a re-analysis of datasets from similarly contrasting Mediterranean sites (Cassis and La Spezia). Our results reveal distinct site-specific microbial signatures, but no differences in alpha diversity or dispersion between seaport and the MPA. However, significant compositional shifts occurred in the impacted Barcelona seaport, characterized by a reconfiguration of the dominant symbiont genus Endozoicomonas and an enrichment of Spongiibacteraceae_clade BD1-7. Similarly, Endozoicomonas strain abundances differed between Cassis and the high-runoff environment of La Spezia, which exhibited increased Mycoplasma abundance. Collectively, these findings suggest a high degree of microbiome flexibility. This microbiota plasticity, alongside predicted functional pathways, suggests a contribution to preserving and acquiring key holobiont functions, highlighting the capacity of L. sarmentosa to persist in disturbed habitats through strategic microbial reconfiguration. This study provides crucial insights into the mechanisms underlying coral acclimation; essential for developing conservation strategies and predicting the long-term viability of Mediterranean marine biodiversity.},
}

@article {pmid42314820,
year = {2026},
author = {Du, Z and Yang, J and Li, W and Huang, C},
title = {Selection-Driven Shifts in Airborne Bacterial Communities and Potentially Pathogenic Genera Across Environmental and PM2.5 Gradients in Urban Beijing.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128603},
doi = {10.1016/j.envpol.2026.128603},
pmid = {42314820},
issn = {1873-6424},
abstract = {Air pollution poses the greatest public health threat among environmental risks, and fine particulate matter with diameter ≤ 2.5 μm (PM2.5) is one of the most harmful air pollutants. PM2.5 is often associated with airborne microorganisms, making their investigation important for both microbial ecology and potential exposure assessment. In this study, airborne bacterial communities in PM2.5 samples collected during autumn and winter in urban Beijing were analyzed using 16S rRNA gene sequencing, null-model community assembly analysis, and co-occurrence network analysis. Distinct differences in microbial communities were observed between autumn and winter sampling periods based on PCoA and PERMANOVA analyses (p < 0.05), whereas no consistent differences between daytime and nighttime samples were detected. Community assembly shifted from stronger stochasticity in autumn to greater homogeneous selection in winter, with homogeneous selection contributing 47.22% and 53.33% in winter daytime and nighttime samples, respectively . We further characterized microbial composition and identified potentially pathogenic genera under different environmental conditions. Most pathogens were less abundant in winter. However, Streptomyces, Saccharopolyspora, and Nocardiopsis were enriched under low temperature and absolute humidity conditions, and their abundance further increased with high PM2.5 levels, as supported by microbial community composition analyses. Co-occurrence network analysis further revealed more interconnected positive microbial associations in autumn, whereas winter communities exhibited greater modularity and increased negative correlations under colder and drier conditions. These findings provide insights into airborne microbial diversity, community assembly, community composition, and co-occurrence patterns across contrasting environmental conditions and their associations with air quality, with potential relevance for understanding airborne microbial exposure and respiratory health concerns in urban environments.},
}

@article {pmid42315001,
year = {2026},
author = {Weltz, TK and Peng, S and Larsen, A and Bak, EEF and Tran, JVQ and Gudjonsdottir, LR and Hemmingsen, MN and Ørholt, M and Mielke, LV and Trillingsgaard, J and Elberg, JJ and Hölmich, LR and Jensen, LT and Vester-Glowinski, P and Bjarnsholt, T and Trivedi, U and Clemens, MW and Li, X and Sørensen, SJ and Herly, M},
title = {Breast implant surface texture is associated with distinct implant microbiome profiles in humans.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2026.06.038},
pmid = {42315001},
issn = {1878-7568},
abstract = {Surface topography of silicone breast implants modulates foreign body responses, but its connection to implant-associated microbial communities remains unclear. We analyzed the microbiome of 391 explanted breast implants from 221 patients with different surface textures using 16S rRNA gene sequencing. We found that the surface texture is associated with distinct microbial communities depending on a surface roughness gradient. Rougher surfaces had lower microbial diversity, driven by lower evenness and a higher relative abundance of Staphylococcus than smoother surfaces. Compositional differences across surface groups followed this gradient. In a subset of samples, absolute bacterial quantification using digital PCR showed increasing total bacterial burden with increasing surface roughness. Smooth and minimally textured implants displayed similar microbiome profiles despite large differences in implantation time. Together, these findings suggest that surface roughness is associated with the local microbial microenvironment, linking material design with microbial burden and the foreign body response. STATEMENT OF SIGNIFICANCE: Breast implant surface topography may influence implant-associated microbial communities, but human evidence across commonly used textures is limited. Using 16S rRNA gene sequencing of 391 explanted implants from multiple manufacturers, we found that microbial diversity and composition varied systematically with a surface roughness gradient. Rougher textures showed lower diversity driven by reduced evenness and a higher relative abundance of Staphylococcus, while compositional differences across surface groups followed the same gradient. Quantitative digital PCR further suggested a higher total bacterial burden on rougher surfaces. In contrast, smooth and minimally textured implants displayed similar microbiome profiles despite large differences in implantation time. These findings link implant surface design to microbial ecology and may help explain texture-associated differences in foreign body responses.},
}

@article {pmid42315252,
year = {2026},
author = {Lin, Y and Liu, YK and Mi, P and Zhao, XL and Lin, JH and Cheng, XS and Liang, LY and Huang, YD and Huo, YN and Xie, GJ and Ye, ZY and Guleng, B},
title = {Integrin CD11b/CD18 reprograms macrophage polarization by suppressing ERK/STAT3 signaling to enhance antitumor immunity in colitis-associated colorectal cancer.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {6},
pages = {},
doi = {10.1136/jitc-2025-014026},
pmid = {42315252},
issn = {2051-1426},
mesh = {Animals ; *STAT3 Transcription Factor/metabolism ; *CD11b Antigen/metabolism/genetics ; *CD18 Antigens/metabolism/genetics ; Mice ; *Macrophages/immunology/metabolism ; Humans ; *Colitis-Associated Neoplasms/immunology/pathology/metabolism ; *Colitis/complications ; *Colorectal Neoplasms/pathology/immunology ; Tumor Microenvironment/immunology ; Signal Transduction ; Mice, Knockout ; Male ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Chronic inflammation is a well-established driver of colorectal cancer (CRC), with the resulting inflammatory microenvironment facilitating tumor initiation and progression. The integrin CD11b/CD18, a leukocyte-specific heterodimeric adhesion receptor, mediates critical immunoregulatory functions during inflammatory responses. However, the roles and mechanisms of CD11b/CD18 in colitis-associated colorectal cancer (CAC) remain unclear.

METHODS: To investigate the impact of CD11b/CD18 deficiency on colorectal carcinogenesis, an azoxymethane/dextran sodium sulfate-induced CAC model was established with CD11b and CD18 single-knockout and double-knockout mice. The tumor immune microenvironment was characterized using multicolor flow cytometry. Transcriptomic changes in tumor-associated neutrophils (TANs) and macrophages (TAMs) on CD11b/CD18 ablation were profiled by RNA sequencing. Functional crosstalk between TANs and TAMs was assessed via co-culture experiments. The direct role of CD11b/CD18 in TAM polarization and antitumor activity was evaluated using in vitro agonist assays, and the involvement of the extracellular signal-regulated kinase (ERK)/signal transducer and activator of transcription 3 (STAT3) axis was validated with pathway-specific inhibitors.

RESULTS: Bioinformatics analysis revealed significant downregulation of ITGAM (CD11b) and ITGB2 (CD18) expression in CRC tissues. In the CAC model, CD11b and CD18 exhibited non-redundant and cooperative functions, and double deficiency significantly exacerbated tumor progression, with increased STAT3 phosphorylation and reduced yes-associated protein phosphorylation. Flow cytometric analysis identified neutrophils as the predominant CD11b[+]CD18[+] population within the tumor microenvironment (TME). Mechanistically, CD11b/CD18 deficiency promoted TME remodeling, including protumor skewing of TANs and TAMs, with TAM polarization mediated partly by TAN-TAM crosstalk. Beyond this indirect mechanism, direct activation of CD11b/CD18 in TAMs attenuated the immunosuppressive properties and enhanced their tumoricidal activity. At the molecular level, CD11b/CD18 deficiency activated janus kinase (JAK)-STAT and mitogen-activated protein kinase pathways in TAMs, whereas CD11b/CD18 activation effectively suppressed ERK1/2 and STAT3 signaling. Combined inhibition of ERK1/2 and STAT3 reversed M2 polarization and restored TAM-mediated tumor killing.

CONCLUSIONS: Our findings establish that integrin CD11b/CD18 orchestrates antitumor immunity by modulating the TME, particularly through direct TAM reprogramming and indirect TAN-TAM crosstalk, highlighting its potential as an immunotherapeutic target for CAC.},
}

Animals
*STAT3 Transcription Factor/metabolism
*CD11b Antigen/metabolism/genetics
*CD18 Antigens/metabolism/genetics
Mice
*Macrophages/immunology/metabolism
Humans
*Colitis-Associated Neoplasms/immunology/pathology/metabolism
*Colitis/complications
*Colorectal Neoplasms/pathology/immunology
Tumor Microenvironment/immunology
Signal Transduction
Mice, Knockout
Male
Mice, Inbred C57BL

@article {pmid42315481,
year = {2026},
author = {Thomas, C and Laakkonen, AK and Rast, DR and Sauter, G and Kremer, K and Max, S and Vogel, H},
title = {Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag072},
pmid = {42315481},
issn = {1574-6968},
abstract = {Microbial communities in the subsurface biosphere remain poorly characterized because many taxa lack cultured representatives and genomic references, limiting the accuracy of taxonomy inferred from short-read 16S ribosomal RNA gene sequencing. We tested the hypothesis that long-read 16S sequencing improves taxonomic resolution and detection of rare lineages compared with short-read approaches in low-biomass, diversity-rich sediments. Microbial communities from a sediment core of Lake Arnon (Switzerland) were analyzed using both long-and short-read sequencing, and community composition, diversity metrics, and taxonomic resolution were compared. Sequencing technology influenced observed community structure, but sediment depth also exerted a strong effect. Taxonomic profiles were broadly consistent across methods for most bacterial groups, whereas archaeal diversity was underrepresented in long-read datasets due to primer mismatches. When detected, long reads provided higher taxonomic resolution, frequently to species level, improving ecological interpretation and inference of metabolic potential. Finer-scale analyses, including species contributions to beta diversity and co-occurrence networks, showed greater specificity with long reads. These results demonstrate that long-read sequencing can substantially enhance subsurface microbial characterization, provided that primer design is optimized, and highlight its potential to improve assessments of microbial identity, structure, and function in low-biomass environments.},
}

@article {pmid42315857,
year = {2026},
author = {Buthelezi, ZM and Pierneef, RE and Bezuidt, OKI and Gregori, MNJ and Pesant, S and Iudicone, D and Hanwell, L and Todd, JD and Makhalanyane, TP},
title = {Dimethylsulfoniopropionate metabolism shapes microbial ecology and physiological adaptation during the austral winter in Southern Ocean sea ice and seawater.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42315857},
issn = {2041-1723},
support = {SANAP23042496849//National Research Foundation (NRF)/ ; 110717//National Research Foundation (NRF)/ ; },
mesh = {*Sulfonium Compounds/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Ice Cover/microbiology/chemistry ; *Adaptation, Physiological ; Seasons ; Oceans and Seas ; Bacteria/metabolism/genetics ; },
abstract = {Dimethylsulfoniopropionate (DMSP) is a highly abundant marine organosulfur compound, with important roles in stress protection and climate-cooling gases production. Polar regions, particularly seawater and sea ice interfaces, are critical yet understudied DMSP cycling hotspots. Here, we reveal up to 38-fold higher DMSP concentrations in Southern Ocean sea ice versus seawaters, identifying sea ice as a concentrated reservoir of DMSP with implications for microbial stress tolerance and sulfur recycling. Eukaryotic algae harboring DSYB and DSYE genes were predicted to dominate DMSP production, but diverse and previously unidentified bacterial producers were also detected. This elevated abundance of algal biosynthetic genes likely underpins the higher DMSP concentrations in sea ice. Notably, DMSP catabolism, particularly the dmdA demethylase and dddD and dddK lyase genes, were more abundant than biosynthesis genes. Taken together, these findings reveal the widespread metabolism for DMSP cycling and underscore a dynamic reservoir and transformation hub influencing polar climate-cooling sulfur fluxes.},
}

*Sulfonium Compounds/metabolism/analysis
*Seawater/microbiology/chemistry
*Ice Cover/microbiology/chemistry
*Adaptation, Physiological
Seasons
Oceans and Seas
Bacteria/metabolism/genetics

@article {pmid42317759,
year = {2026},
author = {Jiya, N and Sha, SP and Khudai, W and Yadav, S and Sasane, R and Sah, SP and Ghatani, K and Sharma, A},
title = {Distinct bacterial and fungal communities linked to functional potential in fermented fish and vegetables.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1850075},
pmid = {42317759},
issn = {1664-302X},
abstract = {INTRODUCTION: Traditional fermented foods constitute a vital component of ethnic community diets; consequently, characterizing their specific food microbiome is essential for elucidating their nutritional, functional and health related attributes.

METHODS: In this study, targeted metagenomics was employed to investigate the bacterial and fungal compositions of fermented fish and vegetables from North Bengal, India. The functional predictions of the fermented food microbiomes was performed using PICRUSt2.

RESULTS AND DISCUSSION: High throughput sequencing of 16S rRNA and ITS genes revealed substantial differences in the diversity indices amongst the fermented fishes and vegetables. Fish samples were dominated by Pseudomonadota (23.05%), whereas vegetables were enriched in Bacillota (32.17%), with Psychrobacter and Aliivibrio prevalent in fishes and lactic acid bacteria including Levilactobacillus, Paucilactobacillus and Pediococcus dominant in vegetables. The fungal genera Bisifusarium belonging to Ascomycota and Cystobasidium affiliated to Basidiomycota, were abundant in the fermented fishes and vegetables, respectively. Functional predictions of bacterial and fungal communities revealed enhanced carbohydrate metabolism, biosynthesis pathways related to vitamins, short-chain fatty acids, organic acids, proteolytic enzymes and compounds contributing to organoleptic attributes in these fermented foods. The assessment of microbial communities associated with the traditionally fermented foods of North Bengal revealed the key microbial taxa involved in the fermentation process and their nutritional properties.},
}

@article {pmid42317952,
year = {2026},
author = {Andafa, TW and Imoh, EC and Adekanmbi, SA},
title = {Artificial Intelligence Applied to the Brain-Gut Axis in Irritable Bowel Syndrome: Advancing Toward Clinical Translation.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109142},
pmid = {42317952},
issn = {2168-8184},
abstract = {Irritable bowel syndrome (IBS) is one of the most common functional gut disorders affecting the global population, characterized by chronic abdominal pain and altered bowel habits in the absence of structural disease. The brain-gut-microbiota axis, a bidirectional network integrating central nervous system processing, enteric and autonomic function, immune signaling, and gut microbial ecology, provides a mechanistic framework that helps explain the substantial symptom heterogeneity and variable treatment response observed across patients. Artificial intelligence (AI) and machine learning (ML) approaches offer the ability to model complex, nonlinear relationships across high-dimensional biological datasets generated from this axis, including microbiome composition profiles, resting-state functional MRI connectivity matrices, multiomics data layers, and psychological and clinical feature sets. This narrative review evaluated primary human studies applying AI and ML to brain-gut axis data in IBS, identified through structured searches of PubMed/MEDLINE and Scopus supplemented by citation chaining, with literature included up to April 2026. Across microbiome profiling, neuroimaging, multiomics integration, and psychological feature modeling, ML approaches have demonstrated proof-of-concept performance for IBS classification and, in a smaller number of studies, for prediction of clinically meaningful outcomes, including cognitive behavioral therapy (CBT) response. A notable early signal is the integration of baseline microbiome and brain features to predict CBT response, with high reported discrimination, although these results are derived from small, single-center cohorts with only internal validation and should be regarded as hypothesis-generating. The current evidence base is limited by small single-center cohorts, reliance on internal validation, healthy-control comparators, limited external replication, and substantial overfitting and data-leakage risk in high-dimensional small-sample settings. AI and ML applications in IBS are promising but remain exploratory and are not yet suitable for routine clinical use. Clinical translation will require larger multicenter datasets, harmonized preprocessing pipelines, external validation, calibration reporting, and evaluation against clinically realistic comparators and decision points.},
}

@article {pmid42318064,
year = {2026},
author = {Li, XT and Zhang, X and Liang, ZL and Jiang, Z and Huang, Y and Han, YQ and Tan, ZB and Ying-Liu, and Liu, ZH and Yin, HQ and Liu, SJ and Jiang, CY},
title = {A culturomics biobank decodes extremophile evolution and metabolism in acid mine drainage.},
journal = {Environmental science and ecotechnology},
volume = {32},
number = {},
pages = {100722},
pmid = {42318064},
issn = {2666-4984},
abstract = {Extreme environments such as acid mine drainage (AMD) host highly specialized microbial communities that drive profound biogeochemical cycles. Within these ecosystems, iron- and sulfur-metabolizing taxa catalyze mineral weathering, generating intense acidity and mobilizing heavy metals. However, more than 97% of these microorganisms remain uncultured "microbial dark matter," heavily restricting our understanding of extremophile metabolism and adaptation. Here we present the Microbial Biobank of AMD (mbAMD), a culturomics-derived collection of 652 isolates spanning 42 species-including 21 novel taxa-that achieves 86.7% coverage of the global AMD core microbiome. Functional validation demonstrates that 36 of these taxa possess active iron or sulfur metabolic capacities, including the discovery of the first pure cultures of acid-tolerant sulfate reducers. Comparative genomic analyses across these isolates reveal that extreme environmental adaptation is predominantly driven by pervasive horizontal gene transfer. Specifically, extremophiles preferentially acquire adaptive genes governing acid tolerance and metal resistance from phylogenetically proximal relatives rather than distant donors. These findings elucidate the modular evolutionary strategies of extremophiles and provide critical functional resources for advancing biohydrometallurgy and environmental bioremediation. This mbAMD resource will accelerate biohydrometallurgical process optimization and environmental bioremediation strategies while advancing evolutionary microbial ecology research.},
}

@article {pmid42319473,
year = {2026},
author = {Książkiewicz, Z and Górzyńska, K and Kosicka, E and Wejnerowski, Ł and Rybak, M},
title = {Microbial Resource Regimes Shape Early Survival, Growth, and Reproductive Morphology in a Phally Polymorphic Terrestrial Gastropod.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02814-2},
pmid = {42319473},
issn = {1432-184X},
abstract = {Microorganisms are fundamental components of terrestrial ecosystems, acting not only as symbionts or pathogens but also as key nutritional resources for invertebrates. Despite their ubiquity, their role in shaping early-life survival and phenotypic variation in terrestrial animals remains poorly understood. Here, we investigated how microbial resource regimes act as early-life ecological filters influencing survival, growth, and reproductive morphology in the phally polymorphic wetland microsnail Vertigo antivertigo. Using eggs and early juveniles, life stages characterized by high natural mortality, we conducted a series of laboratory experiments manipulating access to the species' fecal- and litter-associated bacteria, soil and litter fungi, and the cyanobacterium Limnothrix sp. Survival emerged as the most consistent response variable across treatments. Fungal supplementation combined with plant litter supported growth and survival to sexual maturity, whereas bacterial resources alone did not compensate for the absence of intact litter-associated microorganisms. Exposure to Limnothrix sp. resulted in severe growth suppression and complete juvenile mortality, irrespective of bacterial supplementation. Disrupted microbial conditions were also associated with shifts in reproductive morphology, including reduced or absent male copulatory organs. Our findings demonstrate that microbial resource regimes can function as strong early-life ecological filters, shaping survival, growth and reproductive morphology.},
}

@article {pmid42319514,
year = {2026},
author = {Ståhle, M and Johnson, A and Turner, S and Mårtensson, P and Kalinowski, B and Dopson, M},
title = {Multi-Year Biofilm Formation on Granitic Surfaces Reveals Dynamic Microbial Communities in Fennoscandian Shield Deep Groundwaters.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02812-4},
pmid = {42319514},
issn = {1432-184X},
abstract = {The deep terrestrial biosphere is the vast biome beneath the soil layer that contains the majority of the Earth's prokaryotic biomass, yet it is one of the least investigated communities. Although, estimates of deep biosphere biomass suggest biofilm cells outnumber the planktonic biomass by several orders of magnitude, most investigations target planktonic communities captured from groundwaters. This multi-year study used 16S rRNA gene sequencing to compare planktonic and biofilm communities attached to natural granitic rock, demonstrating that biofilm formation selected for taxa with distinct relative abundances and exhibited temporal development. The biofilm communities also showed a decreasing influence of introduced populations on the natural rock surfaces (macadam) present at the onset of the incubations. After two- and four-years of biofilm incubation, a community developed that was dominated by sulfur/sulfate reducing Desulfocapsaceae, Desulfobacteraceae, and BM004 along with the families UBA5619, Rhodocyclaceae, Profunditerraquicolaceae, and UBA2206. This long-term community included populations predicted to be host-associated ultra-small cells. This contrasted with previous studies of early biofilm development in deep Fennoscandian Shield groundwaters that suggested biofilm initiation was mediated by lithotrophic carbon and nitrogen fixing populations. However, metabolic predictions based upon the 16S rRNA gene-based communities also showed an autotrophic and diazotrophic community including sulfur cycling in line with the previous studies. In conclusion, this study showed long-term biofilm composition to be dissimilar to the planktonic communities with a consistent strategy for energy conservation similar to previous studies of early biofilm formation from these groundwaters.},
}

@article {pmid42319657,
year = {2026},
author = {Shon, WJ and Kim, KA and Kim, JS and Kim, BG and Im, JP and Lee, HJ and Kim, SH and Kim, JW and Kang, HW and Kim, KW and Choi, JW and Cheon, DH and Kim, D and Choi, J and Kim, ES and Koh, SJ},
title = {Habitual Ultra-processed Food Intake Is Associated with Gut Dysbiosis and Pro-inflammatory Metabolite Profiles in Korean Patients with IBD.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42319657},
issn = {1573-2568},
abstract = {BACKGROUND AND AIMS: Ultra-processed food (UPF) is increasingly consumed worldwide and may influence gut microbial ecology relevant to inflammatory bowel disease (IBD). However, patient-level multi-omics data remains scarce. We investigated whether habitual UPF intake is associated with specific microbiota and metabolite profiles in Korean patients with IBD.

METHODS: Dietary intake was assessed using a validated food frequency questionnaire, and food was categorized by the NOVA system. UPF intake was expressed as percent of energy, and 313 patients were stratified into UPF low (Q1-Q2) and UPF high (Q3-Q4). Fecal samples of 174 patients underwent 16S rRNA sequencing and untargeted metabolomics. Microbiome differences were tested using PERMANOVA for beta-diversity and Mann-Whitney U tests for taxa. Differential metabolites were defined by p < 0.05 and |fold change|≥ 1.5, followed by Reactome enrichment with FDR correction. Correlations among microbiota, metabolites, and UPF subgroups were examined using Spearman tests with Benjamini-Hochberg adjustment. Associations between UPF intake and clinical characteristics were analyzed using Spearman tests, η[2] from ANOVA and point-biserial correlation.

RESULTS: Microbial beta-diversity differed significantly between UPF low and UPF high participants. UPF high participants showed expansion of pro-inflammatory pathobionts (Escherichia-Shigella, Proteus, Parasutterella, Enterococcus, Fusobacterium, and Clostridium innocuum group) and depletion of anti-inflammatory commensals (Faecalibacterium, Butyricicoccus, Lachnospiraceae ND3007 group, and Bifidobacterium). Metabolomic profiling revealed enrichment of inflammatory pathways (phospholipid metabolism, eNOS/NO signaling, mitochondrial β-oxidation, FMO3-mediated TMA to TMAO, tryptophan catabolism) and reduction of anti-inflammatory metabolites (AHR ligands, BAAT-conjugated bile acids). Integrated analyses demonstrated significant correlations between dysbiotic taxa and inflammatory metabolites. Among NOVA-defined UPF subgroups, sugar-sweetened beverages, ready-to-eat dishes, and packaged snacks and confectioneries showed the strongest associations with these adverse signatures. Analysis of clinical characteristics showed trends between total UPF intake and inflammatory markers (WBC, CRP, fecal calprotectin), and association with upper gastrointestinal tract involvement in patients with CD. Subgroup analysis showed that sugar-sweetened beverage intake was significantly associated with CRP elevation and upper gastrointestinal involvement in patients with CD.

CONCLUSIONS: In IBD, higher UPF intake, particularly from specific NOVA-defined subgroups, is associated with gut dysbiosis and a pro-inflammatory metabolome, which in turn correlates with unfavorable clinical characteristics. These findings provide patient-based multi-omics evidence and underscore clinically relevant dietary targets for IBD management.},
}

@article {pmid42303895,
year = {2026},
author = {Cornelio-Martínez, S and Frade-Pérez, MD and González-Dávalos, ML and Varela-Echavarría, A and Mora-Izaguirre, O},
title = {Diet-Dependent Variations in the Gut Microbiota and Metabolic Pathways of the land slug Deroceras laeve.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02811-5},
pmid = {42303895},
issn = {1432-184X},
support = {IN204526//PAPIIT-UNAM/ ; IN203924//PAPIIT-UNAM/ ; CBF2023-2024-834//SECIHTI/ ; CF-2023-I-1881//SECIHTI/ ; },
abstract = {The slug Deroceras laeve has emerged as a valuable model for biological research, but limited knowledge exists of the microbiota that inhabit the digestive tract of this species. This study assessed the bacterial microbiota of the stomach and intestine of D. laeve fed either a diet formulated for rodents (RD) or a diet of fresh vegetables (VD). Pseudomonadota was the most abundant phylum in both digestive compartments, although it decreased in abundance with the VD diet. The genus Rahnella was the most abundant in both regions with a decrease caused by the VD diet and a concomitant increase in richness. Predicted metabolic pathways indicated that fatty acid biosynthesis predominated in the stomach of slugs fed the RD, whereas pyruvate fermentation and amino acid biosynthesis were enriched in VD animals. In the intestine, aerobic respiration, pyruvate fermentation, fatty acid and amino acid biosynthesis were identified as conserved pathways. Predictive functional profiling revealed that signaling and cellular processes, genetic information processing, and metabolism were predominant functions across all groups. These results reveal a more diverse microbiome in slugs fed VD, paralleling the findings in other animals and providing a good grounding for the study of ecological adaptations of this species to its environment.},
}

@article {pmid42304377,
year = {2026},
author = {Ghodraty, M and Fekri, M and Kiani, M and Esmaeel Zadegan, S and Abdoli Rezaei, S and Mousavi Gilani, SS and Manafi Varkiani, M and Ghafouri, A and Mehrnia, N and Amudi, M and Khodayar, Z and Jouya Talaei, A and Baadkoubehazaveh, M},
title = {Gut microbiota, brown adipose tissue whitening, and obesity: nutritional modulators and metabolic crosstalk.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01152-x},
pmid = {42304377},
issn = {1743-7075},
abstract = {Obesity reflects a chronic imbalance between energy intake and expenditure, accompanied by metabolic inflammation and ectopic lipid deposition. Accumulating evidence indicates that gut microbiota dysbiosis reshapes host nutrient handling and endocrine-immune signaling, with downstream consequences for thermogenic adipose tissues. Brown adipose tissue (BAT) supports energy dissipation via UCP1-dependent adaptive thermogenesis; however, in obesity, BAT often undergoes "whitening," a maladaptive transition characterized by lipid accumulation, mitochondrial dysfunction, and reduced thermogenic capacity. This review synthesizes mechanistic and translational evidence linking obesity-associated microbiota alterations to BAT dysfunction through integrated gut-adipose and gut-liver communication. We discuss how microbially derived metabolites (including short-chain fatty acids and secondary bile acids), endotoxin-driven inflammation, and bile acid receptor signaling (FXR/TGR5) may converge on sympathetic tone, mitochondrial biogenesis, and lipid flux to favor BAT whitening. We further evaluate nutrition- and lifestyle-based strategies (dietary fiber and polyphenols, exercise, pre/pro/postbiotics, and bile acid-targeted approaches) that modulate microbial ecology and metabolic outputs, with potential to preserve BAT thermogenic identity and improve metabolic health. Clarifying the causal pathways and clinically actionable microbial signatures within this gut-adipose-liver network may inform future nutrition-oriented interventions for obesity and related metabolic disorders.},
}

@article {pmid42308545,
year = {2026},
author = {Yuan, Y and Yin, X and Liu, J and Jing, J and Shi, Y and Tao, S and Guo, L and Wang, D and Jiang, W and Liong, MT and Chen, D and Zhang, J},
title = {Bifidobacterium lactis XLTG11 Reduces Eczema and Infections in Infants: A Randomized Trial.},
journal = {QJM : monthly journal of the Association of Physicians},
volume = {},
number = {},
pages = {},
doi = {10.1093/qjmed/hcag148},
pmid = {42308545},
issn = {1460-2393},
abstract = {BACKGROUND: Early-life gut microbiota profoundly influences immune system maturation and disease susceptibility. Perturbations in microbial development have been linked to rising rates of allergic and infectious diseases in children. Probiotic interventions offer a promising strategy to restore microbial-immune homeostasis; however, evidence from rigorously designed, strain-specific randomized trials integrating clinical and microbiome outcomes remains limited.

OBJECTIVE: To evaluate the efficacy of Bifidobacterium animalis subsp. lactis XLTG11 in reducing the incidence of eczema and respiratory infections during early childhood, and to explore its associations with gut microbial ecology and immune function.

METHODS: In this randomized, double-blind, placebo-controlled trial, 352 healthy infants and young children (aged <3 years) were randomly allocated to receive XLTG11 (1 × 1010 CFU/day) or placebo for 180 days. Primary outcome was eczema incidence; secondary outcomes included respiratory and gastrointestinal symptoms, growth parameters, gut microbiota composition (16S rRNA gene sequencing), and gut immune biomarkers.

RESULTS: Children receiving XLTG11 showed significantly lower incidence of eczema (p = 0.017) and erythema (p = 0.028), and a lower incidence of physician-confirmed pneumonia (RR = 0.40, 95% CI 0.17-0.94; p = 0.030) compared with placebo. Probiotic supplementation improved stool consistency (p = 0.018) without affecting growth. 16S rRNA gene sequencing revealed enrichment of Faecalibacterium, Akkermansia, and other short-chain fatty acid-producing taxa, alongside suppression of Helicobacter and Citrobacter. Predictive functional profiling suggested enrichment of pathways related to energy metabolism, vitamin biosynthesis, and antimicrobial peptide (DEFB2, LL-37) production, alongside preservation of secretory IgA.

CONCLUSIONS: Daily B. lactis XLTG11 supplementation safely reduces eczema and respiratory infection risk in early childhood by remodeling the gut microbiome and reinforcing mucosal immunity. These findings support its use as a preventive strategy for allergy and infection via gut-immune modulation.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT07490587).

ETHICS APPROVAL: Shanghai Sixth People's Hospital Human Ethics Committee (No. 2023-142).},
}

@article {pmid42308849,
year = {2026},
author = {Noman, MA and Adyel, TM and Callahan, DL and He, D and Macreadie, PI and Trevathan-Tackett, SM},
title = {Microplastics and co-occurring nitrogen synergistically accelerate blue carbon loss.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142641},
doi = {10.1016/j.jhazmat.2026.142641},
pmid = {42308849},
issn = {1873-3336},
abstract = {Blue carbon ecosystems (BCEs)-including seagrass meadows, mangroves, and salt marshes-store vast amounts of organic carbon, yet their carbon sink function is increasingly threatened by hazardous microplastics and co-occurring nitrogen pollution. Here, we used a controlled microcosm experiment and multi-omics analysis (16S rRNA amplicon sequencing, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, and Ultra-Performance Liquid Chromatography-Mass Spectrometry) to investigate how two common microplastics-polyethylene terephthalate (PET) and polylactic acid (PLA)-interact with nitrogen fertiliser (N-dominated fertiliser with co-delivered nutrients) to influence seagrass soil biogeochemistry. We showed that PLA combined with N-fertiliser increased CO2 emissions from seagrass soil by 106% relative to nitrogen alone and by 195% compared to controls (p < 0.01), while PET addition had negligible effects. PLA degradation released carboxylic acid and derivatives, supporting putative sulphate-reducing and fermentative bacteria, and increasing the formation of organic-oxygen compounds (e.g., disaccharides, o-glycosyl compounds). N-fertiliser addition further enriched putative organic matter-degrading microbial taxa, particularly Clostridia and Bacteroidia, and elevated microbial metabolic potential across pathways. Combined PLA and nitrogen treatments resulted in the lowest (-37% vs control) residual dissolved organic carbon concentrations, indicating accelerated carbon loss. These findings suggest that microplastics, especially PLA biopolymer, and nitrogen act as hazardous co-contaminants that enhance microbial mineralisation of soil organic matter, potentially weakening blue carbon storage. Plastic waste and fertiliser inputs should therefore be considered together in future risk assessments of coastal carbon stocks and in the development of strategies to safeguard BCEs.},
}

@article {pmid42309236,
year = {2026},
author = {Ali, S and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D},
title = {Following the mobile genome: plasmids as a missing layer in surveillance of carbapenemase-producing Enterobacterales.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.06.010},
pmid = {42309236},
issn = {1469-0691},
}

@article {pmid42311765,
year = {2026},
author = {Xu, H and Hu, J},
title = {Traditional Chinese medicine-based modulation of gut microbiota in coronary heart disease: probiotic synergy and translational perspectives.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1857702},
pmid = {42311765},
issn = {2297-055X},
abstract = {Gut microbiota has emerged as an important contributor to the pathogenesis and progression of coronary heart disease (CHD). Increasing evidence indicates that gut dysbiosis promotes atherosclerosis and cardiovascular dysfunction through microbiota-derived metabolites, including trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and bile acid-related pathways, as well as through effects on inflammation, cholesterol metabolism, endothelial injury, and intestinal barrier integrity. In recent years, phytomedicine, particularly Traditional Chinese Medicine (TCM), has attracted growing attention as a microbiota-modulating strategy because of its multi-component, multi-target, and system-level regulatory properties. In parallel, probiotics may provide targeted supplementation of beneficial strains and functional pathways. This review summarizes the major microbiota-mediated mechanisms involved in CHD and examines how phytomedicine regulates gut microbial composition, microbial metabolism, host inflammatory responses, and barrier function. We further discuss the complementary potential of phytomedicine and probiotics, highlighting their possible synergistic roles in restoring microbial ecology and improving cardiometabolic homeostasis. In addition, we critically evaluate current limitations in the field, including insufficient standardization of phytomedicine-probiotic combinations, heterogeneity of host-microbiota responses, limited clinical evidence, and unresolved long-term safety issues. Overall, this review provides an ethnopharmacology-oriented and mechanistically integrated perspective on microbiota-targeted interventions in CHD, and suggests that phytomedicine-based modulation, alone or in combination with probiotics, may represent a promising direction for future precision prevention and management of CHD.},
}

@article {pmid42297811,
year = {2026},
author = {Senoo, DKJ and Acton, L and Hall, LJ},
title = {From diet to function: using synthetic microbial communities to map gut microbial interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01012-9},
pmid = {42297811},
issn = {2055-5008},
support = {220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/Y011619/1; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Diet shapes gut microbial ecology and function, but causal mechanisms are hard to resolve in native communities. Synthetic microbial communities provide defined systems to test how dietary substrates alter community structure, metabolism, and host responses. This review summarises SynCom design, experimental platforms, and dietary applications, highlights multi-omics and modelling approaches, proposes reporting standards, and considers challenges and future directions, including multi-kingdom and AI-enabled function-first SynComs.},
}

@article {pmid42300034,
year = {2026},
author = {Dhakal, D and Liang, Z and Zhang, P and Barr, JJ and Subedi, D and Dhital, S},
title = {Microbiota dynamics and their impact on the metabolite in lupin oat yoghurt analogues.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo05594f},
pmid = {42300034},
issn = {2042-650X},
abstract = {The growing demand for nutritious, flavour-rich plant-based yoghurt analogues calls for innovative fermentation strategies. This study examined the impact of three probiotic combinations-Y1 (Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus and Lactobacillus rhamnosus), Y2 (Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus and Lactobacillus paracasei) and Y3 (Lactobacillus plantarum and Bifidobacterium sps.)- on microbial dynamics and metabolite formation in lupin-oat yoghurt analogues, using unfermented milk analogues as a control. Samples were assessed during fermentation and throughout 28 days of refrigerated storage (4 °C) using microbial enumeration, 16S rRNA sequencing, acidification profiling, and mass spectroscopy-based metabolomics. Fermentation increased volatile compounds, from 23 in the control to 28 (Y1), 41 (Y2) and 54 (Y3). Probiotic combination Y3 exhibited the most complex and stable aroma profile, enriched in pleasant volatiles such as butanoic acid, phenylacetaldehyde, and butyl esters which effectively masked off-flavours like hexanal and heptanal. Microbiota analysis revealed stable formulation-specific communities, with- Streptococcus dominating in yoghurt analogues Y1 and Y2, and Bifidobacterium prevailing in yoghurt analogues Y3. KEGG-based functional prediction linked these transformations to microbial enzymatic activities within metabolic pathways. Notably, Bifidobacterium dominance in Y3 facilitated enhanced ester biosynthesis and conversion of aldehydes to acids, highlighting the "bifid shunt" as a key contributor to flavour enhancement. This integrated multi-omics approach highlights the critical role of targeted probiotic selection in modulating fermentation biochemistry, microbial ecology, and sensory attributes in plant-based lupin-oat yoghurt analogues. Notably, Bifidobacterium-driven fermentation in Y3 offers a promising strategy for improving the flavour profile and consumer acceptance of lupin-oat yoghurt analogues.},
}

@article {pmid42301310,
year = {2026},
author = {Cosoveanu, A and González-Carracedo, MA and Sopena Lasala, J and Pérez Pérez, JA and Cabrera, R},
title = {Shaping Fungal Communities in Cenchrus setaceus: Host Condition and Habitat Filtering.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02805-3},
pmid = {42301310},
issn = {1432-184X},
abstract = {We investigated the leaf-associated fungal communities of Cenchrus setaceus across a host condition gradient (high- vs. low-condition plants) and environmental zones (coast vs. hill; trade-wind exposure) on Tenerife (TF) and La Palma (LP). We hypothesized that community assembly reflects both host-driven deterministic filtering and abiotic promotion of richness in favourable environments via two mechanisms: (i) high-condition plants promote stable, guild-structured communities; (ii) humid, topographically buffered zones enhance fungal richness, especially for endophytes and saprotrophs. Nanopore sequencing and functional guild annotation revealed island- and zone-specific fungal assemblages. In TF, low-condition plants were associated with genera linked to stressed or exposed conditions whereas high-condition plants, especially in humid northern hills, supported more recurrent yeast-like and niche-associated taxa. In LP, high-condition plants in eastern hill zones were associated with distinct taxa, while drier western coastal low-condition plants were enriched in stress-related fungi. Fungal genera richness (Hill0) was consistently higher in low-condition plants (TF: 146 vs. 95; LP: 94 vs. 76; p < 0.05), while Shannon diversity diverged: greater in high-condition plants on LP (3.29 vs. 2.98), but lower on TF (3.10 vs. 3.28; p < 0.05). Community structure was shaped primarily by host condition in TF (PERMANOVA R[2] = 8.6%, p < 0.05), and by zone in LP (R[2] = 15.0%, p < 0.05). On TF, low-condition plants hosted significantly higher richness of saprotrophic, endophytic and plant-pathogenic genera (all p ≤ 0.001), whereas in LP zone × condition effects shaped guild richness patterns, with saprotroph richness increasing 2.66-fold in high condition plants from eastern hills relative to the eastern coast. Overall, high-condition plants supported less diverse but compositionally more stable fungal communities, while favourable environments enhanced guild richness independently of host condition.},
}

@article {pmid42302619,
year = {2026},
author = {Kim, M and Al Hakeem, WG and Rothrock, MJ},
title = {Random forest modeling to identify key farm-to-fork factors influencing Campylobacter ecology in pastured poultry systems.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107274},
doi = {10.1016/j.psj.2026.107274},
pmid = {42302619},
issn = {1525-3171},
abstract = {Campylobacter in poultry flocks poses significant food safety challenges, yet the drivers of its prevalence and load across the farm-to-fork continuum are not well understood. This study applied two-part random forest models to identify key factors influencing Campylobacter prevalence and load in pastured poultry systems. Data were collected from 11 farms in the southeastern United States between 2014 and 2017. The study included 1,942 broiler samples across five types: pasture soil, feces, ceca, whole carcass rinse after processing (WCR-P), and after storage (WCR-F). Two predictor sets were evaluated by 5-fold stratified cross-validation: farming practices with soil physicochemical properties and meteorological variables. Partial dependence plots were used to assess directional trends for key predictors. Models showed strong overall classification and regression performance across most sample types. Subsequent analyses focused on feces, ceca, and WCR-F to focus on the broiler specific farm-to-fork continuum. Classification models consistently identified farm as the dominant predictor of Campylobacter prevalence. This suggests the cumulative effect of site-specific management and processing practices unique to each farm. Flock age was the second most important predictor for fecal samples. Prevalence increased as birds matured. Day of year was another leading predictor for cecal and WCR-F samples, predicting the highest prevalence during summer. Regression models identified flock age as the top predictor of Campylobacter load in feces and the second most important predictor in ceca. Campylobacter load declined with bird age in feces whereas cecal loads continued to accumulate as an internal reservoir. Meteorological models showed that sustained high wind speed reduced fecal Campylobacter prevalence. Lower rolling-average humidity and higher rainfall on the sampling day were each associated with lower fecal loads. These findings indicate that Campylobacter prevalence and load are affected by distinct drivers at each production stage. Targeted interventions such as optimizing flock management schedules and implementing farm-specific biosecurity measures could improve Campylobacter control throughout the pastured poultry production continuum.},
}

@article {pmid42294705,
year = {2026},
author = {Wang, J and Jiang, P and Yan, J and Shen, H and Wu, L and Wei, F and Lin, X and Xu, L},
title = {Spatial ecology meets quality control: a GIS-integrated strategy for visualizing and managing microbial contamination in sterile pharmaceutical cleanrooms.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0026826},
doi = {10.1128/spectrum.00268-26},
pmid = {42294705},
issn = {2165-0497},
abstract = {To enhance contamination source identification in sterile drug manufacturing, this study innovatively developed an integrated strategy combining geographic information system (GIS) spatial visualization with microbial contamination control. Between 2022 and 2025, researchers collected 1,117 environmental microbial isolates from sterile preparation workshops, analyzing their population structure, distribution patterns, and potential risks through 16S rRNA/ITS sequencing. GIS technology was employed to associate strain data with workshop spatial information, thereby providing a visual representation of microbial quantity, species composition, and distribution patterns. Results showed that Staphylococcus and Micrococcus dominated in clean areas, with microbial diversity highest in Controlled Not Classified (CNC) environments and lowest in A-grade areas. The microbial community structure in A-grade areas significantly differed from that in CNC/C/B-grade areas, while CNC/C/B-grade areas exhibited relative similarity. In the case study, the environmental microbial distribution maps clearly demonstrated regional variations and aggregation patterns. By identifying critical control areas and transmission pathways through contamination risk analysis, targeted interventions were designed and implemented, reducing the microbial contamination rate in target C-grade areas from 4.3% to 2.2%, thereby validating the strategy's effectiveness. This study targets the deficiency of "spatial visualization analysis" in clean area environmental monitoring. The proposed comprehensive strategy effectively fills the methodology gap in spatial analysis and contamination control for current clean area microbial monitoring. It provides a feasible framework for transforming environmental monitoring in the pharmaceutical industry from a passive surveillance system to an active early-warning system, assisting in enhancing the sterility assurance level of pharmaceutical production.IMPORTANCEAnalyzing the spatial distribution characteristics of microorganisms is crucial for developing effective pollution control strategies. However, existing environmental monitoring methods have limitations in revealing these spatial distribution patterns. This paper proposes an innovative strategy that integrates geographic information system (GIS) spatial analysis with microbial ecology research to enhance the accuracy and scientific rigor of pollution source identification and risk control. This approach enables the visualization of environmental microbial quantities, types, and spatial distribution, providing a quantitative tool for analyzing microbial contamination patterns and tracing transmission pathways. The developed "GIS-integrated strategy" methodology promotes a paradigm shift from merely confirming "microbial presence" to systematically analyzing the multidimensional relationships among "microorganism-environment-control." This study not only provides a scientific basis for formulating pollution control protocols in the pharmaceutical industry, contributing to improved sterility assurance, but also serves as a practical example of interdisciplinary integration between microbial ecology and spatial information science, demonstrating significant theoretical value and industry application prospects.},
}

@article {pmid42294914,
year = {2026},
author = {Miller, MGA and Bergmann, GE and Alcalá Briseño, RI and Lan, Y-H and Søndreli, KL and Busby, PE and LeBoldus, JM},
title = {The interaction between Septoria stem canker and the mycobiome of Populus trichocarpa stems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0005526},
doi = {10.1128/msystems.00055-26},
pmid = {42294914},
issn = {2379-5077},
abstract = {UNLABELLED: Sphaerulina musiva, a fungal pathogen causing leaf spot and canker disease of poplar trees (Populus spp.), was recently introduced to the Pacific Northwest, where it threatens commercially valuable plantations and native riparian ecosystems. Vascular tissue was collected from the stems of 410 symptomatic and asymptomatic trees in an S. musiva-infested Populus trichocarpa plantation. Resident fungal endophyte communities were characterized with ITS amplicon sequencing. Canker expression and S. musiva presence corresponded with reduced fungal diversity across multiple indices. Fungal endophyte communities of symptomatic tissues were frequently dominated by S. musiva and thus compositionally distinct from those of asymptomatic tissues. Asymptomatic-tissue communities from healthy and diseased stems did not differ in composition or diversity, indicating disease-associated low-diversity mycobiome states are local to the cankered site. The relative abundance of S. musiva was positively correlated with stem cankering. S. musiva was negatively correlated with key non-pathogenic fungal endophytes, which were themselves strongly inter-correlated. Our results illustrate S. musiva's ability to exploit the vascular microhabitat of susceptible Populus trichocarpa stems and dominate resident fungal assemblies at the site of infection.

IMPORTANCE: Plant-associated microbial communities can both mediate and be modified by pathogen infection. Thus, understanding disease outcomes of complex plant pathosystems requires characterization of pathogen-phytobiome interactions. Efforts to characterize these interactions have yielded microecological insights with applied relevance for disease management in herbaceous leaf- and root-associated pathosystems. However, pathogen-phytobiome interactions in the vascular tissues of hardwood stems remain largely unexplored. Our findings illuminate the ecological organization of the Populus trichocarpa stem mycobiome under S. musiva disease pressure and advance understanding of microfungal community dynamics in the Septoria stem canker pathosystem. Additionally, we identify potentially interactive fungal taxa that may disproportionately shape mycobiome structure and disease dynamics in Populus trichocarpa stems.},
}

@article {pmid42294941,
year = {2026},
author = {Friebel, L and Knepper, J-P and Becker, NS and Abbaszade, G and Stückrath, K and Soltwisch, J and Müller, S and Dreisewerd, K and Mascher, T},
title = {Cannibalism shapes biofilm structure and composition in Bacillus subtilis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0052526},
doi = {10.1128/mbio.00525-26},
pmid = {42294941},
issn = {2150-7511},
abstract = {UNLABELLED: In Bacillus subtilis colony biofilms, phenotypic diversification confers tissue-like properties and enhanced competitive fitness within a structural framework that allows both colony expansion and long-term survival via endospore formation. Cannibalism is a sporulation delay strategy, in which one subpopulation produces the sporulation delay protein SDP, the sporulation killing factor SKF, and the epipeptide EPE. These toxins are thought to lyse susceptible nonproducers, thereby releasing nutrients to prevent premature sporulation. However, the molecular mechanisms orchestrating this bacterial type of programmed cell death during biofilm development are poorly understood. Here, we comprehensively characterized mutants defective in either toxin production or the corresponding autoimmunity by a multiscale approach, combining luminescence reporters, colony biopsy, multi-parameter flow cytometry, and MALDI-mass spectrometry imaging to resolve cannibalism function and distribution. The toxins are produced in distinct, only partially overlapping areas of the colony, and are interdependent in their spatial distribution. Both EPE and SDP, but not SKF, are crucial for delaying sporulation. Loss of EPE or SDP autoimmunity resulted in severe morphological changes and stress-induced occurrence of suppressor mutants. The absence of all three toxins led to small, hyper-sporulating colonies with excessive wrinkle formation, indicating that cannibalism is essential for maintaining biofilm structure and lateral expansion. Our results provide the first evidence for the complex interactions between the three cannibalism toxins that shape biofilm architecture through bacterial programmed cell death. Localized toxin production and its spatial distribution affect the spatiotemporal organization, morphology, and subpopulation dynamics within B. subtilis biofilms.

IMPORTANCE: Programmed cell death (PCD) is a ubiquitous and crucial mechanism to structure eukaryotic multicellular tissues. PCD-like processes have also been described in bacteria, but their contribution to multicellular development is poorly understood. Cannibalism in Bacillus subtilis has been described as a sporulation delay strategy, in which one subpopulation produces antimicrobial peptides that kill susceptible nonproducing siblings. Their lysis is thought to release nutrients that delay the sporulation in the producing subpopulation. This study comprehensively analyses the role of the three cannibalism toxins in shaping colony biofilms. By combining MALDI-mass spectrometry imaging, colony biopsy, flow cytometry, and luminescence reporters, we demonstrate that cannibalism toxins are crucial for biofilm structure. They show a discrete and interdependent localization within the colonies. While cannibalism inhibits sporulation and causes severe envelope stress within biofilms, our data challenge the established role of cannibalism-dependent killing as the mechanism behind this sporulation delay.},
}

@article {pmid42295802,
year = {2026},
author = {Zhang, S and Jiang, Q and Ma, J and Zou, J and Wang, F and Lv, F and Huang, Y and Wang, Y and Xu, Z},
title = {A Single-Cell Transcriptomic Atlas of the Ovine Rumen Microbiome Characterizes Lineage-Specific Metabolic Shifts Associated with Host Heat Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76152},
doi = {10.1002/advs.76152},
pmid = {42295802},
issn = {2198-3844},
support = {8257030475//National Natural Science Foundation of China/ ; 2025M770277//China Postdoctoral Science Foundation/ ; 2025YFF0512800//National Key R&D Program of China/ ; 2024C03005//Pioneer R&D Programs of Zhejiang/ ; 2024SSYS0022//Key R&D Program of Zhejiang/ ; nycytxgxcxtd-2021-09//Guangxi Innovation Team Construction Project of National Modern Agricultural Industry Technology System/ ; AB2506910008//Science and Technology Major Project of Guangxi/ ; },
abstract = {The adaptation of complex, host-associated microbiomes to environmental perturbations is a critical determinant of ecosystem stability and resilience to climate change, as exemplified in ruminants. While single-microbe RNA sequencing advances community interrogation, complex microbial cell walls severely constrain unbiased single-cell transcriptomic profiling in the rumen. In this study, we developed an optimized 25 min time-resolved enzymatic lysis strategy using smRandom-seq to map the sheep rumen microbiome at single-cell resolution. By profiling 60 748 cells across 21 samples, we captured previously intractable lineages, resolving the transcriptional states of 213 genera and 662 species, achieving a physiologically relevant 0.303% recovery of methanogenic archaea. Unsupervised clustering partitioned the ecosystem into seven cross-species functional clusters, uncovering a spatial coupling between microbial lifestyle and metabolic specialization. Applying this framework to a model of host thermal adaptation demonstrated that host resilience was associated with rapid transcriptional activation of key energy-metabolism clusters. Notably, a lineage-specific metabolic shift toward a glycolytic phenotype in Anaerovibrio lipolyticus contributes to a compensatory "nutritional sparing" effect associated with host resilience. This dataset provides a foundational resource for rumen microbial ecology and establishes a technical framework for dissecting phenotypic plasticity within complex microbiomes.},
}

@article {pmid41831128,
year = {2026},
author = {Zhao, Y and Bi, J and Zhao, Y and Wang, C and Li, Y},
title = {Characterization of capillary water absorption in microbially modified strongly weathered phyllite under the effect of thermal fatigue.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41831128},
issn = {1573-0972},
support = {52164001, 52364004, 52464005//National Natural Science Foundation of China/ ; No. QianKeHeJiChu-ZK[2024]YiBan011//Guizhou Provincial Basic Research Program (Natural Science)/ ; [2023]40//the Basic Research Project of Guizhou University/ ; No. GCC[2022]005-1//the Guizhou Provincial Science and Technology Foundation/ ; No. 202412//the Special Research Fund of Guizhou University/ ; No. QianJiaoJi[2024]18//The Youth Talent Growth Project of Guizhou Provincial Department of Education/ ; },
abstract = {Phyllite, when used as a cement subgrade, is susceptible to thermal fatigue degradation due to temperature fluctuations resulting from prolonged exposure to natural environments. However, limited research exists on the anti-seepage properties of microbial-modified phyllite. This study investigates the capillary water migration characteristics of two types of strongly weathered modified phyllite subjected to thermal fatigue cycles, focusing on their anti-seepage performance and structural integrity for use as roadbed fillers or in infrastructure applications. Through spontaneous imbibition and thermal fatigue experiments, the effects of microbial modification on phyllite’s permeability were explored. The results indicated that microbial modification reduced phyllite’s porosity, improved its internal pore structure, and enhanced its anti-seepage performance. Compared to unmodified phyllite, the modified materials exhibited greater resistance to capillary water absorption. This study highlights the potential of microbial treatment as a sustainable method to enhance the properties of weathered phyllite. By combining knowledge of phyllite and microbial ecology, we aim to foster a deeper understanding of the relationship between these fields and better assess how microorganisms affect phyllite’s permeability.},
}

@article {pmid41843084,
year = {2026},
author = {Madhusoodhanan, R and Raman, K and Akbar, R and Pambayan Ulagan, M and Mariadoss Arokia, VA and P, T},
title = {Modulating gut microbiota in type 2 diabetes mellitus: advances and challenges in precision medicine.},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
pmid = {41843084},
issn = {1432-5233},
abstract = {Type 2 Diabetes Mellitus (T2DM) is increasingly recognized as increasingly recognized as not only a metabolic disorder, but also a disease of microbiome–host dysregulation. While the role of the gut microbiota in T2DM has been extensively studied, the emerging convergence of precision medicine and microbiome modulation has not been systematically integrated into prior reviews. This work provides a critical synthesis that unites the classical concepts of dysbiosis with cutting-edge insights into microbial metabolites, strain-specific effects, and host–microbe–drug interactions, including the influence of metformin on microbial ecology and the therapeutic potential of Akkermansia muciniphila. We further discuss the underexplored domains, such as the gut virome, microbial gene editing, and short-chain fatty acid subtype-targeted interventions, which may transform T2DM management. We propose a novel conceptual framework for microbiome-guided, individualized T2DM care by framing gut microbiota as a dynamic, patient-specific therapeutic target. The review concludes with a roadmap for translating microbiota signatures into predictive biomarkers and tailored interventions, emphasizing standardized methodologies, multi-omics integration, and cross-disciplinary clinical trials. This perspective shifts the field from descriptive correlations to actionable precision-guided microbiome therapeutics in T2DM. Notably, this review extends beyond existing summaries by integrating emerging concepts, including gut virome contributions, microbial metabolite engineering, and host–microbe–drug interaction frameworks, to position the gut microbiota as a precision-modifiable therapeutic axis. This synthesis not only reviews established associations but also identifies underexplored therapeutic frontiers, including the gut virome, mycobiome, and microbial genome editing, which could reshape precision T2DM management.},
}

@article {pmid42020676,
year = {2026},
author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR},
title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020676},
issn = {1867-1314},
abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.},
}

@article {pmid42050727,
year = {2026},
author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S},
title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00577-2},
pmid = {42050727},
issn = {2524-4671},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces. RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected. CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.},
}

@article {pmid42182427,
year = {2026},
author = {Lu, C and Tashev, SA and Pessoa, P and Kruithoff, R and Shepherd, DP and Presse, S},
title = {Stochastic colonization and host-to-host transmission shape gut bacterial variability.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42182427},
issn = {2692-8205},
abstract = {Understanding the kinetic processes that govern bacterial population dynamics within hosts is critical in developing effective strategies to control microbiota. However, inferring population dynamics is challenging due to large host-to-host bacterial population variability stemming from stochastic colonization events, as well as the inability to continuously monitor the bacterial population without disturbing the host. Using C. elegans fed E. coli under different diets, we show that early colonization acts as a stochastic bottleneck that drives substantial divergence in host-level bacterial loads, and that the spreading of bacteria from colonized worms to sterile ones regulates this variability by altering effective colonization pressure. These conclusions are reinforced using a simulation-based inference framework that quantifies stochastic within-host population dynamics from discrete snapshot data, enabling inference of effective colonization and growth rates across heterogeneous hosts with variable carrying capacities. Applying this framework, we further demonstrate that the bacterial predator B. bacteriovorus reduces average gut bacterial loads by two orders of magnitude, primarily by suppressing environmental recolonization and subsequent host-to-host transmission rather than eliminating established intra-host populations. Together, these results reveal that host-associated microbial population dynamics are strongly impacted by environmental colonization processes that modulate stochastic entry events.},
}

@article {pmid42278620,
year = {2026},
author = {Lu, Z and Chen, G and Chang, M and Wang, N and Xia, T and Zhang, Y and Xu, G and Zhao, Q and Shen, P and Zhou, W and Ni, Z and Gao, Y},
title = {Effects of High-Altitude Environments on Gut Microbiota and Their Mechanisms in Immune Regulation and High-Altitude Adaptation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278620},
issn = {1422-0067},
support = {2025YFC3507500//National Natural Science Foundation of China/ ; 2025YFC3507502//National Natural Science Foundation of China/ ; zyyzdxk-2023311//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; },
mesh = {Humans ; *Altitude ; Animals ; *Gastrointestinal Microbiome/immunology ; *Acclimatization ; *Adaptation, Physiological ; Intestinal Barrier Function ; Dysbiosis ; Homeostasis ; },
abstract = {High-altitude environments, characterized by hypoxia, low temperature, and intense ultraviolet radiation, profoundly disrupt host intestinal homeostasis and reshape the gut microbiota, thereby influencing immune regulation and acclimatization. This review systematically summarizes the dynamic compositional and functional changes in the gut microbiota in high-altitude natives, immigrant populations, short-term visitors, and relevant animal models. Current evidence indicates that long-term high-altitude adaptation is associated with directional microbial remodeling, including the enrichment of anaerobic and short-chain fatty acid (SCFA)-associated taxa, which may support energy metabolism and immune homeostasis. In contrast, acute high-altitude exposure more readily induces dysbiosis, impairs intestinal barrier integrity, and promotes the translocation of endotoxins and bioactive metabolites. Mechanistically, the gut microbiota and its metabolites participate in high-altitude adaptation and high-altitude-related disease pathogenesis by modulating barrier function, inflammatory responses, oxidative stress, and immune signaling, and by mediating interorgan communication-characterized by metabolite-driven systemic inflammation or tolerance-through the gut-lung, gut-heart, gut-brain, gut-kidney, and gut-testis axes. SCFAs, bile acids, amino acid-derived metabolites, and succinic acid may control immune homeostasis and inflammatory responses through pathways including TLR4/NF-κB and NLRP3. Although the causal relationships, core microbial effectors, and population-specific heterogeneity remain incompletely defined, microbiota-targeted interventions, including probiotics, prebiotics, and fecal microbiota transplantation, have shown promise for promoting acclimatization and preventing high-altitude-related disorders. Overall, this review provides an integrated framework linking environmental stress, gut microbial ecology, and host immune-metabolic adaptation at high altitude, and highlights future directions for mechanistic and translational research in high-altitude medicine.},
}

Humans
*Altitude
Animals
*Gastrointestinal Microbiome/immunology
*Acclimatization
*Adaptation, Physiological
Intestinal Barrier Function
Dysbiosis
Homeostasis

@article {pmid42282557,
year = {2026},
author = {Adelfio, M and Bonzanni, M and Callen, GE and Diaz, AR and Paster, BJ and He, X and Hasturk, H and Ghezzi, CE},
title = {Profiling Gingival Inflammation in a 3D Oral Tissue Model Reveals Early Features of Disease Progression.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.05.730462},
pmid = {42282557},
issn = {2692-8205},
abstract = {Gingival health depends on a balanced interplay among the gingival epithelium, immune system, and oral microbiome. Disruption of this equilibrium through sustained biofilm accumulation and host inflammatory responses leads to gingivitis, a highly prevalent yet reversible condition which if left untreated could progress into more severe and irreversible condition called periodontitis. The early onset of gingivitis remains poorly defined due to subtle clinical presentation and pronounced interindividual variability. Current diagnostic approaches rely largely on clinical assessment and endpoint biomarkers, limiting insight into the early host-microbiome interactions that drive disease initiation. Here, we employ a previously validated, physiologically relevant oral tissue model (OTM) to longitudinally investigate epithelial-microbiome interactions following inoculation with patient-derived dysbiotic microbiomes from early-stage gingivitis. The OTM maintained host tissue integrity and microbial viability over a seven-day period, preserving epithelial barrier function, dynamic inflammatory responses, and disease-associated microbial signatures. Notably, we establish, for the first time in an in vitro platform, clinical calibration against gingival crevicular fluid (GCF), demonstrating that OTM responses recapitulate inoculum-dependent inflammatory signatures, increased microbial dissimilarity under dysbiotic conditions, and coordinated host-microbiome metabolic interactions. While pro-inflammatory responses were most pronounced at early time points, subsequent modulation toward anti-inflammatory states highlights the temporal complexity of host responses and suggests that longer culture durations may further resolve disease trajectories. Collectively, these findings validate the OTM as a robust, physiologically relevant platform that captures key features of periodontal health and inflammation. By integrating host viability, microbial ecology, and clinical benchmarking, this system enables mechanistic interrogation of early disease-driving processes and provides a translational framework for advancing predictive diagnostics and preventive therapeutic strategies in periodontal disease.},
}

@article {pmid42283811,
year = {2026},
author = {Costanzo, M and Di Gregorio, L and Tabacchioni, S and Bevivino, A and Visca, A},
title = {Mobile Genetic Elements as Key Drivers of Bacterial Evolution and Adaptation in Agroecosystems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02803-5},
pmid = {42283811},
issn = {1432-184X},
abstract = {Mobile genetic elements (MGEs), including plasmids, transposons, integrative and conjugative elements, and phage-derived sequences, are central drivers of bacterial evolution in agroecosystems. By enabling horizontal gene transfer, MGEs allow soil- and plant-associated bacteria to rapidly acquire complex functional traits, facilitating adaptation to fluctuating environmental conditions and different agricultural management practices. In agricultural soils, MGEs underpin key microbial functions such as nutrient acquisition and cycling, stress tolerance, rhizosphere competence, and interactions with plant hosts, thereby influencing soil fertility and crop performance. Selective pressures in agroecosystems extend beyond antimicrobial exposure and include fertilizers, pesticides, plant defense compounds, recurrent biotic and abiotic stress, as well as high-yielding crop varieties. These pressures generate co-selection dynamics that shape mobilome composition and activity, linking traits such as resistance, pathogenicity, and biocontrol to broader ecological functions relevant to plant health. Rather than acting as exceptional genetic entities, MGEs form a dynamic and environmentally responsive genetic network that enables rapid ecological tuning while preserving core genome stability. Comparative genomics has revealed that major lifestyle transitions in agroecosystem-associated bacteria, from free-living to commensal, mutualistic, or pathogenic states, are frequently mediated by the gain and loss of genomic islands and other MGEs. This review synthesizes the latest research on the ecological functions and evolutionary dynamics of MGEs in agroecosystems and explores how mobilome-informed approaches can support microbial-based strategies for sustainable agriculture.},
}

@article {pmid42283827,
year = {2026},
author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K},
title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02807-1},
pmid = {42283827},
issn = {1432-184X},
support = {No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; },
abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.},
}

@article {pmid42287050,
year = {2026},
author = {Gao, J and Li, W and Li, X and Tan, Y and Li, Y and Duan, L and Wu, T and Chen, D and Hu, Y and Wang, M},
title = {[Association between wearable-derived physical activity patterns and gut microbiota in older adults].},
journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences},
volume = {58},
number = {3},
pages = {551-559},
pmid = {42287050},
issn = {1671-167X},
mesh = {Humans ; Aged ; *Wearable Electronic Devices ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Exercise/physiology ; Male ; Female ; Feces/microbiology ; China ; },
abstract = {OBJECTIVE: To identify real-world physical activity patterns in older adults using objective measurements from wearable devices, and to analyze the associations between these patterns and gut microbiota composition.

METHODS: Based on data collected from a real-world health management project, a total of 743 participants from Eastern, Central, and Northern China were enrolled between January 2018 and June 2025. A 180-day objective physical activity dataset prior to fecal sampling was collected via smart wearable devices to extract features including mean daily steps, coefficient of variation of steps, and the proportion of active days. Fecal samples underwent 16S ribosomal RNA (rRNA) gene (V3-V4 region) amplicon sequencing to obtain genus-level relative abundance matrices. Covariates, including demographics, lifestyle, and chronic disease history, were collected via questionnaires and physical examinations. The discriminative dimensionality reduction via learning a tree (DDRTree) algorithm combined with K-means clustering was applied to identify physical activity phenotypes. Alpha diversity was evaluated using the Shannon index (Kruskal-Wallis test), and beta diversity was assessed using covariate-adjusted permutational multivariate analysis of variance (PERMANOVA) based on Bray-Curtis distance. Multivariable linear regression with false discovery rate (FDR) correction was used to screen differential taxa. A microbial risk score (MRS) was constructed based on taxa with a raw P < 0.05, defined as the difference between the standardized abundance of beneficial and harmful taxa. Co-occurrence networks were constructed to evaluate micro-ecological topological structures.

RESULTS: The cohort comprised 381 (51.3%) individuals aged 60-74 years and 362 (48. 7%) aged ≥75 years. Compared with the 60-74 group, the ≥75 group had higher prevalences of hypertension (45.9% vs. 36.7%, P=0.045) and heart disease (34.0% vs. 25.2%, P=0.032), higher systolic blood pressure (median 130 mmHg vs. 120 mmHg, P < 0.001), and fewer mean daily steps (median 6 200 steps vs. 7 000 steps, P < 0.001). Clustering identified three activity patterns: active group (n=143, 19.2%; high steps, low variation, high adherence), moderate group (n=429, 57.7%), and irregular group (n=171, 23.0%; low steps, high variation, low adherence). The active group exhibited the lowest prevalences of hypertension (35.0%) and heart disease (21.7%), and the lowest systolic blood pressure (mean 124.4 mmHg), whereas the irregular group showed the highest values (51.5%, 40.4%, and 127.6 mmHg, respectively). Alpha diversity showed no significant differences among the groups. After adjusting for covariates, physical activity patterns showed no statistically significant effect on beta diversity (R[2]=0.003 7, P=0.115). Compared with the irregular group, two genera in the active group showed significant differences (P < 0.05). Specifically, the relative abundance of Roseburia in the active group was significantly lower than that in the irregular group (P < 0.05), and the relative abundance of Butyricimonas was also significantly lower than that in the moderate group (P < 0.01). However, these differences did not remain statistically significant after FDR correction. The MRS exhibited a significant gradient distribution across the groups, with the active group scoring the highest (P < 0.001). Co-occurrence network analysis revealed that the active group had the highest network density and proportion of positive correlations (84.5%), whereas the irregular group had the lowest (60.3%).

CONCLUSION: Physical activity patterns identified from wearable device data are associated with gut microbiota composition and ecological network characteristics in older adults. Active and regular physical activity patterns indicate a higher MRS and more stable microbial co-occurrence networks, suggesting potential associations between activity regularity and gut microbial ecology, though causal inference requires longitudinal confirmation.},
}

Humans
Aged
*Wearable Electronic Devices
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Exercise/physiology
Male
Female
Feces/microbiology
China

@article {pmid42287443,
year = {2026},
author = {Pires, D and Castañeda, F and Galvez, L and Balendres, MA},
title = {Soil as a Battlefield and a Reservoir: Linking Soil Components to the Epidemiology of Soilborne Plant Diseases.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02810-6},
pmid = {42287443},
issn = {1432-184X},
abstract = {This paper focuses on how microbial diversity, soil organic matter, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. Microbial diversity, soil organic matter, and soil structure are soil components that can reshape plant-pathogen-soil interactions by altering nutrient dynamics and the composition of the soil microbiome. When beneficial microorganisms are enriched in soil ecosystems, suppression of soilborne pathogens may be enhanced, thereby decreasing disease incidence and severity. However, microbial diversity, soil organic matter, and soil structure may also promote pathogen growth or facilitate cooperative microbial interactions that improve pathogen persistence, thereby elevating disease risk. Future progress requires a shift from descriptive surveys toward functional and predictive approaches, as these soil components influence epidemiological processes that can either suppress or intensify the development of plant diseases caused by soilborne plant pathogens. Rather than acting as deterministic drivers of disease outcomes, microbial diversity, soil organic matter, and soil structure modify the ecological context in which host-pathogen interactions occur, altering the likelihood of pathogen establishment, persistence, and transmission. This paper highlights the importance of soil management in regulating microbial community dynamics and supporting plant disease control within this probabilistic ecological framework.},
}

@article {pmid42287449,
year = {2026},
author = {Mertin, AA and Blackall, LL and Brumley, DR and Liew, ECY and van der Merwe, M},
title = {Host Species Mediate Distinct Seed Microbiome Responses to Restoration.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02802-6},
pmid = {42287449},
issn = {1432-184X},
abstract = {Microbial diversity is a key driver of ecosystem function, yet it remains poorly integrated into ecological restoration frameworks. While seeds are the primary dispersal unit of plants and the foundation of most restoration programs, the microbial communities they carry are rarely considered. Here, we assess whether sites that have undergone restoration have altered seed-associated microbial communities. We do this by comparing bacterial and fungal seed microbiomes across natural and restored landscapes. Using a landscape-scale sampling design, seeds were collected from multiple plant host species and populations across 41 sites spanning a broad latitudinal gradient. High-throughput sequencing of the 16S rRNA gene and ITS2 region was used to characterise bacterial and fungal communities, respectively, and differences in diversity, composition, and network structure were assessed using multivariate and network-based approaches. Seed microbiomes differed between natural and restored sites, but the magnitude and nature of these changes varied among host species. Restored sites were associated with shifts in microbial diversity, community composition, and network structure, including changes in the retention of putative keystone taxa. In some species, restoration was linked to pronounced restructuring of seed-associated microbial communities, whereas in others, microbiomes remained comparatively stable. Together, these results demonstrate that restoration can alter seed microbial communities in ways that are not consistently predicted by soil-focused restoration outcomes and that host identity mediates these responses. Incorporating seed microbiome data into restoration monitoring may therefore provide a complementary and previously overlooked indicator of restoration success, with implications for improving plant germination and health.},
}

@article {pmid42287489,
year = {2026},
author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A},
title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42287489},
issn = {1573-0972},
mesh = {*Fungi/classification/genetics/isolation & purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.},
}

*Fungi/classification/genetics/isolation & purification
*DNA Barcoding, Taxonomic
*Biodiversity
*Wetlands
*Mycobiome
Basidiomycota/genetics/classification
Geologic Sediments/microbiology
*Rhizophoraceae/microbiology
Ecosystem
Ascomycota/genetics/classification/isolation & purification
Phylogeny

@article {pmid42289496,
year = {2026},
author = {Liu, J and Zhao, Y and Wang, Y and Shi, Y and Zhi, Q and Chen, L and Ke, Y and Ren, J},
title = {ARHI as a key regulator of EMT and metastasis in pancreatic cancer via the Notch-1 pathway.},
journal = {Human genetics},
volume = {145},
number = {1},
pages = {},
pmid = {42289496},
issn = {1432-1203},
support = {81772630//the National Natural Science Foundation of China/ ; 2017J01377//the Natural Science Foundation of Fujian Province/ ; 2024GZL-GG36//Xiamen Young and Middle-Aged Key Talents Program for High-Quality Development/ ; 2022050901//the Science and Technology Programs of the Tan Kah Kee Innovation Laboratory/ ; },
mesh = {*Pancreatic Neoplasms/pathology/genetics/metabolism ; *Epithelial-Mesenchymal Transition/genetics ; *Receptor, Notch1/metabolism/genetics ; Humans ; Animals ; Mice ; Signal Transduction ; Cell Line, Tumor ; Neoplasm Metastasis ; Gene Expression Regulation, Neoplastic ; *rho GTP-Binding Proteins/genetics/metabolism ; Liver Neoplasms/secondary/genetics ; Neoplasm Invasiveness ; Cell Proliferation ; },
abstract = {Pancreatic cancer cell metastasis is a major factor influencing prognosis. A Ras homologue member I (ARHI) was reported to regulate proliferation and apoptosis in pancreatic cancer; however, its role in invasion remains unclear. This study aimed to explore the role and related mechanisms of ARHI in pancreatic cancer metastasis. We revealed that in pancreatic cancer ARHI expression levels were consistent with aggressive cellular phenotypes, and that changes in endogenous ARHI protein expression led to corresponding alterations in epithelial-mesenchymal transition (EMT) markers. Furthermore, ARHI accelerated tumor invasion in pancreatic cancer cells and in a mouse hepatic metastasis model. Notably, this unusual promoting effect of ARHI on EMT and invasion in pancreatic cancer was primarily exerted through the Notch-1 signaling pathway. Collectively, our findings provide insight into the function and molecular mechanisms of ARHI in pancreatic cancer metastasis.},
}

*Pancreatic Neoplasms/pathology/genetics/metabolism
*Epithelial-Mesenchymal Transition/genetics
*Receptor, Notch1/metabolism/genetics
Humans
Animals
Mice
Signal Transduction
Cell Line, Tumor
Neoplasm Metastasis
Gene Expression Regulation, Neoplastic
*rho GTP-Binding Proteins/genetics/metabolism
Liver Neoplasms/secondary/genetics
Neoplasm Invasiveness
Cell Proliferation

@article {pmid42292476,
year = {2026},
author = {Zhou, Y and Li, Z and Chu, Y and Zhou, Z and Zhang, T and Yi, N and Sun, W and Yan, J and Yan, Z and Zhu, A},
title = {Reframing precision nutrition in irritable bowel syndrome: a mechanism-informed conceptual framework for responder prediction and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1809221},
pmid = {42292476},
issn = {1664-3224},
mesh = {Humans ; *Irritable Bowel Syndrome/diet therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; FODMAP Diet ; *Precision Medicine/methods ; Multiomics ; Translational Research, Biomedical ; },
abstract = {BACKGROUND: The low-Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is widely used for irritable bowel syndrome (IBS), but response varies markedly across patients. This heterogeneity has shifted the field from testing average efficacy toward forecasting individual benefit and translating microbiome science into practical precision-nutrition tools.

METHODS: We present a conceptual analysis grounded in evidence mapping from human IBS studies that paired dietary interventions (primarily low-FODMAP pathways) with baseline microbiome and/or multi-omics measurements. Findings are organized within a "microbiome-to-model" roadmap that specifies responder endpoints, candidate data layers (taxa, functions, metabolites and volatile signatures), modeling choices, and the validation and implementation requirements needed for clinical decision support.

RESULTS: Three recurring signals emerge across cohorts. Baseline microbial ecology can stratify response, but taxonomic features alone often fail to transport across studies. Functional readouts, including metabolites and volatile signatures, are closer to symptom mechanisms and can improve interpretability; however, clinical deployment is still limited by endpoint heterogeneity, imperfect exposure and adherence measurement, batch effects, and insufficient external validation and calibration.

CONCLUSION: IBS is well suited for microbiome-informed responder prediction, provided that models are developed with deployment in mind. Progress will depend on validation-first study designs, harmonized responder endpoints and adherence capture, robust multi-omics pipelines, and biologically interpretable decision rules that can be prospectively tested and monitored for temporal instability in real-world care.},
}

Humans
*Irritable Bowel Syndrome/diet therapy/microbiology/metabolism
*Gastrointestinal Microbiome
FODMAP Diet
*Precision Medicine/methods
Multiomics
Translational Research, Biomedical

@article {pmid42293159,
year = {2026},
author = {Ike, I and Teymouri, F and Crook, C and Guzman, S and Hazeltine, M and Castillo, D and Li, D and Brar, G},
title = {The interplay between bile acid metabolism and gut microbiome in biliary tract cancers.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1774429},
pmid = {42293159},
issn = {2813-4338},
abstract = {The gut microbiota and bile acids (BAs) exist in a tightly regulated, bidirectional relationship that influences host metabolism, immune function, and disease. Primary BAs synthesized in the liver are chemically transformed by intestinal microbes into a diverse pool of secondary BAs, which exert antimicrobial effects and activate host signaling pathways including Farnesoid X Receptor (FXR), Takeda G protein-coupled receptor 5 (TGR5), and sphingosine-1-phosphate receptor 2 (S1PR2). These pathways regulate BA homeostasis, epithelial barrier integrity, inflammation, and carcinogenesis. Disruption of this BA-microbiome axis has been implicated in biliary tract cancers (BTCs), a group of aggressive malignancies with rising global incidence and limited therapeutic options. Secondary BAs and BA receptor signaling contribute to tumor initiation and progression through NF-κB activation, oxidative stress, and altered cell survival, whereas reduced FXR signaling and obstructed enterohepatic circulation further promote inflammatory dysregulation. Emerging evidence demonstrates that microbial dysbiosis and altered BA metabolism are associated with distinct BTC microbial profiles, enriched in taxa such as Fusobacterium, Salmonella, Prevotella, and Actinomyces, alongside depletion of commensals including Lactobacillus. These taxa influence inflammatory signaling, BA transformation, and epithelial injury, contributing to carcinogenesis. Microbiome-BA interactions also shape anti-tumor immunity and responses to immune checkpoint inhibitors (ICIs). Specific microbial signatures-particularly enrichment of Lachnospiraceae, Erysipelotrichaceae, Bacteroidetes, and Alistipes-correlate with enhanced immune activation and improved clinical outcomes in hepatobiliary cancers. Modulation of gut microbiota through antibiotics, probiotics, or fecal microbiota transplantation can influence BA composition, immune surveillance, and therapeutic efficacy. Collectively, these data highlight the central role of the BA-microbiome axis in BTC pathogenesis and treatment response. Microbial and BA metabolite profiling represent promising avenues for biomarker development, while targeted manipulation of BA signaling and microbial ecology offers potential therapeutic strategies to improve BTC outcomes.},
}

@article {pmid42293552,
year = {2026},
author = {Aldriwesh, MG and Bin Shuraym, H and Asiri, NY and Asiri, WY and Abukhalid, NF and Alasiri, A and Alghoribi, MF},
title = {Microbiome and One Health in GCC countries: current status, research gaps, and future directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821688},
pmid = {42293552},
issn = {1664-302X},
abstract = {BACKGROUND: Microbiome science has emerged as a central component of the One Health framework, linking human, animal, and environmental health. Although global microbiome research has expanded rapidly, a comprehensive evaluation of microbiome research development and integration across the Gulf Cooperation Council (GCC) countries remains lacking. This systematic review aimed to characterize microbiome research in the GCC countries, identify major research gaps, and evaluate alignment with One Health principles while proposing a strategic framework to support coordinated regional development.

METHODS: This systematic review followed PRISMA 2020 guidelines. A structured search of PubMed, ScienceDirect, Google Scholar, and EBSCO databases identified microbiome-related studies published up to January 31, 2025. Eligible studies included original research conducted in the GCC countries (Saudi Arabia, Qatar, Kuwait, United Arab Emirates, Oman, and Bahrain) investigating human, animal, or environmental microbiomes. Findings were synthesized descriptively to assess study distribution, research design, analytical methodologies, and thematic focus.

RESULTS: A total of 110 studies met the inclusion criteria. Human microbiome studies accounted for 49% of publications, followed by environmental microbiome studies (40%) and animal microbiome studies (11%). Research output increased substantially after 2020 but remained uneven among the GCC countries, with Saudi Arabia contributing 44% of publications, whereas Bahrain and Oman together accounted for fewer than 7%. Most studies were observational and primarily used 16S rRNA gene sequencing on Illumina platforms. Human studies focused mainly on gut and oral microbiomes and frequently investigated metabolic disorders such as obesity and diabetes. Animal microbiome research was limited and largely centered on camels, with minimal investigation of livestock relevant to food security. Environmental studies predominantly examined soil and desert environments. No included study simultaneously investigated human, animal, and environmental microbiomes within an integrated One Health study design.

CONCLUSION: Microbiome research in the GCC countries is growing but remains uneven and largely disconnected across human, animal, and environmental studies, with limited adoption of One Health approaches. A coordinated regional strategy integrating governance, infrastructure, funding, and workforce development is needed to advance translational microbiome research and strengthen the GCC's contribution to global health, food security, and environmental sustainability.},
}

@article {pmid42294667,
year = {2026},
author = {Aponte Rolón, B and Kristy, B and Shade, A and Stopnisek, N and Lebeis, SL and Howe, A and Benucci, GMN},
title = {BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0025126},
doi = {10.1128/mra.00251-26},
pmid = {42294667},
issn = {2576-098X},
abstract = {Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.},
}

@article {pmid42294679,
year = {2026},
author = {Henkel, JV and Røy, H and Jørgensen, BB and Rotaru, A-E and Jovicic, D and Marshall, IPG and Jiang, C and Nielsen, PH and Singleton, CM and Arz, HW and Plewe, S and Kjeldsen, KU},
title = {Desulfatiglans-related bacteria associated with conductive mineral particles in marine subsurface sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0083826},
doi = {10.1128/mbio.00838-26},
pmid = {42294679},
issn = {2150-7511},
abstract = {UNLABELLED: Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Recent observations suggest that acetate is oxidized syntrophically in the methanic zone of marine sediments, and that electrically conductive mineral particles could provide niches for electroactive microbial communities that perform this process. We combined radiotracer measurements, a novel procedure for ferromagnetic mineral particle extraction, and metagenomic analyses to examine this process in Baltic Sea sediments. Our results confirm that acetate is oxidized syntrophically across and below the sulfate-methane transition zones of the sediments, where the transfer of reducing equivalents from acetate oxidation to CO2 fuels methanogenesis. Ferromagnetic particles consistently occurred throughout the geochemical zones and mainly consisted of the electrically conductive minerals magnetite and pyrite-greigite. The microbial communities associated with ferromagnetic particles were dominated by members phylogenetically affiliated with the bacterial genus Desulfatiglans. Known Desulfatiglans species are dissimilatory sulfate reducers; however, metagenome-assembled genomes indicate that Desulfatiglandales populations associated with ferromagnetic particles lack genetic potential to respire sulfate. Instead, they may grow by acetate oxidation coupled with extracellular electron transfer, consistent with a conductive mineral-associated lifestyle. We hypothesize that Desulfatiglans relatives are acetate-oxidizing partners in a syntrophic process facilitated by interspecies electron transfer via conductive particles. We identified cytochrome-rich ANME-1 archaea as the predominant methane-cycling microorganisms associated with ferromagnetic particles; however, their potential role as methanogenic syntrophic partners remains uncertain. Overall, our study reveals that distinct microbial communities are associated with ferromagnetic particles and shows conductive minerals as a niche for electroactive microorganisms in marine sediments.

IMPORTANCE: Acetate is a central intermediate in the anaerobic breakdown of organic matter. In Baltic Sea sediments at and below the sulfate-methane transition zone, we observed acetate oxidation to carbon dioxide at rates similar to methane formation from carbon dioxide reduction, a pattern indicative of syntrophic acetate oxidation. Previous enrichment studies suggest that electrically conductive mineral surfaces can facilitate this process. Motivated by this observation, we extracted ferromagnetic conductive particles from sediments and compared particle-attached microbial communities with bulk sediment. Particle-attached communities were distinct and enriched in the bacterial genus Desulfatiglans. Their genomes lacked genes for sulfate respiration, yet encoded traits consistent with acetate oxidation and extracellular electron transfer. Our findings suggest conductive minerals as distinct microbial niches and highlight Desulfatiglans-related bacteria as a potential key organism in particle-associated acetate oxidation.},
}

@article {pmid42294682,
year = {2026},
author = {Ai, C and Tang, X and Han, H and He, Y and Zhang, H and Liu, C and Liao, H and Zhou, S},
title = {Active prophages as key drivers of microbial adaptation in global soil ecosystems.},
journal = {mBio},
volume = {},
number = {},
pages = {e0069326},
doi = {10.1128/mbio.00693-26},
pmid = {42294682},
issn = {2150-7511},
abstract = {Soils harbor the most complex microbial diversity on Earth, in which bacteria are ubiquitously infected by temperate phages. While integrated prophages often enhance host fitness, active (inducible) prophages are traditionally perceived as "molecular time bombs" due to their intrinsic lysis threat. This dual nature has raised fundamental questions about the true contribution of temperate phages to microbial adaptation and ecosystem stability. To address this gap, we conducted a global-scale integrative analysis by synthesizing 123,207 high-quality bacterial genomes, 183 soil-specific viromic data sets, and 3,749 metagenomes. We established the Global Soil Active Prophage Database (GSAPD), comprising 21,397 high-confidence active prophages, which we found to represent 34.3% of the total soil viral population within our analytical framework. Our comparative genomic analysis reveals that active prophages possess significantly larger genomes and greater genetic complexity compared with their dormant counterparts. Crucially, by mapping phage-encoded auxiliary metabolic genes (AMGs) across diverse biomes, we found that active prophages are disproportionately enriched in key pathways for carbon, nitrogen, and sulfur cycling, as well as specialized resistance mechanisms against heavy metal toxicity. These findings suggest that active prophages act as dynamic reservoirs of functional diversity. We demonstrate that their lytic potential is not merely a survival risk, but a sophisticated mechanism underpinning host environmental adaptation and niche expansion. Ultimately, this study provides a comprehensive global catalog of soil viral pathways and redefines the role of temperate phages as pivotal drivers of microbial evolution and biogeochemical cycling in terrestrial ecosystems.IMPORTANCESoils contain immense microbial diversity, yet the ecological role of temperate phages-especially their active (inducible) forms-remains poorly understood. This study provides the first global-scale assessment of active prophages in soils, revealing that they are widespread and functionally distinct from dormant forms. By building a comprehensive database and integrating multi-omics data, we show that active prophages are enriched in genes linked to key biogeochemical processes and stress resistance. These findings challenge the traditional view of active prophages as purely harmful agents and instead highlight their role as dynamic contributors to microbial function and adaptation. Our work offers new insights into how viruses shape ecosystem processes and provides a valuable resource for future studies on soil microbial ecology and nutrient cycling.},
}

@article {pmid42294696,
year = {2026},
author = {Han, J and Li, Y and Xu, Y and Li, S and Zeng, J},
title = {Reliable delineation of Clostridioides difficile and related members of the family Peptostreptococcaceae using phylogenomics and spore coat protein-specific molecular markers.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0418525},
doi = {10.1128/spectrum.04185-25},
pmid = {42294696},
issn = {2165-0497},
abstract = {Traditional bacterial classification relies on phenotypic traits (e.g., morphology and metabolic profiles), but these methods lack resolution for closely related taxa and are biased by culture conditions. While 16S rRNA gene sequencing is a widely used molecular complement, it fails to resolve closely related Peptostreptococcaceae species, including Clostridioides difficile. These limitations have caused family-level taxonomic confusion and ambiguous Clostridioides genus boundaries, hindering clinical identification of pathogenic strains and posing public health risks. To address these limitations, we developed an integrated approach combining multi-scale phylogenomic and protein-based molecular evidence, adopting a hierarchical workflow: first, constructing a 16S rRNA phylogeny of 151 Firmicutes strains to demonstrate traditional marker inadequacies; second, generating a whole-genome protein phylogeny of 51 representative Peptostreptococcaceae genomes and defining taxonomic boundaries via average amino acid identity (AAI); third, analyzing spore-associated protein patterns across C. difficile isolates and related genomes. Results revealed high conservation of C. difficile spore coat/exosporium proteins and clear genus-level phylogenetic distinctiveness of these proteins. Combined with AAI-validated whole-genome data, our findings support key Peptostreptococcaceae taxonomic revisions: redefining polyphyletic Romboutsia, reassigning Eubacterium tenue to Paraclostridium, and elevating Alkalithermobacter to genus status. This study establishes spore coat proteins as core taxonomic markers for spore-forming bacteria, with our integrated strategy overcoming traditional limitations to improve classification accuracy and C. difficile surveillance.IMPORTANCEConventional classification struggles to resolve closely related Peptostreptococcaceae species (e.g., Clostridioides difficile). We developed an integrated framework combining 16S rRNA sequencing, whole-genome protein analysis, and spore trait assessment, with a key innovation: identifying spore coat/exosporium proteins as robust, conserved taxonomic markers. This approach enabled three pivotal Peptostreptococcaceae revisions-redefining Romboutsia, reassigning Eubacterium tenue to Paraclostridium, and elevating Alkalithermobacter to genus rank. The findings resolve a longstanding microbial systematics bottleneck for spore-forming bacteria, provide critical taxonomic context for C. difficile's precise monitoring and prevention, and expand taxonomic markers beyond nucleic acid-based methods. This advances classification precision, critical for microbial ecology, pathogenesis, and industrial microbiology research.},
}

@article {pmid42277415,
year = {2026},
author = {Prada, J and Pereira-Dias, L and Santos, JA and Santos, C},
title = {Influence of Environment and Rootstock On the Rhizosphere Bacterial Communities in Four Vineyards of the Douro Demarcated Region.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02798-z},
pmid = {42277415},
issn = {1432-184X},
abstract = {The Douro Demarcated Region (DDR) is a worldwide acknowledged winemaking region. Climate change is threatening the sector, as climatic shifts are expected. This work analyzed environmental and genetic traits modulating the rhizobiome of four vineyards in the DDR, focusing on understanding the hierarchy of ecological conductors for these communities. These vineyards' terroir was environmentally, genetically, and culturally characterized. Rhizosphere bacterial community composition was analyzed using 16S metabarcoding from soil samples collected between July 2022 and January 2024. Results support the hypothesis of an ecological profiling hierarchy. The soil physicochemical properties likely acted as a primary environmental modulator, determining the composition of the bacterial microbiome and contributing to the diversity and richness of the bacterial communities. The major drivers among the soil's physiochemistry were organic/inorganic profile, mainly influenced by organic matter content and pH. Rootstock genotype appears to exert a secondary selection on the microbiome, focusing on the microorganisms' functional traits. The 1103-P rootstock positively influenced the abundance of copiotrophic bacteria, compared to the R110, demonstrating that the first recruits a more versatile, exploratory, and expansionist microbiome, whilst the second focuses on attracting a highly specialized community, more focused on maximizing energy gathering and optimizing resource use. This work demonstrates that the microbial terroir is a result of multiple factors, promoting abiotic modulation and host-mediated selection, which establishes a very specific community for each scenario. The assessment of these holistic dynamics is fundamental to establishing a baseline for future precision viticulture strategies, namely bio-inoculants, to support and promote a better grapevine adaptation to climate change.},
}

@article {pmid42270219,
year = {2026},
author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y},
title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119489},
doi = {10.1016/j.foodres.2026.119489},
pmid = {42270219},
issn = {1873-7145},
mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; },
abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.},
}

China
Fermentation
*Hot Temperature
*Microbiota
*Taste
*Food Microbiology
Bacteria/metabolism/classification/genetics
Rivers
Flavoring Agents
*Fermented Foods/microbiology

@article {pmid42274251,
year = {2026},
author = {Zhu, C and Wei, T and Lin, Y and Yan, G and Qian, P-Y},
title = {The patterns of microbial community distribution and co-occurrence in water columns and sediments of Haima cold seep.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0025626},
doi = {10.1128/spectrum.00256-26},
pmid = {42274251},
issn = {2165-0497},
abstract = {Deep-sea cold seeps are essential components of global biodiversity and biogeochemical cycles, whereas the community distribution and co-occurrence patterns of cold seep microorganisms remain poorly understood. Here, we investigated the microeukaryotic and prokaryotic communities across different water layers and benthic habitats in the Haima cold seep of the South China Sea and revealed distinct vertical and horizontal patterns in microbial distribution and co-occurrence between the water columns and sediments. Prokaryotic intra-domain interactions predominated over inter-species correlations in networks, and bacteria-microeukaryote interactions were more abundant in the network of water columns than in sediments, indicating that environmental preferences of microorganisms differed between these environments. The environmental factors and deterministic processes appeared to exert a more pronounced influence on the distribution patterns of microeukaryotes than on prokaryotes in the water columns, whereas the opposite was observed in the sediments. Additionally, microbial co-occurrence patterns were segregated and primarily shaped by deterministic processes. The species interactions were more complex in the euphotic zone and clam (one of the most dominant megabenthos) habitats than those in other water layers and benthic habitats, and the microbial co-occurrence patterns in the euphotic zone and mussel beds were likely influenced by strong selection factors such as light, organic carbon, mussel activities, and high methane concentrations. Our study provides new perspectives on how microorganisms adapt to the different environmental conditions in deep-sea cold seeps, deepening our understanding of microbial ecology in deep-sea extreme environments.IMPORTANCEOur study revealed the vertical and horizontal patterns of microbial community distribution and co-occurrence, highlighting how different ecological processes shape microbial communities in the water column and sediments, as well as between microeukaryotes and prokaryotes. This indicated that the balance of deterministic and stochastic processes was influenced by the environment and taxonomic classification in deep-sea cold seeps. The species interactions in the euphotic zone and clam habitat were more complex than those in other water layers and benthic habitats, and the euphotic zone and mussel beds served as hotspots of intense environmental selection. Our findings revealed that microorganisms responded to these challenging environments in deep-sea cold seeps through various strategies, including different environmental preferences. By elucidating the mechanisms driving the microbial community diversity and species coexistence, this work provides new perspectives on how microorganisms adapt to the environments in deep-sea cold seeps.},
}

@article {pmid42274959,
year = {2026},
author = {Gianaris, A and Ramalho, MO and de Oliveira, AA and de Castro Morini, MS and Martins, C and Bueno, OC},
title = {Bacterial Diversity in Leaf-Cutter Ant Species: Host-Microbe Interactions and Environmental Effects.},
journal = {Neotropical entomology},
volume = {55},
number = {1},
pages = {},
pmid = {42274959},
issn = {1678-8052},
support = {NSF DEB 1900357//Natural Science Foundation/ ; },
mesh = {Animals ; *Ants/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Bacteria/classification/genetics ; *Host Microbial Interactions ; *Biodiversity ; Fungi ; },
abstract = {Historically, studies have sought to identify host-specific factors in host-microbe interactions as a means of understanding evolutionary success. The genus Atta, comprising leaf-cutter ants, is native to the southern Neotropics and obligately mutualistic with cultivated fungi. It hosts a remarkably diverse range of bacterial communities, yet this variability remains poorly understood. Using high-throughput amplicon sequencing of the 16S rRNA genes of the whole worker, we showed significant difference between the bacterial communities among 4 dominant Atta species: Atta sexdens (Linnaeus), Atta laevigata (Smith), Atta capiguara (Gonçalves), and Atta bisphaerica (Forel). We also discovered significant differences in bacterial communities from laboratory conditions, pesticide treatment, and the fungal garden symbiont of Atta sexdens. Surprisingly, bacterial communities of Atta sexdens kept in the laboratory were not significantly different from pesticide-treated Atta sexdens, laying the groundwork for potential refinement of standard research methods.},
}

Animals
*Ants/microbiology
RNA, Ribosomal, 16S/genetics
Symbiosis
*Bacteria/classification/genetics
*Host Microbial Interactions
*Biodiversity
Fungi

@article {pmid42277207,
year = {2026},
author = {Su, H and Liu, DH and Shang, HY and Huang, D and Liang, C and Wang, ZH and Zhai, JN and Zhang, XT and Jiang, HL and Shum, FY and Chen, HY and Qin, N and Xu, ZH and Liu, XD and Tan, LK and Zhang, L and Ho, KM and Chan, MTV and Wu, WKK and Chen, HR},
title = {METTL3 loss exacerbates colitis via m[6]A-dependent Slc39a8 regulation and epithelial lineage depletion.},
journal = {Acta pharmacologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {42277207},
issn = {1745-7254},
abstract = {The intestinal epithelium maintains host-microbiota homeostasis, while inflammatory conditions, such as inflammatory bowel disease (IBD), induce pathological shifts in intestinal epithelial cell (IEC) subtypes. We unveil METTL3, an RNA m[6]A methyltransferase, as a pivotal regulator of this balance. METTL3 is enriched in intestinal stem cells and transit-amplifying cells (TACs), and upregulated in patients with IBD and a mouse model of IBD. DSS-challenged, intestine-specific Mettl3 knockout mice exhibited exacerbated colitis as exemplified by more weight loss, elevated disease activity index (DAI), and higher extent of colon shortening. Single-cell transcriptomics of colonic tissues from DSS-challenged intestine-specific Mettl3 knockout mice revealed that Mettl3 ablation depleted epithelial lineages (TACs, goblet cells, enterocytes) but amplified immune infiltration (macrophages, neutrophils, T cells) within the intestinal mucosa. Crucially, METTL3 loss impaired TAC multipotency and increased epithelial-neutrophil crosstalk mediated by the TNF pathway. Mechanistically, METTL3-mediated m[6]A modification increases Slc39a8 expression, whose knockdown in colon organoids phenocopied METTL3 deficiency in impairing self-renewal. Our work establishes METTL3 as a dual guardian of intestinal homeostasis-preserving epithelial regeneration and restraining inflammation by calibrating epithelial-immune dialogue. The former is mediated at least in part by regulating Slc39a8 expression through m[6]A modification.},
}

@article {pmid42000857,
year = {2026},
author = {Krishnakumar, A and Juárez-Castelán, CJ and Vélez-Ixta, JM and Benitez-Guerrero, T and Murugesan, S and Piña-Escobedo, A and Rico-Arzate, E and Castro-Arellano, JJ and Romero-Maldonado, S and Cruz-Narváez, Y and Pizano-Zárate, ML and García-Mena, J},
title = {Maternal obesity modifies the vertical transmission of gut microbiota and metabolites: Insights from mother-infant dyads in a mexican cohort.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42000857},
issn = {2045-2322},
support = {CONACyT 302670 INFR-2019//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; CONACyT FORDECYT-PRONACES/6669/2020_Programa Presupuestario F003-Ciencia de Frontera 2019//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; CONACyT 163235 INFR-2011-01//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; },
abstract = {UNLABELLED: Maternal obesity is increasingly recognized as an important modulator of early-life microbial and metabolic environments. This study investigates the association between maternal body mass index (BMI) and the microbiota and metabolite profiles of colostrum and neonatal feces in a Mexican mother–infant cohort. Milk and fecal samples were collected from dyads of obese and normal-weight mothers. Bacterial microbiota composition was characterized by sequencing the 16 S rRNA gene (V3 region) using Ion Torrent technology, and metabolomic profiling was performed using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The results provide evidence consistent with vertical microbial and metabolic transmission, with Firmicutes and Patescibacteria predominating in Colostrum. Neonates born to obese mothers exhibited reduced relative abundances of Lactobacillus in neonatal fecal samples, alongside increased levels of Lactobacillus and Staphylococcus in both colostrum and mother´s feces. Overall microbial diversity across maternal stool, colostrum, and neonatal stool samples was not significantly associated with maternal BMI; however, distinct metabolite signatures linked to maternal obesity, like oligopeptides, glycoside-related compounds, Phosphatidic Acid (PA) Derivatives, bioactive molecules such as enkephalinamide derivatives, were observed. These findings highlight the role of breastfeeding as a key interface in shaping the neonatal gut microbiota and metabolome and suggest potential pathways linking maternal metabolic status with early-life microbial and metabolic programming. This study advances understanding of maternal–infant microbial ecology and supports further investigation into the long-term health implications of maternal obesity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-49183-x.},
}

@article {pmid42266678,
year = {2026},
author = {Rao, X and Zou, L and Cai, X and Yao, Y and Zhong, L},
title = {Microbiome-orchestrated cross-organ immunity in autoimmunity: from metabolites to therapeutic targets.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1761834},
pmid = {42266678},
issn = {1664-3224},
abstract = {Autoimmune diseases are systemic disorders in which barrier-site immune activation, especially in the gut, can reshape inflammatory programs in distant organs. This review advances a metabolite-centered, cross-organ framework for understanding how gut microbial ecology influences autoimmunity beyond individual gut-organ axes. We synthesize evidence that short-chain fatty acids, bile acid derivatives, tryptophan catabolites, polyamines and related microbial products act as mobile biochemical checkpoints linking intestinal barrier integrity, pattern-recognition signaling, immune-cell metabolism and tissue-specific inflammation in joints, kidneys, skin, lungs and the central nervous system. Across these axes, shared mechanisms include barrier failure, altered microbial metabolite pools, dysregulated MAMP sensing, trafficking or systemic conditioning of lymphoid and myeloid cells, and local stromal imprinting in target organs. We also discuss sex-dependent microbiome-immune interactions, including the microgenderome concept, as a framework for explaining why microbiome composition, hormone metabolism and immune responses may shape autoimmune risk and treatment response differently in females and males. Finally, we evaluate multi-omics, single-cell and spatial profiling, organ-on-chip platforms and causal computational tools, and we outline translational strategies ranging from diet, probiotics, fecal microbiota transplantation and engineered consortia to pharmacologic targeting of metabolite receptors. By treating microbial metabolites as actionable cross-organ immune checkpoints, this review highlights opportunities and limitations for biomarker-guided, metabolite-focused precision therapy in autoimmunity.},
}

@article {pmid42266934,
year = {2026},
author = {Bautista, J and Lara-Hernández, ME and Hidalgo-De La Cruz, M and Andino-Araque, V and León-Rivera, M and López-Cortés, A},
title = {Host-microbiome interactions in breast cancer progression and treatment response.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1827694},
pmid = {42266934},
issn = {2296-858X},
abstract = {Breast cancer (BC) is a biologically heterogeneous disease in which tumor progression and therapeutic response vary substantially across patients and molecular subtypes. Alongside genetic, endocrine, and immunological determinants, microbial ecosystems have been proposed as components of the host environment that interact with tumor biology. Microorganisms detected in breast tissue, the gastrointestinal tract, and the oral cavity coexist with epithelial and immune compartments and participate in metabolic and inflammatory processes relevant to mammary physiology. Differences in microbial composition have been reported between non-malignant and malignant breast tissue, while intestinal microbial metabolism generates bioactive compounds capable of interacting with immune regulation and systemic endocrine signaling. Microbial enzymatic activity involved in estrogen deconjugation further connects intestinal ecology with hormone-responsive disease. Microbiome-related variation has also been examined in relation to systemic therapies, where differences in microbial composition have been observed alongside variability in therapeutic outcomes. This review examines current knowledge on host-microbiome interactions across breast, gut, and oral environments and discusses how microbial ecology intersects with inflammatory signaling, metabolic regulation, and endocrine pathways relevant to breast cancer progression and treatment response. Methodological challenges and future research directions for microbiome-informed oncology are also considered.},
}

@article {pmid42267103,
year = {2026},
author = {Min, L and Ablitip, A and Wang, Q and Li, T and Di, Q and Ma, X and Fang, W},
title = {Combined heat and exercise stress disrupt gut microbiota and promote microbial translocation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779295},
pmid = {42267103},
issn = {1664-302X},
abstract = {PURPOSE: The incidence of exertional heat stroke (EHS) has increased markedly in recent decades. Although intestinal barrier dysfunction and gut microbiota alterations are increasingly implicated in EHS pathophysiology, the respective contributions of heat exposure and physical exercise to these processes remain incompletely defined.

METHODS: Male C57BL/6 mice were assigned to Control (C), Exercise (E), Heat shock (H), or Exercise + Heat shock (HE) groups. Exercise and/or heat exposure were applied to induce exertional heat stress. Intestinal injury and permeability were assessed by histopathology and circulating D-lactate levels. Gut and blood microbial profiles were characterized using 16S rRNA gene sequencing, and associations between microbial signatures and intestinal injury markers were analyzed.

RESULTS: Both heat exposure and exercise induced intestinal injury and increased circulating D-lactate levels, with the most severe effects observed in the combined HE group. Heat exposure was associated with pronounced alterations in gut microbial diversity and community structure, whereas exercise was associated with increased microbial diversity and gut-associated microbial signatures detected in blood samples. Differential abundance analyses revealed distinct taxonomic profiles associated with heat, exercise, and their combination. Correlation analyses demonstrated significant associations between intestinal injury markers and circulating microbial profiles.

CONCLUSION: These findings indicate that heat exposure and exercise exert distinct yet interacting associations with intestinal barrier integrity and microbial community distribution. Heat stress primarily disrupts gut microbial ecology and barrier function, whereas exercise is more closely associated with increased systemic detection of gut-derived microbial signatures. Together, these results highlight the gut microbiota-barrier axis as a key interface linking environmental and physiological stressors to systemic responses during exertional heat stress.},
}

@article {pmid42267567,
year = {2026},
author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL},
title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.},
journal = {Zoological research},
volume = {47},
number = {3},
pages = {827-842},
doi = {10.24272/j.issn.2095-8137.2025.141},
pmid = {42267567},
issn = {2095-8137},
abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.},
}

@article {pmid42267811,
year = {2026},
author = {Gołębiowska, J and Woodhouse, JN and Tobias-Hünefeldt, SP and Grossart, H-P},
title = {Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0080726},
doi = {10.1128/aem.00807-26},
pmid = {42267811},
issn = {1098-5336},
abstract = {UNLABELLED: Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web.

IMPORTANCE: Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.},
}

@article {pmid42269463,
year = {2026},
author = {Liu, B and Leekitratanapisan, W and Pardon, M and Theus, A and Daenen, R and Jia, M and Kundu, K and Springael, D and Cabooter, D and De Schamphelaere, KAC and Boon, N},
title = {Hydrogen supplementation enhances microbial removal of selected organic micropollutants, reduces associated ecotoxicity, and improves nutrient removal in domestic wastewater effluent.},
journal = {Water research},
volume = {303},
number = {},
pages = {126211},
doi = {10.1016/j.watres.2026.126211},
pmid = {42269463},
issn = {1879-2448},
abstract = {Organic micropollutants (OMPs) compose a group of emerging contaminants that occur in environmental waters at trace concentrations (μg/L to ng/L) with suspected adverse effects on ecosystems and human health. Conventional wastewater treatment plants (WWTPs) are not designed to eliminate the more recalcitrant OMPs. As such, WWTP-effluents are a major source of OMPs in the aquatic environment, and sustainable advanced treatment options are required. One option concerns the biodegradation of OMPs, but several studies show that it might be constrained by the residual low energy content in effluent waters. Since molecular hydrogen (H2) has been identified as a universally available energy source utilised by various bacteria in oligotrophic environments, supporting mixotrophic growth, we examined the hypothesis that H2 can enhance OMP-removal and concomitant ecotoxicity from domestic wastewater effluent. To this end, a lab-scale biological trickling filter supplemented with H2 (1.5% in the aeration with ambient air) was operated in continuous mode for treating a field-collected domestic WWTP-effluent. In total, 51 OMPs were detected in the WWTP-effluent, of which azithromycin and clarithromycin contributed to 76.5% of the total ecotoxic effects, as demonstrated in a cyanobacterial growth inhibition assay. The H2-supplemented trickling filter enhanced the removal of azithromycin and clarithromycin by (69.5 ± 1.5)% and (46.0% ±2.9)%, respectively, and increased the reduction of total OMP-associated ecotoxic effects by 56.5%, compared to the non-H2-supplemented control. Moreover, H2 supplementation improved PO4[3-] and NO3[-] removal by a factor of 2.3 and 1.5, respectively. These findings demonstrate that H2 supplementation may support microbial processes involved in OMP-removal from domestic wastewater in a microbial treatment system, thereby reducing concomitant ecotoxicity.},
}

@article {pmid42270181,
year = {2026},
author = {Wejnerowski, Ł and Pełechata, A and Rybak, M and Piasecka, A and Antonowicz, JP and Belniak, G and Kamiński, O and Dziuba, MK and Koreivienė, J and Meriluoto, J and Dawidowicz, P},
title = {From lakes to the sea: testing the survival of freshwater bloom-forming cyanobacteria and cyanotoxin-related risk in Baltic coastal waters under a changing climate.},
journal = {Harmful algae},
volume = {157},
number = {},
pages = {103144},
doi = {10.1016/j.hal.2026.103144},
pmid = {42270181},
issn = {1878-1470},
abstract = {Brackish coastal waters are increasingly susceptible to harmful cyanobacterial blooms and toxin contamination, and climate change may enhance the persistence of bloom-forming species across salinity gradients. The Baltic Sea, one of the world's largest brackish basins is characterised by distinct salinity gradients, high productivity, and pronounced sensitivity to cyanobacterial blooms. Cyanobacteria are highly adaptable and tolerat of diverse environmental conditions. However, the response of freshwater strains to brackish water from various Baltic coastal sites, and the extent to which such conditions limit their persistence, remains uncertain. This study addressed three main objectives: (1) evaluating the ability of common freshwater bloom-forming filamentous cyanobacteria to grow in water from different Baltic coastal sites; (2) examining the combined effects of warming and CO2 enrichment on their performance under simulated brackish conditions; and (3) testing whether selected freshwater strain can persist in pairwise co-culture with the resident Baltic cyanobacterium Nodularia spumigena. Results showed that several freshwater strains grew in water from both the fresher northern and more saline southern Baltic coastal sites. However, their responses varied by strain and were influenced by site-specific water properties, climate conditions, and biotic interactions. Notably, a cylindrospermopsin-producing strain of Aphanizomenon gracile from an eutrophic inland lake showed the highest performance and also grew in co-culture with Nodularia. Simulations indicate that certain freshwater cyanobacteria can tolerate brackish water from different Baltic coastal sites under controlled short-term conditions. Moreover, findings suggest that freshwater strains capable of persisting under brackish conditions may contribute to cyanotoxin presence risk. This risk may affect water from both the fresher northern and saltier southern Baltic coasts, highlighting an emerging ecological and public health concern. The simplified, nature-safe experimental approach provides a foundation for more complex, field-based studies assessing the ecological relevance of freshwater cyanobacteria in transitional brackish coastal systems.},
}

@article {pmid42095674,
year = {2026},
author = {Robes, JMD and Liebergesell, TCE and Medvedeva, VP and Puri, AW},
title = {Inverse stable isotope labeling (InverSIL) links predicted catecholate siderophore gene clusters to their products in diverse bacteria.},
journal = {mBio},
volume = {17},
number = {6},
pages = {e0339125},
doi = {10.1128/mbio.03391-25},
pmid = {42095674},
issn = {2150-7511},
support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; R35 GM147018/GM/NIGMS NIH HHS/United States ; 00006628//Simons Foundation Early Career Investigator in Aquatic Microbial Ecology and Evolution/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; },
abstract = {UNLABELLED: Bacteria produce high-affinity, iron-chelating secondary metabolites called siderophores to access insoluble Fe(III) in their environments. Genome mining has revealed many predicted siderophore biosynthetic gene clusters (BGCs) in bacterial genomes; however, the structures of their siderophore products remain mostly undetermined. This limits our molecular-level understanding of how bacteria acquire iron. Here, we apply inverse stable isotope labeling (InverSIL) to rapidly connect predicted siderophore BGCs to their products. With InverSIL, bacteria are grown on [13]C-substituted carbon sources and then fed predicted biosynthetic precursors at their natural isotopic abundance to identify BGC products by mass spectrometry, removing issues with the availability of isotopically substituted precursors. We use InverSIL to determine the structures of the siderophore products of predicted BGCs from the methylotrophic genera Methylophilus and Methylorubrum, as well as the siderophores produced by the opportunistic pathogen Chromobacterium violaceum, which were previously shown to be essential for virulence yet remained structurally uncharacterized. We next use this approach to reveal the unexpected production of enterobactin by the genera Kushneria and Paracoccus, which was difficult to predict from genome sequences due to the distributed nature of the biosynthetic genes within the genomes. Finally, we use InverSIL to discover new siderophores, the cellulochelins, from the cellulose-degrading plant symbiont Cellulomonas sp. strain Leaf334. These findings demonstrate the utility of InverSIL for functional BGC characterization and expand our molecular understanding of bacterial iron acquisition strategies.

IMPORTANCE: Iron acquisition is important for microbial survival, and bacteria produce secondary metabolites called siderophores to scavenge iron from the environment. While bacterial genome sequences show many predicted genes for making siderophores, most remain unlinked to their metabolic products. Understanding which siderophores bacteria produce is critical for elucidating microbial iron acquisition strategies, ecological interactions, and potential roles in host-microbe interactions. Here, we demonstrate how inverse stable isotope labeling (InverSIL) can rapidly link predicted siderophore gene clusters to their corresponding metabolites. By applying InverSIL to diverse bacterial strains, we validate known siderophore products and uncover unexpected products, highlighting the limitations of current in silico predictions. This study highlights the value of combining experimental approaches with genome mining to advance our understanding of how bacteria acquire iron from their environment.},
}

@article {pmid42260218,
year = {2026},
author = {Chauhan, PK and Tomar, S and Kumari, S and Srivastava, AK},
title = {Climate Warming and Plant Disease: Mechanistic Insights Into Pathogenic Stress Resilience.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70648},
pmid = {42260218},
issn = {1365-3040},
abstract = {Climate warming is rapidly reshaping plant-pathogen interactions, leading to increased disease incidence and substantial crop losses worldwide. This review examines how rising temperature, humidity and shifting precipitation patterns intensify plant disease, while highlighting advances in sustainable microbe-based and molecular strategies to enhance plant immunity and crop resilience. A systematic literature-based synthesis highlights the role of root-adhering microbes (RAM), plant-microbe-environment crosstalk under combined stresses and engineered microbial consortia. It also explores advanced molecular tools, including CRISPR/Cas9 and RNA Interference (RNAi), for precise targeting of pathogen virulence and regulation of host defence pathways. Evidence shows that RAM and tailored microbial consortia enhance induced systemic resistance (ISR) and systemic acquired resistance (SAR), improving tolerance to multiple stresses. Meanwhile, molecular approaches are accelerating the development of climate-resilient, disease-resistant crop genotypes. Integrating beneficial microbes with precision molecular innovations offers a transformative path toward climate-smart agriculture. Strengthening links between plant immunity, microbial ecology and genetic technologies will be essential for building resilient food systems in a warming world.},
}

@article {pmid42260689,
year = {2026},
author = {Wang, K and Peng, Q and Geng, L and Zhang, F and Liu, R and Liu, X and Zhang, J and Shu, C},
title = {Protaetia brevitarsis larvae frass affects substrate microecological systems via two suggestive pathways to enhance cherry tomato growth.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00915-6},
pmid = {42260689},
issn = {2524-6372},
support = {2023YFD1701502//National Key Research and Development Program of China/ ; 32570599//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The identification and development of high-quality humus sources to enhance the productivity and performance of substrate-based vegetable cultivation systems remains a significant challenge in sustainable agriculture. Protaetia brevitarsis larvae (PBL) exhibit exceptional efficiency in decomposing decaying crop straw and produce nutrient-rich frass with high humic acid content and a complex microbial community. However, its impacts on substrate microecological systems and the underlying functional mechanisms remain unclear, limiting its rational application in substrate cultivation. This study aimed to investigate the effects of PBL frass on substrate microecology and elucidate the associated mechanisms using cherry tomato (Lycopersicon esculentum Mill. var. cerasiforme Alef) pot experiments.

RESULTS: Incorporation of 2% or 4% (w/w) PBL frass into cherry tomato cultivation substrates significantly promoted plant growth, characterized by reduced plant height (indicating more robust, dwarf-type growth) and increased aboveground (stem) and belowground (root) biomass. Furthermore, PBL frass application enhanced substrate microbial diversity through two distinct, complementary pathways: (ⅰ) Frass-derived microbes, which possess specific colonization capabilities, directly augmented microbial communities in both the rhizoplane and bulk substrate; and (ⅱ) Organic compounds in PBL frass may have activated a broad range of microbes, enriching the rhizosphere microbiome. This enhanced microbial diversity was associated with an increased abundance of plant-beneficial taxa, which likely contributed to growth promotion and substrate health maintenance.

CONCLUSIONS: This study uncovers the multifaceted contributions of PBL frass to substrate microbial ecology and reveals its two suggestive regulatory pathways. These results provide a theoretical basis for the sustainable utilization of PBL frass and advance the development of eco-friendly amendments for modern vegetable production.},
}

@article {pmid42261086,
year = {2026},
author = {Wang, B and Yang, F and Zhou, L and Li, ZZ and Zhang, S and Zhang, N and Liang, J and Mu, BZ},
title = {Pilot-Scale Biodesulfurization of Natural Gas: Microbial Ecology and Community Dynamics of an In Situ Enriched System.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag136},
pmid = {42261086},
issn = {1365-2672},
abstract = {AIMS: This study investigated the microbial ecology of a biodesulfurization system inoculated with indigenous (rather than commercial) sulfur-oxidizing bacteria (SOB), aiming to assess their rapid enrichment feasibility and identify optimization strategies.

METHODS AND RESULTS: Pilot-scale Shell-Paques reactors were established to remove hydrogen sulfide from natural gas, using an inoculum of indigenous SOB. Microbial community dynamics were tracked via high-throughput sequencing, while ecological interactions were analyzed by combining co-occurrence network analysis and niche overlap indices. Indigenous SOB were successfully enriched to an abundance of ~30% within 13 days. Thioalkalimicrobium emerged as the dominant SOB genus, differing from strains typically employed in commercial technologies. A key finding was the production of bipyramidal elemental sulfur with a rhombic structure as the primary product. Both network and niche overlap analyses revealed complex ecological interactions, indicating potential competition and mutualism between Thioalkalimicrobium and other dominant genera.

CONCLUSIONS: Indigenous SOB can be rapidly enriched within two weeks to achieve effective desulfurization and sulfur recovery. The ecological insights lay the groundwork for optimizing enrichment through targeted microbiota management.},
}

@article {pmid42261608,
year = {2026},
author = {Shelat, VG},
title = {Microbial ecology and hepatocellular carcinoma: should a subset be viewed as a microbiome-conditioned malignancy?.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2026.2687711},
pmid = {42261608},
issn = {1747-4132},
}

@article {pmid42262077,
year = {2026},
author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y},
title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113225},
doi = {10.1128/spectrum.01132-25},
pmid = {42262077},
issn = {2165-0497},
abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.

IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.},
}

@article {pmid42264080,
year = {2026},
author = {Abdullah, M and Jayadevan, K and Therayil, A and Kumaraguruparan, N and Kavyasree, PKV and Dilna, P and Faiza, A},
title = {Pharmaco-microdynamics (PMD): Redefining Dose, Exposure, and Control for Living Drug Carriers.},
journal = {Annales pharmaceutiques francaises},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pharma.2026.06.002},
pmid = {42264080},
issn = {2772-803X},
abstract = {Living drug delivery systems including probiotics, engineered microbial therapeutics, and live biotherapeutic products represent a rapidly emerging therapeutic modality whose behavior fundamentally diverges from the assumptions underlying classical pharmacokinetics and pharmacodynamics (PK/PD). Unlike chemically defined, non-replicating drugs, living therapeutics persist, replicate, adapt, and generate bioactive molecules in situ, such that therapeutic exposure is not externally imposed but biologically generated over time. As a result, administered dose functions only as an initiating condition, while realized exposure emerges from population dynamics, ecological establishment, spatial localization, and regulated functional output. These properties render concentration-based PK/PD frameworks insufficient for predicting efficacy, safety, and controllability of living drug carriers. We introduce pharmaco-microdynamics (PMD) as a quantitative delivery-science framework designed to define, measure, and control exposure for living therapeutics. PMD is operationalized through a set of formal metrics including the functional exposure integral (F-AUC), colonization efficiency (CE), residence-time-weighted activity (RTWA), effective functional concentration (EFC50), and the genetic stability index (GSI)that serve as living-system analogues of AUC, bioavailability, mean residence time, EC50, and product-identity specifications. PMD reconceptualizes exposure as a time-integrated biological process governed by four interdependent axes: population kinetics, functional output kinetics, spatial pharmacology, and evolutionary dynamics. By integrating principles from pharmacology, microbial ecology, synthetic biology, biomaterials science, and systems modeling, PMD provides an operational vocabulary for translating adaptive biological agents into predictable and engineerable delivery systems. We further delineate PMD from adjacent frameworks such as quantitative systems pharmacology (QSP) and ecological microbiome modeling, and critically discuss boundary conditions under which classical PK/PD remains applicable to non-replicating or transient microbial interventions. This review critically examines the limitations of classical PK/PD in modeling living drug carriers, formalizes the core principles of PMD, and illustrates them through three quantitative case studies: SYNB1618 for phenylketonuria, synchronized-lysis bacterial tumor therapies, and fecal microbiota transplantation for recurrent Clostridioides difficile infection. Regulatory and clinical implications are addressed, emphasizing the need to shift from dose- and concentration-centric evaluation toward functional biomarkers, persistence metrics, and model-informed assessment of biological activity. Collectively, pharmaco-microdynamics establishes a unifying conceptual and quantitative foundation for the rational development of living medicines.},
}

@article {pmid42265261,
year = {2026},
author = {Pazos, T and Moya, P and Chiva, S and Škaloud, P and Kantnerová, V and Barreno, E and Garrido-Benavent, I},
title = {The Impact of Visible Symptoms of Thallus Damage on the Phycobiota of Mediterranean Epiphytic Lichens.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02794-3},
pmid = {42265261},
issn = {1432-184X},
abstract = {Lichens are excellent bioindicators of overall ecosystem health. The symbiotic nature of their thalli enables tracking changes in humidity, temperature, habitat disturbance and air pollution, often before larger plants do. Sensitive species usually show visible thallus damage, such as bleaching or changes in colour (including total or partial necrosis, and death of the photosynthetic component of the symbiosis), slow growth, and/or biases in reproductive strategies. Particularly, the extent to which these damages are associated with changes in the microscopic photosynthetic community inhabiting lichen thalli (phycobiota) remains poorly understood. Here, we combined Sanger and Illumina sequencing techniques to characterize the diversity and community structure of the eukaryotic phycobiome in selected epiphytic macrolichens showing different levels of thallus damage. Phylogenetic analyses revealed a high microalgal diversity, largely dominated by a few Trebouxia species, which are the most prevalent lichenized microalgae, accompanied by several low-abundance co-occurring genera. Notably, microalgal diversity peaked at intermediate levels of thallus damage. This pattern is consistent with disturbance-mediated modulation of microalgal community evenness rather than a categorical shift in symbiotic composition. These findings reveal previously unrecognized variability within the lichen phycobiota, providing new insights into the ecological dynamics and stress responses of these communities. In conclusion, our work offers a new perspective on the potential of lichens as sensitive bioindicators of air quality and ecosystem health.},
}

@article {pmid42265539,
year = {2026},
author = {Schoeman, C and Roodt, D and Mc Menamin, A and Bezuidt, O and Dithugoe, C and Pinard, D and Mizrachi, E},
title = {Conserved symbiosis-associated genes in the cycad Encephalartos natalensis suggest co-option for cyanobacterial symbiosis.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71311},
pmid = {42265539},
issn = {1469-8137},
support = {116239//National Research Foundation/ ; 118981//National Research Foundation/ ; },
abstract = {Plant-cyanobacterial symbioses have evolved independently at least four times across land plants, yet their underlying molecular mechanisms remain largely elusive. Here, we elucidate the pathways involved in this specialised symbiosis and nutrient exchange within coralloid roots (CRs) of Encephalartos natalensis. Using anatomical analysis and RNA sequencing, we characterise the structural and transcriptional features of CRs harbouring active, heterocyst-rich, nitrogen-fixing Nostoc cyanobacteria. Notably, no fungal hyphae or arbuscular structures were observed under the sampled conditions. CR-associated upregulation of core common symbiosis signalling pathway (CSSP) genes was evident, genes shared across multiple nodulating symbioses. Transcriptome-wide analysis further revealed elevated expression of citrulline and ornithine biosynthesis genes, indicating host assimilation of Nostoc-fixed ammonia. Together, these findings demonstrate that cycads retain and transcriptionally upregulate conserved symbiosis signalling genes during cyanobacterial associations. Building on the evolutionary link between CSSP genes and the ancient arbuscular mycorrhizal (AM) signalling toolkit, our results support differential retention of these genes across plant lineages. Specifically, in E. natalensis, CSSP gene expression in CRs suggests transcriptional co-option for cyanobacterial symbiosis in CRs. This study provides a framework for understanding the role of ancient molecular pathways in driving plant-microbe symbiosis evolution and diversification.},
}

@article {pmid42266025,
year = {2026},
author = {Campillo-Cora, C and Rodríguez-Seijo, A and Arias-Estévez, M and Santás-Miguel, V and Fernández-Calviño, D},
title = {Relevance of pollution-induced community tolerance (PICT) methodology in the soil assessment of heavy metal pollution. A review.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag097},
pmid = {42266025},
issn = {1551-3793},
abstract = {Heavy metal (HM) accumulation in soils may negatively affect soil microbial communities and ecosystem functioning. Several microbial-based methodologies have been applied to assess HM pollution in soils. However, it is often difficult to distinguish whether microbial responses are driven by HM accumulation or soil properties influence, particularly in field studies. In this context, methodologies specifically linked to HM toxicity, such as the pollution-induced community tolerance (PICT) approach, represent useful tools for environmental assessment. The PICT methodology is based on determining microbial community tolerance to a pollutant by comparing previously exposed communities with unexposed reference communities, enabling the identification of pollutant-induced effects on microbial communities. This review provides and updated overview of the conceptual basis, strengths, and limitations of the PICT approach for assessing HM-contaminated soils. In particular, it has been addressed the influence of soil properties on both PICT phases (selection and detection), methodological artifacts that may led to over- or underestimation of microbial community tolerance, as well as the occurrence of co-tolerance mechanisms among pollutants. Finally, current limitations and future perspectives for the application of PICT in soil ecotoxicology are discussed.},
}

@article {pmid42266442,
year = {2026},
author = {Sun, G and Shen, H and Xiao, Z and Yang, C},
title = {Gut Microbiota and Hypertension: Mechanisms, Drug Interactions, and Translational Directions for Individualized Therapy.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {613324},
pmid = {42266442},
issn = {1178-7074},
abstract = {Hypertension remains a major global health challenge, with suboptimal treatment and blood pressure (BP) control rates and apparent or confirmed resistant hypertension (RHT) affecting approximately 10-20% of treated patients. Increasing evidence suggests that the gut microbiota may contribute to BP regulation through interconnected metabolic, immune-inflammatory, intestinal barrier, gut-brain, and gut-kidney pathways. Short-chain fatty acids (SCFAs) may support vasodilation, renal sodium handling, epithelial barrier integrity, and anti-inflammatory signaling through receptor- and tissue-specific mechanisms, whereas trimethylamine N-oxide (TMAO) has been associated with adverse vascular and cardio-renal phenotypes but may function either as a pathogenic mediator or as a biomarker of altered microbial-host metabolism or impaired renal clearance. Beyond the SCFA-TMAO axis, bile acid metabolism, tryptophan/indole derivatives, phenylacetylglutamine, uremic toxins, and the nitrate-nitrite-nitric oxide pathway provide additional mechanistic links between microbial ecology and BP phenotypes. This review synthesizes mechanistic, pharmacological, clinical, and translational evidence on microbiota-hypertension interactions, with particular emphasis on drug-microbiota bidirectionality. We propose a three-layer framework in which bacterial enzymatic transformation, host metabolic regulation, and epithelial transport/barrier functions jointly shape antihypertensive drug exposure and response. Human interventional evidence remains preliminary: colon-targeted acetylated and butyrylated high-amylose maize starch increased circulating SCFAs and reduced 24-hour systolic BP by approximately 5-6 mmHg in a small, short-duration trial of untreated essential hypertension, whereas probiotics and prebiotics generally show modest BP reductions of approximately 1-3 mmHg systolic and 1-2 mmHg diastolic in meta-analyses. These findings support microbiota-informed hypertension research and risk stratification, but clinical implementation, particularly in well-defined RHT populations, remains investigational.},
}

@article {pmid42266459,
year = {2026},
author = {Van Landuyt, J and Oosterlinck, J and De Vrieze, J},
title = {The anaerobic digestion microbiome is robust toward variation in the waste activated sludge feed.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf072},
pmid = {42266459},
issn = {2730-6151},
abstract = {Anaerobic digestion stands out as the foremost technology for maximizing the valorization of waste activated sludge (WAS) to recover energy and recover resources. The physical/chemical and microbial makeup of WAS is susceptible to seasonal fluctuations, due to the open-air nature of wastewater treatment facilities, potentially impacting subsequent digester performance and the quality of the resulting digestate. This study delved into a comprehensive analysis of both the initial WAS and the digestate produced by 12 full-scale digesters during both a summer and winter sampling campaign. A significant influence of seasonal variations was observed on the physical/chemical and microbial composition of WAS. Interestingly, the digestate microbiome exhibited a high resilience with minimal seasonal fluctuations, but instead showed variations between different digesters. In summary, this research demonstrates that while WAS composition manifests in specific physical/chemical attributes, it does not exert a discernible influence on the microbial composition of the resulting digestate.},
}

@article {pmid42257736,
year = {2026},
author = {Di Nezio, F and Di Cesare, A and García-Cobo, M and Brankovits, D and Sabatino, R and Borgomaneiro, G and Fresno-López, Z and Neunschwander Kurtz, M and Boulamail, S and Cozzoli, F and Fumarola, L and Gonzalez, BC and Roldán, A and Camacho, C and García-Herrero, A and Moro, L and Valdivia, C and Mateo-Mederos, E and García-Gómez, G and Fontaneto, D and Corno, G and Eckert, EM and Martínez, A},
title = {Multilayered Human Activities Shape the Microbial Communities of Groundwater-Dependent Ecosystems on an Arid Oceanic Island.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02797-0},
pmid = {42257736},
issn = {1432-184X},
abstract = {Island coastal aquifers, though spatially limited, sustain key ecosystem functions linked to locally critical provisioning, maintenance and cultural ecosystem services. These functions are largely dependent on the presence of highly adapted biological communities, whose microbial components remain poorly understood. Here, we describe bacterial communities across groundwater-dependent ecosystems on Lanzarote (Canary Islands, Spain), spanning habitats with contrasting environmental conditions and degrees of human influence, using 16 S rRNA gene amplicon sequencing. We then infer the processes shaping community variation by integrating diversity partitioning, indicator species analysis, and machine-learning classification. Bacterial taxonomic diversity varied significantly among habitats, with community composition primarily structured by turnover, consistent with environmental filtering. In contrast, predicted human-associated and potentially pathogenic taxa showed patterns dominated by nestedness, indicating localized enrichment linked to anthropogenic inputs. Caves, enclosed marine bays, and hypersaline systems hosted the most compositionally distinct microbial communities, whereas wells and anchialine pools showed greater overlap in community composition. Together, our results suggest that groundwater microbial communities are influenced by the interplay between environmental filtering and anthropogenic inputs, and that coastal aquifers can act simultaneously as reservoirs of natural biodiversity and sinks of human-associated bacteria. These findings highlight the need for integrative monitoring and conservation strategies that incorporate both hydrological and biological components to safeguard groundwater-dependent ecosystems on oceanic islands.},
}

@article {pmid42259270,
year = {2026},
author = {Bonte, D and Van de Peer, Y},
title = {A three-step model for the establishment of polyploid plants.},
journal = {Current biology : CB},
volume = {36},
number = {11},
pages = {R553-R564},
doi = {10.1016/j.cub.2026.03.078},
pmid = {42259270},
issn = {1879-0445},
abstract = {Polyploidy, the result of whole genome duplication, is widespread in plants. Over long timescales, polyploids seem to go extinct more often than diploids. Clear genomic signs of long-term polyploid success exist across plants, but they are comparatively rare within individual lineages. To address the 'polyploid paradox' - early success followed by long-term decline - we propose a three-step framework. The first step is 'Supply', the rate at which new polyploids arise, which can spike in stressful conditions because of elevated formation of gametes with unreduced genomes and relatively weak ecological filtering of the generated polyploids. The second step is 'Bridging', which can occur in one or other of two ways: a short-term route, in which genome duplication increases phenotypic and genetic variation and rarely produces phenotypes that fit the new environment; or a longer-term route, when processes that normally exclude rare cytotypes are weakened and polyploids can persist despite the early costs. The third and last step, 'Consolidation' determines evolutionary outcomes, where some polyploids achieve niche divergence and persist alone or jointly with diploids, while many are removed by long-term costs. As a result, even though polyploids often succeed in the short term, relatively few persist over macroevolutionary timescales. We refer to this sequence as Supply-Bridging-Consolidation (SBC). In this view, polyploid success reflects demographic assembly and ecological opportunity; adaptation usually follows establishment, rather than causing it. The framework yields testable predictions and offers a unified understanding of when polyploids flourish and when they falter, and why only a small fraction is ultimately retained.},
}

@article {pmid42259455,
year = {2026},
author = {Wang, Y and Huang, Y and Yin, D and Gong, B and Fan, G},
title = {A segmented electron donor dosing strategy for enhancing thiosulfate-driven partial denitrifying efficiency: Insights into sulfur oxidation pathway, electron transfer and metagenomic microbial ecology.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135106},
doi = {10.1016/j.biortech.2026.135106},
pmid = {42259455},
issn = {1873-2976},
abstract = {Thiosulfate-driven partial denitrification (TPD) is a highly efficient denitrification process that exhibits good stability when coupled with Anammox. This study aimed to enhance the performance of the TPD system by employing different electron donor dosing strategies. The data show that the NO3[-]-N removal efficiency (NRE) and NO2[-]-N accumulation efficiency (NAE) in the segmented dosing group reached 98 % and 90 %, respectively. The study indicates that segmented electron donor dosing significantly enhances the activity of the electron transport chain. Specifically, Complex I and Complex III are associated with electron utilization by nitrate reductase (Nar) and nitrite reductase (Nir). The increased activity of Complex I and the inhibited activity of Complex III in the segmented dosing group contribute to improved NRE and NAE. Metagenomic analysis revealed that Thiobacillus predominated and served as the key functional species for Nar, Nir, and sulfur oxidation. Combined with qPCR analysis, segmented dosing significantly increased the expression levels of functional genes and elevated the NarG/(NirK + NirS) ratio, which further facilitated the accumulation of NO2[-]-N. Furthermore, the segmented dosing group possessed a complete sulfur oxidation pathway capable of fully oxidizing S2O3[2-] to SO4[2-], suggesting a reduced metabolic potential for S[0] production within the system. Overall, this study offers a potential strategy for ensuring a stable supply of nitrite in future anaerobic ammonium oxidation processes.},
}

@article {pmid42259791,
year = {2026},
author = {Koch, H and Clavel, T and Mayr, C and Coltman, BL and Schloter, M and Vorholt, JA and Sanz, Y and Cernava, T and Beattie, GA and Lange, L and Chaillou, S and Kovács, ÁT and Smidt, H and Pieterse, CMJ and Kostic, T and Finkel, OM and Lawson, CE and Cocolin, L and Mercado-Blanco, J and Finn, RD and Papadopoulou, KK and Ryan, M and Candela, M and Cotter, PD and Berg, G and O'Sullivan, O and Delgado-Baquerizo, M and Trivedi, P and Charles, TC and Singh, BK and Brader, G and Marian, M and Sessitsch, A},
title = {From "synthetic" to defined microbial communities for clearer terminology.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74251-1},
pmid = {42259791},
issn = {2041-1723},
support = {doi.org/10.55776/COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/P36288//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; doi.org/10.55776/COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; doi.org/10.55776/COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101083671//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101084485//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101060218//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101166968//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101060693//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101094353//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101084163//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 395357507 - SFB1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013 - SFB1382//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 460129525 - NFDI4Microbiota//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CL 481/17-1 - SPP2474//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SPI.2022.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
}

@article {pmid42244647,
year = {2026},
author = {Zeng, X and Meng, X and Weakley, AM and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and Fischbach, MA},
title = {A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.23.727446},
pmid = {42244647},
issn = {2692-8205},
abstract = {The complexity of the gut microbiome has made it challenging to define the role of individual species in community-level function. Here, we constructed 56 single-strain dropout variants of a defined 118-member community and used each one to colonize a group of germ-free mice. In many cases, removing a single strain triggered a large reordering of a small group of species, which in turn altered the community's metabolic output. En bloc removal of the eight-strain acetogen compartment markedly reduced acetate production and caused intestinal H 2 accumulation and bloating; a specific subset of four acetogens was sufficient to relieve bloating and restore acetate production. Together, these data show that small disturbances in community composition can trigger a confined ecological reorganization with a large chemical phenotype, and they reveal novel strategies for engineering communities with altered metabolic output.},
}

@article {pmid42246391,
year = {2026},
author = {Ramadier, G and Chakraborty, S and Fonquernie, I and Dessauvages, TT and Boudoux, C and Brun, YV and Berne, C and Weiss, LE},
title = {Single-Cell Probing of Nanoscale Bacterial Adhesion in Real-Time Using Optical Tweezers.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.6c03697},
pmid = {42246391},
issn = {1936-086X},
abstract = {Bacterial biofilms are organized microbial communities that profoundly impact medicine, industry, and microbial ecology. Biofilm formation begins with nanoscale adhesion events between single bacteria and a surface, and the earliest stages of surface colonization involve reversible interactions that transition to irreversible attachment through the secretion of specialized nanoscale bioadhesins. Understanding and controlling the initial interactions between adhesin and surface is key to control and prevent biofilm formation. Here, we investigate the nanoscale adhesion dynamics of single Caulobacter crescentus cells, a dominant early colonizer in environmental biofouling, focusing on its holdfast, a strong nanoscale adhesive organelle that mediates irreversible attachment within seconds of contact. To characterize the time-dependent mechanical properties of holdfast, we developed the Trapezoid, a custom optical tweezers platform that combines nanometer spatial precision with millisecond temporal control of cell position, contact timing, and applied force on defined surfaces. We implemented a trapezoidal temporal profile of these programmed contact cycles, in which a single cell is brought into contact with the surface, maintained for a defined duration, retracted, and subjected to controlled pulling forces. This approach enables real-time quantification of nanoscale adhesion onset, holdfast deployment kinetics, and influence of surface chemistry at the level of individual live adhesion events. Our results dissect the physical and biochemical determinants of bacterial adhesion, providing a quantitative framework for the rational design of antiadhesive coatings, nanoscale biofouling control strategies, and bioinspired adhesives functional in wet environments.},
}

@article {pmid42247161,
year = {2026},
author = {Fablet, L and Belcour, A and Stephant, S and Michel, C and Ropers, D and Cerna, K and Bombach, P and Riha, J and Tremosa, J and An-Stepec, BA and Fadrhonc, K and Dopffel, N and Rad, S},
title = {Microbial-geochemical Interactions in Underground Reservoirs: Implications for Hydrogen Storage.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02800-8},
pmid = {42247161},
issn = {1432-184X},
support = {No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; ANR-23-CETP0002//Agence Nationale de la Recherche/ ; },
abstract = {Understanding microbial life in deep geological environments is essential for assessing natural biogeochemical processes and their implications for subsurface activities such as underground hydrogen storage. This study investigates the water chemistry, microbial community composition, and metabolic potential of two contrasting geological settings: porous reservoirs and salt caverns. This study is among the first to provide a large-scale comparison of microbial and geochemical processes across reservoirs. Our results show that porous reservoirs, particularly those with carbonate facies, are characterized by carbonate-rich fluids and host anaerobic microbial communities dominated by methanogenic archaea, fermentative bacteria, and acetogens. In contrast, the studied salt caverns contain salt-saturated brines and are dominated by halophilic and chemoorganotrophic microorganisms adapted to oligotrophic, high-salinity conditions. Some reservoirs showed atypical microbial profiles influenced by anthropogenic activities or hydrogeological connections, which alter local geochemistry and microbial structures. This study highlights the influence of salinity, carbon availability, temperature, and human impact on microbial community structure and metabolic functional potential. The presence of hydrogenotrophic microorganisms raises concerns about their potential to consume injected hydrogen and alter gas quality. These findings underscore the need to move beyond detection toward activity-based assessments of microbial hydrogen consumption, in order to anticipate biogeochemical dynamics and develop effective mitigation strategies. A better understanding of the interplay between reservoir chemistry, geology, and microbiology is crucial for ensuring safe and efficient underground hydrogen storage.},
}

@article {pmid42250808,
year = {2026},
author = {Sabina, R and Kharmawphlang, IM and Charan, K and Hussain, N},
title = {Per- and polyfluoroalkyl substances stress in soil ecosystems: decoding microbial dysbiosis mechanisms and advanced remediation strategies.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135036},
doi = {10.1016/j.biortech.2026.135036},
pmid = {42250808},
issn = {1873-2976},
abstract = {Per- and polyfluoroalkyl substances (PFAS), the so-called "forever chemicals," are emerging contaminants that severely disrupt soil ecosystems by rewiring microbial networks that sustain biogeochemical processes. This review deciphers the mechanisms underlying PFAS-induced microbial dysbiosis, revealing how these contaminants reconfigure community architecture, metabolic functions, and enzyme-mediated processes critical for biogeochemical cycling. It further integrates multi-omics approaches, spanning genomics to metabolomics, to elucidate molecular signatures and adaptive responses that govern microbial resilience and vulnerability across trophic hierarchies. Furthermore, the review examines PFAS biotransformation pathways, emphasising oxidoreductase-mediated mechanisms, kinetic bottlenecks, and catalytic constraints within complex soil matrices. By bridging microbial ecology with advanced material science, the review introduces a transformative paradigm of hybrid catalytic systems, including nanozyme-enabled transformations, engineered enzymes, and photocatalytic assemblies for targeted PFAS degradation. Thus, by linking microbial dysfunction with engineered catalytic innovation, the review offers a systems-level blueprint for sustainable and efficient strategies to restore PFAS-contaminated soils. Notably, this review highlights the urgent need for integrated multidisciplinary approaches to mitigate PFAS-induced ecological risks and advance sustainable soil restoration technologies.},
}

@article {pmid42252423,
year = {2026},
author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ},
title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05199-x},
pmid = {42252423},
issn = {1471-2180},
support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Química Valaner-MGI Mexico/ ; },
abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.},
}

@article {pmid42252693,
year = {2026},
author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W},
title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag145},
pmid = {42252693},
issn = {1751-7370},
abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.},
}

@article {pmid42253950,
year = {2026},
author = {Han, X and Guo, XL and Qiu, J},
title = {From gut-reproductive microbiota to ferroptosis: a comprehensive insight into the molecular-pathogenicity of endometriosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1762013},
pmid = {42253950},
issn = {1664-3224},
abstract = {Endometriosis (EMS) is a highly heterogeneous chronic gynecological disease characterized by pain, infertility, and relapse, with its etiology and pathogenesis not yet fully elucidated. Traditional theories, including "retrograde menstruation," "implantation theory," and "abnormalities in immune tolerance," struggle to adequately explain the complex lesion behavior, diverse phenotypic characteristics, and accompanying immune-metabolic disorders. In recent years, the key roles of imbalances in the gut and reproductive microbiomes, abnormal iron metabolism, and the newly proposed ferroptosis in the occurrence and development of EMS have gradually gained attention, suggesting that this disease may be a systemic condition involving the interplay of microbial ecology, iron metabolism, and cell death. Existing studies indicate that the gut-reproductive microbiome profoundly influences the body's iron homeostasis and iron load by regulating mucosal immunity, systemic inflammatory responses, and metabolic environments. This, in turn, activates the ferroptosis pathway through iron-dependent lipid peroxidation and cell membrane damage, participating in the formation, maintenance, and inflammatory microenvironment shaping of ectopic lesions. Based on these findings, this article systematically reviews the interactions between gut-reproductive microbiome imbalance and iron metabolism disorders, integrating multi-omics evidence such as microbiome analysis, metabolomics, and iron metabolism/ferroptosis-related molecular markers. It proposes a new pathological mechanism framework of "dysbiosis-iron overload-ferroptosis" incorporating microecological imbalance and ferroptosis into a unified picture of the pathogenesis of EMS. Furthermore, this article discusses potential therapeutic strategies and application prospects surrounding microbiome remodeling (such as probiotics, fecal microbiota transplantation, dietary and lifestyle interventions) and pharmacological targeting of key ferroptosis-related molecules. Through a comprehensive and critical analysis of existing evidence, this review aims to provide a more systematic theoretical framework for the mechanistic research of EMS and offer ideas and directions for future clinical translation of precise classification, individualized intervention, and novel treatment plans.},
}

@article {pmid42254836,
year = {2026},
author = {Xu, L and Sun, X and Zakem, EJ},
title = {Dependency-competition tradeoffs structure microbial niches and nitrogen cycling.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag134},
pmid = {42254836},
issn = {2730-6151},
abstract = {The marine nitrogen cycle is regulated by ecological interactions among diverse microbial populations. In anoxic zones, populations carrying out anaerobic metabolisms, mainly multi-step denitrification and anammox, drive the loss of bioavailable nitrogen, some of which is emitted as the potent greenhouse gas nitrous oxide ([Formula: see text]). While competition for limiting resources is well studied, the combined effects of competition and dependencies, where a "feeder" population supplies a required resource to a "recipient," remain poorly understood. Here, we develop a trait-based consumer-resource framework to test how recipient populations reshape the ecological niches of their feeders and competitors. Our analysis demonstrates how recipients may expand either their feeder's or their feeder's competitor's niche, depending on relative competitive abilities on limiting resources. We analyze and identify equilibrium co-existence regions, threshold regimes, and the dominant pathways of nitrogen loss as a function of varying both organic matter (OM) and nitrate supply, rather than just their ratio. Examining this 2D supply space identifies a distinct zone where OM and nitrate co-limitation results in [Formula: see text] production but not consumption, and thus an ecological niche for [Formula: see text] accumulation. Additionally, the model suggests that anammox bacteria occupy a wider range of OM and nitrate supply regimes than denitrifying populations, consistent with their more frequent detection across diverse marine environments. The results link microbial interaction networks to biogeochemical fluxes relevant at global scales and extend ecological theory to multi-resource systems with nested competitive and dependent interactions.},
}

@article {pmid42254896,
year = {2026},
author = {Vaggi, C and Vötterl, JC and Lerch, F and Yosi, F and Koger, S and Ricci, S and Verhovsek, D and Metzler-Zebeli, BU},
title = {Characterization of fecal bacterial microbiomes according to fecal color, consistency, and sample type in piglets before and after weaning.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1815748},
pmid = {42254896},
issn = {2297-1769},
abstract = {Fecal samples are widely used as a proxy for the large intestinal microbiota; however, phenotypic characteristics (e.g., color and consistency) may be associated with divergent microbial profiles, especially around weaning, when diet and physiological adaptation rapidly alter gut function. The relationship between fecal phenotype, sample type, and piglet gut microbiota under physiological conditions remains poorly understood. This study investigated the bacterial communities in different fecal phenotypes of piglets shortly before and immediately after weaning. The fecal consistency of 192 piglets across two replicate batches was scored daily from day of life (DoL) 28 to 36, and fecal or rectal swab samples were collected at DoL28 and DoL33. The samples were classified by type (feces/swab), color (brown/yellow), and consistency (balls/liquid). DNA was extracted for quantification of total bacterial gene copies and 16S rRNA gene sequencing, and microbial composition was analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2), Statistical Analysis System (SAS), and R. Fecal consistency changed markedly over time, shifting from predominantly ball-shaped on DoL28-32 to softer feces thereafter (p < 0.001). Age strongly influenced microbiota structure, with marked increases in relative abundance of Prevotella and Alloprevotella from DoL28 to DoL33, whereas the abundance of Escherichia, Methanobrevibacter, and Fusobacterium declined. Microbial communities differed between sample types, with swabs potentially reflecting mucosa-associated taxa more closely than fecal samples. Shannon and Simpson indices indicated reduced diversity in yellow and liquid feces on DoL28 (p < 0.001). Swabs and yellow liquid feces on DoL28 showed higher relative abundances of Escherichia, Bacteroides, and Fusobacterium, whereas brown ball-shaped feces were enriched in Lachnospiraceae, Prevotella, and Lactobacillus on both sampling days (p < 0.05). Overall, each fecal phenotype exhibited a distinct bacterial signature, and the sample type influenced the composition of the captured community. Monitoring fecal phenotypes alongside selecting appropriate sample types may enhance the interpretation of microbiome data and offer a practical, non-invasive approach to assess gut health during the critical weaning period.},
}

@article {pmid42256221,
year = {2026},
author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V},
title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826972},
pmid = {42256221},
issn = {2235-2988},
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.},
}

@article {pmid42256599,
year = {2026},
author = {Keum, HL and Sul, WJ and Kim, HS},
title = {Comparison of skin microbiota profiles in chronic scratch lesions using tape strip and swab sampling.},
journal = {JAAD international},
volume = {27},
number = {},
pages = {19-20},
pmid = {42256599},
issn = {2666-3287},
}

@article {pmid42243144,
year = {2026},
author = {Qin, Z and Wang, Q and Yang, Q and Wang, Q and Li, Y and Ma, H and Gao, J and Li, X},
title = {Agricultural fungicides shape soil and sediment reservoirs of multidrug-resistant fungi.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73958-5},
pmid = {42243144},
issn = {2041-1723},
support = {42277409//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Fungicide resistance in environmental fungi represents a growing One Health challenge, yet its ecological extent and clinical relevance remain poorly studied. Here, we integrate residue monitoring, community profiling, large-scale culture isolation, and mechanistic assays to investigate the resistance of fungi in agricultural soils and adjacent river sediments. The results indicate that fungicides are widely detected in environmental samples and pose substantial ecological risks, particularly carbendazim and tebuconazole. Resistant fungi are also widespread and account for a large proportion of the genera detected in fungal communities. Among >3,900 resistant isolates, we recover 358 multidrug-resistant (MDR) strains showing cross-resistance to multiple agricultural fungicides. Transcriptomic, qPCR, and molecular docking analyses suggest that environmental MDR phenotypes arise from synergistic effects of target-gene alterations, efflux pump overexpression, and adaptive stress responses. Notably, triazole exposure coordinately upregulates virulence genes and mycotoxin biosynthetic clusters, indicating transcriptional activation of genes associated with virulence and secondary metabolism. Together, these findings highlight agricultural landscapes as reservoirs of fungicide-resistant fungi and underscore the need to re-evaluate fungicide practices to protect crop health, ecosystem stability, and the effectiveness of clinical antifungals.},
}

@article {pmid42026592,
year = {2026},
author = {Li, Y and Zhu, Y and Zhang, F and Huang, C and Wang, Z},
title = {The interaction between microbes and cytokines in cancer: unraveling the underlying effects.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42026592},
issn = {1479-5876},
support = {Nos. 32370628,92159302, 32170592//National Natural Science Foundation of China/ ; Nos. 2022ZDZX0018, 2023NSFSC004,2024NSFSC0402//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; No. 2023-YF09-00039-SN//National Science and Technology Planning Project/ ; No. ZYGD22009//1.3.5 project for Disciplines of Excellence, West China Hospital, Sichuan University/ ; },
abstract = {An increasing number of studies have found that microbes are involved in the development and treatment of tumors, and the impact of microbes on the tumor microenvironment has emerged as a prominent field in cancer studies. Although microbiome–immunity interactions in cancer have extensively reviewed in previous studies, the molecular integration of microbes with cytokines within the tumor microenvironment remains insufficiently resolved. This review examines how microbes influence the immunological and inflammatory regulatory systems in cancer. The activation of important signaling axes, such as IL-6/STAT3, TNF-α/NF-κB, and interferon pathways, by microbial components and metabolites (LPS, SCFA, and EPS) changes immune surveillance, encourages immune evasion, and affects the spread of metastases. Recent studies indicate that Microbiota-induced alterations in cytokine signaling increasingly influence cancer immunotherapy, suggesting that microorganisms and their metabolites may emerge as potential targets for novel anti-tumor immunotherapy. Evidences from multiple cancer types, combined with studies on specific non-malignant diseases, reveals synergistic alterations in microbial communities and cytokine networks. These interactions form a microbe-cytokine axis linking inflammation, tumor progression, and treatment response. Understanding the mechanisms underlying the interplay between microbial ecology and host cytokines may provide strategic guidance for enhancing precision cancer immunotherapy.},
}

@article {pmid42241895,
year = {2026},
author = {Hodžić, A and Cizek, V and Kunert, M},
title = {Gut immune and redox transcriptional responses to Borrelia infection in questing Ixodes ricinus.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {4},
pages = {102668},
doi = {10.1016/j.ttbdis.2026.102668},
pmid = {42241895},
issn = {1877-9603},
abstract = {Ticks of the genus Ixodes are major vectors of pathogens of medical and veterinary importance, including the causative agents of Lyme borreliosis. While much is known about tick immune responses during feeding, the molecular mechanisms that enable pathogen persistence during the off-host period remain poorly understood. Here, we investigated the gut immune landscape of questing Ixodes ricinus females naturally infected with members of the Borrelia burgdorferi sensu lato species complex. Transcriptional profiling of gut tissues revealed sustained upregulation of the NF-κB transcription factor dorsal and redox-associated genes in Borrelia-infected individuals, whereas other selected immune signalling pathway genes and antimicrobial peptides remained unchanged. Correlation analyses further indicated that Borrelia load was positively associated with gene expression levels, while redox genes were strongly co-regulated, indicating a coordinated control of oxidative homeostasis. These findings point to a targeted immune response that supports gut homeostasis rather than triggering broad antimicrobial activity. However, the limited number of Borrelia-positive questing ticks analyzed in this study highlights the need for further investigations with larger sample sizes, multiple developmental stages, and additional infection experiments to validate and expand these findings.},
}