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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42389292,
year = {2026},
author = {Wang, Y and Liu, X and Zhang, Z and Jing, R and Zhao, X and Han, W and Huang, C and Yang, Q},
title = {In-sewer microplastics drive microbial metabolic shifts toward enhanced methanogenesis.},
journal = {Environmental science and ecotechnology},
volume = {32},
number = {},
pages = {100726},
pmid = {42389292},
issn = {2666-4984},
abstract = {Microplastics (MPs) in sewer systems can be transported extensively before entering wastewater treatment plants. Sewer systems harbor complex microbial communities under low-oxygen, sulfide-rich conditions that drive key biogeochemical cycles. These conditions drive microplastic aging, whereas these particles concurrently perturb sewer microbial ecology and metabolic functions. However, the underlying mechanisms of in-sewer microplastic aging and their subsequent impacts on sewer microbiomes remain unclear. Here we show that hydroxyl radicals preferentially attack ester bonds (C-O) in polyethylene terephthalate (PET) and polybutylene adipate terephthalate (PBAT) MPs, increasing surface roughness, reducing particle size, promoting surface oxidation, and ultimately inducing polymer chain scission. Exposure to PET and PBAT MPs at 30-500 particles L[-1] intensified oxidative stress, disrupted membrane integrity and permeability, impaired microbial activity, and suppressed sulfide production in a dose-dependent manner. These disruptions coincided with weakened microbial co-occurrence networks and a shift from stochastic toward deterministic community assembly. High doses of PET and PBAT MPs reduced hydrolytic/fermentative bacteria and sulfate-reducing bacteria by up to 63.4% and 49.7%, respectively, while enriching hydrogen-producing acetogenic bacteria and methanogenic archaea by 48.4-67.0%, consistent with reduced sulfidogenic potential and enhanced methanogenic potential. Changes in genes related to antioxidant defense, SOS response, quorum sensing (e.g., sodA, katG, lexA, and luxS), and redox signaling suggested potential mechanisms of microbial metabolic perturbations aggravated by PET and PBAT MPs. Our results indicate that sewer systems are not passive conduits but active reactors that promote MP aging, and that MPs reshape microbial functions. Microplastic control may therefore help reduce downstream particle pollution and limit perturbations to urban sewage biogeochemistry.},
}

@article {pmid42390568,
year = {2026},
author = {Pepori, AL and Berto, H and Gionni, A and Luchi, N and Pecori, F and Santini, A},
title = {Exploring Metabolic Interaction between Ophiostoma novo-ulmi and Geosmithia spp.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02822-2},
pmid = {42390568},
issn = {1432-184X},
abstract = {Dutch elm disease (DED), caused by the invasive vascular pathogen Ophiostoma novo-ulmi, is one of the most devastating pandemics affecting elms. Within beetle galleries and on elm bark beetle vectors, O. novo-ulmi co-occurs with fungi of the genus Geosmithia, yet the functional significance of this association remains poorly understood. This study investigates metabolic interactions between O. novo-ulmi and Geosmithia spp. using in vitro dual-culture experiments and phenotype microarray analysis to elucidate ecological mechanisms potentially influencing disease development and vector ecology. Dual-culture assays on dH2O agar revealed that O. novo-ulmi subsp. novo-ulmi exhibited significantly enhanced radial growth rates when cultured in proximity to Geosmithia isolates. Phenotypic analysis revealed distinct metabolic strategies: O. novo-ulmi subsp. novo-ulmi utilised substrates within 12-24 h and preferred polyols and simple carbohydrates, while G. pumila adopted a progressive colonization strategy, ultimately utilising 92 substrates in 90 h and demonstrating greater utilisation of nitrogen-enriched substrates, nucleosides and complex organic acids. Co-culture revealed utilization of adenosine and nitrogen-rich compounds, but antagonistic interactions for polyols and amino sugars. Niche overlap analysis showed asymmetric resource partitioning: O. novo-ulmi subsp. novo-ulmi utilized 98% of G. pumila's substrates versus 81% reciprocal overlap, while fungal competitiveness analysis indicated G. pumila superiority. The distinct metabolic strategies and complementary patterns of substrate utilisation suggest niche construction and the functional partitioning of resources. These findings provide evidence supporting the hypothesis of a functional association within the DED pathosystem. The results highlight the ecological importance of microbial community complexity in pathogenic interactions and suggest that understanding these multitrophic relationships is essential for the development of effective disease management strategies.},
}

@article {pmid42390575,
year = {2026},
author = {Cukier, S and Gawor, J and Grzesiak, J},
title = {Gut Microbiota and Feeding Patterns of the Antarctic Fairy Shrimp (Branchinecta gaini Daday, 1910): A Metabarcoding Perspective.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02820-4},
pmid = {42390575},
issn = {1432-184X},
abstract = {Understanding how feeding ecology and environmental conditions shape gut microbiota is essential for interpreting host-microbe interactions in extreme environments. Here, we investigated the diet and gut-associated bacterial communities of the Antarctic fairy shrimp Branchinecta gaini across multiple postglacial freshwater ponds on King George Island. We combined microscopic gut content analysis with 18 S and 16 S rRNA gene metabarcoding and distinguished between gut content and gut tract-associated bacterial fractions in pooled, pond-level samples to assess the relative roles of diet, host filtering, and environmental context in structuring gut-associated communities. Our results reveal pronounced dietary flexibility of B. gaini, with strong site-specific differences in consumed eukaryotic taxa reflecting local resource availability. This trophic variability was mirrored by highly variable gut-associated bacterial communities, characterized by low taxonomic overlap among ponds and the absence of a stable core microbiota at the pooled sample level. Although bacterial assemblages differed between gut contents and gut tract, consistent at the composite-sample scale, this pattern suggests limited evidence for strong host filtering. Gut-associated communities retained pond-specific signatures, indicating a dominant role of environmental sourcing. Environmental drivers influenced different aspects of gut microbiome organization: hydrological connectivity and associated conductivity gradients were linked to shifts in bacterial community composition, whereas water temperature showed a non-linear association with bacterial alpha diversity but not with overall community structure. Water pH showed no detectable effect on either metric. Together, these findings indicate that gut-associated bacterial communities of B. gaini, as captured by pooled samples, largely reflect environmentally acquired assemblages shaped by opportunistic feeding and local environmental filtering. This ecological flexibility may represent a key strategy enabling persistence of B. gaini across highly heterogeneous Antarctic freshwater ecosystems.},
}

@article {pmid42391470,
year = {2026},
author = {Plominsky, AM and Peoples, LM and Norenberg, M and Ramirez-Flandes, S and Podell, S and Mullane, KK and Casagrande, D and Roman, C and Pockalny, R and Smith, DC and Belser, C and Poulain, J and Allen, EE and Glud, RN and Ulloa, O and Barber, N and D'Hondt, S and Bartlett, DH},
title = {Minimising decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag064},
pmid = {42391470},
issn = {1751-7370},
abstract = {The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimising pressure and temperature effects. When compared to samples collected under pressurised conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a > 20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurised (e.g., members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g., Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.},
}

@article {pmid42393338,
year = {2026},
author = {Cornell, CR and Olatinwo, RO and Kozhar, O and Wharton, K and Stewart, JE},
title = {Emerging Threats in Southern U.S. Pine Plantations: Temporal Dynamics of Fungal Communities and the Impact of Lecanosticta acicola.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02825-z},
pmid = {42393338},
issn = {1432-184X},
abstract = {Globally, pine forest ecosystems are under increased threat of foliar fungal pathogens. This includes brown spot needle blight (BSNB), caused by Lecanosticta acicola. High disease severity of BSNB has been observed in loblolly pine plantations across the Southeastern U.S., causing substantial declines in productivity. Because foliar disease outcomes depend on phyllosphere community interactions, shifts in community composition under climate variation may influence outbreak potential of L. acicola. To investigate these interactions, fungal communities in first- and second-year symptomatic and asymptomatic needle tissue were examined over two years across six loblolly pine plantations in central Louisiana. L. acicola was consistently enriched in symptomatic needles and emerged as a strong indicator of disease, including increasing crown dieback, particularly in first-year needles. Disease progression was associated with reduced fungal diversity and pronounced shifts in community composition, consistent with microbiome dysbiosis. Additional fungi, including Lophodermium and Soleella, were enriched in symptomatic needles, likely representing opportunistic associates with a potential role in disease. There were distinct differences in the relationship with climate variables for symptomatic and asymptomatic communities. Symptomatic communities were associated with higher humidity, higher minimum temperatures, and reduced solar radiation, whereas asymptomatic communities were correlated with warmer, drier conditions. Our findings demonstrate that BSNB severity reflects both L. acicola infection and broader needle fungal community disruption, with first-year needles being especially vulnerable. These results underscore the need to integrate microbial community dynamics and climate into disease monitoring and management, as increasing humidity, warmer nights, and more variable precipitation likely elevate fungal pathogen risk.},
}

@article {pmid42395019,
year = {2026},
author = {Li, X and Zhao, Y and Liu, N and Zhang, Y and Liu, R and Shan, W and Zhang, J and Chen, T},
title = {Panax ginseng as a microbial ecosystem modulator: implications for systemic health via the gut-organ axes.},
journal = {Journal of ginseng research},
volume = {50},
number = {4},
pages = {101059},
pmid = {42395019},
issn = {1226-8453},
abstract = {Panax ginseng C.A. Meyer, a renowned medicinal herb, exerts many of its systemic effects through intricate interactions with the gut microbiota, a relationship that also addresses the challenge of its own limited oral bioavailability. This review comprehensively examines the role of ginseng and its bioactive constituents in modulating gut microbiota and their subsequent influence on host health through key gut-organ axes. Based on an in-depth analysis of literature, we summarize how ginseng intervention is associated with a modulated gut microbial ecology-characterized by enriched beneficial taxa and suppressed pathogens-and is further linked to enhanced barrier integrity, regulated microbial metabolites, and reduced inflammation and oxidative stress. These mechanisms underlie its protective effects across multiple organ systems, including the gut-brain, gut-liver, gut-lung, gut-heart, and gut-kidney axes, ameliorating conditions such as cognitive decline, hepatic inflammation, pulmonary fibrosis, atherosclerosis, and renal injury. Clinical evidence further associates ginseng with improved metabolic and cognitive parameters correlated to microbial changes. We conclude that the therapeutic activity of ginseng appears to involve, and is likely modulated by, its prebiotic-like influence on the gut microbiota. However, the degree to which its efficacy is microbiota-dependent varies across different organ systems, as established by current evidence. Further mechanistic and clinical studies, particularly those employing causal models, are essential to definitively validate its potential in treating chronic diseases via microbiota-based strategies.},
}

@article {pmid42396625,
year = {2026},
author = {San Román, AX and Chen, G and Ronda, K and Muratore, T and Knorr, MA and Frey, SD and Wang, J and Simpson, AJ and Simpson, MJ},
title = {High-Resolution Molecular Analyses Reveal Non-additive Impacts of Chronic Warming and Nitrogen Addition on Soil-Derived Dissolved Organic Matter.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04800},
pmid = {42396625},
issn = {1520-5851},
abstract = {Dissolved organic matter (DOM) plays a central role in soil carbon (C) cycling as the most mobile and reactive C fraction in forests, regulating the microbial metabolism, nutrient availability, and C export. However, molecular-level DOM responses to environmental stressors such as warming and nitrogen (N) deposition remain poorly constrained, particularly under their combined influences. Thus, we investigated how 14 years of soil warming, N-addition, and combined heat + N influence soil-derived DOM quantity and chemistry. Using solution-state NMR spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry, we resolved DOM composition across molecular size, biochemical class, mobility, and oxidation state. While the DOM quantity remained unchanged, warming enhanced microbial processing and oxidative transformation, yielding DOM enriched in oxidized, structurally complex compounds, whereas N-addition suppressed decomposition, limiting the release of plant-derived biopolymers and shifting DOM toward more microbial-derived constituents. Heat + N produced the most compositionally diverse DOM, with molecular shifts more closely resembling warming-induced responses, indicating that temperature-driven decomposition dominates under interacting stressors. These results demonstrate that chronic warming and N addition influence C cycling through distinct, yet nonadditive molecular pathways not captured by single-factor studies. This underscores the necessity of multifactor experiments to accurately capture the current and future ecosystem responses to interacting environmental stressors.},
}

@article {pmid42379814,
year = {2026},
author = {Eilers, T and Van Rillaer, T and Wittouck, S and Tuyaerts, I and Michiels, K and Victor, M and Gehrmann, T and Bron, PA and Van Beeck, W and Lebeer, S},
title = {From diversity to dominance: how salt and CO2 shape LAB-dominated ecosystems in vegetable fermentations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0357825},
doi = {10.1128/spectrum.03578-25},
pmid = {42379814},
issn = {2165-0497},
abstract = {UNLABELLED: Research on microbial ecosystems is often challenging due to the high diversity of microbial taxa present and the complexity of controlling environmental variables. Fermented foods offer simpler and more reproducible model ecosystems in which both community composition and environmental factors can be more precisely controlled and manipulated. In this study, we focused on fermented vegetables, which are typically dominated by lactic acid bacteria (LAB). However, it remains unclear why LAB consistently drive the spontaneous fermentation of vegetables and how factors such as vegetable substrates, salt addition, and carbon dioxide levels shape microbial community dynamics. We characterized the temporal microbial succession in standardized spontaneous fermentations of 11 different vegetables (including beetroot, bell pepper, cabbage, carrot, cucumber, fennel, green asparagus, leek, parsnip, sunroot, and tomato), revealing a robust and recurrent dominance of Leuconostoc and other LAB across substrates. Additionally, we investigated the impact of varying salt concentrations and found that lower salt levels delayed the establishment of the typically LAB-dominated community, while promoting a higher abundance of Weissella and multiple Enterobacterales taxa. Notably, these salt reduction-induced effects were mitigated by CO2 injection, which reduced Enterobacterales levels and increased the overall abundance of Lactobacillales. Together, these findings demonstrate how targeted manipulation of environmental parameters, such as salinity and gas composition, can be used to uncover ecological principles governing microbial succession and community assembly in reproducible fermentation-based model ecosystems.

IMPORTANCE: Understanding the ecological principles that shape microbial community assembly is essential for advancing our knowledge of microbial ecosystems. Fermented vegetables, which are increasingly popular among the general population, provide a tractable and reproducible model system to study microbial succession. By systematically manipulating variables such as vegetable substrate, salinity, and gas composition, we identified the effects of these factors on microbial dynamics throughout the fermentation. These insights not only enhance our understanding of the microbial ecology of these man-made food systems but also suggest directions for novel strategies to optimize fermentation processes for the production of faster, safer, and more flavorful foods.},
}

@article {pmid42383736,
year = {2026},
author = {Zhang, C and Hammer, BK},
title = {Microbial Primer: The T6SS, a deadly bacterial harpoon.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {7},
pages = {},
doi = {10.1099/mic.0.001721},
pmid = {42383736},
issn = {1465-2080},
}

@article {pmid42384095,
year = {2026},
author = {Hernández-Zulueta, J and Raygoza-Alcantar, LN and Avila-Castro, E and Rodríguez-Zaragoza, FA and Cáceres, I and Delgado-Hernández, JI and Bonilla-Urzúa, MG},
title = {Biotechnological potential of marine invertebrate-associated bacteria with antibacterial activity against aquaculture and human pathogens.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42384095},
issn = {1678-4405},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/metabolism ; *Bacteria/isolation & purification/classification/metabolism/genetics ; Aquaculture ; Humans ; *Aquatic Organisms/microbiology ; Biotechnology ; Microbial Sensitivity Tests ; Phylogeny ; *Anthozoa/microbiology ; Sea Urchins/microbiology ; },
abstract = {Marine invertebrates harbor diverse bacterial communities that contribute to host defense by producing antibacterial compounds. In this study, 258 cultivable bacterial isolates from corals (Porites panamensis, P. lobata), the sea urchin Echinometra vanbrunti, and the ctenophore Mnemiopsis leidyi were screened against aquaculture and human pathogens. 14% (37 isolates) exhibited antibacterial activity, predominantly from E. vanbrunti and M. leidyi. Multiple assays revealed strong, broad-spectrum inhibition, particularly against aquaculture pathogens such as Listonella anguillarum, Photobacterium damselae, and Vibrio parahaemolyticus, whereas human pathogens showed limited sensitivity. Notably, isolates MT26 and MT43 displayed the widest inhibitory spectra, and EV78 and MM7 demonstrated high inhibition rates in growth assays. Taxonomic analysis showed that Bacillus was the dominant genus (65%), followed by Vibrio and Pseudoalteromonas. These findings highlight marine invertebrate-associated bacteria as promising sources of bioactive compounds with potential applications in aquaculture and biotechnology.},
}

Animals
*Anti-Bacterial Agents/pharmacology/metabolism
*Bacteria/isolation & purification/classification/metabolism/genetics
Aquaculture
Humans
*Aquatic Organisms/microbiology
Biotechnology
Microbial Sensitivity Tests
Phylogeny
*Anthozoa/microbiology
Sea Urchins/microbiology

@article {pmid42384698,
year = {2026},
author = {Wang, J and Ai, C and Tiedje, JM and Ge, Y},
title = {A molecular timescale for evolution of cobamide biosynthesis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {27},
pages = {e2610446123},
doi = {10.1073/pnas.2610446123},
pmid = {42384698},
issn = {1091-6490},
support = {32322076//MOST | National Natural Science Foundation of China (NSFC)/ ; Y2026QC22//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023YFD1700803//MOST | National Key Research and Development Program of China (NKPs)/ ; DBI-1759892//Us NSF grant DBI-1759892 computational/ ; 42307162//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Cobamides/biosynthesis/genetics ; *Evolution, Molecular ; Phylogeny ; Bayes Theorem ; },
abstract = {Cobamides are essential nutrients for most organisms but are only biosynthesized by a limited number of taxa through aerobic and anaerobic pathways. Although the origin of these widespread shared cofactors changed ecosystems and the metabolisms of living organisms, little evolutionary information is available about the biosynthetic genes and the producers. Here, we established a timeframe for the emergence of cobamide biosynthesis genes and producers, using a series of Bayesian molecular clock analyses combined with phylogenetic reconciliation. We revealed the partial producers of tetrapyrrole precursor and corrin ring were earlier than the oldest cobamide producer, suggesting the possibility that cobamide-like compounds may have existed before the emergence of their de novo producers. We also found that the anaerobic de novo producers and corrin ring producers emerged first (Pelobacter, around 2458 Mya), and that the Great Oxidation Event postdated emergence of aerobic producers (Kribbella, around 1784 Mya). These findings reveal the chronology of cobamide biosynthesis, which greatly changed global ecological frameworks and resulted in the current biosphere, and can guide the exploration of cross-feeding and the origin of diverse organisms on the planet.},
}

*Cobamides/biosynthesis/genetics
*Evolution, Molecular
Phylogeny
Bayes Theorem

@article {pmid42385456,
year = {2026},
author = {Hodžić, A and Cizek, V and Kunert, M and Berry, D and Collingro, A},
title = {Qualitative profiling of the gut-specific chlamydial population in Ixodes ricinus ticks.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {4},
pages = {102679},
doi = {10.1016/j.ttbdis.2026.102679},
pmid = {42385456},
issn = {1877-9603},
abstract = {Members of the phylum Chlamydiota are obligate intracellular bacteria increasingly recognized across a wide range of arthropod hosts, including ticks. In this study, we investigated the diversity and distribution of chlamydiae in Ixodes ricinus ticks and their potential association with Lyme borreliosis spirochetes. A total of 250 questing nymphal and female I. ricinus ticks were collected from three recreational sites in Vienna, Austria. Individual tick guts were screened for chlamydiae using pan-Chlamydiota PCR assays targeting the 16S rRNA gene, followed by sequencing for taxonomic identification. The presence and abundance of Borrelia burgdorferi sensu lato were quantified by specific qPCR to evaluate potential co-occurrence patterns. Chlamydiota DNA was detected in ticks from all investigated areas, with prevalence varying according to geography and developmental stage. Phylogenetic analyzes revealed high chlamydial diversity within the gut microbiome, predominantly comprising members of the metagenomic family MCF-D, followed by Parachlamydiaceae, Endochlamydiaceae, and Parasimkaniaceae. A positive, albeit not statistically significant, association between Chlamydiota and Borrelia was also observed. These findings indicate that the I. ricinus gut microbiome harbours a diverse assemblage of chlamydiae, suggesting potential ecological and functional relevance. Overall, our study highlights the importance of tissue-specific, single-tick analyzes for elucidating microbiome complexity and advances current understanding of Chlamydiota diversity in the tick vector. Further experimental and multi-omics studies are warranted to elucidate the biological roles of these bacteria in tick physiology and pathogen infection dynamics.},
}

@article {pmid42386020,
year = {2026},
author = {Fousekis, F and Lianos, GD and Stavropoulou, E and Patrikiou, E and Vradelis, S and Cassimos, D and Tsigalou, C},
title = {Decoding gut microbiome alterations in celiac disease: Implications for pathogenesis and treatment.},
journal = {Autoimmunity reviews},
volume = {25},
number = {9},
pages = {104127},
doi = {10.1016/j.autrev.2026.104127},
pmid = {42386020},
issn = {1873-0183},
abstract = {Celiac disease (CD) is a chronic immune-mediated disorder triggered by dietary gluten in genetically predisposed individuals and characterized by intestinal inflammation, epithelial damage, and loss of immune tolerance. While a strict lifelong gluten-free diet (GFD) remains the cornerstone of treatment, accumulating evidence indicates that it does not consistently restore gut microbiome composition or function, and many patients experience persistent symptoms despite good dietary adherence. The gut microbiome has emerged as a key modulator of immune homeostasis, intestinal barrier integrity, and gluten metabolism, implicating microbial dysbiosis in both the initiation and progression of CD. Alterations in microbial composition and metabolic activity have been documented in genetically at-risk individuals prior to disease onset, in patients with active disease, and in treated patients on a GFD, suggesting a potential role of the microbiome in early pathogenesis, disease heterogeneity, and symptom persistence. In this review, we summarize current evidence on the bidirectional interactions between the gut microbiome and CD, including microbial-mediated gluten degradation, microbiome signatures associated with genetic susceptibility and disease activity, and the effects of a GFD on microbial ecology. We further discuss emerging strategies aimed at modulating the gut microbiome, including probiotics, prebiotics, postbiotics and precision probiotics, as potential adjunctive therapeutic approaches. A better understanding of microbiome-host interactions in CD may support the development of personalized therapeutic strategies that go beyond gluten avoidance and aim to restore microbial balance and immune regulation, thereby improving long-term outcomes.},
}

@article {pmid42387523,
year = {2026},
author = {de Amorim, JE and Ferronatto, JA and Polydoro, LS and Batista, CF and Toledo-Silva, B and Costa, LBSBC and Heinemann, MB and Blagitz, MG and Della Libera, AMMP},
title = {Ovine milk-derived non- aureus Staphylococcus and Mammaliicoccus spp. (NASM) isolates and their cell-free supernatants inhibit major mastitis pathogens in vitro.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05683-6},
pmid = {42387523},
issn = {1746-6148},
abstract = {BACKGROUND: Innovative strategies to control ovine mastitis pathogens and reduce dependence on conventional antimicrobials are globally essential for One Health and sustainable livestock production. Non-aureus Staphylococci and Mammaliicoccus spp. (NASM) are commonly isolated in cases of ovine mastitis and may influence the microbial ecology of the mammary gland. This study evaluated the inhibitory potential of these microorganisms against key ovine mastitis pathogens, Staphylococcus aureus and Escherichia coli, through two experimental approaches. In experiment 1, 30 isolates of NASM were screened for their inhibitory activity using the cross-streaking method, assessing total, partial, or absent inhibition of S. aureus and E. coli. In experiment 2, the antimicrobial effect of cell-free supernatants from non-aureus Staphylococcus cultures (NAS CFS) cultures was tested at varying concentrations (12.5%, 25%, and 50%) under different treatments (heat treatment, pH adjustment, combined heat treatment + pH adjustment, and control). Pathogen growth was quantified by colony forming unit (CFU)/mL counts after incubation, and data were analyzed via ANOVA followed by Tukey's test.

RESULTS: Results from experiment 1 revealed that 36.7% of the isolates partially or totally inhibited S. aureus, while 20% partially inhibited E. coli. In experiment 2, the combined heat treatment and pH adjustment at a concentration of 12.5% significantly reduced S. aureus and E. coli CFU/mL when tested, for example, in the presence of S. xylosus (p < 0.01 for both cases).Results from experiment 1 revealed that 36.7% of the isolates partially or totally inhibited S. aureus, while 20% partially inhibited E. coli. In experiment 2, the combined heat treatment and pH adjustment at a concentration of 12.5% significantly reduced S. aureus and E. coli CFU/mL when tested, for example, in the presence of S. xylosus (p < 0.01 for both cases).

CONCLUSIONS: These findings highlight the preliminary potential of antimicrobial compounds derived from NASM for ovine mastitis control, while underscoring the need for further studies to confirm their applicability as sustainable strategies alongside conventional approaches.},
}

@article {pmid42388110,
year = {2026},
author = {Gross, M and Koll, U and Sonntag, B and Stoeck, T},
title = {From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70177},
doi = {10.1111/1755-0998.70177},
pmid = {42388110},
issn = {1755-0998},
support = {STO 414/13-3//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Polymerase Chain Reaction/methods ; *Gene Dosage ; *Ciliophora/genetics/classification ; *Ecology/methods ; Fresh Water/parasitology ; *Oligohymenophorea/genetics ; },
abstract = {Quantifying abundances of unicellular eukaryotes (protists) remains a central challenge in microbial ecology, as methodological differences can strongly influence abundance estimates and ecological interpretation. Although molecular tools have thus far greatly improved our understanding of protists, high rRNA gene copy numbers limit quantitative inferences. Digital PCR (dPCR) has emerged as a promising tool for absolute quantification, yet its application for unicellular eukaryotes and its comparability to established cell-based methods remain insufficiently explored. Here, we develop species-specific dPCR assays for two important freshwater ciliates (Urotricha castalia and Urotricha pseudofurcata) and establish gene copy number correction factors to enable highly accurate quantitative abundance estimates. We assess assay performance using controlled laboratory experiments and apply the approach to environmental samples, directly benchmarking dPCR against catalyzed reporter deposition-FISH (CARD-FISH). Under controlled conditions, dPCR and CARD-FISH yielded comparable accuracy, with dPCR showing superior precision. In field applications, method-dependent differences emerged, reflecting both methodological constraints and biological variability. Notably, dPCR provided an overall higher sensitivity, enabling robust detection of low-abundance taxa. Our results highlight dPCR as a scalable and sensitive approach that, when combined with appropriate correction strategies, represents a significant step towards more reliable molecular quantification of protists. At the same time, differences between methods underscore the value of integrating molecular and microscopy-based approaches. We propose that combining dPCR with tools such as CARD-FISH can offer complementary insights into protist population dynamics. Such integrative frameworks provide a powerful path forward for improving abundance estimates and advancing quantitative microbial ecology.},
}

*Polymerase Chain Reaction/methods
*Gene Dosage
*Ciliophora/genetics/classification
*Ecology/methods
Fresh Water/parasitology
*Oligohymenophorea/genetics

@article {pmid42361920,
year = {2026},
author = {Petrognani, C and Mariën, Q and Vos, L and Oijen, MV and Boon, N and Ganigué, R},
title = {CO2 availability as process tool to enhance isobutyric acid production in methanol fermentation by Clostridium luticellarii.},
journal = {Bioresource technology},
volume = {459},
number = {},
pages = {135255},
doi = {10.1016/j.biortech.2026.135255},
pmid = {42361920},
issn = {1873-2976},
abstract = {The bioconversion of CO2‑derived methanol into higher‑value chemicals offers an attractive route for hybrid catalytic-biotechnological carbon capture and utilization (CCU). Clostridium luticellarii is one of the few acetogens able to produce isobutyric acid. However, operational and metabolic factors driving its production are poorly understood. This work investigates how CO2 availability shapes the product spectrum of C. luticellarii during methylotrophic growth and assesses whether CO2 supply can be used as a process lever to promote isobutyric acid formation. Batch experiments with varying initial bicarbonate concentrations revealed that conditions leading to CO2 limitation (i.e., DIC depletion at ≤ 30 mM NaHCO3) redirected carbon and electron fluxes away from acetic acid toward butyric and isobutyric acids, with the latter accounting for up to 41% of total products. This metabolic switch was not observed when CO2 was in excess (>45 mM). High acetic acid supplementation (100 mM) triggered isobutyric acid production even while CO2 was still available, indicating a combined regulation of dissolved inorganic carbon (DIC) and acetic acid availability. Net acetic acid consumption took place in all isobutyric acid-producing experiments. These observations were reproduced in 3-L bioreactors and further exploited through a fed‑batch strategy in which an initial acetic‑acid‑accumulating phase was followed by CO2‑limited feeding. This approach achieved complete conversion of methanol and CO2 and yielded an isobutyric acid titer of 2.70 ± 0.04 g·L[-1]. Controlling CO2 availability is a viable operational tool to steer C. luticellarii metabolism toward isobutyric acid production, in interaction with electron acceptor availability.},
}

@article {pmid42378725,
year = {2026},
author = {Marques, HM},
title = {The chemistry of the cobalt corrinoids - Recent advances and emerging themes. Part 3. Cobalamins and health.},
journal = {Journal of inorganic biochemistry},
volume = {283},
number = {},
pages = {113395},
doi = {10.1016/j.jinorgbio.2026.113395},
pmid = {42378725},
issn = {1873-3344},
abstract = {Vitamin B12 (cobalamin) is an essential micronutrient whose biological importance extends beyond its traditional classification as a haematinic vitamin. This third and final part of a review covering work published between 2020 and 2025 synthesises selected illustrative studies that have advanced understanding of B12 physiology, nutrition, deficiency, delivery, and systems-level biology. At the molecular level, B12 functions as a cofactor in one‑carbon metabolism and mitochondrial pathways, influencing DNA synthesis, methylation capacity, and energy metabolism. These biochemical roles translate into organism-level consequences, particularly in the nervous system, where deficiency may cause irreversible neurological injury even in the absence of overt haematological abnormalities.Population-level analyses show that B12 status reflects the interaction of didetary intake, absorption efficiency, life stage, and food-system dynamics. Although animal-source foods remain the most reliable sources, shifts towards plant-based diets and inconsistent fortification practices are altering risk profiles. Clinical evidence further indicates that B12 deficiency is heterogeneous, frequently under-recognised, and complicated by the limitations of conventional biomarkers. Advances in delivery science point towards more controlled and targeted interventions, including encapsulation technologies, alternative administration routes, and receptor-mediated transport strategies. Emerging evidence also suggests biological activities for cobalamin derivatives beyond classical cofactor function, while microbiome research increasingly implicates corrinoid metabolism in host-microbe interactions relevant to immune and metabolic regulation. These developments support an integrated systems-level view of B12 biology spanning dietary supply, physiology, microbial ecology, and therapeutic innovation. SYNOPSIS: The final part of this review examines recent advances in vitamin B12 biology, spanning physiology, nutrition, deficiency, biomarker limitations, therapeutic delivery, and microbiome-linked corrinoid metabolism. These developments support an integrated systems-level view linking molecular function, dietary ecology, population health, and emerging therapeutic opportunities.},
}

@article {pmid42378946,
year = {2026},
author = {Vila, JC and Estrela, S},
title = {From coarse-grained metabolic rules to fine-grained control of microbial communities.},
journal = {Current opinion in microbiology},
volume = {92},
number = {},
pages = {102788},
doi = {10.1016/j.mib.2026.102788},
pmid = {42378946},
issn = {1879-0364},
abstract = {Over the past decade, microbial ecology has revealed remarkable coarse-grained regularities in community assembly and metabolic function. Across diverse systems, distinct taxonomic compositions can converge on similar functional outputs, and simple physiological principles can predict steady-state outcomes. These findings suggest that complex microbiomes may, in some regimes, be governed by emergent simplicity and therefore be predictable. Yet many of the traits we want to understand or engineer seem to depend on fine-grained dynamics that may be transient, strain-specific, and history dependent. Here, we argue that bridging the gap between coarse-grained metabolic rules and fine-grained metabolic complexity is essential for a predictive and engineering-oriented microbiome ecology. While progress is limited by the lack of (or insufficient) temporal, spatial, and chemical resolution, we highlight both conceptual advances and emerging technologies that may help fill that gap by providing temporal, spatial, single-cell resolved, dynamic, quantitative measurements.},
}

@article {pmid42379319,
year = {2026},
author = {Zhu, Y and Vrieze, J and Li, Y and Wang, S and Li, D and Zhang, Z and Dong, R and Li, X},
title = {Comparative assessment of endogenous, integrated, and exogenous biomethanation strategies: performance, microbial community and metabolic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135179},
doi = {10.1016/j.biortech.2026.135179},
pmid = {42379319},
issn = {1873-2976},
abstract = {Biological methanation is a promising approach for enhancing methane production rates and upgrading biogas during anaerobic digestion. However, few studies have examined the key biological rate-limiting factors or systematically compared different CO2 biomethanation strategies. In this study, anaerobic digestion of rice straw was subjected to H2/CO2 supplementation to evaluate three CO2 biomethanation strategies, i.e., endogenous, exogenous, and integrated. All CO2 biomethanation strategies increased methane production rate and achieved methane content over 83.9 %. Exogenous CO2 biomethanation achieved the highest methane production rate of 983 ± 68 mL·L[-1]·d[-1], which was 121 % and 41 % higher than endogenous and integrated CO2 biomethanation, respectively. In the integrated strategy, CO2 addition supplied buffer capacity to limit the pH increase. Rice straw hydrolysis and specific acetoclastic methanogenic activity was partially inhibited. In the CO2 biomethanation system, Methanobacterium formicicum was enriched, which is the dominant archaeal genus (50 %-69 % relative abundance). The relative abundance of 5,10-methylenetetrahydromethanopterin reductase (EC:1.5.98.2) suggested a potential functional limitation within the hydrogenotrophic methanogenesis pathway. Overall, this comparative assessment of these biomethanation strategies offers valuable references to optimizing full-scale biogas upgrading systems.},
}