@article {pmid42523320,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Daerwish, AA and Pérez, MP and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential Metabolite Production Underlies Disruption of the Cystic Fibrosis Airway Microbiota by Pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42523320},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) is a multisystem disease characterized by the accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. Culture-independent approaches have revealed that the CF airway harbors a complex microbiota, including opportunistic pathogens and bacteria that colonize the oropharynx. Here, we reanalyzed 5,260 16S rRNA gene microbiota datasets to infer ecological associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are more likely to form persistent communities. Further, we found higher diversity and increasing numbers of inferred interactions were positively associated with lung function. In contrast, pathogens were negatively associated both with each other and with oropharyngeal bacteria, suggesting that they may disrupt the microbiota. To validate these predictions, we cultured 1,597 bacterial isolates from 96 people with CF and performed 12,542 coculture assays against eight representative CF pathogenic and oropharyngeal bacteria. 23% of these interactions resulted in growth inhibition. While Pseudomonas isolates were, on average, the most inhibitory, we observed variable activity among isolates. We then confirmed that Pseudomonas aeruginosa isolates, even those from the same donor and timepoint, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and bloom in part through differential metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbial communities.},
}

@article {pmid42743742,
year = {2026},
author = {Guan, K and Xiao, Y and Xu, C and Zhang, H and Wu, S and Song, Z and Cao, S},
title = {Phosphorus alleviates age-associated osteoporosis in laying hens by reshaping bone metabolism and modulating cecal microbial communities.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107678},
doi = {10.1016/j.psj.2026.107678},
pmid = {42743742},
issn = {1525-3171},
abstract = {Osteoporosis in aged laying hens poses a major constraint on long-term egg production system. This study investigated the efficacy and underlying mechanisms of dietary phosphorus (P) in alleviating age-associated osteoporosis. A completely randomized design was employed, with 300 Hy-Line Brown laying hens (58 weeks of age) randomly assigned to one of three dietary treatments: a low-phosphorus diet (LP, 0.12% non-phytate phosphorus [NPP]), a regular-phosphorus diet (RP, 0.32% NPP), or the LP diet supplemented with 10,000 FTU/kg phytase (PHY, 0.12% NPP). Each treatment comprised 10 replicates of 10 hens. Following a 2-week adaptation period, the experiment lasted for 12 weeks. The results showed that dietary P reduction or phytase supplementation had no significant effect (P > 0.05) on egg production performance or egg quality throughout the experimental phase. However, at the end of the trial, hens fed the LP diet exhibited significantly lower serum P concentration and alkaline phosphatase (ALP) activity, along with reduced tibial P and magnesium (Mg) contents (P < 0.05), compared with the RP group. Conversely, serum calcium (Ca) level and tartrate-resistant acid phosphatase (TRACP) activity were significantly elevated in the LP group (P < 0.05). In contrast, phytase supplementation in the PHY group significantly increased serum ALP activity and tibial P and Mg contents relative to the LP group (P < 0.05). Notably, the PHY group also showed higher serum Ca concentration than the RP group (P < 0.05). Histomorphological examination revealed progressive cortical bone thinning accompanied by irregular erosion and increased demineralized areas in the tibiae of LP-fed hens, whereas only mild pathological changes were observed in the PHY group. Analysis of cecal microbiota indicated that dietary P modulation significantly altered microbial community structure: principal coordinate analysis (PCoA) showed distinct clustering for the LP and PHY group at week 8 and week 12, respectively (P < 0.05). Linear discriminant analysis effect size (LEfSe) further revealed that the LP group was enriched with pro-inflammatory taxa and microbes associated with nutrient metabolism stress. The RP group harbored a more complex and diverse microbial community, while the PHY group was characterized by an enrichment of beneficial bacteria involved in short-chain fatty acid (SCFA) production. Spearman correlation analysis demonstrated significant associations between specific bacterial genera and tibial health parameters. Genera such as Phascolarctobacterium, Rikenellaceae_RC9_gut_group, and Bacteroides were positively correlated with tibial mineral content and structural integrity, whereas Lactobacillus, Olsenella, and Prevotellaceae_Ga6A1_group showed negative correlations with these bone traits (P < 0.05). Collectively, these findings indicate that chronic P deficiency induces severe skeletal deterioration and gut microbiota dysbiosis in aged laying hens. Phytase supplementation partially counteracts the adverse effects of low-P diet by improving P utilization and reshaping the cecal microbiota toward a more beneficial composition. Nevertheless, long-term feeding of P-deficient diet even with phytase remains insufficient to fully preserve skeletal health. Therefore, ensuring adequate dietary P supply is essential for alleviating age-associated osteoporosis in aged laying hens, likely through integrated regulation of bone metabolic homeostasis and gut microbial ecology.},
}

@article {pmid42743793,
year = {2026},
author = {Andersen, JE and Iturbe-Espinoza, P and Ellegaard-Jensen, L and Sapkota, R and Winding, A},
title = {Protists introduce distinct temporal patterns in a synthetic bacterial community consistent with known feeding traits.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128728},
doi = {10.1016/j.micres.2026.128728},
pmid = {42743793},
issn = {1618-0623},
abstract = {Through predation, protists act as strong determinants of bacterial communities, yet their role in shaping synthetic communities (SynCom) remains unclear. We present the effects of three predator protists - a ciliate (Colpoda steinii), a flagellate (Neobodo designis), and an amoeba (Acanthamoeba castellanii) on the temporal dynamics of bacterial SynCom using a microtiter plate-based design. We asked whether predation contributes to the maintenance of SynCom richness, alters trajectories, and whether these effects depend on the identity of the protist. Bacterial community structure and composition in absolute abundances were estimated by 16S rRNA gene metabarcoding. Protist 18S and bacterial 16S rRNA gene copy numbers were quantified by qPCR, respectively. Using five sampling points, we found that bacterial 16S rRNA gene abundance did not change significantly over time when cultured alone, whereas protist 18S rRNA gene abundance altered at later time points, decreasing in ciliates, remaining stable in amoebae, and increasing in flagellates. Further, using 16S rRNA gene metabarcoding, we found that protists significantly reshaped bacterial community structure across the temporal scale. Protist predation was associated with community richness and species-specific SynCom dynamics: C. steinii induced broad suppression, whereas N. designis exerted more restricted effects, both preferentially targeting initially dominant taxa, while A. castellanii showed a minor impact. These results highlight the importance of accounting for trophic interaction and point to prioritizing protists with a narrower feeding range when creating SynCom to maintain community diversity over time.},
}

@article {pmid42740563,
year = {2026},
author = {Feruza, J and Otajon, M and Shaxobiddin, M and Mamura, A and Aziz, K and Nargiza, K and Alimova, Z},
title = {The Oral Microbiome-Inflammaging Axis in Elderly Periodontitis: Emerging Immunopathogenic and Systemic Mechanisms.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70493},
pmid = {42740563},
issn = {1601-0825},
abstract = {BACKGROUND: Periodontitis prevalence increases with age, yet "elderly periodontitis" is not merely cumulative plaque exposure. Aging remodels mucosal immunity, elevates chronic inflammation, and promotes senescent cell accumulation with pro-inflammatory secretory phenotypes.

OBJECTIVE: To critically evaluate the self-reinforcing oral microbiome-inflammaging axis in elderly periodontitis.

METHODS: Narrative synthesis of mechanistic studies, human cohorts, and preclinical models investigating interactions between oral microbial ecology, immunosenescence, cellular senescence, and inflammaging.

RESULTS: Dysbiotic biofilms deliver persistent pressure interpreted by aged immune-stromal networks with heightened inflammatory gain. Mechanistic studies implicate aging-sensitive TLR9 sensing, age-amplified inflammasome-linked macrophage responses to P. gingivalis, and senescent niches that potentiate inflammation. Microbes directly induce senescence programs, including epithelial senescence and exosome-mediated paracrine immune senescence. Systemically, periodontitis induces multi-organ frailty-like phenotypes, neuroinflammatory changes, persistent gut dysbiosis, and altered metabolomes despite local therapy.

CONCLUSION: Elderly periodontitis represents a geroscience-relevant disorder where dysbiosis and biological aging jointly establish a self-sustaining inflammatory ecosystem. Priority gaps include longitudinal elderly cohorts integrating microbiome function with senescence markers and stratified trials combining biofilm control with host modulation.},
}

@article {pmid42740589,
year = {2026},
author = {Yu, J and Li, H and Zeng, H},
title = {Association of a Dietary Index for Gut Microbiota With Epilepsy Among US Adults Aged 40 and Over: A Cross-Sectional Study.},
journal = {Behavioural neurology},
volume = {2026},
number = {1},
pages = {e5311940},
pmid = {42740589},
issn = {1875-8584},
mesh = {Humans ; Cross-Sectional Studies ; Female ; *Epilepsy/epidemiology/microbiology ; Male ; *Gastrointestinal Microbiome/physiology ; *Diet ; Adult ; Middle Aged ; United States/epidemiology ; Nutrition Surveys ; Aged ; Prevalence ; },
abstract = {BACKGROUND: Epilepsy remains difficult to control in some patients, motivating interest in modifiable factors linked to seizure biology. Because diet can shape gut microbial ecology and gut-brain signaling, we examined whether the dietary index for gut microbiota (DI-GM) was associated with prevalent epilepsy in US adults aged ≥ 40 years.

METHODS: This cross-sectional study included 5025 participants from NHANES 2013-2016. DI-GM was constructed from 14 predefined dietary components reflecting microbiota-supportive or microbiota-adverse intake. NHANES sampling weights were applied. Multivariable logistic regression evaluated associations between DI-GM and prevalent epilepsy. Restricted cubic splines, subgroup analyses, and weighted quantile sum (WQS) regression were used to examine dose-response shape, effect heterogeneity, and component contributions.

RESULTS: In the fully adjusted model, DI-GM showed an inverse association with prevalent epilepsy (OR per 1-point increase, 0.80; 95% CI, 0.69-0.93; p = 0.008). Compared with Q1, Q4 had lower epilepsy odds (OR, 0.29; 95% CI, 0.10-0.87; p = 0.033). The spline analysis did not support nonlinearity (p = 0.663). The inverse association was mainly seen among adults without hypertension or diabetes, with significant interaction by hypertension (p < 0.001) and diabetes status (p = 0.003). WQS results highlighted cranberries, chickpeas, avocados, soybeans, and lower processed meat intake as major contributors.

CONCLUSIONS: Higher DI-GM adherence was associated with lower odds of prevalent epilepsy, particularly in metabolically healthier subgroups. Prospective and intervention studies are needed to test temporality and clinical relevance.},
}

Humans
Cross-Sectional Studies
Female
*Epilepsy/epidemiology/microbiology
Male
*Gastrointestinal Microbiome/physiology
*Diet
Adult
Middle Aged
United States/epidemiology
Nutrition Surveys
Aged
Prevalence

@article {pmid42741332,
year = {2026},
author = {Wang, QH and Liu, YF and Wang, B and Xiao, Q and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Oil composition determines microbial preference for carbon source between hydrocarbons and Necromass in water droplets within crude shale oil.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag242},
pmid = {42741332},
issn = {2730-6151},
abstract = {Water droplets entrapped in crude oil have recently been recognized as unexpected but metabolically active microbial habitats in shale oil reservoirs. However, the key environmental drivers that shape the community composition and metabolic profiles of these droplet microorganisms remain poorly understood. Here, we investigated three shale oil samples from Jiangsu oilfield, all of which contained abundant water droplets (>10[5] droplets/ml oil) of ancient formation water origin. Integrated microscopy, metagenomics, and metabolomics revealed that the physicochemical properties of the enclosing oil, primarily API gravity and viscosity, are associated with droplet size and may influence the droplet microbiomes. These factors appear to jointly drive a fundamental metabolic dichotomy, where in light oil with low-salinity water, communities are enriched with hydrocarbon degraders together with molecular signatures of active petroleum hydrocarbon metabolism. In more viscous, light-to-medium oil with high-salinity water, however, communities shift towards necromass recycling and strong genetic adaptations to osmotic stress. Our findings demonstrate that microbial life in water droplets enclosed in shale oil is widely found in the shale oil reservoirs examined, and selected by carbon quality and environmental pressure. This study provides a mechanistic framework for understanding microbial ecology and biogeochemical processes in shale oil reservoirs and offers insights for microbial enhanced oil recovery in heavy oil reservoirs.},
}

@article {pmid42741352,
year = {2026},
author = {Monge-Loría, M and Brady, C and Wu, H and Aron, A and Garg, N},
title = {Computational mass spectrometry and genome mining guided discovery of metallophores produced by Microbulbifer.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag238},
pmid = {42741352},
issn = {2730-6151},
abstract = {Iron is an essential component of cellular biology. Thus, iron's low bioavailability is a key evolutionary pressure guiding microbial dynamics in the marine environment. Among marine bacteria, Microbulbifer is a chemically underexplored and functionally versatile bacterial genus, which is commonly associated with sponges, algae, corals, and sediments. Previously, genome analyses have revealed that Microbulbifer spp. can degrade polymers and synthesize natural products. Despite their recognized potential to produce secondary metabolites, siderophores are yet to be identified in Microbulbifer, and their iron acquisition strategies remain largely unknown. Here, we developed a comprehensive mass spectrometry-based query language code to determine siderophore production by Microbulbifer spp. in mono- and mixed cultures. Using this workflow, we discovered a new metallophore, which we named bulbichelin, as well as a suite of previously unreported petrobactins containing an unprecedented longer chain length acylation on the central spermidine moiety. We applied genome mining methods to describe the biosynthesis of these compounds. Using metal infusion mass spectrometry, we show that bulbichelins bind a variety of metals. Notably, neither of these compounds were produced in a co-culture of Microbulbifer with coral-derived pathogen Vibrio coralliilyticus Cn52-H1. Understanding how siderophores shape interspecies interactions between Microbulbifer spp. and other marine organisms will aid in unraveling the chemical and catalytic versatility of this genus and adaptation in nutrient deplete marine environment.},
}

@article {pmid42742455,
year = {2026},
author = {Chen, J and Ren, S and Tong, Z and Guan, Z and Zhang, W and Ren, S and Ma, L and Kong, L and Chong, H and Wang, Z and Yong, X and Yan, S and Wang, Y and Zhou, J},
title = {An integrated culturomic and genomic database and analysis platform for methanogenic archaea.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42742455},
issn = {1758-0463},
support = {U24A20543//National Natural Science Foundation of China/ ; 32371538//National Natural Science Foundation of China/ ; JASTIF, CX [23]1038//Jiangsu Agriculture Science and Technology Innovation/ ; XTSW4C01//Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture/ ; },
mesh = {*Genome, Archaeal/genetics ; *Databases, Genetic ; *Archaea/genetics/metabolism ; *Genomics/methods ; Biocuration ; *Methane/metabolism ; },
abstract = {Methanogenic archaea research is challenged by limited strain resources, fragmented genomic data, inconsistent genome quality, substantial uncultured lineages, and difficulties in laboratory culturing, hindering advances in biogas production, climate mitigation, and microbial ecology. These archaea play crucial roles in global carbon cycling and anaerobic environments, yet scattered data and unculturable strains limit systematic studies and applications. To address this, we created MethArDB (Methanogenic Archaeal Genome Database), a specialized database for methanogenic archaea, compiling 3919 genomes, 87 host-associated plasmids, and 42 phages, with standardized quality classifications (complete, scaffold, draft), protein sequences, and metadata on geography, habitats, metabolism, and inheritable elements. Integrated MethArCT (Methanogenic Archaeal Culturomics Toolkit) employs a dual-threshold orthologous/paralogous protein analysis to evaluate metabolic pathway completeness, predicting cultivation parameters and suggesting candidate cultivation strategies, including potential medium formulations and conditions, to support strain isolation. Overall, MethArDB and MethArCT form an integrated platform combining genomics and culturomics to facilitate methanogenic archaea research. Database URL: http://methardb.cn.},
}

*Genome, Archaeal/genetics
*Databases, Genetic
*Archaea/genetics/metabolism
*Genomics/methods
Biocuration
*Methane/metabolism

@article {pmid42743290,
year = {2026},
author = {Stoll, MF and Dentz, M and Stocker, R and Jimenez-Martinez, J},
title = {Porous medium heterogeneity favors chemotaxis to nutrient hotspots in flow.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {38},
pages = {e2616336123},
doi = {10.1073/pnas.2616336123},
pmid = {42743290},
issn = {1091-6490},
support = {956457//EC | Horizon 2020 Framework Programme (H2020)/ ; 956457//EC | Horizon 2020 Framework Programme (H2020)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; NA//Eidgenössische Technische Hochschule Zürich (ETH)/ ; NA//Eidgenössische Technische Hochschule Zürich (ETH)/ ; },
mesh = {*Chemotaxis/physiology ; Porosity ; *Nutrients/metabolism ; *Azospirillum brasilense/physiology ; Hydrodynamics ; Soil Microbiology ; },
abstract = {Natural porous environments, such as soils and aquifers, are often highly heterogeneous, exposing microorganisms to variable fluid flow and nutrient landscapes. Chemotactic bacteria can locate nutrient hotspots and thereby accelerate subsurface reactions, yet how chemotaxis is affected by pore-scale flow remains poorly understood. Here, we show that pore-scale heterogeneity enhances the foraging benefits afforded to bacteria by motility and chemotaxis, compared to nonmotile cells advected by the flow. Using a microfluidic porous medium with localized steady nutrient sources, mimicking those found in natural porous media, we systematically test the effects of hydrodynamic heterogeneity, flow magnitude, and bacterial traits on nutrient exposure and pore-scale transport by directly tracking single cells of the soil bacterium Azospirillum brasilense. By introducing an advantage index that quantifies nutrient exposure compared to that of nonmotile cells, we find that the chemotactic gain in nutrient exposure increases with hydrodynamic heterogeneity by 1.5-fold. The underlying mechanism is due to swimming bacteria preferentially occupying low-velocity regions, where they can swim against the flow to climb the chemical gradient. The heterogeneous flow field in porous systems additionally causes chemotaxis to remain advantageous across a wider range of flow rates than in uniform, grain-free systems at the same mean fluid speed. These findings highlight how, due to the strong heterogeneity in the flow field, the quenching effect of flow on chemotaxis is much weaker in porous media than in homogeneous environments, with implications for biogeochemical cycling and predictive modeling of the transport of chemotactic bacteria and contaminants in porous media.},
}

*Chemotaxis/physiology
Porosity
*Nutrients/metabolism
*Azospirillum brasilense/physiology
Hydrodynamics
Soil Microbiology

@article {pmid42714937,
year = {2026},
author = {McDougall, FK and Paranagama, K and Boardman, WSJ and Wyres, K and Power, ML},
title = {Detection of opportunistic bacterial pathogens with intrinsic amoxicillin- and cephalosporin-resistance in wild koala faecal microbiomes.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42714937},
issn = {1465-2080},
mesh = {Animals ; *Phascolarctidae/microbiology ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Amoxicillin/pharmacology ; *Cephalosporins/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/drug effects/isolation & purification/genetics/classification ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; Animals, Wild/microbiology ; *Gastrointestinal Microbiome/drug effects ; Third Generation Cephalosporins ; },
abstract = {Opportunistic bacterial pathogens frequently associated with human clinical infections, including antimicrobial-resistant strains, are infiltrating the microbiomes of wild animals, where they have the potential to negatively impact wildlife health. Bacterial genes conferring resistance to amoxicillin have previously been reported in koala (Phascolarctos cinereus) faecal DNA. Koalas are facing several key threats, including wildfires, and affected individuals may receive amoxicillin therapy to treat burn wounds. This study aimed to identify the species of amoxicillin-resistant bacteria in koala gut microbiomes and determine if they are opportunistic pathogens. Faecal samples collected from 98 wild-caught koalas were cultured using amoxicillin-supplemented media to isolate amoxicillin-resistant Gram-negative enteric bacteria. Isolates were screened using 16S rRNA PCR and Sanger sequencing to identify opportunistic pathogenic species, which then underwent whole-genome sequencing and antimicrobial susceptibility testing. Intrinsically amoxicillin-resistant opportunistic pathogens were obtained from 9.2% (9/98) of koala faecal samples and comprised Klebsiella oxytoca (6/98, 6.1%), Klebsiella pneumoniae (1/98, 1.0%) and Citrobacter spp. (2/98, 2.0%). Seven of nine amoxicillin-resistant opportunistic pathogens also exhibited cephalosporin resistance. Four K. oxytoca isolates belonged to lineages associated with human clinical infections, which also have the potential to cause disease in koalas, including fatal systemic infections in pouch young. The presence of amoxicillin- and cephalosporin-resistant strains may also increase the risk of gut dysbiosis and opportunistic infections when penicillins or cephalosporins are required to treat bacterial infections in koalas, highlighting the importance of good antimicrobial stewardship. The study findings demonstrate the One Health perspective of microbial pathogens and the intertwined microbial ecology between humans and wildlife.},
}

Animals
*Phascolarctidae/microbiology
*Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Amoxicillin/pharmacology
*Cephalosporins/pharmacology
RNA, Ribosomal, 16S/genetics
*Bacteria/drug effects/isolation & purification/genetics/classification
Microbial Sensitivity Tests
*Drug Resistance, Bacterial
Animals, Wild/microbiology
*Gastrointestinal Microbiome/drug effects
Third Generation Cephalosporins

@article {pmid42715205,
year = {2026},
author = {Nauwynck, W and Faust, K and Boon, N},
title = {Accessible, robust ultrahigh-throughput microbiome analysis via integration of uniform droplet-templated emulsification and FACS.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0356887},
pmid = {42715205},
issn = {1932-6203},
mesh = {*Flow Cytometry/methods ; Emulsions/chemistry ; *Microbiota ; *High-Throughput Screening Assays/methods ; },
abstract = {Microbial phenotypes vary at the single-cell level, shaping key community traits like resilience and adaptability. Yet, current methods either lack resolution (e.g., culturing, sequencing), are too costly, or technically complex, limiting widespread use. To address this gap, we introduce and validate a workflow called DE-SWIRL (Double Emulsion-Sorting Workflow with sImple, Rapid emuLsification), an accessible, low-cost workflow enabling ultrahigh-throughput (~107 microcultures/experiment) screening of individual microbial cells. DE-SWIRL integrates a published droplet-templated emulsification protocol producing uniform double emulsions from monodisperse single emulsions with Fluorescence-Activated Cell Sorting (FACS). We validated that double emulsions of 6 and 24 pL can be reliably formed, with ~45% droplet survival. To address persistent large-particle contaminants, we validated a gating strategy and show it enables accurate screening and sorting. When starting from a monodisperse single emulsion population, oil layer variability is higher for droplet-templated emulsification than for on-chip microfluidics, but maintains a comparably uniform core emulsion while offering substantial time savings. We demonstrate DE-SWIRL's utility by isolating viable strains from a synthetic community with up to 99% sorting purity and isolating droplet cocultures from a mixed community. This workflow provides a fast, accessible, and affordable workflow for screening entire microbiomes at a single-cell level using a fluorescent assay of interest.},
}

*Flow Cytometry/methods
Emulsions/chemistry
*Microbiota
*High-Throughput Screening Assays/methods

@article {pmid42719130,
year = {2026},
author = {Dai, Y and Li, H and Wang, H and He, Y and Cai, K and Wu, X and Zou, H and Wang, Y and Cai, L and Wu, X and Shamsi, IH},
title = {Insights into the changes of soil microorganism communities and carbon cycle metabolic functions caused by the application of L-glufosinate-ammonium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1920057},
pmid = {42719130},
issn = {1664-302X},
abstract = {L-glufosinate-ammonium (L-GLA), a widely used herbicide, exerts detrimental non-target effects on crops, soil microorganisms, and ecosystems. However, its impacts on soil microbial communities and metabolic functions remain poorly understood. In this study, we applied L-GLA at two concentrations-600 g a.i. hm[-2] (low, L) and 3,000 g a.i. hm[-2] (high, H)-to yellow-brown soil and investigated its effects on microbial community composition, carbon cycle-related metabolic functions, and soil metabolites using integrated metagenomics and soil environmental pseudotargeted metabolomics at 30 and 60 days post-application. The degradation rate of L-GLA was concentration-dependent, with half-lives of 18.8 days (L) and 29.7 days (H). Both doses significantly reduced soil organic matter (SOM) and available potassium (AK) content, and markedly altered microbial community richness, structure, and composition. L-GLA exposure also disrupted the complexity of soil microbial co-occurrence networks and the activities of carbon-cycle-related enzymes. Metabolomic analysis further revealed significant (p < 0.05) and dose-dependent alterations in the soil metabolite profile. Correlation analysis indicated strong associations between characteristic microbial taxa and differential metabolites. Our findings provided critical insights into how L-GLA influences the soil microecological environment and contributed to a deeper understanding of soil microbial ecology in the context of modern agricultural practices.},
}

@article {pmid42724485,
year = {2026},
author = {Zhang, H and Zhang, T and Pan, Z and Zhang, Y and Liang, T and Liu, H and Wang, B and Yu, Y and Wang, S},
title = {Microbiota-associated metabolic networks in gut-kidney communication and renal immune regulation: mechanisms and therapeutic potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1899977},
pmid = {42724485},
issn = {1664-302X},
abstract = {Kidney disease development and progression involve not only local inflammation, immune dysregulation, and fibrosis but also alterations in gut microbiota composition and metabolic function. Microbiota-associated metabolic signals connect the intestinal ecosystem, host metabolism, and the renal immune microenvironment through their associations with intestinal barrier integrity, renal tubular epithelial homeostasis, immune cell function, and inflammatory-fibrotic responses. Depending on their biological origin, receptor engagement, target-cell specificity, and disease context, these signals may either support immune homeostasis and tissue repair or contribute to persistent inflammation and tissue remodeling. Representative mediators include short-chain fatty acids, tryptophan-derived metabolites, bile acid-related signaling molecules, indoxyl sulfate, p-cresyl sulfate, trimethylamine N-oxide, succinate, and other host-microbiota-associated metabolites. Their biological effects, however, cannot be interpreted independently of renal function because circulating metabolite levels are also influenced by impaired renal clearance, systemic inflammation, dietary factors, and host metabolism. Conversely, kidney dysfunction reshapes intestinal barrier integrity, microbial ecology, and metabolic output, establishing a dynamic gut-kidney metabolic-immune feedback network. In this Review, we summarize current evidence linking microbiota-associated metabolic networks to renal immune remodeling across different kidney diseases, highlighting metabolite origin, shared target-cell responses, disease-specific and context-dependent mechanisms, and current evidence limitations. We further discuss therapeutic strategies targeting this axis and emphasize key translational challenges, including distinguishing causal metabolic drivers from secondary metabolic alterations and developing precision interventions based on metabolic and immune phenotypes.},
}

@article {pmid42724737,
year = {2026},
author = {Raval, R and Hejmadi, S and Hettiarachchi, M and Chandna, S and Mehta, AC},
title = {Gut-lung axis in chronic respiratory diseases: a narrative review of emerging insights.},
journal = {Journal of thoracic disease},
volume = {18},
number = {8},
pages = {967},
pmid = {42724737},
issn = {2072-1439},
abstract = {BACKGROUND AND OBJECTIVE: The gut-lung axis is a bidirectional network through which intestinal microbial ecology, mucosal immunity, epithelial barrier function, microbial metabolites, and neurohumoral signalling influence pulmonary inflammation. This narrative review summarizes the mechanistic basis of gut-lung communication, compares the strength of evidence across major chronic respiratory diseases (CRDs), and evaluates emerging microbiome-targeted interventions.

METHODS: PubMed, Embase, and Google Scholar were searched for peer-reviewed English-language literature published from January 2010 through June 2024 using combinations of terms related to the gut-lung axis, microbiome, asthma, chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), short-chain fatty acids (SCFAs), intestinal permeability, bile acids, tryptophan metabolites, vagal signalling, and glucagon-like peptide-1 (GLP-1). Human and animal original studies, randomized trials, cohort studies, mechanistic studies, and relevant narrative or systematic reviews were considered; case reports, non-English articles, and studies without respiratory outcomes were excluded. Reference lists of key papers were also hand-searched.

KEY CONTENT AND FINDINGS: Evidence is strongest for biologically plausible immune and metabolic pathways linking intestinal dysbiosis to pulmonary disease. In asthma, early-life depletion of SCFA-producing taxa may impair regulatory T-cell development and promote allergic sensitization. In COPD, gut dysbiosis, increased intestinal permeability, and systemic endotoxin exposure are more consistently associated with inflammatory phenotype and exacerbation burden. Evidence in ILD remains preliminary but supports a possible role for gut-derived pathogen-associated molecular patterns in profibrotic signalling. After lung transplantation (LT), antibiotic exposure, immunosuppression, and microbial loss may interact with allograft inflammation and chronic lung allograft dysfunction (CLAD). Dietary modulation, probiotics, prebiotics/synbiotics, post-biotics, and fecal microbiota transplantation (FMT) remain investigational, with heterogeneous and generally limited clinical evidence.

CONCLUSIONS: Current data support mechanistic plausibility but do not justify routine microbiome-directed treatment of CRDs. Future trials should standardize microbiome profiling, incorporate metabolomic and disease-specific clinical endpoints, and stratify responders to define where gut-lung axis interventions can add clinically meaningful benefit.},
}

@article {pmid42725769,
year = {2026},
author = {Van Rossum, U and Heyndrickx, M and Demaître, N and Sadiq, FA and Boon, N and Rasschaert, G and Cools, A and De Reu, K},
title = {Biofilm formation and multispecies interactions of bacteria recovered from drinking water systems in broiler houses and piglet nursery units.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0108426},
doi = {10.1128/spectrum.01084-26},
pmid = {42725769},
issn = {2165-0497},
abstract = {The presence of biofilms on the surfaces of drinking water systems in livestock housing can compromise the microbiological quality of drinking water. Understanding the biofilm microbiome and the biofilm-forming capacity of its dominant species is therefore essential, particularly for identifying species that coexist and enhance biofilm formation through interactions. This study investigated 248 bacterial isolates representing the dominant microbiota of biofilm samples collected from drinking water systems in broiler houses and pig nursery units. Biofilm formation was assessed in both single-species cultures and 341 multispecies combinations. Of the tested isolates, 80% formed biofilms in single culture; however, only 25% were classified as strong biofilm formers. In multispecies combinations with up to four species or isolates, antagonistic or competitive interactions were dominant, whereas biofilm mass enhancement was observed in only a limited number of combinations. These included opportunistic pathogens, with Citrobacter freundii and Staphylococcus nepalensis identified as key species driving the interactions. Our research highlights the importance of specific microbial interactions in biofilm development and provides a potentially practice relevant four-species model to guide future research aimed at improving strategies for controlling biofilms in livestock drinking water systems.IMPORTANCEEnsuring the quality of drinking water on livestock production farms benefits animal production and health. Persistent biofilms on water line surfaces can lead to microbial contamination, resulting in lower-quality drinking water. This study examines bacteria commonly found in biofilms within livestock drinking water systems in pig nursery units and broiler houses. Most bacterial isolates can form biofilms in monoculture. Specific interactions among certain species primarily mediate bacterial interactions that enhance biofilm biomass in multispecies communities. Identifying these key interactions enables the development of a synthetic model to guide research on controlling biofilms in livestock drinking water systems.},
}

@article {pmid42728625,
year = {2026},
author = {Schroeder, BG and Bhattacherjee, R and Bonatelli, ML and da Rocha, UN and Sträuber, H and Harms, H and Nikolausz, M},
title = {Anaerobic mono-digestion of wheat straw in a three-stage semi-continuous system inspired by a beetle larva gut.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {19},
number = {1},
pages = {},
pmid = {42728625},
issn = {2731-3654},
support = {nº 88887.161417/2017-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Based on the efficient digestive system of the larva of the sun beetle (Pachnoda marginata) in utilizing lignocellulose-rich biomass, a reactor system was designed to partially mimic processes that occur in the larval gut. We aimed developing a process with this system for anaerobic mono-digestion of wheat straw to produce volatile fatty acids (VFAs) and biogas. Three stirred tank reactors connected in series were customized with polyurethane foam and operated at 37 °C. The first two reactors were designed to mimic the midgut of the larva with enhanced VFA production and the third one to resemble the hindgut and optimized for methanogenesis. The system was fed in a semi-continuous regime with ground wheat straw in an alkaline medium. Enrichment cultures from midgut and hindgut of the larva were used as inocula and three conditions with increasing organic loading rate were tested. The highest biomass to methane conversion occurred at the lowest organic loading rate and highest retention time, when a methane yield of 148 mLNorm g[-1]VS was obtained and VS degradation reached 44%. The microbial community was enriched toward cellulose and hemicellulose degrading taxa, including Dysgonomonadaceae, Lachnospiraceae, Marinilabiliaceae and Ruminococcaceae. The methanogenic community shifted from predominance of Methanosarcina to Methanobacterium and Methanoculleus. A comparison with other studies investigating straw utilizing bioreactors confirmed that a core microbiome composed of the phyla Firmicutes, Bacteroidetes and Proteobacteria effectuates the anaerobic digestion of lignocellulose-rich materials, regardless of the source of the inoculum and the process conditions. The designed process was stable and capable to convert wheat straw into methane and carboxylates. Further adaptations are suggested to improve the anaerobic digestion and decrease assembly and operating costs.},
}

@article {pmid42729561,
year = {2026},
author = {Ji, F and Wang, S and Wang, L and Zhao, Y and Zhong, J and Wang, R and Qu, J and Lu, Y and Yuan, N and Zhang, Q},
title = {The impact of short-term intensive fasting on physical health and gut microbiota in obese individuals.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1873000},
pmid = {42729561},
issn = {2296-861X},
abstract = {OBJECTIVES: This study aimed to characterize how a 7-day complete water-only fast followed by structured refeeding was associated with changes in body weight, hydration-dependent bioelectrical-impedance estimates, physical test performance, cardiovascular indicators, and gut microbial ecology in adults with obesity and normal-weight controls.

METHODS: Seventy-two eligible volunteers formed prespecified BMI sampling strata (normal weight, n = 36; obesity, n = 36), from which 14 participants were randomly selected within each stratum before the intervention and before outcome collection (N = 28). All selected participants completed a supervised 7-day water-only fast followed by a 7-day structured refeeding period. Physical indicators were assessed pre-fasting, post-fasting, and post-refeeding and analyzed using two-factor mixed-design repeated-measures models; gut microbiota (16S rRNA) was profiled pre- and post-fasting.

RESULTS: BMI-group-by-time interactions were significant for body weight and BMI (both p < 0.001) but not for BIA-derived fat mass, body-fat percentage, or muscle mass (all p > 0.05). Dynamometer-recorded grip, knee-flexion, and knee-extension scores increased over time (all time-effect p < 0.001), but none showed a BMI-group-by-time interaction (all p ≥ 0.340). Gut microbial alpha diversity remained largely stable apart from an FDR-significant ACE-index reduction in the normal-weight group (q = 0.021); most taxonomic findings did not survive FDR correction, and beta-diversity analysis showed no community-level convergence between groups.

CONCLUSION: Supervised seven-day water-only fasting followed by structured refeeding was associated with reduced body weight, particularly in participants with obesity. Changes in body composition were BIA-derived estimates, while higher dynamometer scores represented measured test performance that may have been influenced by familiarization. Gut-microbiota alpha diversity was largely stable, with exploratory compositional changes supporting further investigation in controlled studies.},
}

@article {pmid42733080,
year = {2026},
author = {Li, C and Wang, Y and Zhou, ASK and Pan, X and Zhu, Y and Zhang, X and Chen, T and Xiong, A and Ho, YW and Liu, J and Zhou, Z and Wang, J and Adyel, TM and Fang, JK and Bank, MS and Rillig, MC and Jin, LN},
title = {Unraveling the coastal marine plastisphere archaeome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42733080},
issn = {2041-1723},
mesh = {*Archaea/genetics/classification ; *Seawater/microbiology ; Crenarchaeota/genetics/classification ; Phylogeny ; Euryarchaeota/genetics/classification ; Metagenomics ; Ecosystem ; Biodiversity ; Methane/metabolism ; },
abstract = {Plastic pollution has created an expanding anthropogenic microbial niche, the plastisphere, raising questions about microbial ecology and associated impacts. Archaea, the third domain of life with fundamental ecological and evolutionary significance, remain poorly understood in this habitat. Here, using paired plastic debris and bulk-water samples from coastal marine ecosystems, key archaeal habitats increasingly threatened by plastic pollution, we characterize the plastisphere archaeome through archaeal amplicon sequencing and metagenomics. We show that the archaeome is significantly reshaped in the plastisphere, exhibiting higher taxonomic diversity, greater community heterogeneity, and selective enrichment of Euryarchaeota and Crenarchaeota. Archaeal genes involved in methane, nitrogen, and sulfur cycling are enriched in the plastisphere. Taxonomic and functional divergence between the plastisphere and bulk water increases with anthropogenic chemical stress. These findings suggest that plastic pollution could alter marine archaeal diversity, biogeography, and biogeochemical potential, extending understanding of plastisphere impacts to the archaeal domain.},
}

*Archaea/genetics/classification
*Seawater/microbiology
Crenarchaeota/genetics/classification
Phylogeny
Euryarchaeota/genetics/classification
Metagenomics
Ecosystem
Biodiversity
Methane/metabolism

@article {pmid42734183,
year = {2026},
author = {Chen, W and Pan, Y and Chen, M and Zhou, S and Liu, X and Sun, M and Yang, Z and Zhi, Y},
title = {Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726620},
pmid = {42734183},
issn = {1949-0984},
mesh = {Humans ; *Stroke/complications/metabolism ; Metabolomics ; Metagenomics ; *Depression/metabolism/etiology/microbiology ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Middle Aged ; Aged ; Cytokines/blood ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Biomarkers/blood ; },
abstract = {Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.},
}

Humans
*Stroke/complications/metabolism
Metabolomics
Metagenomics
*Depression/metabolism/etiology/microbiology
Female
Multiomics
Male
*Gastrointestinal Microbiome
Inflammation/metabolism
Middle Aged
Aged
Cytokines/blood
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
Biomarkers/blood

@article {pmid42736476,
year = {2026},
author = {Li, L and Ma, L and Zhang, Z},
title = {Global Research Trend of Axillary Osmidrosis: A Bibliometric and Visualized Analysis.},
journal = {Aesthetic plastic surgery},
volume = {},
number = {},
pages = {},
pmid = {42736476},
issn = {1432-5241},
abstract = {BACKGROUND: Axillary osmidrosis is a common condition with significant psychosocial implications. Despite growing research interest in recent years, no bibliometric analysis has been conducted in this field. This study aims to provide a knowledge framework and identify research hotspots in this domain using bibliometric methods.

METHODS: Publications related to axillary osmidrosis from 1990 to 2025 were retrieved from the Web of Science Core Collection and PubMed. Bibliometric analyses were conducted using VOSviewer, Bibliometrix package of R, and Microsoft Excel.

RESULTS: A total of 252 publications on axillary osmidrosis were included. China led in both publication output (n = 119) and total citations (n = 1321). Chang Gung Memorial Hospital was the most prolific institution (n = 12). Aesthetic Plastic Surgery ranked first in both publication output and h-index among journals. Highly cited literature primarily focused on foundational research, including odor components, microbiological mechanisms, and genetic susceptibility. Keyword analysis revealed a thematic shift from foundational research on odor chemistry, microbial ecology, and genetics toward clinical application of minimally invasive therapies and patient-centered outcome assessments.

CONCLUSIONS: Research on axillary osmidrosis has entered a phase of rapid development, with increasing focus on minimally invasive treatments and individualized care. Future efforts should prioritize cross-regional collaboration, high-quality clinical trials, and translation of mechanistic insights into clinical practice.

LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .},
}

@article {pmid42737277,
year = {2026},
author = {Zhang, S and Guo, Y and Zhao, J and Zhao, J and Guo, Y and Yan, W},
title = {Lacticaseibacillus paracasei LPB27: Effectively Enhances the Immune System by Improving the Intestinal Environment.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737277},
issn = {2304-8158},
support = {2023YFF1103802//National Key Research and Development Program of China/ ; ZK10202501//Key Projects and Major Training Programs of Beijing Union University/ ; },
abstract = {Lacticaseibacillus paracasei LPB27 is a novel probiotic isolated from the intestines of healthy infants and young children. In this study, healthy mice were used as a model to systematically investigate the immune regulatory effects of LPB27 mediated by the microbiota-gut-immune axis, with a focus on evaluating its immune-enhancing potential. The safety evaluation showed that, at a dose of 0.50 g/kg/day, LPB27 caused no observable toxicity or adverse reactions. The evaluation of immune function indicated that in terms of cellular immunity, high-dose LPB27 increased the delayed-type hypersensitivity response and lymphocyte proliferation by 69% and 35%, respectively; in terms of humoral immunity, the number of hemolytic plaques and hemolysin titer increased by 42% and 36%, respectively; in terms of innate immunity, the carbon clearance capacity, CRBC phagocytosis rate, and macrophage phagocytic index increased by 13%, 33%, and 66%, respectively. Serum IgA, IgG, and IL-6 levels were significantly elevated in the high-dose group, whereas TNF-α was significantly reduced. Overall, LPB27 supplementation enhanced multiple immune indicators in mice. By comparing the gut microbiota composition at different time points, the study found that continuous intake of LPB27 was associated with an enrichment of multiple beneficial bacterial genera, including Akkermansia, Lactobacillus, Muribaculum, and Lachnospiraceae_NK4A136_group, together with a reduction of potentially pathogenic taxa, indicating an overall improvement in the intestinal microbial ecology. Changes in the abundance of these beneficial taxa were positively correlated with the predicted activation of metabolic pathways related to the synthesis of immune-related proteins. These findings support the further development of LPB27 as an immune-regulating ingredient.},
}

@article {pmid42737331,
year = {2026},
author = {Olanbiwoninu, AA and Awotundun, TA and Afolabi, JF and Fashogbon, RO and Fagunwa, O},
title = {Ethnogeographic Distribution of Nigerian Fermented Foods and the Prospects for Bioeconomy Improvements.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737331},
issn = {2304-8158},
abstract = {Fermented foods and beverages represent a cornerstone of Nigerian food culture, yet their scientific documentation remains fragmented, and their potential within global bioeconomy frameworks is largely unrealised. This review addresses two interrelated gaps: the absence of a comprehensive ethnogeographic analysis of Nigerian fermented foods that integrates ecological, cultural, and agricultural drivers of regional diversity, and the limited examination of these foods as models for circular bioeconomy development. Using a narrative synthesis of peer-reviewed literature spanning 1986-2025, we systematically map the distribution of fermented tuber, cereal, legume, dairy, and fruit products across Nigeria's major geopolitical zones, demonstrating that agroecological endowment, ethnic composition, trade routes, and cross-cultural interactions shape regional variation. Beyond their socio-cultural significance, Nigerian fermented foods contribute meaningfully to food security by extending shelf life, enhancing nutrient bioavailability, and reducing post-harvest losses. This review further positions ogi (fermented maize gruel) and garri (fermented cassava granules) as model systems for circular bioeconomy integration, demonstrating how by-product valorisation can generate value-added outputs, including animal feed, bioethanol, biodegradable packaging, and organic acids. Key challenges, including food safety deficits, absence of standardised production protocols, and limited regulatory frameworks, are critically assessed. Three priority research directions are identified: metagenomics-based microbiome profiling, development of culturally appropriate starter cultures, and formulation of gender-responsive regulatory instruments. Nigerian fermented foods, properly documented and integrated into innovation systems, represent an underutilised asset for sustainable food system transformation in Sub-Saharan Africa.},
}

@article {pmid42738923,
year = {2026},
author = {Klain, A and Cascone, S and Grella, C and Cattivera, V and Fabiano, C and Galletta, F and Manti, S and Senatore, AA and Licari, A and Miraglia Del Giudice, M and Marseglia, GL and Indolfi, C and , },
title = {Prenatal, Perinatal and Postnatal Exposures and Clinical Factors of Food Allergy Prevention: A Review for the First 1000 Days of Life from the SIAIP Primary and Secondary Prevention of Allergic Diseases Commission.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42738923},
issn = {2072-6643},
mesh = {Humans ; *Food Hypersensitivity/prevention & control ; Female ; Pregnancy ; Infant ; Infant, Newborn ; Breast Feeding ; *Prenatal Exposure Delayed Effects ; Risk Factors ; Diet ; Developmental Origins of Health and Disease ; },
abstract = {Food allergy prevention is no longer understood as the simple avoidance of allergenic foods. The first 1000 days (from conception to, approximately, 24 months of age) include prenatal, perinatal and postnatal windows in which diet, epithelial barrier integrity, microbial ecology, immune maturation and family-level implementation interact. This narrative review was developed as a Commission-proposed SIAIP-oriented clinical framework, rather than a formal guideline or consensus statement. Evidence from guidelines, systematic reviews, randomised trials, birth cohorts and mechanistic studies was organised by developmental window and interpreted according to endpoint validity, confounding, feasibility and clinical readiness. Prenatal factors include maternal allergen non-avoidance, whole-diet quality, micronutrient and fatty acid status, antibiotic exposure, environmental context and maternal microbiome. Perinatal factors include mode of delivery, intrapartum and neonatal antibiotics, gestational maturity, early colonisation, breastfeeding initiation and routine vaccination. Postnatal factors include eczema, skin barrier inflammation, the timing and regularity of allergen introduction, breastfeeding management, infant diet diversity, siblings, daycare, pets, smoke and pollution, physical activity and equitable implementation. The strongest actionable evidence remains eczema-linked risk recognition and timely, sustained oral exposure to peanut and well-cooked egg. Maternal and environmental factors are clinically important, but many are contextual rather than prescriptive; they should guide non-restrictive, non-blaming counselling rather than deterministic risk labelling.},
}

Humans
*Food Hypersensitivity/prevention & control
Female
Pregnancy
Infant
Infant, Newborn
Breast Feeding
*Prenatal Exposure Delayed Effects
Risk Factors
Diet
Developmental Origins of Health and Disease

@article {pmid42739013,
year = {2026},
author = {Buzatu, GD and Dodocioiu, AM and Ciupeanu-Călugaru, ED and Radulescu, D and Trască, ET},
title = {Dietary Nitrate Bioactivation at the Diet-Microbiota-Host Interface: The Enterosalivary Cycle, Food Matrix, Microbial Determinants and Health Implications-A Narrative Review Supported by a Structured Literature Search.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42739013},
issn = {2072-6643},
mesh = {Humans ; *Nitrates/metabolism ; *Diet ; *Gastrointestinal Microbiome/physiology ; Nitrites/metabolism ; Nitric Oxide/metabolism ; *Intestinal Mucosa/metabolism ; Animals ; },
abstract = {Background/Objectives: Dietary nitrate, long framed through food-safety concerns about N-nitroso compound formation, is now also recognised as a substrate of the nitrate-nitrite-nitric oxide pathway. This review aims to define the mechanistic, dietary and host conditions under which nitrate bioactivation becomes functionally relevant, with particular attention to its microbial determinants and to the level of inference the evidence actually supports. Methods: We conducted a narrative review supported by a structured literature search (PubMed, Scopus and Web of Science; 1 January 1976 to 14 February 2026; full-text, peer-reviewed, English-language, human-relevant sources; 148 sources retained, of which 93 contributed to the evidence synthesis), with narrative synthesis of mechanistic, interventional, observational and regulatory sources addressing dietary source and food matrix, enterosalivary metabolism, oral and gut microbial function, and health-related outcomes. A PRISMA-style flow diagram summarises the documented screening and inclusion process, and the complete database-specific search strategies are provided in Supplementary Table S1; no meta-analysis was performed because of substantial heterogeneity in designs and outcomes. Results: Within the canonical enterosalivary pathway, nitrate-to-nitrite bioactivation is predominantly microbiota-dependent and downstream conversion is chemically conditional: within the enterosalivary cycle, nitrate-reducing bacteria on the tongue dorsum generate the nitrite required for downstream nitric oxide formation, and its conversion in the stomach depends on pH and on matrix constituents. Dietary source and food matrix therefore govern both the delivered dose and the chemistry that follows, so vegetables, beetroot products, inorganic salts, drinking water and processed meat are not interchangeable exposure models. The oral microbiota is the principal microbial determinant of the response, whereas the gut microbiota acts as a context-dependent modifier of intestinal redox tone, barrier function and microbial ecology, supported by markedly weaker human evidence. Nitrate-rich sources reproducibly raise nitrate and nitrite biomarkers, with variable effects on blood pressure, vascular function and exercise efficiency, limited or inconsistent effects on cognition, cerebral blood flow and metabolic endpoints, and a safety profile whose interpretation depends on food matrix, dose, exposure pattern and host context rather than concentration alone. Conclusions: We propose the Source-Matrix-Microbiota-Host (SMMH) framework, in which biological impact depends on the interaction between dietary source and dose, food matrix, microbial nitrate-reducing capacity and host susceptibility, rather than on nitrate dose alone, and in which pathway-level, physiological and clinical evidence are kept explicitly distinct. The evidence base is mechanistically robust for the oral microbiota, considerably less defined for the gut microbiota, and variable at the level of validated clinical endpoints; it does not yet support source-independent guidelines or population-level recommendations.},
}

Humans
*Nitrates/metabolism
*Diet
*Gastrointestinal Microbiome/physiology
Nitrites/metabolism
Nitric Oxide/metabolism
*Intestinal Mucosa/metabolism
Animals

@article {pmid42739046,
year = {2026},
author = {Szabó, J and Maróti, G and Solymosi, N and Andrásofszky, E and Tuboly, T and Bersényi, A and Bruckner, G and Fébel, H},
title = {Effects of Dietary Glucose, Fructose, and Monosaccharide-to-Lard Energy Ratios on Cecal Microbiota Composition and Ecological Organization in Rats.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42739046},
issn = {2072-6643},
mesh = {Animals ; *Fructose/administration & dosage/pharmacology ; *Cecum/microbiology ; Male ; *Glucose/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Monosaccharides/administration & dosage/pharmacology ; *Dietary Fats/administration & dosage ; Rats, Sprague-Dawley ; *Dietary Carbohydrates/administration & dosage ; Bacteria/classification ; Diet ; Energy Intake ; },
abstract = {Background: Although dietary fat and carbohydrates are major determinants of gut microbiota composition, their interactive effects across changing dietary monosaccharide-to-lard energy ratios remain incompletely understood. This study descriptively examined treatment-level cecal microbiome profiles across dietary gradients in which lard (L) was progressively replaced with glucose (G) or fructose (F). Methods: A carbohydrate-free, lard-rich control diet was formulated, and lard was progressively replaced with glucose or fructose while maintaining a constant protein-to-energy ratio. Cecal contents from eight rats per dietary group were pooled in equal amounts, yielding one composite microbiome sample per treatment. Pooled samples were characterized by shotgun metagenomic sequencing. Sequencing/classified read counts (CRs) and relative abundance (RA) were treated as complementary sequencing-derived representations rather than measures of absolute bacterial abundance. Microbiome outcomes were interpreted descriptively at the treatment level. Results: Across the pooled treatment profiles, CRs and RA showed non-linear patterns and did not consistently change in parallel, providing complementary descriptions of treatment-level taxonomic responses. CR patterns indicated a combined effect of L and monosaccharide content, with several mixed L-monosaccharide diets showing lower CRs than both the L6.03 reference and the lard-free endpoints. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions, although their magnitude and direction varied among taxa. Hierarchical clustering and exploratory correlation networks provided complementary descriptions of treatment-level community organization. Conclusions: The pooled treatment-level microbiome profiles revealed non-linear responses to changing dietary L-monosaccharide composition, with CRs and RA providing partly different information on taxonomic patterns. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions.},
}

Animals
*Fructose/administration & dosage/pharmacology
*Cecum/microbiology
Male
*Glucose/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Rats
*Monosaccharides/administration & dosage/pharmacology
*Dietary Fats/administration & dosage
Rats, Sprague-Dawley
*Dietary Carbohydrates/administration & dosage
Bacteria/classification
Diet
Energy Intake

@article {pmid42739438,
year = {2026},
author = {Liu, M and Feng, X and Wang, H and Tan, Z and Liang, X and Wang, Q and Wang, Y and Wang, J},
title = {Effects of the Lower Irrigation Limit and Drip Irrigation Flow Rate on Root Traits and Bacterial Community Structure of Tomatoes Grown in Coconut Coir.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42739438},
issn = {2223-7747},
support = {52509081//the National Natural Science Foundation of China/ ; 8254048//the Natural Science Foundation of Beijing/ ; 2023B02024-2//the Research and Demonstration of Key Technologies for Green Development of Ecological Agriculture in Gobi/ ; No. 2024TSYCTD0019//the Tianshan Talent Science and Technology Innovation Team Project of Xinjiang Uygur Autonomous Region/ ; 2023AB071//the Science and Technology Plan Project of Xinjiang Production and Construction Corps/ ; No. 2024TSYCQNTJ005//the Tianshan Talent Youth Support Program of Xinjiang Uygur Autonomous Region/ ; 2026-2030//the Agricultural Science and Technology Innovation Program/ ; },
abstract = {Water management is a key factor affecting crop physiology and rhizosphere microbial ecology in protected agriculture. However, the responses of root development and bacterial community structure to different lower irrigation limits and drip irrigation flow rates in coir substrates remain poorly understood. This study investigated greenhouse-grown tomatoes in the Gobi region under three lower irrigation limits (30%, 50%, and 70% of substrate water-holding capacity) and two drip irrigation flow rates (1 and 2 L·h[-1]). Substrate moisture, root traits, bacterial community structure, co-occurrence networks, and functional potential were evaluated. Increasing the lower irrigation limit maintained higher and more stable substrate moisture and generally enhanced root length, root surface area, root tip number, and root activity. W3Q1 promoted greater spatial expansion of the root system, whereas W2Q2 produced the largest root volume and maintained relatively high root activity. Irrigation combination significantly altered bacterial community structure but had limited effects on bacterial richness. W2Q1 enriched Bacillota-related taxa, whereas W2Q2 enriched Pseudomonadota and exhibited greater bacterial network connectivity and modularity. FAPROTAX-based functional prediction indicated that the bacterial communities were mainly associated with chemoheterotrophy, organic matter decomposition, and nitrogen transformation. Overall, the lower irrigation limit primarily regulated substrate moisture and root traits, whereas the effects of drip irrigation flow rate were trait- and irrigation-limit-dependent, with significant main and interaction effects on root volume. These findings provide a basis for optimizing precision irrigation in coir-substrate tomato cultivation in arid greenhouse systems.},
}

@article {pmid42714191,
year = {2026},
author = {Dyczko, D and Jawień, P and Kiewra, D},
title = {Mosquito diversity in an urban landscape: species composition and a new record of Culiseta longiareolata ław, Poland.},
journal = {Annals of parasitology},
volume = {72},
number = {},
pages = {},
doi = {10.17420/ap72.553},
pmid = {42714191},
issn = {2299-0631},
mesh = {Animals ; Poland ; *Culicidae/classification/physiology ; *Biodiversity ; Cities ; Seasons ; Animal Distribution ; },
abstract = {Climate change, globalisation, and land use transformation are driving the redistribution of mosquito species (Diptera: Culicidae), with urban areas becoming hotspots for both native and invasive taxa. This study assessed mosquito species diversity in Wrocław, SW Poland, based on CDC trap collections from 14 sites between May and October 2024. A total of 17,104 adult mosquitoes were collected, of which 16,728 (97.8%) were identified to species level. Fifteen species across five genera were recorded, with Aedes vexans dominating the assemblage (68.7%), followed by Coquillettidia richiardii (9.8%). Molecular analyses confirmed all morphologically identified species. Mosquito abundance peaked in July and August, although some locations showed earlier seasonal maxima. Species such as Ae. vexans, Cq. richiardii, and Culex pipiens s.l./Cx. torrentium were present at all sites, while others were more localised. Notably, Culiseta longiareolata, previously unrecorded in Poland, was detected at a single urban site, contributing to recent evidence of a northward shift in its European distribution. Although based on only two individuals, this finding may indicate an early signal of a northward range of extension rather than evidence of established populations. These results underscore the value of continuous urban mosquito surveillance for documenting changes in species composition, detecting potential range shifts, and assessing public health risks under changing environmental conditions.},
}

Animals
Poland
*Culicidae/classification/physiology
*Biodiversity
Cities
Seasons
Animal Distribution

@article {pmid42714846,
year = {2026},
author = {Cui, Y and Zhang, B and Jiang, X and Rehemujiang, H and Xu, G and Li, Y and Wang, B},
title = {Perilla seed oil reshapes the rumen microbiome and increases fermentation end-products in vitro.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag233},
pmid = {42714846},
issn = {1365-2672},
abstract = {AIMS: The effect of Perilla frutescens seed oil (PSO) on an in vitro rumen microbial ecosystem was evaluated by integrating fermentation measurements, microbiome profiling, metagenomics, and untargeted metabolomics.

METHODS AND RESULTS: Rumen inoculum was incubated for 24 h with a control TMR substrate (CK), TMR supplemented with 23.7 mg of Perilla seeds per bottle (PS), or TMR supplemented with 8.5 μL of Perilla seed oil per bottle (PSO), with the PS and PSO treatments providing equivalent amounts of seed oil. Fermentation kinetics and volatile fatty acids were measured, and microbial and metabolic responses were characterized using 16S rRNA gene sequencing, metagenomics, KEGG and CAZy annotation, untargeted metabolomics and MetOrigin2 source tracing. PSO increased maximum gas production and total volatile fatty acid concentrations while maintaining pH within the physiological range. Community diversity was unchanged, but PSO altered microbial composition, including increases in Firmicutes, Verrucomicrobia, Vagococcus, Clostridium and Lactobacillus and decreases in Shigella sonnei and Methanosarcina sp. Ant1. PSO also altered microbial functional profiles and increased several lipid- and vitamin-associated metabolites, including linoleic acid, 13-HODE, 9-oxoODE, pantothenic acid and thiamine, while reducing lactate.

CONCLUSIONS: PSO changed rumen microbial community structure and functional potential in parallel with increased fermentation end-products and extensive metabolic shifts. These in vitro findings identify microbial and metabolic responses that warrant validation in vivo.},
}

@article {pmid42712928,
year = {2026},
author = {Bautista, J and Hernández-León, R and Valencia-Valverde, A and López-Cortés, A},
title = {The gut microbiome-cardiometabolic axis: insights into obesity, type 2 diabetes, and hypertension.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1948038},
pmid = {42712928},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Obesity/microbiology/metabolism ; *Hypertension/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; },
abstract = {Alterations in gut microbial ecology have been linked to obesity, type 2 diabetes (T2D), and hypertension, but their biological significance remains difficult to separate from diet, medication use, adiposity, and other host factors. We synthesize evidence on intestinal barrier dysfunction, microbial translocation, low-grade inflammation, and microbiota-derived metabolites as interconnected mechanisms across these disorders. SCFAs, bile acids, trimethylamine N-oxide, tryptophan derivatives, branched-chain amino acid metabolites, and phenylacetylglutamine influence epithelial function, immune activation, insulin signaling, lipid handling, vascular tone, and renal physiology. Cross-cohort comparisons identify the greatest taxonomic overlap between obesity and T2D, whereas hypertension is characterized more consistently by shifts in community structure than by reproducible disease-specific taxa. Dietary modification, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation produce modest and variable benefits, often shaped by baseline microbial features and clinical phenotype. The mechanistic and comparative data position the microbiome as a context-dependent contributor rather than an independent cause of cardiometabolic dysfunction. Progress requires longitudinal cohorts, repeated sampling, integrated multi-omics, standardized protocols, diverse populations, and prospective validation of functional biomarkers and treatment-response signatures before translation into clinical practice.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism
*Obesity/microbiology/metabolism
*Hypertension/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Animals

@article {pmid42713785,
year = {2026},
author = {Thakur, R and Dhar, H and Kiran, S and Gulati, A},
title = {Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70416},
doi = {10.1002/mbo3.70416},
pmid = {42713785},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; *Tea/microbiology ; Metagenomics ; Sequence Analysis, DNA ; Biodiversity ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; China ; DNA, Fungal/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.},
}

*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
*Tea/microbiology
Metagenomics
Sequence Analysis, DNA
Biodiversity
Phylogeny
DNA, Bacterial/genetics/chemistry
China
DNA, Fungal/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
DNA, Ribosomal Spacer/genetics/chemistry

@article {pmid42705711,
year = {2026},
author = {Du, J and Du, X and Wang, Y and Zhou, C and Zhang, Y and Teng, W and Wang, J and Zhuang, S and Cao, J},
title = {Microbial and flavor modulation of Jinhua ham at the fermentation stage by a synthetic mold and yeast community.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120202},
doi = {10.1016/j.foodres.2026.120202},
pmid = {42705711},
issn = {1873-7145},
mesh = {*Fermentation ; Odorants/analysis ; Animals ; Penicillium/metabolism ; *Food Microbiology/methods ; *Meat Products/microbiology/analysis ; *Taste ; Volatile Organic Compounds/analysis ; *Yeasts/metabolism ; Penicillium chrysogenum/metabolism ; Aldehydes/analysis ; Rhodotorula ; },
abstract = {This study investigated the effect of individual inoculation with Penicillium (Penicillium aethiopicum & Penicillium chrysogenum, PP), yeast (Candida parapsilosis & Rhodotorula mucilaginosa, CM) and their co-inoculation (MI) on the microbial ecology and flavor of Jinhua ham. Inoculation established target fungal populations (>6.0 log CFU/g) successfully increased lipase activity (peak in MI) and inhibited lipid oxidation, peroxide values and Aspergillus community to <10% compared to the control. PP accelerated the release of free fatty acid, especially unsaturated fatty acids, driving total volatile aldehyde concentrations by 5.0-, 1.5-, and 2.2-fold in PP, CM, and MI, respectively, compared to the control. Consequently, hams in the PP group exhibited stronger green and meaty odor scores, lower off-odor scores, and enhanced W1S, W2S and W3S sensor responses. In contrast, CM and MI increased monounsaturated fatty acids, alcohols, aldehydes, carboxylic acids, esters and pyrazines contents with stronger mellow, green & meaty odor scores, as verified by robust W1W, W1S, W3S and W5S sensor responses than the control. These findings indicate that targeted Penicillium or yeast multi-species combination strategies promoted the formation of desirable aldehydes, ketones, esters and pyrazines contents and produced green, meaty and mellow flavor profile of Jinhua ham.},
}

*Fermentation
Odorants/analysis
Animals
Penicillium/metabolism
*Food Microbiology/methods
*Meat Products/microbiology/analysis
*Taste
Volatile Organic Compounds/analysis
*Yeasts/metabolism
Penicillium chrysogenum/metabolism
Aldehydes/analysis
Rhodotorula

@article {pmid42709016,
year = {2026},
author = {Duysburgh, C and Govaert, M and Azmi, P and Finn, R and Simmons, N and Marzorati, M},
title = {Comparison of the Bioaccessibility of Two Formulations of Magnesium Bisglycinate Using an In Vitro Simulation of the Upper Gastrointestinal Tract.},
journal = {Journal of dietary supplements},
volume = {23},
number = {5},
pages = {690-704},
doi = {10.1080/19390211.2026.2727023},
pmid = {42709016},
issn = {1939-022X},
mesh = {Humans ; *Magnesium/pharmacokinetics ; Biological Availability ; *Upper Gastrointestinal Tract/metabolism ; *Dietary Supplements ; *Glycine/pharmacokinetics/analogs & derivatives ; Intestinal Absorption ; Models, Biological ; Gastrointestinal Transit ; Capsules ; },
abstract = {Modern diets are often deficient in magnesium, making magnesium supplementation an important consideration for overall human health. However, the efficiency of magnesium release and absorption in the small intestine varies among different magnesium formulations. The objective of this study was therefore to assess whether using the same magnesium salt type in different formulations could affect efficiency of magnesium release and passive diffusion in the simulated human intestine. This study utilized an in vitro simulation of the upper gastrointestinal tract under fasted conditions to evaluate capsule dissolution and levels of bioaccessible and dialyzable magnesium during transit for two magnesium bisglycinate supplements containing a similar magnesium content (Chelamax[®] and Albion[®]). For this purpose, the validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) technology platform was used and magnesium fractions were determined by inductively coupled plasma optical emission spectroscopy following sample extraction. Analytical validation proved that the model was fit for purpose (94-102% recovery, RSD ≤ 2.4%, R2 > 0.999, LOQ 0.04 mg/kg). Visual capsule scoring found that the Chelamax[®] product dissolved later in gastrointestinal transit than the Albion[®] product. Magnesium bioaccessibility was higher for the Chelamax[®] versus Albion[®] product in early phases of the gastrointestinal tract (i.e. duodenum), resulting in 17% higher overall Mg availability after the small intestinal incubation was complete. The level of dialyzable magnesium at the end of the small intestinal incubation was significantly higher with the Chelamax[®] versus Albion[®] product (53 mg vs. 39 mg; p = 0.0009). These results demonstrate that the Chelamax[®] product showed significantly higher in vitro efficiency of potentially absorbable magnesium, even upon using the same magnesium salt type, suggesting the crucial role of product formulation. Even though a proven valid in vitro methodology for the prediction of effectiveness of magnesium availability was used, future in vivo studies should confirm these findings.},
}

Humans
*Magnesium/pharmacokinetics
Biological Availability
*Upper Gastrointestinal Tract/metabolism
*Dietary Supplements
*Glycine/pharmacokinetics/analogs & derivatives
Intestinal Absorption
Models, Biological
Gastrointestinal Transit
Capsules

@article {pmid42709402,
year = {2026},
author = {van Neerbos, FAC and Cusumano, A and Lievens, B and de Bobadilla, MF},
title = {Honeydew microbial ecology: A neglected frontier in multitrophic networks.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag104},
pmid = {42709402},
issn = {1574-6941},
abstract = {Honeydew, the sugary excretion produced by sap-feeding Hemiptera, is one of the most common carbohydrate resources in many plant-based food webs. Honeydew supports a wide range of organisms, including ants, pollinators, (hyper-)parasitoids wasps, predatory insects, and microbes. As a sugar-rich resource, honeydew is frequently colonized by specific microbes (i.e., bacteria and fungi), which consume its sugars and other nutritional constituents. Recent research suggests that microbes within honeydew may modify its traits. Thereby driving microbial succession and acting as important "hidden players" in multitrophic ecological interactions. Yet its role as a dynamic microbial habitat remains largely unexplored. Here, we synthesize current evidence on the microbial ecology of honeydew and propose that honeydew is a dynamic rapidly changing microbial habitat. We further propose a four-stage successional model to frame its temporal dynamics. We discuss how the honeydew microbiome alters nutritional composition. Further, we discuss how the honeydew microbiome may mediate multitrophic interactions through the emission of volatile organic compounds that attract natural enemies of honeydew-producing insects. We propose that this process may pose a trade-off between the microbial secondary metabolism and its dispersal capacity of some microbes. We aim to stimulate research that will establish honeydew microbial ecology as a new frontier in plant-insect-microbe interactions.},
}

@article {pmid42705452,
year = {2026},
author = {Tummala, R and Kondapalli, N and Katari, V and Manandhar, I and Dalal, K and Adapala, R and Paruchuri, S and Joe, B and Thodeti, C},
title = {TRPV4 deletion remodels the gut microbiota and increases colonic ammonia levels.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124671},
doi = {10.1016/j.lfs.2026.124671},
pmid = {42705452},
issn = {1879-0631},
abstract = {AIMS: The transient receptor potential vanilloid 4 ion channel is widely expressed in the gastrointestinal tract and contributes to epithelial barrier regulation, mechanosensation and innate immune signaling. However, its role in shaping gut microbiota composition and intestinal metabolic homeostasis remains unclear. This study aimed to determine whether deletion of TRPV4 influences gut microbial composition and intestinal ammonia levels.

MATERIALS AND METHODS: Fecal microbiota from wild type and TRPV4 knockout mice were analyzed using taxonomic profiling and microbial diversity approaches. Alpha diversity and beta diversity metrics were used to evaluate microbial richness, evenness, phylogenetic diversity and community structure. Ammonia concentration and pH were measured in cecal and colonic contents.

KEY FINDINGS: Phylogenetic diversity differed significantly between wild type and TRPV4 knockout mice whereas microbial richness and evenness were not altered. Beta diversity analysis revealed marked differences in microbial community composition between genotypes. The ratio of Bacillota to Bacteroidetes was reduced by approximately 50 % in TRPV4 knockout mice due to decreased Bacillota and increased Bacteroidetes abundance. In addition, TRPV4 knockout mice exhibited significantly elevated ammonia levels in both the colon and cecum compared with wild type mice.

SIGNIFICANCE: Deletion of TRPV4 alters gut microbial community structure and intestinal nitrogen metabolism without affecting overall microbial richness or evenness. These findings identify TRPV4 as a novel regulator of gut microbiota composition and metabolic homeostasis and suggest that ion channel dependent signaling contributes to the regulation of gut microbial ecology and metabolite balance.},
}

@article {pmid42701922,
year = {2026},
author = {Zhang, L and Tian, Q and Du, C},
title = {γ-Butyrolactones and γ-butenolides as autoregulatory systems: key mediators of intraspecific, interspecific, and interkingdom communication in Streptomyces.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42701922},
issn = {1432-072X},
support = {Grant No.: 32572911//National Natural Science Foundation of China/ ; Grant No.: LH2024C096//Heilongjiang Provincial Natural Science Foundation/ ; },
mesh = {*4-Butyrolactone/analogs & derivatives/metabolism/chemistry ; *Streptomyces/metabolism/genetics/physiology ; *Quorum Sensing ; Gene Expression Regulation, Bacterial ; Anti-Bacterial Agents/biosynthesis ; Signal Transduction ; },
abstract = {Streptomyces represent a phylogenetically coherent group of aerobic, Gram-positive, high-GC-content bacteria occupying diverse terrestrial and aquatic environments. They are renowned for their exceptional capacity to biosynthesize structurally diverse secondary metabolites, many of which serve as clinically essential antibiotics, antifungals, immunosuppressants, and anticancer agents, with broad applications in pharmaceuticals, agriculture, food, and industrial biotechnology. Quorum sensing (QS) represents a fundamental regulatory paradigm governing both intraspecies coordination and interspecies crosstalk in Streptomyces. Within this framework, gamma-butyrolactones (GBLs) and gamma-butenolides (GBNs) function as structurally analogous, receptor-specific signaling molecules that autoregulate antibiotic biosynthesis, morphological differentiation, and stress adaptation. However, despite growing insights into their intraspecies functions, the ecological range, molecular determinants, and functional outcomes of GBL- and GBN-mediated interspecies communication remain largely underexplored. This review summarizes recent advances in the chemical diversity and regulatory mechanisms of microbial GBLs and GBNs. Based on current empirical evidence, we categorize their interspecies communication functions into four distinct themes: experimentally validated ligand-receptor pairs, exogenous compound-mediated receptor responses, extract- or coculture-mediated complementation, and Streptomyces-fungi communication hypotheses. Furthermore, we propose a forward-looking research agenda integrating multi-omics, synthetic biology, and microbial ecology to decipher the mechanistic foundation of interspecies QS networks-ultimately facilitating the rational activation of silent biosynthetic gene clusters, the discovery of novel bioactive natural products, and the mitigation of antimicrobial resistance.},
}

*4-Butyrolactone/analogs & derivatives/metabolism/chemistry
*Streptomyces/metabolism/genetics/physiology
*Quorum Sensing
Gene Expression Regulation, Bacterial
Anti-Bacterial Agents/biosynthesis
Signal Transduction

@article {pmid42702405,
year = {2026},
author = {Šulčius, S and Kuznecova, J and Kasperovičienė, J and Alzbutas, G and Šimoliūnas, E and Voss, M and Jürgens, K and Dziga, D},
title = {Cyanophage lysis reshapes nitrogen cycling and microbiome composition in diazotrophic cyanobacterium Aphanizomenon flos-aquae.},
journal = {Harmful algae},
volume = {159},
number = {},
pages = {103186},
doi = {10.1016/j.hal.2026.103186},
pmid = {42702405},
issn = {1878-1470},
mesh = {*Aphanizomenon/virology/metabolism/physiology/genetics ; *Bacteriophages/physiology ; *Microbiota ; Nitrogen Fixation ; *Nitrogen Cycle ; Nitrogen/metabolism ; },
abstract = {Although it is presumed that viruses play a significant role in nutrient cycling and bacterial community dynamics, this has only rarely been addressed in studies of diazotrophic cyanobacteria. In this study, we therefore examined how cyanophage infection affects the expression of nitrogen (N) cycling genes, N2 fixation rates, and population structure in the diazotrophic cyanobacterium Aphanizomenon flos-aquae, a prevalent bloom-forming species in temperate brackish and freshwater ecosystems. We also assessed the influence of A. flos-aquae lysis on co-occurring bacterial assemblages throughout an incubation experiment. We found that nitrogen fixation, its release, and the relative availability of different nitrogen forms (e.g. ammonium versus nitrate/nitrite) varied substantially during cyanophage infection, population lysis, and recovery phases. Interestingly, resistant A. flos-aquae subpopulation emerged during viral infection, showed increased expression of N fixation (e.g. nitrogenase (nifH) and heterocyst differentiation regulator (hetR)) and assimilation (e.g. glutamine (glnA) and glutamate (gltB) synthase) genes, as well as higher cell-specific N2 fixation rates. These changes were accompanied by a fast recovery of A. flos-aquae population structure (e.g. filament length and heterocyte-to-vegetative cell ratio) to pre-infection level, indicating A. flos-aquae ability to quickly compensate for short-term population decline. Lysis of the cyanobacterial host significantly altered the successional trajectory and increased diversification of the co-occurring bacterial community. The compositional changes corresponded well with the prevalent inorganic nitrogen form, implying a substantial, nitrogen-driven reorganization of the microbial network and its interactions within the A. flos-aquae microbiome. This study improves our understanding of nitrogen cycling and microbial dynamics within cyanobacteria-driven communities disturbed by viral infections and lysis.},
}

*Aphanizomenon/virology/metabolism/physiology/genetics
*Bacteriophages/physiology
*Microbiota
Nitrogen Fixation
*Nitrogen Cycle
Nitrogen/metabolism

@article {pmid42702754,
year = {2026},
author = {Sengupta, S and Ghorai, S and Bose, S and Hazra, S and Mukhopadhyay, A and Majumdar, A and Roychowdhury, T},
title = {Integrating Plant Physiology and Microbiome Engineering for Climate-Resilient Crops: Bridging Knowledge Gaps in Multi-Stress Tolerance.},
journal = {Physiologia plantarum},
volume = {178},
number = {5},
pages = {e71088},
pmid = {42702754},
issn = {1399-3054},
mesh = {*Crops, Agricultural/physiology/microbiology ; *Stress, Physiological/physiology ; *Microbiota/physiology ; Climate Change ; *Plant Physiological Phenomena ; },
abstract = {Climate change is intensifying the frequency and co-occurrence of abiotic and biotic stresses, posing significant challenges to global crop productivity and stability. Conventional approaches based on single-stress responses are increasingly insufficient for addressing complex field environments where plants experience multiple simultaneous stresses. This review synthesizes current knowledge on plant physiological responses, microbiome interactions, and emerging technological interventions to develop an integrative framework for climate-resilient agriculture. It highlights how stress perception, hormonal regulation, metabolic adjustments, and epigenetic mechanisms collectively shape plant adaptation under multi-stress conditions. The review further examines the role of plant-associated microbiomes in enhancing nutrient acquisition, regulating stress signaling, and improving resilience through mechanisms such as phytohormone modulation, antioxidant activity, and induced systemic resistance. Advances in microbiome engineering, including synthetic microbial communities and computational prediction frameworks, are discussed as promising strategies for improving stress tolerance. In addition, emerging tools such as nanotechnology-assisted delivery systems and biosensing platforms are considered for precision management of plant-microbe systems. By identifying critical knowledge gaps in multi-stress physiology, microbiome assembly, and field-level predictability, this review proposes an interdisciplinary approach that integrates plant physiology, microbial ecology, and technological innovations to support sustainable crop production under changing climatic conditions.},
}

*Crops, Agricultural/physiology/microbiology
*Stress, Physiological/physiology
*Microbiota/physiology
Climate Change
*Plant Physiological Phenomena

@article {pmid42703030,
year = {2026},
author = {de Lorenzo, V},
title = {Environmental Release of Genetically Intervened Microorganisms: Towards a New Narrative.},
journal = {Microbial biotechnology},
volume = {19},
number = {9},
pages = {e70441},
pmid = {42703030},
issn = {1751-7915},
support = {CL6-2021-UE 101060625//HORIZON EUROPE Excellent Science/ ; },
mesh = {*Microorganisms, Genetically-Modified/genetics ; Genetic Engineering/legislation & jurisprudence ; *Containment of Biohazards ; Biotechnology/legislation & jurisprudence ; },
abstract = {The deliberate release of genetically engineered microorganisms for environmental applications has remained largely blocked since the early days of recombinant DNA technology, when limited ecological knowledge, lack of success stories and public apprehension shaped a culture of caution and restrictive regulation. Despite profound advances in microbial ecology, synthetic biology and genetic design, current frameworks still rely on outdated assumptions and legacy regulations that equate engineered microbes with inherent danger and demand unrealistic forms of absolute containment. This review examines how laboratory-trained microorganisms exist on a continuum with naturally evolved life, and that their risks are neither categorically different nor greater. Rather than pursuing unachievable containment, governance should shift towards traceability, stewardship and long-term monitoring through genomic barcodes, digital twins and transparent oversight. The vision moves from domination and control to care and partnership recognizing engineered microbes as live amendments capable of restoring degraded ecosystems. Achieving this transformation requires new terminology, phased field-trial frameworks, improved scaling methods, and the integration of epistemological perspectives that emphasize reciprocity and coexistence with nature. Reframing biotechnology in this way could finally unlock the capacity of engineered microorganisms to contribute responsibly and effectively to planetary repair in an era of escalating environmental crises.},
}

*Microorganisms, Genetically-Modified/genetics
Genetic Engineering/legislation & jurisprudence
*Containment of Biohazards
Biotechnology/legislation & jurisprudence

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42704659,
year = {2026},
author = {Cahill, N and Kovarova, A and Alfahl, Z and O'Connor, L and Morris, D},
title = {Antimicrobial resistance in wastewater-impacted coastal waters: implications for environmental surveillance and public health.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42704659},
issn = {1465-2080},
mesh = {*Wastewater/microbiology ; Ireland ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/drug effects/isolation & purification ; *Seawater/microbiology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Public Health ; Anti-Bacterial Agents/pharmacology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; beta-Lactamases/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a global public health concern, and wastewater-impacted aquatic environments are recognized as reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and genes (ARGs). However, harmonized environmental AMR surveillance frameworks that integrate culture-based ARB enumeration with molecular ARG monitoring across wastewater and receiving surface waters remain limited. This pilot study, conducted in Ireland as part of a European harmonized monitoring initiative, assessed ARB and ARG abundances in wastewaters and surface waters. Wastewater treatment plant influent (n=3), effluent (n=3) and surface waters upstream and downstream of the discharge point (n=3 each) were sampled on three occasions in late 2024. Culture-based methods enumerated total and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, while quantitative real-time PCR quantified 16S rRNA and five AMR-associated genes (intI1, ermB, aadA1, bla CTX-M-1 and vanA). Total E. coli concentrations were highest in influent (~10[5]-10[6] c.f.u. dl[-1]), decreased in effluent (~10[3]-10[5] c.f.u. dl[-1]) and lowest in surface waters (~10[1]-10[2] c.f.u. dl[-1]). ESBL-producing E. coli were consistently detected in influent (~10[4] c.f.u. dl[-1]) and effluent (~10[1]-10[3] c.f.u. dl[-1]) but were not recovered from seawater. ARG abundances were highest in influent, reaching up to ~10[11] copies dl[-1] for intl1, remained elevated in effluent (up to ~10[10] copies dl[-1]) and were ~2-3 orders of magnitude lower in surface waters relative to effluent. Downstream seawater exhibited higher ARG levels than upstream freshwater despite low culturable E. coli. Peak ARG concentrations in effluent and surface waters were observed following a period of heavy rainfall; however, the limited number of sampling events precluded assessment of any statistical association. These findings highlight the impact of wastewater discharges on environmental AMR dissemination and suggest that faecal indicator-based monitoring may underestimate emerging risks, supporting integration of AMR indicators into EU water quality frameworks.},
}

*Wastewater/microbiology
Ireland
*Environmental Monitoring
*Drug Resistance, Bacterial/genetics
Escherichia coli/genetics/drug effects/isolation & purification
*Seawater/microbiology
*Bacteria/genetics/drug effects/isolation & purification/classification
Public Health
Anti-Bacterial Agents/pharmacology
Pilot Projects
RNA, Ribosomal, 16S/genetics
Water Microbiology
beta-Lactamases/genetics

@article {pmid42698632,
year = {2026},
author = {Park, J and Cheon, S and Choi, YS and Kim, J and Ahn, SJ and Chung, JE},
title = {Anaerobic antibiotic exposure and risk of maculopathy: a nationwide dual design study.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1840229},
pmid = {42698632},
issn = {1663-9812},
abstract = {The pathogenesis of maculopathy remains incompletely understood, and emerging evidence implicates the gut-eye axis in retinal and macular diseases. Given that antibiotics with anti-anaerobic activity may disrupt gut microbial ecology, this study investigated their association with the risk of incident maculopathy. We conducted a nationwide population-based study using the National Health Insurance Service-National Sample Cohort of South Korea. A retrospective cohort study was used to assess cumulative systemic anaerobic antibiotic exposure during a 5-year baseline period and subsequent incident maculopathy from 2007 to 2019. After 1:1 propensity score matching, hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression. A nested case-control study was also conducted using risk-set sampling and 1:10 propensity score matching. Anaerobic antibiotic exposure during the 365 days before the index date was assessed, and odds ratios (ORs) and 95% CIs were estimated using conditional logistic regression. Duration-response relationships were evaluated using formal trend analyses. Sensitivity analyses included age restriction, Fine-Gray competing risk models, extended exposure assessment windows, lag-time analyses, and a negative control comparator analysis using first-generation cephalosporins. In the retrospective cohort study, 326,436 anaerobic antibiotic users were matched to 326,436 non-users. Anaerobic antibiotic use was associated with an increased risk of incident maculopathy in the fully adjusted model (HR, 1.07; 95% CI, 1.03-1.12), with a significant duration-response trend and the highest risk observed for ≥57 days of cumulative use (HR, 1.24; 95% CI, 1.09-1.42). In the nested case-control study, 55,776 cases were matched to 557,760 controls. Anaerobic antibiotic use within 365 days before the index date was associated with increased odds of maculopathy (OR, 1.04; 95% CI, 1.02-1.07), also showing a significant duration-response trend. Sensitivity analyses and first-generation cephalosporin comparator analyses, generally supported the robustness of the findings. Systemic exposure to antibiotics with anti-anaerobic activity was associated with an increased risk of incident maculopathy, with a duration-response pattern across cumulative exposure categories. These findings suggest further investigation into gut microbiome disruption and the gut-eye axis as potential pathways involved in maculopathy.},
}

@article {pmid42699672,
year = {2026},
author = {Wu, D and Dong, T and Chen, X and Lin, Z and Pan, Q and Wei, J and Liang, J and Wei, J},
title = {Insights into microbiome and ARGs diversity in patients with upper and lower respiratory tract infections by targeted next-generation sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21615},
pmid = {42699672},
issn = {2167-8359},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Male ; Middle Aged ; Adult ; *Bacteria/genetics/drug effects/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Drug Resistance, Bacterial/genetics ; Coinfection/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Respiratory tract infections (RTIs) cause substantial global morbidity and mortality, with antimicrobial resistance presenting an increasing challenge to the effective management. Characterizing the differences in microbiome composition and antimicrobial resistance genes (ARGs) between upper respiratory tract infections (URTIs) and lower respiratory tract infections (LRTIs) may inform site-specific diagnostic and therapeutic strategies. We retrospectively analyzed 1,340 URTIs samples (nasopharyngeal swab) and 699 LRTIs samples (bronchoalveolar lavage fluid) admitted to a single medical center to characterize the epidemiology of the respiratory microbes and ARGs using targeted next-generation sequencing (tNGS). Microbiome diversity, ARGs profiles, and coinfection patterns were compared between LRTIs and URTIs groups. Random forest machine learning was employed to identify discriminating species. LRTIs patients exhibited significantly higher microbiome abundance and ARGs diversity than URTIs patients (P < 0.001. Beta-lactam, multidrug, phenicol, and fluoroquinolone resistance genes were significantly more abundant in LRTIs (P < 0.01). Bacteria-virus coinfections predominated in both LRTIs (39.3%) and URTIs (54.6%). Thirty species were identified as potential discriminators between LRTIs and URTIs, with an Area Under Curve (AUC) of 0.852 in the training set. These findings reveal distinct microbial and ARGs profiles between URTIs and LRTIs patients, and provide a foundation for understanding site-specific microbial ecology in RTIs for clinical diagnosis and antimicrobial stewardship.},
}

Humans
*Respiratory Tract Infections/microbiology
*Microbiota/genetics
Female
High-Throughput Nucleotide Sequencing
Retrospective Studies
Male
Middle Aged
Adult
*Bacteria/genetics/drug effects/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Drug Resistance, Bacterial/genetics
Coinfection/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid42694744,
year = {2026},
author = {Rajakaruna, S and Howard-Varona, C and Urvoy, M and AminiTabrizi, R and Ayala-Ortiz, C and Gittrich, M and Solonenko, N and Burris, M and Sanderson, C and Noel, C and Leopold, J and Quillin, L and Doshi, K and Walker, LR and Sullivan, MB and Tfaily, MM},
title = {Metabolome restructuring reveals distinct virocell infection strategies in bacteriophage-host interaction.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag223},
pmid = {42694744},
issn = {2730-6151},
abstract = {Viral infection transforms microbial cells into metabolically reprogrammed "virocells," yet the metabolic architecture underlying this transition remains poorly resolved. Here we investigate how bacteriophages reshape host metabolism in Cellulophaga baltica across time and phage types, uncovering coordinated metabolic reorganization during infection that includes pathway-level patterns consistent with membrane remodeling, amino-acid recycling, and redistribution of cellular resources. Temporal analyses further distinguished infection strategies: efficient phages produced structured, phased metabolic shifts indicative of controlled host reprogramming, whereas inefficient infection triggered abrupt metabolic collapse. These results suggest that the organization and timing of host metabolome restructuring represent defining features of the virocell state and may reflect underlying viral life-history strategies. These biological patterns were made accessible by an integrative annotation framework that combines previously validated computational tools, substantially expanding interpretable metabolite coverage beyond conventional approaches. This approach reveals coherent infection signatures that would otherwise remain hidden, demonstrating how expanded metabolite interpretability can uncover functional principles of virus-host interactions. The analytical strategy presented here is readily transferable to other virus-host systems and complex microbial communities, providing a path toward mechanistic interpretation of untargeted metabolomic data in microbial ecology.},
}

@article {pmid42695145,
year = {2026},
author = {Van Etten, J and Han, S and Burns, JA and Lhee, D and Willoughby, AC and Stephens, TG and Chille, E and Sleith, RS and Bhattacharya, D and Yoon, HS},
title = {Crawling under the radar: Two novel Paulinella species expand knowledge about the ecology and evolution of a primary plastid-containing amoeba lineage.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70230},
pmid = {42695145},
issn = {1529-8817},
support = {80NSSC19K1542/NASA/NASA/United States ; RS-2022-NR068987//National Research Foundation of Korea/ ; RS-2022-NR070837//National Research Foundation of Korea/ ; RS-2025-25434508//National Research Foundation of Korea/ ; NJ01180//USDA National Institute of Food and Agriculture Hatch Formula/ ; 2410274//National Science Foundation/ ; 2410358//National Science Foundation/ ; RS-2025-02304428//Korea Institute of Marine Science and Technology promotion/ ; },
abstract = {The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes.},
}

@article {pmid42696299,
year = {2026},
author = {Román, R and Maestre, FT and Couradeau, E},
title = {Rainfall-induced microbial resuscitation reveals functional decoupling across biocrust succession.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag231},
pmid = {42696299},
issn = {1751-7370},
abstract = {Dryland ecosystems rely on infrequent rainfall pulses to activate soil microbial communities, yet the fraction and identity of microbes resuscitating after hydration remain unclear. We applied bioorthogonal non-canonical amino acid tagging coupled with fluorescence-activated cell sorting (BONCAT-FACS) and 16S rRNA gene sequencing to identify translationally active bacteria in early (L-BSC) and late (D-BSC) successional cyanobacteria-dominated biocrusts subjected to 3 mm simulated rainfall under light and dark conditions. Our results reveal that only a small subset of the microbial community resumes activity within six hours, with higher active cell abundances in mature crusts. Microbial activity patterns were largely independent of light exposure and showed partial decoupling from total community composition, indicating that presence does not predict short-term function. These findings suggest that biocrust maturity shapes microbial activation dynamics and that functional responses to precipitation pulses are governed by a conserved pool of fast responders, informing predictions of dryland soil microbiome resilience under changing precipitation regimes.},
}

@article {pmid42696594,
year = {2026},
author = {Glasl, B and Kitzinger, K and Luter, HM and Legin, A and Schuster, S and Salas, E and Heldwein, N and Damjanovic, K and Rutsch, M and Vekeman, B and Geerlings, NMJ and Pjevac, P and Séneca, J and Watzka, M and Wanek, W and Speth, DR and Wagner, M},
title = {Branched-chain amino acid assimilation enables mixotrophy of ammonia-oxidizing archaeal sponge symbionts.},
journal = {Science advances},
volume = {12},
number = {36},
pages = {eaef9450},
doi = {10.1126/sciadv.aef9450},
pmid = {42696594},
issn = {2375-2548},
mesh = {Animals ; *Ammonia/metabolism ; *Symbiosis ; *Archaea/metabolism/physiology ; *Amino Acids, Branched-Chain/metabolism ; *Porifera/microbiology/metabolism ; Oxidation-Reduction ; },
abstract = {Marine sponges and ammonia-oxidizing archaea (AOA) represent one of the earliest animal-microbe symbioses. AOA are considered metabolically constrained chemolithoautotrophs that remove nitrogenous waste within the sponge holobiont. Here, we expand this view by demonstrating that symbiotic AOA assimilate branched-chain amino acids (BCAA) as additional carbon and nitrogen sources. By combining stable isotope probing with fluorescence and chemical imaging, we trace the assimilation of [13]C- and [15]N-labeled BCAA (leucine, isoleucine, and valine) in the sponge holobiont Ianthella basta at single-cell resolution. We show that the ability to take up, degrade, and biosynthesize BCAA is a common adaptation among symbiotic AOA lineages. This ability may enable symbiotic AOA to modulate BCAA concentrations in their auxotrophic sponge hosts. Modulation of BCAA availability by symbionts may regulate the leucine-sensitive mTOR (mechanistic target of rapamycin) signaling pathway in sponges.},
}

Animals
*Ammonia/metabolism
*Symbiosis
*Archaea/metabolism/physiology
*Amino Acids, Branched-Chain/metabolism
*Porifera/microbiology/metabolism
Oxidation-Reduction

@article {pmid42697479,
year = {2026},
author = {Luo, Y and Jiang, Y and Tingting, Z},
title = {Targeting Nrf2 in oxidative liver injury: expanding the role of gut microbiota and metabolites.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.09.006},
pmid = {42697479},
issn = {2090-1224},
abstract = {BACKGROUND: Liver diseases are a major cause of illness and death worldwide. Oxidative stress is a pivotal driver in the pathogenesis of a spectrum of liver diseases, including alcoholic liver disease (ALD), metabolic dysfunction-associated fatty liver disease (MAFLD), drug-induced liver injury (DILI), and hepatocellular carcinoma (HCC). The transcription factor Nrf2, a master regulator of cellular antioxidant responses, plays a central yet context-dependent role in modulating this injury. Additionally, the gut-liver axis is a critical regulator of hepatic homeostasis.

AIM OF REVIEW: This review presents recent advances to propose a refined gut-microbiota-Nrf2 axis as a key mechanistic link in the treatment of liver injury. We detail how specific gut-derived microbial metabolites, such as short-chain fatty acids (SCFAs), tryptophan derivatives, and urolithins, directly or indirectly activate the hepatic Keap1/Nrf2 signaling pathway. This activation orchestrates a cytoprotective program that enhances the redox balance, promotes detoxification, and induces selective autophagy, thereby protecting against oxidative liver injury. Conversely, we examine the dual role of Nrf2, highlighting how its dysregulated and constitutive activation in established HCC can paradoxically promote tumor progression and ferroptosis resistance. Finally, we evaluate the therapeutic potential of targeting this axis using microbiome-modulating strategies, including probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), dietary intervention, and synergy with Nrf2-targeting drugs.

This review provides an integrated framework that connects gut microbial ecology with host redox signaling, offering novel mechanistic insights and translational perspectives for the prevention and treatment of oxidative liver diseases.},
}

@article {pmid42697798,
year = {2026},
author = {Ho, PM and Nazeer, RR and Askenasy, I and Quinn, RA and Welch, M},
title = {Microbial content versus microbial interaction: the impact of medications on CF airway microbial ecosystems.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.011},
pmid = {42697798},
issn = {1873-5010},
abstract = {BACKGROUND: The airways of people with cystic fibrosis (pwCF) are often colonized by a variety of different microbes. Although much effort has been put into cataloguing the impact of medication on the identities and abundances of these microbes, far less has been directed towards examining this from an ecological perspective, i.e., examining how medications affect the network and types of interactions between microbes.

METHODS: In the current work, we generated an ecological model of the CF airway microbiome and examined how medications affect interactions between co-habiting airway microbiota in six pwCF. Ecological interactions were inferred from a generalized Lotka-Volterra model, and the impact of medications was determined by principal component(s) regression analysis.

RESULTS: For the majority of the subjects studied, antimicrobial interventions had relatively little impact on the CF airway microbial ecology, and even appeared to stabilize ecological interactions between the microbiota. However, the microbial ecosystem in some individuals was more sensitive to external perturbations. More surprisingly, we found that some non-antimicrobial medications, and also certain carriers and excipients affect the ecosystem.

CONCLUSIONS: Medications affect the ecology of the CF airway microbiota. These impacts appear to be very patient-specific. We also note that some nominally non-bioactive ingredients in medications can also potentially impact the CF airway ecosystem. Our data highlight the importance of collecting patient-specific data and in employing suitable computational frameworks for disentangling medication-microbiota interactions in vivo.},
}

@article {pmid42693120,
year = {2026},
author = {Burian, A and Wilson, R and Kratina, P and Ábrám, Ö and Afonina, E and Alcocer, J and Alfonso, MB and Anderson, T and Anufriieva, E and Balci, N and Barbosa, LG and Baxter, BK and Bazarova, B and Bazhenov, Y and Beckmann, M and Boros, E and Borzenko, S and Bucher, EH and Camacho, A and Casamayor, EO and Chao, X and Coleman, P and Colla, MF and Datson, B and Echaniz, S and Farias, ME and Fetahi, T and García, CM and Golovatyuk, L and Hudson, P and Hueso-Kortekaas, K and Johnston, J and Karimov, BK and Kalioujnaia, I and Komova, A and Krienitz, L and Kulshreshtha, S and Larson, R and Lipka, O and Matyugina, E and Mauvisseau, Q and Melack, J and Mills, K and Morant, D and Moreno, E and Namsaraev, Z and Oren, A and Rogers, C and Ryves, DB and Sánchez, MI and Camacho-Santamans, A and Santamans, AC and Schagerl, M and Selivanova, E and Shadrin, N and Sima, S and Tashlykova, N and Teubner, K and Tsybekmitova, G and Timms, B and Ulanova, S and Vidal Quini, NE and Vignatti, A and Wurtsbaugh, WA and Zapitis, C and Zechmeister, T and Zhang, C and Zadereev, E},
title = {The overlooked conservation values of saline lakes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42693120},
issn = {2041-1723},
mesh = {*Lakes/chemistry ; Biodiversity ; *Conservation of Natural Resources ; Animals ; Ecosystem ; Endangered Species ; Salinity ; },
abstract = {Saline lakes are hypersensitive to changes in their water balance and therefore show amplified responses to climatic and land-use changes in their catchment. Despite often dramatic ecological impacts, saline lakes rank low on policy agendas as they are assumed to support few ecosystem services and low levels of biodiversity. Here, we challenge this view and evaluate ecosystem services and threatened species in 85 saline lakes distributed across the globe. We show that saline lakes support, additionally to threatened aquatic biota, a diverse range of red-listed terrestrial species that contribute together with a large beta diversity to their conservation value. Further, our results highlight that saline lakes provide a number of culturally and economically important ecosystem services but several of them are 'hidden' and difficult to quantify. We conclude our analysis with best-practice recommendations for sustainable management of saline lakes. Their local adaptation and implementation will be key for safeguarding biodiversity and ecosystem services of these valuable and highly sensitive ecosystems.},
}

*Lakes/chemistry
Biodiversity
*Conservation of Natural Resources
Animals
Ecosystem
Endangered Species
Salinity

@article {pmid42694728,
year = {2026},
author = {Bautista, J and Iñiguez-Ramírez, A and Villegas-Chávez, JA and Bunces-Larco, D and López-Cortés, A},
title = {Skin microbiome and cutaneous aging mechanisms and clinical implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917816},
pmid = {42694728},
issn = {1664-302X},
abstract = {The skin microbiome is an integral component of the cutaneous ecosystem and contributes to barrier, immune, and metabolic homeostasis. Available evidence is examined across three distinct levels: microbial community structure, functional activity, and host biological response. This ecological-functional distinction is necessary because taxonomic abundance alone does not establish microbial activity, biological effects, or causality. Age-associated microbial variation is considered within the physiological context of cutaneous aging, including reduced sebaceous activity, altered hydration and surface pH, impaired barrier recovery, chronic low-grade inflammation, oxidative stress, and extracellular matrix deterioration. Microbial alterations reported in acne, atopic dermatitis, and rosacea further illustrate how changes in the cutaneous environment can modify host-microbiome interactions and contribute to clinically relevant phenotypes. Translational developments in dermatology and aesthetic medicine include microbiome-compatible skincare, prebiotic and postbiotic formulations, live biotherapeutic approaches, and strategies intended to preserve microbial and barrier recovery after dermatological procedures. Interpretation of the available literature remains limited by low microbial biomass, anatomical and interpersonal heterogeneity, contamination risk, differences in sampling and sequencing methods, and limited functional and longitudinal resolution. Observed microbial remodeling should be interpreted within a bidirectional host-microbiome relationship. Physiological changes that accompany aging can reshape microbial ecology, whereas microbial products may modify barrier and immune responses. Current evidence does not establish whether these microbial alterations are causes, consequences, or correlates of cutaneous aging. Integration of strain-resolved microbiome data with microbial gene expression, metabolite measurements, host molecular responses, and clinical phenotypes will be required to identify biologically relevant microbial functions and determine their value in dermatological practice.},
}

@article {pmid42691813,
year = {2026},
author = {Hoebinger, C and Semmler, G and Petrenko, O and Rajcic, D and Hoffelner, DK and Duckova, T and Baranovskyi, T and Goederle, L and Khuu, MP and Paeslack, N and Reinhardt, C and Pjevac, P and Séneca, J and Mieczkowski, K and Burger, K and Bergheim, I and Gensluckner, S and Völkerer, A and Reiberger, T and Scheiner, B and Aigner, E and Wernly, B and Datz, C and Binder, CJ and Hendrikx, T},
title = {Corrigendum to: 'Alcohol intake reprograms hepatic immune-metabolic circuits to exacerbate murine atherosclerosis and human cardiovascular risk' [JHEP Reports (2026) 19;8(9):101932].},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {10},
pages = {102001},
doi = {10.1016/j.jhepr.2026.102001},
pmid = {42691813},
issn = {2589-5559},
}

@article {pmid42692668,
year = {2026},
author = {Vanzetti, G and Traina, C and Rantsiou, K and Muñoz-Labrador, A and Gabaldón, M and Moreno, FJ and Peron, AC and Lemois, M and Landaud-Liautaud, S and Rossi, F and Ferrocino, I and Cocolin, L},
title = {Development of autochthonous yeast starter cultures for Taggiasca table olives: Microbial ecology and metabolomic profile under standard and reduced-salt fermentation conditions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120246},
doi = {10.1016/j.foodres.2026.120246},
pmid = {42692668},
issn = {1873-7145},
mesh = {*Fermentation ; *Olea/microbiology ; *Food Microbiology/methods ; *Metabolomics ; *Yeasts/metabolism/classification ; *Sodium Chloride/metabolism ; Metabolome ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Italy ; Random Amplified Polymorphic DNA Technique ; Saccharomycetales ; },
abstract = {Taggiasca table olives are a native variety to Liguria (Italy) that undergo spontaneous fermentation in a traditional manner. The autochthonous microbiota of Taggiasca olives is typically dominated by yeasts, while lactic acid bacteria are often unable to compete probably due the high phenolic content of this variety. Consequently, the fermentation kinetics and metabolomic profile are determined primarily by indigenous yeasts. This study evaluated three autochthonous yeast starter cultures for Taggiasca fermentation under standard (10% w/v) and low (6% w/v) salt conditions. Three yeast strains (Pichia membranifaciens TUCC00000520, Candida diddensiae TUCC00000529, and Wickerhamomyces anomalus TUCC00000536), previously isolated from Taggiasca fermentations, were inoculated in different formulations. Dynamics of the microbial community were monitored with an integrated approach, using culture-dependent (plate counts, MALDI-TOF MS, and RAPD-PCR) and culture-independent methods (metataxonomics approach). The metabolome was characterized at the final stage of fermentation via organic acid determination, [1]H NMR and untargeted volatile organic compounds (VOCs) analysis. Results highlighted an influence of the selected yeasts on the microbial dynamics and metabolomic profile of the final product with P. membranifaciens TUCC00000520 isolated until late stages of fermentation. Overall, this study validates the feasibility of autochthonous yeast-driven, cultivar-specific starters and provides a strategic framework for optimizing Taggiasca olive fermentation.},
}

*Fermentation
*Olea/microbiology
*Food Microbiology/methods
*Metabolomics
*Yeasts/metabolism/classification
*Sodium Chloride/metabolism
Metabolome
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Italy
Random Amplified Polymorphic DNA Technique
Saccharomycetales

@article {pmid42680398,
year = {2026},
author = {Mao, Y and Wang, C and Zhang, L and Zou, B and Han, M and Wang, Z},
title = {Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {400-412},
doi = {10.1016/j.jes.2025.12.004},
pmid = {42680398},
issn = {1001-0742},
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; China ; Bacteria ; Eutrophication ; *Microbial Interactions ; *Environmental Monitoring ; Nitrogen Cycle ; },
abstract = {Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.},
}

*Lakes/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
China
Bacteria
Eutrophication
*Microbial Interactions
*Environmental Monitoring
Nitrogen Cycle

@article {pmid42680626,
year = {2026},
author = {Liu, Y and Ji, M and Chen, Y and Liu, K and Liu, P and Liu, Y and Yao, T},
title = {Prokaryotic biogeography across atmospheric, aquatic, and terrestrial ecosystems in the Mount Everest region.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.07.065},
pmid = {42680626},
issn = {2095-9281},
abstract = {The Mount Everest region encompasses one of the world's most fragile cryospheric landscapes, comprising diverse and interconnected habitats across atmospheric, aquatic, and terrestrial ecosystems. Despite growing interest in high-mountain microbial ecology, basin-scale assessments remain scarce. Here, we conducted a microbial survey in the Rongbuk River basin (3699-7000 m a.s.l.), analyzing 677 samples from aerosols, snow, stream water, stream sediments, and soils via 16S rRNA gene amplicon sequencing. We identified 58,141 operational taxonomic units (OTUs) across 67 prokaryotic phyla, dominated by Pseudomonadota, Actinomycetota, and Bacteroidota. Elevational diversity patterns were ecosystem-specific: richness declined with elevation in aerosols and stream water, showed a U-shaped pattern in snow, peaked at mid-elevations in soils, and remained stable in stream sediments. Evenness and Shannon diversity, however, displayed distinct elevational trends and environmental determinants compared to richness. Community assembly was largely stochastic in snow, aquatic, and soils but strongly deterministic in aerosols. Source-tracking analysis revealed strong landscape-scale connectivity, with snow serving as a microbial vector linking atmospheric inputs to downstream ecosystems (contributing 6.6%-12.0%). Soils served as a potential microbial reservoir, harboring 42% of the unique OTUs and contributing 3%-11.8% of communities to other habitats. While stream water and sediments showed reciprocal exchange, aerosols remained largely uncharacterized in terms of their sources. Collectively, these findings demonstrate that although prokaryotic responses to elevation are ecosystem-specific, these habitats are ecologically interconnected across the high-mountain landscape, providing a comprehensive overview of the prokaryotic biogeography of the region.},
}

@article {pmid42681282,
year = {2026},
author = {Berruto, F and Bortolot, M and Lumini, E and Bianciotto, V},
title = {From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3045},
number = {},
pages = {185-208},
pmid = {42681282},
issn = {1940-6029},
mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Soil Microbiology ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {In recent years, DNA sequencing technologies have advanced considerably with the rise of Next-Generation Sequencing (NGS) platforms, which have transformed microbial ecology research. These approaches enable the characterization of entire communities by using DNA traces to identify organisms taxonomically from a single sample. Arbuscular mycorrhizal fungi (AMF) are no exception and represent one of the most extensively studied groups of soil fungi. This chapter presents protocols for high-throughput, sequence-based analysis of AMF communities, covering the complete workflow from DNA extraction in plant or soil samples to the bioinformatic processing of sequencing data. It particularly focuses on rRNA gene metabarcoding, the most common strategy to provide estimates of AMF diversity and community composition through the amplification of DNA with taxon-specific primers followed by sequencing of barcode regions. Alternative strategies are described to accommodate different research objectives, including the selection of molecular markers.},
}

*Mycorrhizae/genetics/classification/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Soil Microbiology
DNA Barcoding, Taxonomic/methods
DNA, Fungal/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid42681999,
year = {2026},
author = {Harrison, F and Wheatley, RM},
title = {A special issue of Essays in Biochemistry on the social lives of bacteria.},
journal = {Essays in biochemistry},
volume = {70},
number = {3},
pages = {295-299},
pmid = {42681999},
issn = {1744-1358},
mesh = {*Bacteria/metabolism ; *Microbial Interactions ; *Bacterial Physiological Phenomena ; },
abstract = {The study of bacterial sociality, understanding when and how bacteria interact and the consequences of those interactions, has rapidly grown in popularity over the last 20 years. This has revealed that bacteria engage in a remarkable variety of social interactions, including complex cell-cell communication, the exchange of an arsenal of inhibitory molecules, and the sharing of metabolites. These interactions can have significant consequences for the host or environment they reside in, and numerous mechanisms of interaction have attracted significant interest for their therapeutic potential. The present special issue contains eight review articles addressing three major questions in bacterial sociality (Who is where? How are they interacting? And what are the implications of this?) alongside five methods-focused articles that introduce some particularly valuable approaches for the study of bacterial interactions.},
}

*Bacteria/metabolism
*Microbial Interactions
*Bacterial Physiological Phenomena

@article {pmid42682509,
year = {2026},
author = {Ren, C and Xiu, Y and Zhang, Y and Wang, X and Zhao, H and Tang, J and Li, Q and Zhang, S and Zhao, F},
title = {Gut microbiome-immune-metabolic mechanisms in cerebrovascular disease: evidence-graded insights from cerebral small vessel disease, ischemic stroke, and intracerebral hemorrhage.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1927904},
pmid = {42682509},
issn = {1664-302X},
abstract = {Cerebrovascular disease is increasingly being examined in relation to the gut microbiome, but the field has not advanced evenly across disease phenotypes. A central challenge is to distinguish broad dysbiosis-based associations from microbial functions, host-facing metabolites, epithelial barrier injury, and immune pathways that may plausibly influence neurovascular vulnerability or recovery. This distinction is particularly important because cerebral small vessel disease, acute ischemic stroke, and intracerebral hemorrhage differ in time scale, vascular pathology, clinical exposure, and available microbiome evidence. This review evaluates gut microbiome-immune-metabolic mechanisms across these cerebrovascular contexts with a focus on microbial ecology, intestinal barrier dysfunction, microbial translocation, short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acid derivatives, tryptophan-linked metabolites, lipopolysaccharide (LPS)-related inflammatory signaling, and emerging multi-kingdom signals, including the gut virome and mycobiome. Current evidence is most convincing in acute ischemic stroke, where human cohort studies and experimental perturbation models link microbiome disruption, microbial metabolites, immune programming, and functional outcome. Evidence for imaging-defined cerebral small vessel disease remains more limited and is largely cross-sectional, whereas intracerebral hemorrhage is an emerging but mechanistically distinct domain. Virome- and mycobiome-related mechanisms remain exploratory and require longitudinal, multi-omics, and perturbation-based validation. This review argues that cerebrovascular microbiome research should move beyond taxonomic association toward time-resolved microbial function, host-facing metabolites, disease-specific host-microbe interfaces, and experimentally testable mechanisms. Candidate microbiome-directed interventions-including dietary, prebiotic, probiotic, postbiotic, fecal microbiota transplantation, defined microbial consortia, metabolite-targeted, and phage-based approaches-remain investigational. Their translation will require disease- and time-window-specific evaluation of biological target engagement, safety, and clinically meaningful outcomes. Longitudinal multi-omics cohorts, disease-specific models, and careful control of diet, antibiotics, vascular medications, hospitalization, and frailty will be essential for determining which gut microbiome-related pathways are causal, context-specific, modifiable, and therapeutically actionable.},
}

@article {pmid42683650,
year = {2026},
author = {Almalki, M and De Pierri, CR and Méric, T and Mkaouar, H and Slimani, D and Mariaule, V and Tebassi, S and Akermi, N and Maguin, E and Hernandez, J and Raittz, RT and Rhimi, M and Asnicar, F},
title = {Protease-serpin-microbiome interactions in inflammatory bowel disease: toward integrated biomarkers of gut health.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726641},
pmid = {42683650},
issn = {1949-0984},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/immunology ; *Serpins/metabolism ; Biomarkers/metabolism ; Intestinal Barrier Function ; *Gastrointestinal Microbiome ; Animals ; *Peptide Hydrolases/metabolism ; Intestinal Mucosa/microbiology/metabolism/immunology ; Bacteria/enzymology/classification/genetics/metabolism/isolation & purification ; *Serine Proteases/metabolism ; Immunity, Mucosal ; },
abstract = {Proteolytic imbalance involving host and microbial serine proteases and their inhibitors (serpins) contributes to intestinal barrier disruption and chronic inflammation in inflammatory bowel disease (IBD). However, the interplay among these components remains insufficiently characterized. Here, we survey 13,304 publications over five decades, to map protease-serpin-microbiome literature in IBD. Our analysis reveals a fragmented literature structure, with uneven coverage and limited cross-domain integration among host proteases, microbial proteases, and inhibitory pathways. We synthesize evidence linking these components to intestinal barrier integrity, mucosal immunity, extracellular-matrix remodeling, and microbial ecology. Considering the protease-serpin-microbiome axis may provide an integrative direction for future studies of IBD pathogenesis, including the investigation of mechanisms underlying disease heterogeneity, prioritizing future biomarker and therapeutic studies.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/immunology
*Serpins/metabolism
Biomarkers/metabolism
Intestinal Barrier Function
*Gastrointestinal Microbiome
Animals
*Peptide Hydrolases/metabolism
Intestinal Mucosa/microbiology/metabolism/immunology
Bacteria/enzymology/classification/genetics/metabolism/isolation & purification
*Serine Proteases/metabolism
Immunity, Mucosal

@article {pmid42683775,
year = {2026},
author = {Bao, X and Wang, R and Qian, X and Wang, Y and Li, T and Wang, Q and Liu, S and Niu, S and Guo, J},
title = {Penicillium-mediated toxicity and microbial dysbiosis are associated with fruiting body abortion in artificially cultivated Chinese cordyceps.},
journal = {Virulence},
volume = {},
number = {},
pages = {2728527},
doi = {10.1080/21505594.2026.2728527},
pmid = {42683775},
issn = {2150-5608},
abstract = {Chinese cordyceps consists of fruiting body and sclerotia (larvae part) formed through the parasitism of the insect Hepialidae by the fungus Ophiocordyceps sinensis, but artificial cultivation is hindered by fruiting body abortion, severely impacting yield and quality. The interactions between the fungus, its host insects, and soil are critical for its development. Multi-omics analyses were conducted to compare normally and abnormally developing samples, examining microbial communities and metabolites in fungus-colonized host larvae and the mycosphere soil. Abnormal fruiting body development was associated with profound shifts in microbial ecology: fungal diversity increased significantly in both endophytic larvae and mycosphere soil, whereas bacterial diversity decreased within host larvae. The microbial composition in and around abnormal samples was markedly altered, characterized by a high enrichment of Penicillium fungi and a depletion of Bacillus bacteria. Cross-kingdom microbial network analysis showed fewer connections and lower stability in abnormally developing samples. Untargeted metabolomic profiling revealed significant accumulation of the antibiotics N1-hydroxy-roquefortine C and glandicoline A, both roquefortine C derivatives characteristic of Penicillium metabolism, along with enriched pathways involved in antibiotic biosynthesis. Exploratory Partial Least Squares Structural Equation Modeling (PLS-SEM) analysis supported an associative pathway in which Penicillium-mediated toxicity is correlated with microbial dysbiosis, which in turn is associated with fruiting body abortion. Conversely, Bacillus may play a critical role in suppressing Penicillium overgrowth and maintaining microbial homeostasis, representing a promising target for biocontrol strategies. This study is the first to reveal potential links between Penicillium‑mediated toxicity, microbial imbalance, and developmental disorders of Chinese cordyceps.},
}

@article {pmid42686967,
year = {2026},
author = {Corinaldesi, C and Anantharaman, K and Aronson, JC and Baker, BJ and Candela, M and Cardinale, B and Dell'Anno, A and Gasol, JM and Grossart, HP and Laiolo, E and Levin, LA and Nomaki, H and Nunoura, T and Pusceddu, A and Ripple, WJ and Snelgrove, PVR and Suttle, CA and Zhang, R and Danovaro, R},
title = {Grounding microbial conservation in ecological principles.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42686967},
issn = {2058-5276},
}

@article {pmid42678152,
year = {2026},
author = {Grettenberger, CL and Williams, C and Hamilton, TL},
title = {The distribution of acidophilic iron oxidizers is consistent with environmental filtering, dispersal limitation, and competition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0035126},
doi = {10.1128/msphere.00351-26},
pmid = {42678152},
issn = {2379-5042},
abstract = {UNLABELLED: Acid mine drainage (AMD) is a global pollution problem characterized by low pH and high concentrations of metals. Active remediation is often cost-prohibitive, but Fe(II)-oxidizing microbes may be used for passive bioremediation. To leverage these species, we must understand the factors that control their distribution. Here, we examined the environmental and ecological factors that control these species with the aim of determining if microbial seeding is a viable remediation strategy. Although stochastic processes appeared to control the distribution of the majority of taxa inhabiting AMD ecosystems, the distribution of Fe(II) oxidizers appeared to be driven by environmental filtering and competition. The abundance of all the major Fe(II)-oxidizing genera had significant relationships with pH, with pH explaining 10%-38% of the variation in their abundance. The genera appeared to have pH preferences, with Acidithiobacillus and Leptospirillum preferring environments with pH below 3, Gallionella, Sideroxydans, and Ferritrophicum preferring environments with pH above 3.5, and Ferrovum preferring intermediate-pH environments. Once the effect of pH is removed, genera that share pH preferences were negatively correlated, indicating that they were likely competing for the Fe(II)-oxidizing niche in their preferred environments. Communities were also shaped by dispersal limitation, which suggests that microbial seeding may be possible in these environments. Future seeding attempts should consider species interactions and ecology more generally to inform their efforts.

IMPORTANCE: Acid mine drainage (AMD) is a global pollution problem affecting streams worldwide. One method of remediating AMD is by using naturally occurring microbial communities to remove iron and other metals. However, we do not have a complete understanding of the factors that control the distribution of these species or if it is possible to seed species from one environment into another. Here, we examine the factors that control community assembly in AMD ecosystems. We find that individual species appear to be dispersal-limited; thus, microbial seeding may be a viable method for AMD remediation.},
}

@article {pmid42679733,
year = {2026},
author = {Sun, Y and Zhao, Z and Lv, J and An, L and Yan, W and Wang, J and Li, Q and Qian, X and Tiedje, JM and Gu, J and Wang, X},
title = {Two typical residual surfactants facilitate the dissemination of antibiotic resistance genes: mechanisms of conjugation and community-level implications.},
journal = {Environment international},
volume = {215},
number = {},
pages = {110484},
doi = {10.1016/j.envint.2026.110484},
pmid = {42679733},
issn = {1873-6750},
abstract = {Since the outbreak of the COVID-19 pandemic, the reinforcement of personal hygiene practices has led to a significant increase in surfactant residues in municipal wastewater. As a reservoir of antibiotic resistance genes (ARGs), municipal wastewater has been reported to facilitate the conjugative transfer of ARGs by surfactants. However, the intrinsic mechanisms driving this process and the broader impact of surfactants on ARGs fate in real wastewater systems remain poorly understood. Here, we demonstrate that residual cetyltrimethylammonium bromide (CTAB) and sodium dodecylbenzenesulfonate (SDBS) promote ARGs transfer both between Escherichia coli (E. coli) strains and from E. coli to municipal wastewater indigenous microbiota. Exploration of the underlying mechanisms revealed that CTAB exerts its effects primarily by increasing cell membrane permeability, inducing oxidative stress, and activating the SOS response. Further investigation showed that CTAB increases membrane permeability through direct binding to membrane proteins. SDBS primarily acted by enhancing bacterial motility and reducing barriers to cell contact. Additionally, modulation of glutamate and aspartate metabolism supported the conjugative transfer process by providing supplementary energy. Furthermore, we found that harboring multidrug-resistant plasmids conferred a survival advantage to bacterial hosts in municipal wastewater environments, thereby promoting the enrichment of ARGs. These findings elucidate novel mechanisms underlying surfactant-facilitated dissemination of ARGs, revealing a significant but overlooked environmental risk associated with residual surfactants in wastewater.},
}

@article {pmid42680317,
year = {2026},
author = {Leng, M and Zeng, Z and Zhu, X and Guo, Y and Xu, H and Chen, W and Xiang, X and Huang, W and Huang, R and Zhao, M and Song, C and Jin, S},
title = {Microbial diversity, functional activities, and safety risks in fermented tea: a comprehensive review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {120020},
doi = {10.1016/j.foodres.2026.120020},
pmid = {42680317},
issn = {1873-7145},
mesh = {*Tea/microbiology/chemistry ; *Fermentation ; *Food Microbiology ; Food Safety ; Mycotoxins ; *Fermented Foods/microbiology ; Fungi/metabolism ; },
abstract = {Microbial fermented teas are gaining global popularity due to their unique sensory profiles and health benefits. The quality and safety of these products are governed by complex microbial ecosystems that orchestrate the biotransformation of tea leaf components. This review addresses a critical paradox in the field: the same microbial activities that generate desirable bioactive metabolites, such as theabrownins and organic acids, also create ecological niches for mycotoxigenic fungi, posing significant health risks from contaminants like ochratoxin A, citrinin, and aflatoxins. While extensive research has cataloged the microbial diversity in these systems, a comprehensive framework linking processing environments to microbial community assembly, functional outcomes, and quantifiable safety risks remains elusive. This review systematically bridges this gap by synthesizing current knowledge on the microbial consortia-dominated by Aspergillus, Penicillium, Bacillus, and Lactiplantibacillus species-that drive tea fermentation. We critically analyze their functional roles in enhancing flavor, bioactivity, and potential probiotic activity while simultaneously evaluating the mechanisms of mycotoxin production and accumulation. By integrating microbial ecology, biochemistry, and food safety, we propose a forward-looking perspective focused on transitioning the industry from traditional, spontaneous fermentation to modern, controlled biotechnological processes. This approach, centered on the use of defined starter cultures, predictive modeling, and active biocontrol strategies, provides a roadmap for ensuring the consistent quality and safety of fermented tea products, ultimately unlocking their full potential as high-quality functional foods.},
}

*Tea/microbiology/chemistry
*Fermentation
*Food Microbiology
Food Safety
Mycotoxins
*Fermented Foods/microbiology
Fungi/metabolism

@article {pmid42670971,
year = {2026},
author = {Mahdy, A and Amin, I and Mohamed, HH and Hamdy, M and Abuelhaded, K and Alam-ElDein, KM and Elbakry, OM and Abdelkhalek, A and Elkhawanky, M and Elgebaly, AS and Faraag, AHI and Mohammed, OA and Doghish, AS},
title = {The Dysbiosis-Barrier-Immune Axis: Unraveling the Immune Consequences of Skin Microbial Imbalance.},
journal = {Immunology and cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imcb.70161},
pmid = {42670971},
issn = {1440-1711},
abstract = {The skin microbiota has been reframed as a dynamic and active regulator of cutaneous barrier integrity and immune programming, moving beyond its traditional view as a passive microbial community. Dysbiosis represents a complex functional and ecological imbalance that disrupts barrier integrity and may promote sustained inflammatory immune remodeling. This mechanistic axis, in which disruption of the microbiota contributes to barrier failure and immune dysregulation, underpins chronic inflammatory skin conditions. Conventional antibiotic-centered therapies often fail to restore microbial homeostasis or immune balance, highlighting their limitations. Emerging precision microbiome therapeutics focus on targeted modulation of microbial function, signaling pathways, and ecological restoration to repair barrier defects and recalibrate immune responses. This review synthesizes current evidence linking skin microbiota dysbiosis with barrier dysfunction, inflammatory immune remodeling, and emerging microbiome-directed therapeutic strategies. We propose an integrative framework linking ecological disruption, epithelial barrier injury, and immune dysregulation while highlighting unresolved mechanistic, translational, and knowledge gaps, such as detailed molecular mechanisms of host-microbiota interactions and challenges in translating findings into clinically effective personalized interventions. Future research should prioritize multi-omics integration and biomarker-driven stratification to advance precision dermatology therapeutics grounded in mechanistic insights of skin microbial ecology.},
}

@article {pmid42671214,
year = {2026},
author = {Qi, S and Zhang, S and Hu, Y and Sun, M and Xing, Z and Bao, S and Song, Y and Sun, L and Tong, X},
title = {Architectural confinement and seasonal forcing shape cross-domain pathogen-associated assemblages in complex built environments.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191526},
doi = {10.1128/spectrum.01915-26},
pmid = {42671214},
issn = {2165-0497},
abstract = {Airborne microbial pathogens in built environments (BEs) may pose health threats, yet the ecological mechanisms governing their assembly and persistence across interconnected architectural spaces are less studied. Here, we conducted a year-long, multi-spatial investigation across a university building complex, sampling the exhaust outlets of three indoor environments and adjacent outdoor inlets. By integrating the 16S rRNA gene and ITS sequencing from 437 paired bacterial-fungal samples, we characterized the spatiotemporal dynamics of airborne opportunistic pathogen-containing genera. Our study showed that spatial filtering emerged as the dominant determinant of pathogen community structure, with confined elevator environments serving as reservoirs of potential pathogens, with limited but continuous microbial influx from surrounding spaces. Some potential pathogens exhibited distinct seasonal dynamics, as exemplified by pathogen-associated fungal genera such as Fusarium, which peaked in autumn and winter, possibly driven by enhanced aerosol persistence and dispersal under cooler, drier conditions. In contrast, the bacterial counterparts exhibited greater temporal resilience, with key taxa such as Listeria actively transcribed during winter, predisposing them to increased relative abundance in spring. Cross-domain ecological networks further revealed dynamic associations among potential pathogens, centered on the skeletal structure mediated by the keystone fungal genus Aspergillus, suggesting that coordinated microbial associations may reinforce their persistence across seasons. Together, our findings suggest that the dynamics of pathogen-containing genera within BEs arise from the coupled effects of spatial filtering, climatic modulation, and microbial associations. These results provide a foundation for transitioning from static environmental control toward predictive pathogen management in BEs.IMPORTANCEBuilt environments (BEs) are the primary settings of human microbial exposure, yet the ecological principles governing the persistence of airborne pathogens across interconnected indoor spaces remain poorly resolved. By integrating bacterial and fungal community dynamics across spatial environments over four seasons, this year-long study demonstrates that the ecology of airborne pathogen-associated taxa is not static but is instead mediated by a complex interplay of spatial, climatic, and biological forces. Our findings identify enclosed, high-transit elevator spaces as critical hotspots for the accumulation of potential pathogens and highlight the role of seasonal ecological reorganization in driving airborne health risks. More broadly, this work establishes a system-level ecological framework for understanding the dynamics of airborne pathogen-associated taxa in BEs and provides a conceptual basis for developing more adaptive strategies for indoor microbial risk management.},
}

@article {pmid42672061,
year = {2026},
author = {Acheampong, R and Otu-Ayeboafo, JO},
title = {Dietary Sulfur Compounds and Halitosis: Bridging Food Science, Microbial Metabolism, and Oral Health: A Comprehensive Review.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {17},
pages = {e70526},
pmid = {42672061},
issn = {1613-4133},
mesh = {*Halitosis/microbiology/etiology ; Humans ; *Oral Health ; *Sulfur Compounds/metabolism/adverse effects ; Microbiota ; Biofilms ; *Diet ; Tongue/microbiology ; },
abstract = {Intraoral halitosis is predominantly caused by anaerobic microbes within the tongue biofilm that break down sulfur-containing amino acids, especially cysteine and methionine, to volatile sulfur compounds (VSCs). In addition to microbial activity, there is growing evidence to suggest that dietary factors are able to influence VSC formation by affecting substrate availability, redox equilibrium, and oral ecological stability and that some of these effects are due to extraoral metabolic activity. This review integrates food chemistry, microbial ecology, and oral health to explain how dietary exposures can interact with the oral microbiome to trigger and maintain halitosis. We synthesize current evidence on tongue biofilm ecology, key microbial taxa and metabolic pathways, and the modifying roles of salivary flow, periodontal inflammation, and common beverages and condiments. Diagnostic approaches are discussed with a mechanistic viewpoint, which has focused on combined organoleptic, gas specific analysis, tongue biofilm imaging, and selective provocation testing. Comprehensively, halitosis is presented as a diet modifiable, ecology-driven disease, the diagnostics of which should be guided by phenotype, and the intervention based on microbiomes and tailored care plans should be sustainable so that evidence-based functional foods and personalized care plans can be developed.},
}

*Halitosis/microbiology/etiology
Humans
*Oral Health
*Sulfur Compounds/metabolism/adverse effects
Microbiota
Biofilms
*Diet
Tongue/microbiology

@article {pmid42674646,
year = {2026},
author = {Zuo, Z and Qiao, L and Cen, X and Liu, T and Zheng, M},
title = {Wastewater-Derived Comammox Nitrospira for Next-Generation Wastewater Management.},
journal = {Environmental science & technology},
volume = {60},
number = {33},
pages = {23018-23034},
pmid = {42674646},
issn = {1520-5851},
support = {DE250100621//Australian Research Council/ ; DP230101340//Australian Research Council/ ; PolyU 25238324//Research Grants Council, University Grants Committee/ ; },
mesh = {*Wastewater ; Ammonia ; Oxidation-Reduction ; },
abstract = {The discovery of complete ammonia-oxidizing (comammox) Nitrospira in 2015 marked a major advance in our understanding of the nitrogen cycle and demonstrated that a single microorganism can catalyze the full oxidation of ammonia to nitrate, challenging the long-standing paradigm that separates ammonia- and nitrite-oxidizing microorganisms. Over the past decade, research on comammox has progressed rapidly from genomic discovery to detailed characterization of its physiology, kinetics, and ecological distribution across natural and engineered ecosystems. Wastewater-derived comammox Nitrospira have emerged as influential players in biological nitrogen transformations due to their exceptionally high substrate affinities, metabolic versatility, potentially low nitrous oxide emissions, and resilience under resource-limited conditions. These traits position comammox as promising catalysts for low-energy and sustainable nitrogen management in engineered systems. This review synthesizes the first decade of research on comammox Nitrospira, with a particular focus on wastewater-associated lineages. We examine the ecological niches that enable comammox Nitrospira to thrive in wastewater environments and analyze their competitive and cooperative interactions with canonical ammonia- and nitrite-oxidizing microorganisms. Building on these ecological insights, we discuss emerging comammox-centered biotechnological strategies for next-generation wastewater treatment and resource recovery. By linking microbial ecology with process engineering, this review highlights the potential for comammox-driven innovations to advance circular and energy-efficient nitrogen management in the coming decade.},
}

*Wastewater
Ammonia
Oxidation-Reduction

@article {pmid42677876,
year = {2026},
author = {Van Leeuwen, P and Thinphovong, C and Sluydts, V and Nicolas, A and Kritiyakan, A and Kriengudom, A and Soisook, P and Chaisiri, K and Morand, S and Michaux, J},
title = {Microbiome Insights Into Zoonotic Risk at Wildlife-Human Interfaces in a Transitioning Landscape in Thailand.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70167},
pmid = {42677876},
issn = {1749-4877},
support = {//Thai International Cooperation Agency/ ; ANR-24-CE35-5476//project rewild4Health/ ; 101059483//BCOMING project/ ; //European Union/ ; 40020126//FNRS/ ; },
abstract = {Land-use change is accelerating worldwide and is one of the strongest predictors of emerging zoonotic disease. These ecological transitions can disrupt host microbiomes, change pathogen carriage, and create novel opportunities for spillover at wildlife-livestock-human interfaces. Yet, little is known about how reforested landscapes influence microbiome diversity and the distribution of zoonotic bacteria in key reservoir hosts such as bats, rodents, treeshrews, and domestic dogs. We characterized the rectal microbiome of bats, rodents, and domestic dogs sampled across a land-use gradient in Nan Province, Thailand, spanning caves, forests, reforested zones, plantations, and village habitats. Full-length 16S rRNA sequencing was used to assess host- and habitat-specific patterns at the bacteria species level. Pathogen-associated taxa were identified, and their potential transmission pathways were explored using network analysis and qPCR validation targeting Salmonella spp. From 102 samples, 1816 taxa were identified, including 354 documented human pathogens. Hierarchical Modeling of Species Communities models confirmed that host species explained far more variation in pathogen occurrences than habitat type, with dogs, Menetes berdmorei, and Scotophilus heathii exhibiting particularly high pathogen diversity. Domestic dogs also displayed high network centrality and move freely across habitats, positioning them as a key bridging host. Salmonella screening detected both Salmonella enterica (serovars Newport/Typhimurium) and the reptile-associated Salmonella bongori, the latter unexpectedly in bats and rodents, with variable concordance between metabarcoding and qPCR results. Our findings demonstrate that host identity, more than habitat type, structures pathogen-associated microbiomes across a reforested landscape. Understanding these dynamics is essential to anticipate pathogen flow and strengthen One Health surveillance.},
}

@article {pmid42663042,
year = {2026},
author = {Araujo, ASF and de Almeida Lopes, AC and Martins, LDV and Ferreira, GDNC and da Costa, RM and Rocha, SMB and Mendes, LW and de Medeiros, EV and Pereira, APA},
title = {Phytohormone-microbiome interactions and epigenetic regulation of plant stress responses and priming.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag417},
pmid = {42663042},
issn = {1460-2431},
abstract = {Plants continuously face fluctuating environmental conditions, requiring tightly coordinated regulatory systems to balance growth and stress responses. This review synthesizes current knowledge on phytohormones as central integrators of plant-microbiome interactions, highlighting their dual role as internal regulators and ecological gatekeepers that shape microbiome assembly and function. Phytohormones, such as auxins, cytokinins, gibberellins, abscisic acid, ethylene, salicylic acid, and jasmonates, dynamically regulate plant development, immunity, and rhizosphere chemistry, thereby influencing microbial recruitment and activity. In turn, plant-associated microbes actively modulate hormonal pathways through biosynthesis, degradation, and interference with signaling and transport processes, thereby reconfiguring plant physiological responses. Emerging evidence demonstrates that these interactions underpin microbial priming, enabling enhanced responsiveness to subsequent stresses without constitutive defense costs. Such primed states are frequently associated with epigenetic modifications, including DNA methylation and histone modifications, which contribute to stress memory and may persist across generations. We propose that microbiome-driven hormonal regulation represents a key mechanism for plant adaptation to environmental stress and that its integration can offer promising opportunities to enhance resilience, reduce agrochemical dependence, and improve agricultural sustainability under climate change.},
}

@article {pmid42663479,
year = {2026},
author = {Liu, M and Su, X and Huang, X and Yang, X and Chen, Y and Xu, J and He, Y},
title = {Top-down/bottom-up consortia achieve robust γ-HCH degradation and reduced methanogenic contribution in wetlands.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0113326},
doi = {10.1128/aem.01133-26},
pmid = {42663479},
issn = {1098-5336},
abstract = {UNLABELLED: Generalist non-obligate organochlorine-degrading bacteria (ODB) play an important role in the bioremediation of γ-hexachlorocyclohexane (γ-HCH), yet their ecological roles and functional mechanisms remain underexplored. In this study, we used both "top-down" and "bottom-up" strategies to construct two functional consortia (M and Y13) based on non-obligate ODB. Both consortia demonstrated efficient degradation in sediment microcosms, reducing γ-HCH (C/C0) to 63.0% (M) and 56.1% (Y13). Simultaneously, functional microbial consortia inoculation significantly suppressed the CO2 reduction methanogenesis pathway compared with the non-inoculated group (P < 0.05), as evidenced by a marked decline in the CH4/CO2 ratio in inoculated groups. The well-known degradation gene pceA was enriched in the Y13 group, and the co-localization of pceA-encoding contigs with mobile genetic elements was identified. Notably, Enterococcus was found to have successfully colonized inoculated groups. It has strong environmental evolutionary adaptability and might acquire organochlorine-degrading genes through horizontal gene transfer under pollution stress. The broad applicability of non-obligate ODB (e.g., Enterococcus) makes them a promising candidate for future environmental remediation efforts, breeding new avenues of "One Health" win-win solutions in carbon reduction during pollution remediation for wetlands.

IMPORTANCE: γ‑Hexachlorocyclohexane (γ‑HCH) is a representative organochlorine pesticide and a well‑known persistent organic pollutant that poses significant risks to ecosystems and human health. Microbial anaerobic degradation is a key process in the natural attenuation and engineered cleanup of γ‑HCH contamination. The effective application of obligate organohalide-respiring bacteria often requires precise management. In parallel, newly discovered non‑obligate organohalide-respiring bacteria capable of degrading γ‑HCH have emerged as promising alternatives, yet their performance and ecological interactions in realistic sediment systems remain poorly understood. This study examines the degradation mechanisms and microbial ecology of non-obligate organohalide-respiring bacterial functional consortia in complex media. The findings provide critical insights for developing effective bioaugmentation strategies for lindane‑contaminated coastal wetlands and may offer a useful framework for managing other recalcitrant halogenated pollutants in similar environments.},
}

@article {pmid42664271,
year = {2026},
author = {Lilja, E and Allen, RJ and Waclaw, B},
title = {Simple birth-death-mutation models predict some-but not all-aspects of the experimental evolution of antibiotic resistance.},
journal = {PLoS computational biology},
volume = {22},
number = {8},
pages = {e1014666},
doi = {10.1371/journal.pcbi.1014666},
pmid = {42664271},
issn = {1553-7358},
abstract = {Mathematical modelling of antibiotic resistance plays an important role in understanding the mechanisms of resistance emergence and spreading, testing the feasibility of new treatment protocols, and antimicrobial stewardship. However, many assumptions underlying some of the most commonly used mathematical models have not been rigorously tested experimentally. We verify whether one of these models - a birth-death-mutation process - is able to quantitatively predict the outcome of laboratory experiments. We grow bacteria in a bioreactor in conditions that closely resemble the assumptions of the model, and compare the model predictions with experimental observables such as the probability and time to resistance evolution, mutant number distribution, and the genetic composition of the evolved populations. We show that the model fails to reproduce some aspects of the experiments (failing differently for different antibiotics) but that simple modifications of the model significantly improve its predictive power. These modifications give insight into the population dynamics of resistant mutants for each antibiotic tested, and highlight the importance of quantitative modelling for accurate prediction of antibiotic resistance evolution.},
}

@article {pmid42667435,
year = {2026},
author = {De, P and Chakraborti, S and Bhabai, B and Nath, S and Ghosh, PK and Khatun, N and Asif, SM},
title = {From traditional retting to precision bioprocessing: microbial ecology, enzymatic selectivity, and systems biology of jute retting.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {9},
pages = {},
pmid = {42667435},
issn = {1572-9699},
mesh = {*Systems Biology/methods ; *Lignin/metabolism/chemistry ; Microbial Consortia ; Bacteria/metabolism ; },
abstract = {Jute is one of the world's most important lignocellulosic fibre crops, yet its commercial value remains highly dependent on retting, a biologically mediated fibre extraction process still largely governed by empirical practices and variable environmental conditions. Recent advances in microbial ecology, enzymology, molecular biology, and bioprocess engineering have transformed retting from a traditional post-harvest operation into a controllable lignocellulosic bioconversion process. This review synthesizes current understanding of the structural organization of jute bast fibres, selective degradation of plant cell-wall polymers, microbial succession, extracellular enzyme networks, and physicochemical factors regulating fibre liberation. It highlights the coordinated interactions among cell-wall architecture, microbial communities, enzyme specificity, and environmental conditions that collectively determine retting efficiency and fibre quality. Emerging precision retting strategies, including defined microbial consortia, enzyme-assisted retting, ribbon retting, controlled processing systems, and water-efficient technologies, are critically evaluated for their potential to improve process reproducibility, fibre quality, and environmental sustainability. The review also examines metagenomics, metatranscriptomics, metaproteomics, metabolomics, systems biology, and artificial intelligence as enabling technologies for microbiome-guided process monitoring, predictive modelling, and digital decision support. Furthermore, this review discusses the integration of precision retting within circular bioeconomy frameworks through resource recovery, pollution mitigation, climate-resilient processing, and lignocellulosic biorefineries. Key knowledge gaps, including limited understanding of microbial interactions, lack of standardized microbial consortia, insufficient process-monitoring tools, fragmented multi-omics datasets, and challenges in industrial scale-up, are identified. Overall, this review presents a systems-level framework for advancing jute retting toward standardized, predictive, and environmentally sustainable precision bioprocessing.},
}

*Systems Biology/methods
*Lignin/metabolism/chemistry
Microbial Consortia
Bacteria/metabolism

@article {pmid42667906,
year = {2026},
author = {Barbosa, LMP and Silva, DEO and Ventura, SH and Costa, MKL and Rocha, SMB and Borges, JF and Costa, RM and de Medeiros, EV and Pereira, APA and Mendes, LW and Salles, JF and Araujo, ASF},
title = {Restoration contexts shape the bacterial and fungal soil communities in desertification hotspots in the Brazilian semiarid region.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130831},
doi = {10.1016/j.jenvman.2026.130831},
pmid = {42667906},
issn = {1095-8630},
abstract = {Desertification in the Brazilian semiarid has compromised ecosystem functionality, impacting soil microbial biodiversity. Thus, restoration strategies have been implemented, aiming to mitigate the negative impacts. However, little is known about their effects on soil microbial communities. In this study, we hypothesized that the two restoration contexts would promote distinct trajectories of soil microbial community recovery. We evaluated 36 soil samples collected from two desertification hotspots in the Brazilian semiarid, representing active (Gilbués) and passive (Irauçuba) restoration contexts. Soil DNA was extracted and subjected to 16S and ITS amplicon sequencing to characterize bacterial and fungal communities, respectively. Community differences were assessed using alpha-diversity metrics, redundancy analysis (RDA), and PERMANOVA. The results showed that within Gilbués (active restoration), bacterial and fungal community composition differed among soils under desertification and restoration. In Irauçuba (passive restoration), only native soils differed from both soils under desertification and restoration. Proteobacteria, Actinobacteriota, and Firmicutes (bacteria), and Ascomycota and Basidiomycota (fungi), were the dominant phyla in both hotspots. Bacterial and fungal communities showed distinct taxonomic patterns among native, degraded, and restored soils within each restoration context. Niche occupancy patterns also differed between restoration contexts. In conclusion, the two hotspots followed contrasting microbial recovery trajectories, demonstrating that restoration responses are context-dependent and vary according to the microbial groups, rather than supporting the universal superiority of one restoration strategy over the other.},
}

@article {pmid42668748,
year = {2026},
author = {Cao, C and Ma, B and Show, PL and Ngo, HH and Fu, X and Li, N and Zhou, J},
title = {Marine phycotoxins repurposed as bioresource: their antiviral potentials and molecular mechanisms in aquatic organism.},
journal = {Marine life science & technology},
volume = {8},
number = {3},
pages = {727-741},
pmid = {42668748},
issn = {2662-1746},
abstract = {UNLABELLED: Marine phycotoxins produced by microalgae have traditionally been regarded as water pollutants or hazardous substances. Most studies have focused on their toxicity, with limited exploration of their therapeutic potential. In this study, we demonstrated that domoic acid (DA) exerts antiviral roles against largemouth bass ranavirus (LMBV). Mechanistic analyses revealed that DA disrupts the extracellular structure of LMBV and inhibits intracellular viral assembly. This may be attributed to the ATP depletion caused by the suppression of mitochondrial oxidative phosphorylation. In vivo, DA treatment reduced fish mortality by 12.5% and significantly alleviated pathological lesions in splenic and telencephalic tissues, thereby further confirming its protective effect. Additionally, transcriptomic analysis of liver tissue showed that DA enhanced digestive enzyme activity and activated the complement immune response in LMBV-infected fish. This study uncovers previously unappreciated antiviral activity of marine phycotoxin-DA and elucidates its underlying mechanisms preliminary, laying a foundation for developing marine phycotoxins as antiviral lead compounds.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s42995-026-00412-2.},
}

@article {pmid42655784,
year = {2026},
author = {Xi, H and Liu, J and Wang, J and Zhong, L and Xu, Y and Li, Y},
title = {Virus-Induced Intestinal Barrier Injury: Mechanisms and Therapeutic Perspectives.},
journal = {Veterinary sciences},
volume = {13},
number = {8},
pages = {},
pmid = {42655784},
issn = {2306-7381},
support = {LQ24C180001//Zhejiang Provincial Natural Science Foundation/ ; 32302845//National Natural Science Foundation of China/ ; 2025SZRJJ1032//Hangzhou Natural Science Foundation/ ; ZJSKXQT2025033//Zhejiang Association for Science and Technology/ ; },
abstract = {The intestinal barrier is a key interface maintaining host-microbial segregation and systemic homeostasis. A broad range of viruses, including enteric, respiratory, and systemic pathogens, can disrupt this barrier through effects on epithelial integrity, vesicular transport, immune responses, and microbial ecology. Whether these diverse insults converge on shared regulatory nodes or act through distinct virus-specific pathways that ultimately result in barrier failure remains unclear. Building on this premise, this review systematically delineates the molecular and cellular mechanisms underlying virus-induced disruption of the intestinal barrier. Viral infection disrupts epithelial integrity through multiple converging processes, including disassembly of tight junction architecture, activation of programmed cell death pathways, degradation of the mucus layer, impaired regeneration driven by intestinal stem cells, and dysregulation of transcellular transport. These processes are interconnected and collectively drive epithelial dysfunction and barrier breakdown. Beyond epithelial damage, we further highlight the pivotal contribution of host immune responses to barrier breakdown. Viral infection induces dysregulated cytokine production and aberrant immune activation, which amplify epithelial damage and further increase barrier permeability. In parallel, increasing evidence supports a bidirectional interaction between viral infection and gut microbiota dysbiosis, in which each process reinforces the other to accelerate barrier disruption and disease progression. We also discuss emerging therapeutic strategies aimed at restoring intestinal homeostasis, including antiviral therapies, host-targeted interventions, and microbiota modulation. Despite recent progress, key questions remain, particularly regarding mechanisms of failed barrier repair after viral clearance and the multilayered regulatory networks linking viruses, immunity, and the microbiota. Together, this review provides a framework for understanding virus-induced intestinal barrier dysfunction and identifies potential therapeutic nodes for intervention.},
}

@article {pmid42657533,
year = {2026},
author = {Cristian, RE and Vrancianu, CO and Constantin, M and Paun, M and Milea, EC and Malaescu, D and Chifiriuc, MC},
title = {Microbiome-based therapeutics for Clostridioides difficile infection: additive, subtractive, and modulatory strategies in modern clinical practice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2722482},
pmid = {42657533},
issn = {1949-0984},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Clostridioides difficile/physiology/drug effects ; Fecal Microbiota Transplantation ; Animals ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; Biological Therapy/methods ; },
abstract = {Microbiome-based therapeutics have rapidly evolved into a transformative field at the intersection of infectious diseases, microbial ecology, and precision medicine. Clostridioides difficile infection (CDI) represents the most extensively studied model, providing a framework for understanding microbiome-driven disease and ecological restoration. This review synthesizes three major therapeutic strategies, additive, subtractive, and modulatory, and integrates recent advances from basic, translational, and clinical research. Additive approaches, including fecal microbiota transplantation (FMT), live biotherapeutic products (LBPs), and defined microbial consortia, aim to restore microbial diversity and colonization resistance. Subtractive strategies selectively target C. difficile or its ecological advantages through targeted antibiotics, bacteriocins, bacteriophages, and CRISPR-based antimicrobials. Modulatory therapies reshape host-microbe and microbe-microbe interactions, targeting toxin activity, bile acid metabolism, and spore germination. Together, these approaches reflect a paradigm shift from pathogen-centered treatment toward ecological therapeutics targeting the dysbiotic niche underlying CDI persistence and recurrence. Understanding the similarities and differences between these strategies can help guide the design of future microbiome-targeted interventions and explore their potential beyond CDI across microbiome-mediated diseases.},
}

Humans
*Clostridium Infections/therapy/microbiology
*Clostridioides difficile/physiology/drug effects
Fecal Microbiota Transplantation
Animals
Anti-Bacterial Agents/therapeutic use
*Gastrointestinal Microbiome
Biological Therapy/methods

@article {pmid42660056,
year = {2026},
author = {Nair, PM and Alex, R and Mondal, G},
title = {Hydrogen flux and microbial interactions governing methane formation in the rumen: Implications for mitigation.},
journal = {The Science of the total environment},
volume = {1050},
number = {},
pages = {182213},
doi = {10.1016/j.scitotenv.2026.182213},
pmid = {42660056},
issn = {1879-1026},
abstract = {Enteric methane production in ruminants is the dominant metabolic consequence of microbial hydrogen (H2) disposal during anaerobic fermentation under typical rumen conditions, yet controlling it without disrupting rumen function remains a critical challenge in sustainable livestock production. Methanogenesis is not an isolated metabolic pathway but an emergent property of syntrophic microbial interactions that govern H2 flux within the rumen ecosystem. During ruminal fermentation, fibrolytic bacteria, anaerobic fungi, and ciliate protozoa generate H2 through coordinated carbohydrate degradation, which is continuously transferred to hydrogenotrophic microorganisms, primarily methanogenic archaea, through interspecies H2 transfer mechanisms that are essential for maintaining redox balance and fermentation efficiency. Molecular hydrogen (H2), serves as the primary vehicle for reductant transfer between microbial partners, and its dissolved concentration in rumen fluid governs the thermodynamic feasibility of all major fermentation pathways. This review uniquely frames enteric methane mitigation as a network-level H2 flux control problem, integrating microbial ecology, thermodynamics, hydrogenase biology, and multi-omics evidence within a unified mechanistic framework. Methanogenesis is more comprehensively understood as a system-level outcome of H2 partitioning within a complex microbial network rather than the activity of methanogens alone. H2 is distributed among competing metabolic sinks, including propionate formation, reductive acetogenesis, nitrate reduction, and sulfate reduction, with methanogenesis dominating due to thermodynamic and ecological advantages under standard rumen conditions. Mitigation strategies are evaluated through their effect on H2 flux: approaches that suppress H2 production, redirect H2 toward alternative sinks, or disrupt interspecies transfer are each constrained by microbial functional redundancy and adaptive compensation. Composite strategies simultaneously targeting multiple nodes within the H2 network achieve more consistent and sustained methane reductions. Reconceptualizing methane mitigation as coordinated control of microbial H2 flow provides a mechanistic, systems-level framework for designing interventions that reduce emissions without compromising rumen microbial stability or host productivity.},
}

@article {pmid42662711,
year = {2026},
author = {Marian, M and Stringlis, I and Rolli, E and Barnes, CJ and Compant, S and Sessitsch, A},
title = {Microbiome modulation for sustainable crop production and climate resilience.},
journal = {Sustainable microbiology},
volume = {3},
number = {3},
pages = {qvag032},
pmid = {42662711},
issn = {2755-1970},
abstract = {The microbiome is fundamental to plant performance in agroecosystems, influencing primary productivity and climate resilience. Microbiome modulation refers to the targeted manipulation (or steering) and optimization of microbiota features, including taxonomic structure, diversity, composition, assembly dynamics, stability, functional capacity, interactions, and network architecture. Here, we review the current state-of-the-art knowledge and strategies used for microbiome modulation, encompassing biological interventions such as bacteria, fungi, protists, nematodes, and phages, as well metabolites, compounds, and nutrients derived from plants. We further discuss emerging tools and strategies for next-generation microbiome modulation, including function-oriented, multitrophic defined microbial communities assembled based on ecological traits and interactions across multiple trophic levels to enable their establishment and function within the phytobiome; temperate phages; microbiome transplantation and breeding; and functional synbiotics, defined as combinations of beneficial microorganisms and compounds that improve microbiome health and function. In addition, we highlight key knowledge gaps and research priorities for advancing precision microbiome modulation. Addressing current challenges will require integrated frameworks combining experimental validation in planta and reductionist approaches with in silico modeling and multiomics analyses to better predict, design, and sustain beneficial plant-microbiome outcomes. Overall, microbiome modulation represents a paradigm shift in advancing sustainable and climate-resilient agri-food systems.},
}

@article {pmid42655146,
year = {2026},
author = {Zhang, Z and Yan, C and Li, J and Zhao, L and Li, L and Cai, R and Wei, W and Lu, S},
title = {Advances in Cider Flavor: Integrating Apple Raw Materials, Microbial Ecology, and Process Control.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
pmid = {42655146},
issn = {2076-2607},
abstract = {Cider is a low-alcohol fruit wine produced by partial or complete fermentation of apple juice. In recent years, its consumption has grown significantly, especially in Asia. Its distinctive flavor profile reflects a complex interplay of aroma and non-volatile components. The composition of cider is mainly influenced by three factors: raw materials, starter cultures, and production process. This review begins by outlining the composition of cider, covering both its aromatic compounds and non-volatile components. The primary aroma profile is defined by higher alcohols, esters, fatty acids, and carbonyl compounds, while sugars, organic acids, and polyphenols are the key determinants of its taste. Subsequently, it provides a detailed analysis of how the raw material, the choice of starter cultures, and the applied production processes collectively shape the cider's flavor. Research shows that apple variety and maturity influence the levels of sugars, organic acids, and polyphenols, shaping the flavor foundation of cider. To enhance flavor diversity, inoculation strategies have shifted from single-strain fermentation with Saccharomyces cerevisiae to mixed fermentations using non-Saccharomyces yeasts and lactic acid bacteria, either simultaneously or sequentially. Currently, screening non-Saccharomyces strains has become a key strategy to increase cider flavor complexity. Precise micro-oxygenation and nutrient supply regulate microbial metabolism, thereby controlling the fermentation process and the production of specific flavor compounds. In the future, given the untapped diversity of non-Saccharomyces yeasts and lactic acid bacteria in winemaking traits, research in this direction may be key to improving cider quality. In addition, selecting apple cultivars tailored to specific cider styles and exploring pre-fermentation treatments such as cold maceration and enzymolysis may also contribute to enhancing the flavor diversity of cider.},
}

@article {pmid42655103,
year = {2026},
author = {Yuan, H and Li, B and Shen, C and Xie, L and Hou, F},
title = {Microbiota-Immune Crosstalk in Pneumonia and Acute Lung Injury: Mechanisms, Evidence, and Therapeutic Opportunities.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
pmid = {42655103},
issn = {2076-2607},
support = {YDZJ202501ZYTS283//Jilin Province Science and Technology Department/ ; },
abstract = {Mucosal microbiota contribute broadly to host defense and immune homeostasis, while the lung and gut microbiota form a particularly important bidirectional ecological and immunological network that shapes pulmonary host defense, inflammatory injury, and tissue repair. In pneumonia, loss of colonization resistance and altered microbial metabolite production may weaken innate and adaptive immunity; respiratory infection, antibiotics, and critical-care exposures can, in turn, remodel both microbial communities. In acute lung injury (ALI) and acute respiratory distress syndrome (ARDS), intestinal barrier failure, circulating microbial products, immune cell trafficking and, in selected settings, lymphatic or hematogenous dissemination of gut-derived organisms may aggravate alveolar-capillary injury. Alveolar macrophages integrate these signals through pattern-recognition, metabolic, and epigenetic pathways, linking microbial ecology to pathogen clearance and inflammatory resolution. The evidence, however, remains uneven. Mechanistic causality rests largely on animal studies, most human data are associative, and trials of microbiota-directed interventions are heterogeneous and strain-specific. This Review examines bacterial and viral pneumonia, sepsis-associated ALI and ventilator-associated injury; separates mechanistic, observational, and interventional evidence; and evaluates probiotics, live biotherapeutic products, microbial metabolites, and dietary approaches. Translation will depend on longitudinal sampling, source-resolved microbial tracking, metabolite-informed patient stratification, and adequately powered trials with clinically relevant endpoints.},
}

@article {pmid42655130,
year = {2026},
author = {Rahman, MH and Jeon, H and Kim, H and Lee, S},
title = {Precision Nutrigenomics in Cultured Finfish: Dietary Regulation of Gene Expression, Microbial Ecology, Metabolism, and Immunity.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
pmid = {42655130},
issn = {2076-2607},
support = {2025//Pukyong National University/ ; Global Partnership Exchange and Capacity Building for Overseas Fisheries" program//Ministry of Oceans and Fisheries/ ; },
abstract = {Precision nutrigenomics requires a diet-microbiome-host perspective because microorganisms can transform feed substrates, generate bioactive metabolites, compete with pathogens, and modify intestinal and systemic gene regulation. This structured narrative review synthesizes representative controlled feeding trials, transcriptomic and targeted gene-expression studies, microbiome analyses, and complementary multi-omic evidence concerning dietary regulations in cultured finfish. The available evidence is concentrated particularly on soybean-derived proteins, lipid-source replacements, selected amino acids and micronutrients, functional additives, probiotics, and fermented ingredients in a limited range of cultured finfish species; therefore, the synthesis is not intended to provide exhaustive coverage of every dietary intervention or finfish taxon. Recurrent host responses involve intestinal inflammation and barrier integrity, nutrient transport, lipid and bile-acid metabolism, long-chain polyunsaturated fatty-acid biosynthesis, targets of rapamycin/insulin-like growth factor (TOR/IGF) signaling, and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) antioxidant defense. The expanded microorganism-centered synthesis shows that dietary effects depend on microbial niche, substrate availability, community succession, metabolite production, and strain-specific probiotic or pathobiont activity. Lactic-acid bacteria, Bacillus-associated interventions, butyrate-generating strategies, fermented ingredients, and microbial biomass may support digestion, immune balance, and disease resistance, but taxonomic shifts alone do not demonstrate functional benefit. Current evidence is limited by extensive reliance on 16S ribosomal RNA (16S rRNA) relative-abundance data, inconsistent digesta-versus-mucosa sampling, inadequate feed and water controls, and weak causal validation. Future precision aquafeed studies should combine host transcriptomics with absolute microbial quantification, shotgun metagenomics, metatranscriptomics, metabolomics, culturomics, histology, and pathogen challenge. Integrating microbial function with host phenotype can improve sustainable feed design, intestinal health, and resilience.},
}

@article {pmid42654237,
year = {2026},
author = {Diaz-Garrido, N and Regaldiz, A and Zagmutt, S and Cisternas, P and Bastías-Pérez, M and Cortés-Martín, A},
title = {Intermittent Fasting and the Gut Microbiota: Mechanisms Linking Microbial Remodeling to Metabolic and Immune Regulation.},
journal = {Nutrients},
volume = {18},
number = {16},
pages = {},
pmid = {42654237},
issn = {2072-6643},
mesh = {Humans ; *Intermittent Fasting ; *Gastrointestinal Microbiome/physiology ; Animals ; *Energy Metabolism ; Prebiotics ; Circadian Rhythm ; Fatty Acids, Volatile/metabolism ; *Fasting ; Probiotics/administration & dosage ; Intestinal Barrier Function ; Immune System ; },
abstract = {Intermittent fasting (IF) has gained increasing attention as a dietary strategy to improve metabolic health and prevent cardiometabolic disorders. Accumulating evidence suggests that modulation of the gut microbiota may represent one of the mechanisms underlying the physiological benefits of IF. This review summarizes the current knowledge on the mechanisms by which IF modulates gut microbial ecology and how these changes influence host metabolic and immune functions. We examine the effects of IF on gut microbiota diversity and composition, highlighting shifts in key microbial taxa associated with metabolic regulation. In addition, we discuss how fasting-induced microbial remodeling affects microbiota-derived metabolites, including short-chain fatty acids and bile acids, which play central roles in energy homeostasis, intestinal barrier integrity, and inflammatory signaling. Increasing evidence indicates that IF interacts with circadian rhythms, influencing both microbial oscillations and host metabolic pathways that coordinate nutrient sensing and energy metabolism. Furthermore, we explore the bidirectional crosstalk between the gut microbiota and the intestinal immune system, emphasizing that fasting-driven microbial changes may modulate inflammatory responses, epithelial barrier function, and immune cell activity. Finally, we discuss nutritional strategies that may enhance the beneficial effects of IF, including the incorporation of prebiotics, dietary fiber, and probiotic supplementation, to promote microbial diversity and functional resilience. Collectively, these findings support a model in which IF acts as a key modulator of the gut microbiota-immune-metabolic axis. Future integrative studies combining gut microbiome, metabolomic, and immunological approaches are needed to better understand these interactions and optimize microbiota-targeted dietary interventions.},
}

Humans
*Intermittent Fasting
*Gastrointestinal Microbiome/physiology
Animals
*Energy Metabolism
Prebiotics
Circadian Rhythm
Fatty Acids, Volatile/metabolism
*Fasting
Probiotics/administration & dosage
Intestinal Barrier Function
Immune System

@article {pmid42654492,
year = {2026},
author = {Ingravalle, F and Ciotti, M and Gaetti, G and Morlino, G and Bulfone, G and Bardhi, D and Barbadoro, P and Pica, F and Di Carlo, S and Serafinelli, L and Vinci, A and Maurici, M},
title = {Microbial Epidemiology and Antimicrobial Resistance Trends in Urinary Isolates from a Tertiary Hospital in Rome, Italy: A Retrospective Study (2022-2025).},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {8},
pages = {},
pmid = {42654492},
issn = {1648-9144},
mesh = {Humans ; Retrospective Studies ; Rome/epidemiology ; Tertiary Care Centers/statistics & numerical data/organization & administration ; *Urinary Tract Infections/microbiology/epidemiology/drug therapy ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbial Sensitivity Tests ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; Italy ; Drug Resistance, Bacterial ; },
abstract = {Background and Objectives: Urinary tract infections are common in clinical practice, but in hospital settings, especially among older and catheterized patients, the microbial ecology and resistance burden may differ substantially from community-acquired infections. Local surveillance is therefore essential to support appropriate empirical treatment and antimicrobial stewardship. The objective is to describe the microbiological epidemiology of urinary isolates in a tertiary hospital and evaluate temporal trends in antimicrobial resistance among the most frequently isolated microorganisms. Materials and Methods: This retrospective observational study analyzed microbiology laboratory data from Tor Vergata University Hospital, Rome, Italy, collected from January 2022 to June 2025. After WHONET-based deduplication using a 30-day repeat-isolate rule, 5788 deduplicated urinary isolates and 85,888 microorganism-drug associations were included. Descriptive analyses, cumulative antibiograms/antimycograms, and quarterly resistance trends were assessed using univariable and multivariable regression analyses. Results: The population was predominantly elderly, inpatient, and catheter-exposed. Gram-negative organisms predominated, followed by Gram-positive bacteria and fungi. The most frequent isolates were E. coli, K. pneumoniae, E. faecalis, and C. albicans. Although microorganism distribution remained broadly stable over time, resistance increased in several clinically relevant organism-drug combinations, especially among major Enterobacterales. Conclusions: In this high-complexity hospital population, urinary isolates showed a relatively stable microorganism distribution but progressive changes in susceptibility among selected urinary isolates. These findings support setting-specific microbiological surveillance and stewardship-informed empirical treatment strategies.},
}

Humans
Retrospective Studies
Rome/epidemiology
Tertiary Care Centers/statistics & numerical data/organization & administration
*Urinary Tract Infections/microbiology/epidemiology/drug therapy
Anti-Bacterial Agents/therapeutic use/pharmacology
Microbial Sensitivity Tests
Female
Male
Aged
Middle Aged
Aged, 80 and over
Italy
Drug Resistance, Bacterial

@article {pmid42654747,
year = {2026},
author = {Koukouvini, KA and Fokas, R and Vantarakis, A},
title = {Beyond Infection-Indoor Airborne Pathogens as Contributors to Respiratory Inflammation and Immune Dysregulation: A Narrative Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
pmid = {42654747},
issn = {2076-0817},
mesh = {Humans ; *Air Microbiology ; *Air Pollution, Indoor/adverse effects/analysis ; *Inflammation/etiology ; Fungi ; },
abstract = {Indoor-air research has largely examined infection, microbial ecology, immune effects and antimicrobial resistance separately, leaving the pathway from indoor biological sources to chronic respiratory outcomes insufficiently integrated. This narrative review synthesises evidence on indoor airborne pathogens and non-viable microbial components as health-relevant biological exposures beyond acute infection. Literature published between 2000 and February 2026 was reviewed from PubMed, Scopus and Web of Science, supplemented by guidance from WHO, ECDC, US EPA and ASHRAE. Viable microorganisms and non-viable components, including endotoxin, β-(1→3)-glucans, microbial DNA and extracellular vesicles, engage epithelial pattern-recognition pathways and promote inflammatory signalling. Findings included 6.5% higher TNF-α and 5% higher IL-8 per log-unit increase in fungal-spore exposure among sawmill workers; uncontrolled asthma in 45% of moisture- or mould-exposed versus 33% of non-exposed children; airborne resistance-gene and mobile-element loads of 0.55-479.44 copies/m[3] in hospital departments; and a 32.8% reduction in viral diversity, but no significant reduction in high viral exposure, following classroom HEPA filtration. These findings support biological plausibility but reveal a fragmented evidence base dominated by observational studies, heterogeneous sampling and limited longitudinal exposure-response data. Indoor bioaerosols should be considered continuous exposures within the exposome, requiring research and regulation across microbiology, environmental engineering, medicine and public health.},
}

Humans
*Air Microbiology
*Air Pollution, Indoor/adverse effects/analysis
*Inflammation/etiology
Fungi

@article {pmid42654952,
year = {2026},
author = {Wang, J and Wang, K and Yuan, R and Xu, X and Ma, Q and Chen, K and Jiang, Y and He, X and Zhang, X and Liu, X},
title = {Effects of Combined Application of Mushroom Residue and Chemical Fertilizer on Greenhouse Soil Quality and Microbial Community Structure and Function.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
pmid = {42654952},
issn = {2076-2607},
support = {2025QCY KXJ 128//Construction of the "Scientists+Engineers" Team, Shaanxi Qinchuangyuan/ ; },
abstract = {To explore the effects of different fertilization regimes on physicochemical properties and microbial ecology of greenhouse soil, we set five treatments with original soil (BS) as the control: chemical fertilizer alone (GF), high/low-rate mushroom residue combined with chemical fertilizer (MH, ML), and high/low-rate organic fertilizer combined with chemical fertilizer (OH, OL). Metagenomic sequencing and bioinformatic analyses were adopted to characterize soil nutrients, microbial communities, and C-N-P-S metabolic functions. All treatments increased soil nutrients. MH had the highest organic matter, total nitrogen, nitrate nitrogen, and available phosphorus, while GF contained the most available potassium and ammonium nitrogen. Bacteria dominated the soil microbiota, with Pseudomonadota and Pseudomonas as keystone taxa. Mushroom residue amendments improved microbial richness and diversity. By improving soil physicochemical properties, the combined application of organic fertilizer with chemical fertilizer and mushroom residue with chemical fertilizer both enriched some beneficial microorganisms. Chemical fertilizer alone enhanced anaerobic metabolism, which was reversed by high-rate mushroom residue. Available phosphorus, available potassium, and ammonium nitrogen were key environmental factors driving the differentiation of microbial communities and their functions. Overall, mushroom residue combined with chemical fertilizer is effective for greenhouse soil improvement, with proper dosage and tillage recommended.},
}

@article {pmid42654991,
year = {2026},
author = {Kasimanickam, R and Bhowmik, P and Jiang, Z},
title = {Postpartum Uterine Diseases in Dairy Cattle: Integrating Microbiology, Immunology, and Reproductive Physiology.},
journal = {Microorganisms},
volume = {14},
number = {8},
pages = {},
pmid = {42654991},
issn = {2076-2607},
support = {GF002076//Population Theriogenology Development Fund/ ; //Department of Veterinary Clinical Sciences, Washington State University/ ; },
abstract = {Postpartum uterine diseases are among the most prevalent and economically important reproductive disorders affecting dairy cattle worldwide. These conditions, including metritis, clinical and subclinical endometritis, and pyometra, develop during the postpartum transition period when physiological, metabolic, endocrine, and immunological adaptations increase susceptibility to microbial invasion and persistent uterine inflammation. Although bacterial contamination of the postpartum uterus is nearly universal, healthy cows generally restore uterine homeostasis through coordinated immune responses, microbial regulation, and effective uterine involution. Failure of these defense mechanisms results in microbial dysbiosis, impaired endometrial repair, reduced fertility, and substantial economic loss. Major pathogens associated with postpartum uterine disease include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, Prevotella spp., and other anaerobic bacteria that interact synergistically to promote inflammation, tissue damage, and reproductive dysfunction. Advances in next-generation sequencing, metagenomics, and metatranscriptomics have transformed understanding of the postpartum uterine microbiota and host-microbe interactions involved in disease pathogenesis. This review synthesizes current evidence regarding uterine physiology, microbial ecology, immune regulation, virulence mechanisms, dysbiosis, diagnostic approaches, and emerging omics-based technologies relevant to postpartum uterine disease in dairy cattle. Particular emphasis is placed on the ecological and physiological interactions linking microbial succession, endocrine recovery, metabolic stress, and immune competence during the postpartum period. The review further discusses translational opportunities for precision diagnostics, microbiome-informed interventions, antimicrobial stewardship, and integrated herd management strategies to improve reproductive efficiency, animal welfare, and dairy herd sustainability.},
}

@article {pmid42639367,
year = {2026},
author = {Mulaw, G and Kidanemariam, G and Bara, M and Tesfay, T},
title = {Probiotics in Human Health: Current Evidence, Mechanism of Action, and Future Perspectives.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {1721210},
pmid = {42639367},
issn = {1687-918X},
abstract = {Probiotics are widely recognized for their potential to promote human health through diverse mechanisms that influence host physiology and microbial ecology. This review synthesizes current evidence on the biological functions, mechanisms of action, and therapeutic applications of probiotics. A comprehensive narrative literature review was conducted, with 143 records identified, screened, and assessed for eligibility before inclusion in the final analysis. The available evidence indicates that probiotics exert their beneficial effects through modulation of gut microbiota composition, enhancement of intestinal barrier integrity, competitive exclusion of pathogens, production of antimicrobial metabolites, and regulation of innate and adaptive immune responses. Clinical and experimental studies further suggest potential benefits in the prevention or management of antibiotic-associated diarrhea, lactose intolerance, allergic diseases, hypercholesterolemia, colorectal cancer, neurological disorders, and heavy metal toxicity. Despite promising findings, probiotic efficacy remains strain-specific and influenced by host characteristics, dosage, and treatment duration. Challenges related to strain selection, safety assessment, and standardization continue to limit broader clinical application. Overall, this narrative review provides an integrated overview of current knowledge on probiotic functionality, highlights emerging therapeutic opportunities, and identifies key research gaps that should be addressed to support evidence-based probiotic use.},
}

@article {pmid42642057,
year = {2026},
author = {Mairet, F},
title = {Mitochondrial ribosome content as a proxy for respiration.},
journal = {Biology letters},
volume = {22},
number = {8},
pages = {},
doi = {10.1098/rsbl.2026.0144},
pmid = {42642057},
issn = {1744-957X},
mesh = {*Saccharomyces cerevisiae/metabolism/growth & development ; *Mitochondrial Ribosomes/metabolism ; *Oxygen Consumption ; *Oxygen/metabolism ; Mitochondria/metabolism ; Cell Respiration ; *Ribosomes/metabolism ; },
abstract = {Quantifying cellular activities remains a major challenge across fields ranging from microbial ecology to biotechnology and biomedical sciences. Building on the well-established linear relationship between growth rate and ribosome content-the so-called microbial growth law-this study proposes using organelle ribosome content to infer metabolic activity. In exponentially growing yeast (Saccharomyces cerevisiae), including under overflow metabolism conditions, a strong linear correlation was observed between mitochondrial ribosome content and oxygen uptake rate, underscoring the potential of this approach. Additionally, under fully respiratory conditions, cytoplasmic and mitochondrial ribosome fractions were linearly correlated, whereas overflow conditions fell below this linear relationship, providing a means to identify such metabolic states. Although these findings require broader validation across additional species, organelle ribosome quantification may provide a promising proxy for deciphering cellular metabolism.},
}

*Saccharomyces cerevisiae/metabolism/growth & development
*Mitochondrial Ribosomes/metabolism
*Oxygen Consumption
*Oxygen/metabolism
Mitochondria/metabolism
Cell Respiration
*Ribosomes/metabolism

@article {pmid42643400,
year = {2026},
author = {Medaglia-Mata, A and Rojas-Rodríguez, P and Bystrý, V and Guillén-Watson, R and Gómez-Espinoza, O and Núñez-Montero, K},
title = {PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1909327},
pmid = {42643400},
issn = {2673-7647},
abstract = {BACKGROUND: Environmental microbiome research has advanced through three complementary sequencing modalities, targeted 16S rRNA amplicon sequencing, whole-genome shotgun (WGS) metagenomics, and long-read full-length 16S rRNA profiling, each supported by distinct toolsets with heterogeneous outputs, variable configurations, and different levels of reproducibility documentation. Existing pipelines are typically modality-specific, require substantial configuration expertise, or produce outputs that need further custom scripting before standard ecological analyses can begin. This analytical fragmentation introduces avoidable technical variability and complicates cross-study reproducibility and comparability. PUDU addresses this by integrating all three modalities into a single reproducible workflow with simplified configuration, harmonized outputs across classifiers, and direct compatibility with downstream ecological analysis frameworks.

RESULTS: We present PUDU (Pipeline for Universal Diversity Unveiling), a modular Snakemake workflow that supports amplicon (short-read 16S), shotgun metagenomics (WGS), and long-read 16S analyses from raw reads to standardized outputs for downstream microbial ecology. PUDU performs technology-aware preprocessing and centralized quality control, and integrates established taxonomic approaches, including DADA2 for amplicons, Emu for full-length 16S long reads, and Kraken2/Bracken and Centrifuger for WGS. Across methods, PUDU produces harmonized count and relative-abundance tables at user-defined taxonomic ranks, Krona files, and a standardized Phyloseq-compatible R object to streamline diversity analyses and statistical workflows. PUDU also provides an integrated Shiny interface for metadata-aware alpha/beta diversity, ordination, community composition, and shared-taxa exploration with exportable figures and taxa tables. We demonstrate PUDU on two publicly available environmental datasets spanning rhizosphere WGS and long-read marine sediment 16S, yielding broadly consistent community-level patterns across classifiers (Spearman ρ = 0.936 at phylum level; PERMANOVA R[2] = 0.87-0.95) with peak memory below 45 GB on a standard Linux workstation.

CONCLUSION: PUDU is an end-to-end, reproducible, and extensible framework that enables standardized taxonomic profiling and ecology-oriented analysis across sequencing modalities. By combining harmonized outputs, Phyloseq interoperability, and an integrated visualization layer, PUDU facilitates reproducible, standardized, and comparable environmental microbiome analysis from raw reads to interpretable ecological insights.},
}

@article {pmid42644562,
year = {2026},
author = {Rainey, PB and Timmis, KN and Williams, PA and Karahan, ZC and López-García, P and Chavarria, M and Greening, C and Steward, K and Silva Pereira, C and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H and Hochberg, ME and Berryhill, B and Levin, BR},
title = {Stop paying predatory publishers of academic journals-A policy proposal to restore scientific integrity and transparency.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70451},
pmid = {42644562},
issn = {1873-3468},
abstract = {Scientific publishing is undergoing a systemic breakdown. Thousands of journals now collect article processing charges (APCs)-increasingly paid from public research funds-while providing minimal editorial oversight. This erodes standards, distorts incentives and threatens public trust in science. APC payments to six major publishers exceeded 8 billion dollars between 2019 and 2023, with almost no transparency over how these fees are set or spent. This cannot continue. We propose that public and institutional funds support journals-whether through APCs, subscriptions or bundled agreements-only where they are accredited against a transparent, enforceable quality standard. Implemented in stages and led by funding bodies and learned societies, such accreditation would narrow the space in which predatory journals operate without resorting to blacklists.},
}

@article {pmid42645451,
year = {2026},
author = {Lee, YC and Cheng, YC and Kung, CM and Huang, CJ},
title = {Modulating Oral Microbiota to Prevent Dental Caries: A Microbial Ecology Approach.},
journal = {Dentistry journal},
volume = {14},
number = {8},
pages = {},
pmid = {42645451},
issn = {2304-6767},
abstract = {Background: Dental caries is a highly prevalent, biofilm-mediated disease characterized by microbial dysbiosis, excessive acid production, and progressive enamel demineralization. Although traditionally managed through restorative treatment, increasing attention has shifted toward preventive strategies focused on modulation of the oral microbiota and maintenance of ecological balance within the oral cavity. Methods: This narrative review summarizes current evidence regarding the ecological and mechanistic basis of dental caries and microbiota-centered prevention strategies. Literature published between January 2000 and March 2026 was retrieved from PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar using keywords related to dental caries, oral microbiota, cariogenic bacteria, biofilms, probiotics, prebiotics, salivary diagnostics, metabolomics, quorum sensing, and artificial intelligence. Results: Current evidence demonstrates that dental caries is driven by ecological shifts favoring acidogenic and aciduric microorganisms within cariogenic biofilms. Emerging preventive approaches include dietary modification, oral hygiene optimization, probiotics, prebiotics, synbiotics, and functional dietary agents aimed at restoring microbial homeostasis and inhibiting cariogenic biofilm maturation. In addition, advances in salivary microbiome profiling, metabolomics, artificial intelligence-assisted predictive modeling, and smart responsive materials have shown promising potential for improving early diagnosis, risk assessment, and personalized prevention strategies. Conclusions: Microbiota-based approaches represent a promising paradigm shift in dental caries prevention by emphasizing ecological modulation rather than pathogen eradication alone. Continued interdisciplinary research integrating microbial ecology, diagnostics, biomaterials, and digital technologies may facilitate the development of personalized and preventive oral healthcare strategies.},
}

@article {pmid42645525,
year = {2026},
author = {Larsen, J and Efthymiou, A and Nicolaisen, MH and Jensen, B and Nybroe, O and Gómez-Muñoz, B},
title = {Penicillium aculeatum pre-activated with cellulose and different phosphorus sources promotes maize growth, nutrition and mycorrhiza formation, and decreases Microdochium bolleyi root infection.},
journal = {Current microbiology},
volume = {83},
number = {10},
pages = {},
pmid = {42645525},
issn = {1432-0991},
mesh = {*Zea mays/microbiology/growth & development ; *Cellulose/metabolism ; *Mycorrhizae/growth & development/physiology ; *Plant Roots/microbiology/growth & development ; *Penicillium/metabolism/physiology ; *Phosphorus/metabolism ; Soil Microbiology ; Soil/chemistry ; *Glomeromycota/growth & development/physiology ; },
abstract = {Microbial plant growth promoters often perform inconsistently under natural soil conditions most likely due to their poor establishment after inoculation. Here, we conducted a growth chamber pot experiment with maize using pre-activated inoculum of the P-solubilizing fungus Penicillium aculeatum to facilitate its establishment in a natural non-sterile agricultural soil. Hence, P. aculeatum was preincubated for one week in soil amended with cellulose as a C source and with different P sources, i.e. sewage sludge ash, Ca3(PO4)2, and no P fertilization as control. Control treatments of C and P sources without P. aculeatum were also included. The pre-activated inocula were mixed into natural agricultural soil (1:40 w/w), maize seeds were sown, and plants were grown for 42 days. Measured variables included shoot and root dry weight, nutrient content, and root colonization by arbuscular mycorrhizal fungi (AMF) and root infection with Microdochium bolleyi. Overall, P. aculeatum inoculation enhanced maize growth, nutrient content and AMF root colonization, while reduced root infection with M. bolleyi, independent of P source used. Both P sources increased maize growth and nutrient content, though sewage sludge ash showed stronger effect than Ca3(PO4)2. None of the P sources affected AMF root colonization, but sewage sludge ash decreased M. bolleyi root infection and increased the population density of P. aculeatum. In conclusion, inoculation with pre-activated P. aculeatum (with cellulose and P sources) enhances maize growth and nutrient uptake, and is associated with increased AMF root colonization and reduced root infection by M. bolleyi.},
}

*Zea mays/microbiology/growth & development
*Cellulose/metabolism
*Mycorrhizae/growth & development/physiology
*Plant Roots/microbiology/growth & development
*Penicillium/metabolism/physiology
*Phosphorus/metabolism
Soil Microbiology
Soil/chemistry
*Glomeromycota/growth & development/physiology

@article {pmid42646070,
year = {2026},
author = {Li, H and Jiao, X and Wang, Y and Sun, N},
title = {Co-Application of Organic and Ca, Mg, Zn Fertilizers Reshapes Depth-Stratified Arbuscular Mycorrhizal Fungal Communities in Orchard Soil.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {42646070},
issn = {2309-608X},
support = {KJCX20250926//Beijing Academy of Agricultural and Forestry Sciences/ ; Z191100004019001//Beijing Municipal Science and Technology Commission/ ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are crucial symbiotic microorganisms in terrestrial ecosystems, playing a vital role in maintaining orchard soil health and productivity. However, how organic-and Ca, Mg, Zn fertilizers co-application affect vertical stratification and ecological functions of arbuscular mycorrhizal fungi (AMF) in perennial fruit orchards remains unclear. Based on a five-year in situ peach trial, we established three fertilization regimes: low- (LWF), medium- (MWF), and high-input (HWF) regimes. We systematically analyzed the AMF community structure, diversity, and their correlations with soil physicochemical properties, as well as peach tree physiology, fruit yield, and quality across two soil depths: 0-20 cm (topsoil) and 20-40 cm (subsoil). HWF significantly inhibited AMF root colonization rates and spore density (p < 0.05), while reducing community α-diversity AMF α-diversity (p < 0.05), characterized by the enrichment of genera such as Glomus and a decrease in the relative abundance of Rhizoglomus. Redundancy analysis (RDA) identified available Zn (AZn) and Mg (WMg) as key drivers of this restructuring. Integrating RDA results into depth-specific partial least squares structural equation models (PLS-SEM), we found that subsoil AZn/WMg indirectly boosted yield by reshaping AMF composition (β = 0.34, p = 0.006), mediated via improved canopy status (NDVI, PRI). Total effect analysis confirmed the dominant role of subsoil pathways. These findings challenge the prevailing topsoil-centric view of soil microbial ecology and underscore the importance of considering the full soil profile when evaluating the impacts of agricultural practices on beneficial symbionts. We conclude that sustainable management strategies should account for depth-dependent AMF responses to maintain both productivity and belowground biodiversity across the entire rooting zone.},
}

@article {pmid42646830,
year = {2026},
author = {Liu, J and He, Y and Qiu, K and Zhao, S and Qiu, Z and Gao, S and Nagel, G and Zhu, M},
title = {TrcrtB regulates carotenoid biosynthesis, stress tolerance, conidiation and pathogenicity in the postharvest pink rot fungus, Trichothecium roseum.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-03-26-0608-RE},
pmid = {42646830},
issn = {0191-2917},
abstract = {Trichothecium roseum is a highly destructive postharvest pathogenic fungus that causes pink mold rot in various fruit and leads to significant agricultural and economic losses. Phytoene is crucial for phytopathogens, but the molecular mechanism by which the phytoene synthase gene crtB regulates fungal pathogenicity remains largely unclear. In this study, we evaluated the functions of TrcrtB a phytoene synthase, in T. roseum via in vivo and in vitro assays. Our results showed that knock-out of TrcrtB showed inhibition of production of phytoene and its relevant downstream metabolites, such as lycopene, carotenes and carotenal, resulting in colorless colony and branching at the mycelial edges in the knockout mutant ΔTrcrtB. Compared with the wild type (WT) strain, the colony expansion was significantly reduced 35% at 5 days post-inoculation (dpi), and conidiation was notably decreased to 45%, 36%, and 70% at 3, 5, and 7 dpi in ΔTrcrtB in vitro. Scanning electron microscope observation revealed similar results. Moreover, the ΔTrcrtB showed higher sensitivity to abiotic stresses than WT, as evidenced by inhibition rates of ΔTrcrtB colony expansion up to 71.76% (menadione), 47.73% (Congo red), 23.01% (SDS), and 17.13% (KCl). The pathogenicity of ΔTrcrtB was dramatically impaired by decreasing the rotten area up to 85.26% on apple fruit and 70.30% on pears fruit. These results suggest that TrcrtB and phytoene are critical for development, stress tolerance and pathogenicity of T. roseum. Collectively, our study highlights the roles of TrcrtB and phytoene in the pathogenic fungus T. roseum, providing new insights into the molecular mechanisms of pink rot pathogenesis.},
}

@article {pmid42647083,
year = {2026},
author = {Lv, R and Jiang, Z and Zhong, Y},
title = {The role of gut-lung axis-targeted nursing strategies in immune regulation of COPD.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02947},
pmid = {42647083},
issn = {1588-2640},
abstract = {Chronic obstructive pulmonary disease (COPD) is featured by persistent airflow limitation and chronic inflammation. Considerable evidence highlights the role of the gut-lung axis, suggesting that disruption of gut microbial balance may contribute to aggravated systemic and pulmonary inflammation. This research intended to assess the impacts of a structured gut-lung axis-targeted nursing intervention on immune-inflammatory parameters, gut microbiota, and clinical outcomes in patients with stable COPD. The study involved the randomization of 115 patients to either the intervention or control group in a 1:1 ratio. The intervention group received a 12-week multimodal program, which included personalized high-fiber/probiotic nutrition, customized exercise plans, and stress management techniques. Patients in the control group did not receive the multimodal program and instead received routine care. The findings indicated that the intervention notably lowered serum IL-6, TNF-α, and CRP. Microbiome analysis further revealed that the intervention significantly enhanced α-diversity (Shannon and Chao1), enriched beneficial butyrate-producing genera (Faecalibacterium, Roseburia, and Bifidobacterium), and reduced the relative abundance of potential pathogens (Enterobacteriaceae), indicating a favorable shift in gut microbial ecology. Compared with the control group, the intervention group also experienced fewer moderate-to-severe exacerbations and showed greater sustained improvement in quality of life (SGRQ and CAT scores). In summary, a comprehensive nursing strategy centered on the gut-lung axis can regulate gut microbiota, alleviate systemic inflammation, lead to a reduction in exacerbation frequency and an improvement in the quality of life among patients with stable COPD, thus presenting a promising supplementary strategy to conventional care.},
}

@article {pmid42647465,
year = {2026},
author = {Ali, S and Baig, A and Nagassar, RP and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D},
title = {The Caribbean under the radar? A scoping review of carbapenemase-producing Enterobacterales across the region.},
journal = {PLOS global public health},
volume = {6},
number = {8},
pages = {e0007176},
pmid = {42647465},
issn = {2767-3375},
abstract = {Carbapenemase-producing Enterobacterales (CPE) are a critical antimicrobial resistance (AMR) threat globally. The Caribbean region, despite its high global connectivity, varied healthcare infrastructure and rising antimicrobial use, remains underrepresented in CPE surveillance data. Our study aims to map and characterise the existing literature on CPE in the Caribbean, including bacterial species, carbapenemase types, detection methods, and epidemiological trends. A scoping review was conducted in accordance with PRISMA-ScR guidelines. MEDLINE, EMBASE, Cochrane CENTRAL and Web of Science were searched to 1st July 2025 in addition to grey literature (policy documents, guidelines, websites). Studies were included if they reported carbapenemase production among Enterobacterales from human, animal, or environmental sources in Caribbean nations (defined geophysically). Non-Caribbean studies and non-Enterobacterales organisms were excluded. Fourteen studies published between 2008 and 2024 met inclusion criteria. Reports originated from six countries: Cuba, Puerto Rico, Jamaica, Guadeloupe, the Dominican Republic, and Curaçao. Klebsiella pneumoniae was the most frequently reported species. The most common carbapenemase enzymes were KPC (including KPC-2 and KPC-8), NDM-1, NDM-5 and OXA-48. Co-production of NDM and KPC was documented. Detection was largely hospital-based, though community and environmental isolates were also identified. High levels of AMR were observed, with colistin often the only active agent. Surveillance gaps are evident across many populous Caribbean nations. CPE are established in multiple Caribbean countries, but surveillance remains irregular and limited. Addressing critical gaps in diagnostic capacity, reporting and molecular surveillance is essential to ensure the region's inclusion in the global AMR response.},
}

@article {pmid42649294,
year = {2026},
author = {Sichert, A and Pollak, S and Priest, T and Goyal, A and Miravet-Verde, S and Sunagawa, S and Cordero, OX and Sauer, U},
title = {Synergistic degradation of fucoidans in the ocean.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42649294},
issn = {1476-4687},
abstract = {Fucoidans, a class of complex polysaccharides produced by brown algae and diatoms, contribute to long-term carbon sequestration owing to their resistance to microbial degradation[1,2]. Although individual microorganisms can break down portions of these polysaccharides[3-5], it remains unclear whether complete breakdown is possible in nature and, if so, by what mechanisms. Here we show that fucoidans are degraded through synergistic interactions between specialized bacteria with complementary metabolic functions. Using metabolomic analysis of a reconstructed marine consortium, we uncovered metabolic guilds of bacteria that preferentially degrade either the sulfated fucose backbone or the side branches of rare monomers. This functional division of labour leads to an unexpectedly high number of synergistic interactions between different degraders that enhanced degradation efficiency up to 97.1%. Despite varying fucoidan structures across different types of algae[6], the metabolic functions of degraders remained conserved, enabling quantitative prediction of degradation outcomes based on community and substrate composition. The frequent co-occurrence of functionally complementary fucoidan degraders in ocean metagenomes suggests that synergistic degradation is a globally relevant strategy. Our findings suggest that the environmental turnover of complex biopolymers depends not only on individual metabolic capabilities of degraders but also on ecological interactions shaped by substrate architecture. This work provides a mechanistic framework for understanding carbon cycling in the ocean and for engineering synthetic microbial consortia to degrade recalcitrant polysaccharides.},
}

@article {pmid42650190,
year = {2026},
author = {Godos, J and Caruso, G and Mainas, G and Micek, A and Di Mauro, A and Buccarello, L and Martínez López, NM and Frias-Toral, E and Giampieri, F and Lehoczki, A and Isola, G and Galvano, F and Ungvari, Z and Quiles, JL and Battino, M and Grosso, G},
title = {Oral Microbiota, the Oral-Brain Axis, and Neurodegeneration: Mechanisms and Dietary Modulation.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antiox15080925},
pmid = {42650190},
issn = {2076-3921},
support = {NA//Italian Ministry of Health/ ; },
abstract = {The oral microbiota represents a complex and dynamic microbial ecosystem that plays a critical role in preserving both oral and systemic homeostasis. Emerging evidence suggests that alterations in oral microbial milieu (dysbiosis) may contribute to the pathogenesis of neurodegenerative disorders, especially Alzheimer's disease (AD), through the oral-brain axis. This review synthesizes current evidence on the pathways linking oral microbiota to cognitive decline, integrating microbial, immunological, and vascular perspectives. Oral pathogens may access the central nervous system via hematogenous dissemination or neural routes, including the trigeminal nerve, while simultaneously promoting systemic inflammation, immune activation, and blood-brain barrier disruption. These processes converge on key neurodegenerative mechanisms, including chronic neuroinflammation, amyloid-β accumulation, and tau pathology. In parallel, alterations in oral microbial composition have been linked to disease severity, supporting a potential role of dysbiosis in both initiation and progression of cognitive impairment. Diet emerges as a critical modifiable determinant of oral microbial ecology. Diets rich in refined sugars may promote dysbiosis and inflammatory signaling, whereas (poly)phenols, probiotics, and prebiotics may support microbial eubiosis and exert neuroprotective effects through modulation of host-microbe interactions. Although current evidence remains largely observational and mechanistic, the diet-oral microbiota-brain axis represents a promising target for preventive and therapeutic strategies aimed at mitigating cognitive decline and promoting healthy aging. Future longitudinal and interventional studies are required to establish causality and translate these insights into clinical practice.},
}

@article {pmid42650527,
year = {2026},
author = {Li, S and Yu, X and Huang, H and Wang, C and Yi, C and Zhang, X and Wen, Y and Xiong, B and Jiang, Q and Yu, K and Ma, Y},
title = {Regulatory Effects of Tannin Supplementation on Microbial Succession and Flavor Formation During Xiaoqu Light-Flavor Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/foods15162833},
pmid = {42650527},
issn = {2304-8158},
support = {Y2025067//Sichuan University of Science and Engineering/ ; H72313005//Yibin Agricultural Science and Technology Innovation Project/ ; 2022ZDZX0016//Sichuan Province Major Science and Technology Special Project/ ; },
abstract = {Sorghum tannins have been suggested to influence microbial ecology and flavor formation in Xiaoqu light-flavor Baijiu (XLB), but their specific contribution is difficult to distinguish from confounding, cultivar-dependent variations in macromolecular components. To address this limitation, a controlled fermentation system was established using a uniform, low-tannin substrate. Based on preliminary gradient trials, a 1.0% tannin supplementation level was selected, and high-throughput sequencing combined with HS-SPME-GC-MS was employed to investigate tannin-related microbial and volatile changes. Compared with the group without tannin supplementation, 1.0% tannin supplementation altered bacterial and fungal community succession during the fermentation, reducing the relative abundances of Saccharomyces and Weissella, and enriching taxa including Cyberlindnera and Pantoea. The tannin-supplemented group exhibited a more complex and stable microbial co-occurrence network. Furthermore, PICRUSt2 predictions suggested enhanced metabolic potentials primarily related to carbohydrate and amino acid pathways. FUNGuild analysis further suggested that tannin supplementation shifted fungal trophic-mode composition, particularly saprotrophic and saprotroph-containing groups. At the end of fermentation, total volatile compounds increased from 4.208 μg/g to 4.983 μg/g, total esters and acids increased by 27.0% and 112.3%, respectively, whereas total alcohols decreased by 13.3%. Spearman correlation analysis revealed that the enriched non-Saccharomyces fungi and acid-producing bacteria in the tannin-supplemented group were positively associated with the accumulation of acids and esters, whereas the control microbiota was mainly linked to an alcohol-oriented profile. These findings may provide process-level evidence for tannin-related microbial and volatile changes during XLB fermentation.},
}

@article {pmid42650569,
year = {2026},
author = {Hao, M and Liu, J and Kan, C and Zheng, X and Liu, C and Zhang, Y and Shen, L},
title = {Research Progress, Challenges, and Future Trends of Modified Atmosphere Packaging (MAP) Technology for Food and Agricultural Products: A Bibliometric Analysis (2016-2025).},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/foods15162875},
pmid = {42650569},
issn = {2304-8158},
abstract = {Modified atmosphere packaging (MAP) is a preservation and packaging technology used to extend the shelf life of foods and agricultural products, maintain quality stability, and ensure food safety. To systematically review and summarize the current research landscape, technical challenges, and development trends in the MAP field, this study selected 1568 publications related to MAP from the Web of Science Core Collection (WOSCC) database during 2016-2025 and conducted bibliometric and visualization analysis. The results indicate that research activity in the MAP field has remained robust over the past decade, mainly focusing on four research areas: atmosphere regulation and packaging system design; microbial ecology, safety, and spoilage control; physicochemical deterioration and quality regulation; functional packaging materials and integrated preservation technologies. Countries such as China, Italy, and Spain have demonstrated outstanding performance in terms of publication output and academic influence in the MAP field, forming a solid research foundation in the MAP of perishable foods such as fruit and vegetables, meat products, and aquatic products. Research in the MAP field has gradually shifted from the verification of application effects toward system design and mechanistic analysis. Active packaging, intelligent packaging, bio-based materials, natural functional ingredients, volatile organic compounds, microbial community succession, and quality deterioration mechanisms have gradually become research hotspots, indicating a trend toward precision, sustainability, and functionality. These findings may provide references for future research topic selection, innovative packaging system design, and the development of novel food preservation technologies in the MAP field for foods and agricultural products.},
}