@article {pmid40840251,
year = {2025},
author = {Gui, L and Wang, S and Chen, L and Dou, Y and Fan, Y and Huang, S and Wu, T and Tian, X},
title = {Crumpled polyethyleneimine nanofiltration membranes regulated by thermocapillary effect for efficient magnesium-lithium separation.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124352},
doi = {10.1016/j.watres.2025.124352},
pmid = {40840251},
issn = {1879-2448},
abstract = {The advancement of lithium (Li) extraction from brines is crucial for boosting Li production capacity and meeting the growing demands of emerging energy markets. However, the presence of symbiotic ions, particularly magnesium ions (Mg[2+]), poses significant challenges. Although conventional nanofiltration (NF) membranes have demonstrated considerable potential in magnesium-lithium (Mg[2+]/Li[+]) separation, they often face the inherent trade-off between membrane permeance and salt rejection. In this study, NF membranes with desirable ridge-like structures were fabricated via temperature-gradient-assisted interfacial polymerization. Notably, under the action of thermocapillary effect, the surface morphology of the membranes can be precisely controlled by adjusting the amount of residual aqueous film on the substrate. The separation performances revealed that the unique microscale hollow ridges provided a larger effective filtration area, leading to a substantial improvement in membrane permeance. Compared to conventional polyethyleneimine-based NF membranes, the optimized membrane exhibited a threefold increase in permeance (17.6 L·m[-2]·h[-1]·bar[-1]) while exhibiting a higher Mg[2+] rejection rate (97.6 %) and exceptional Mg[2+]/Li[+] selectivity (SLi[+]/Mg[2+] = 32.2). Additionally, the membrane demonstrated excellent long-term operational and storage stability. These crumpled membranes displayed advantages such as ease of production and high separation efficiency, making them highly promising for practical applications in Mg[2+]/Li[+] separation.},
}

@article {pmid40839311,
year = {2025},
author = {Majhi, P and Prajapati, N and Pradhan, U and Das, SN and Shukla, AK},
title = {Sustainable stress management in crops: unlocking the potential of rhizospheric microbes.},
journal = {Archives of microbiology},
volume = {207},
number = {10},
pages = {233},
pmid = {40839311},
issn = {1432-072X},
mesh = {*Rhizosphere ; *Crops, Agricultural/microbiology/physiology/growth & development ; *Soil Microbiology ; *Stress, Physiological ; *Microbiota ; Symbiosis ; Fungi ; Bacteria ; },
abstract = {Biotic and abiotic stresses pose significant challenges to global agricultural productivity by adversely affecting soil health, plant vitality, and crop yields. These stresses can lead to economic crises, highlighting the urgent need for cost-effective and environmentally sustainable solutions to mitigate their negative impacts. Traditionally, agrochemicals such as pesticides, insecticides, fertilizers, and herbicides have been extensively and often improperly used to protect plants and enhance crop productivity. However, this over-reliance has harmed ecosystems and human health. In response to these challenges, plants have evolved symbiotic relationships with microbes as a natural defense mechanism. Increasingly, attention is being directed toward rhizospheric microbiomes like Bacillus sp., Pseudomonas sp., Pantoea sp., Rhizobium sp., Trichoderma sp., Piriformospora sp., Penicillium sp., Aspergillus sp., etc. for their potential to manage pathogens, such as bacteria, viruses, fungi, parasites, and herbivores responsible for biotic stress and abiotic stresses such as drought, salinity, high temperature, and metal toxicity in a sustainable and eco-friendly manner. Validating these microbial interactions through experimental research is essential to understand their effects on rhizosphere biodiversity, soil heath status, plant growth and crop productivity. This review examines the role of rhizospheric microbes in protecting plants against biotic and abiotic stresses through plant-microbiota symbioses.},
}

*Rhizosphere
*Crops, Agricultural/microbiology/physiology/growth & development
*Soil Microbiology
*Stress, Physiological
*Microbiota
Symbiosis
Fungi
Bacteria

@article {pmid40839117,
year = {2025},
author = {Oravecz, O and Xie, Y and Balogh, A and Posta, M and Harms, C and Farkas, E and Borowski, S and Szekeres-Barthó, J and Than, NG and Blois, SM},
title = {Maternal and placental galectins: key players in the feto-maternal symbiotic tango.},
journal = {Seminars in immunopathology},
volume = {47},
number = {1},
pages = {35},
pmid = {40839117},
issn = {1863-2300},
mesh = {Humans ; Pregnancy ; *Galectins/metabolism/genetics ; Female ; *Placenta/metabolism/immunology ; Animals ; *Maternal-Fetal Exchange/immunology ; Placentation/immunology ; Immune Tolerance ; },
abstract = {Galectins, a family of β-galactoside-binding proteins, are critical in regulating feto-maternal interactions during pregnancy. Their evolutionary trajectory is reflected in their expression patterns and diverse functions in embryo implantation, trophoblast invasion, and maternal immune and vascular adaptation, contributing to healthy placentation and uncomplicated pregnancy. Galectin-1 (gal-1), one of the most ancient galectins, plays a pivotal role in feto-maternal immune regulation, acting predominantly from the maternal side to promote immune tolerance, a function integrated early in placental mammalian evolution. In contrast, anthropoid primates introduced a unique set of fetal (placental) galectins (gal-13, gal-14, and gal-16) through birth-and-death evolution, with these genes localized on human chromosome 19. Notably, these primate species have evolved varying degrees of deep placentation, with humans exhibiting the deepest, which facilitates enhanced nutrient delivery to the fetus, particularly for brain development. Placental galectins have been implicated in the evolution of immune tolerance mechanisms that support deep placentation. During pregnancy, reduced expression of maternal galectins (e.g., gal-1) and placental galectins (e.g., gal-13) has been associated with severe obstetric complications, signaling disruptions in feto-maternal tolerance. This review provides a comprehensive overview of gal-1, gal-13, gal-14, and gal-16, highlighting their shared and unique roles in maternal and placental immune regulation and placental development. Additionally, the review explores the potential of maternal versus placental galectins as biomarkers and therapeutic targets to improve diagnostic and treatment strategies for adverse pregnancy outcomes.},
}

Humans
Pregnancy
*Galectins/metabolism/genetics
Female
*Placenta/metabolism/immunology
Animals
*Maternal-Fetal Exchange/immunology
Placentation/immunology
Immune Tolerance

@article {pmid40837223,
year = {2025},
author = {Tang, HM and Zhang, QL and Qiao, X and Dai, MW and Yuan, YS and Tang, XM and Yang, WJ and Jing, R and Li, XC and Zhang, Q and Yan, X and Ma, YC and Huang, YB and Zhou, LX and Long, J and Peng, NN and Cai, CH and Meng, JH and Luo, KJ},
title = {Innexin DNA-binding domains regulate Microplitis bicoloratus bracoviral transcription in symbiotic wasps.},
journal = {iScience},
volume = {28},
number = {9},
pages = {113276},
pmid = {40837223},
issn = {2589-0042},
abstract = {Bracoviruses have two hosts: symbiotic wasps and infected hosts. Although symbiotic wasps and infected Spodoptera litura larva host bracoviruses, mature virions form only in the wasps after the integrated Microplitis bicoloratus bracovirus (MbBV) proviral genome replicates. However, the associated mechanisms of transcription regulation have not been characterized. Here, we found that innexins (Inxs) of the Microplitis bicoloratus wasp (Mb-Inx1 and Mb-Inx2) contain DNA-binding domains that directly bind to, and regulate transcription promoters of the viral envelope genes MbBVp74 and MbBVe56-1. Transmission electron microscopy revealed that Mb-Inx1 and Mb-Inx2 RNA interference cause abnormal bracoviral virion formation. This led to inhibited virion assembly in wasp ovaries and downregulated envelope genes that are analogous to baculovirus proteins. The ectopic expression of Mb-Inx1 and Mb-Inx2 in the Bac-to-Bac Baculovirus expression system promoted nuclear polyhedra formation. We propose that unique bracoviral transcription strategies regulated by wasp Inx proteins govern virus-wasp interactions.},
}

@article {pmid40837070,
year = {2025},
author = {Bunch, KM and Greeneway, GP and Ansari, DS and Patel, C and Nottmeier, EW and Madhavan, KHS and Pirris, SM and Sama, AA and Brooks, NP},
title = {The symbiosis of robotics, enabling technology and minimally invasive surgery.},
journal = {North American Spine Society journal},
volume = {23},
number = {},
pages = {100769},
pmid = {40837070},
issn = {2666-5484},
abstract = {BACKGROUND: Procedural and technical advances in spinal surgery, such as the utilization of minimally-invasive techniques, have evolved alongside the development and distribution of tools such as navigation, robotics, augmented reality (AR), dynamic visualization, and preoperative planning modules. Each innovative advancement in a surgeon's ability to see, measure, and manipulate human tissue entails an improvement or novel application of existing tools. Similarly, given the enormous economic and opportunity costs associated with the research and development of novel technologies, these efforts must be refined to address existing needs and infrastructure gaps. The successful application of enabling technologies such as robotics, navigation, and minimally-invasive techniques, is therefore dependent upon the expansion of new surgical tools and techniques.

METHODS: We review numerous technological advances (Navigation, Intraoperative Imaging, Robotics, Augmented Reality, Computational Planning and Visualization) within the field of spine surgery and demonstrate their mutually beneficial, yet dependent, relationship with one another in advancing spine surgery technology through both expert opinion and published literature.

RESULTS: We provide an overview of several different domains of enabling technology as they pertain to novel applications in spinal surgery and review current uses, limitations, and areas of potential improvement.

CONCLUSIONS: The integration of augmented reality, robotics, visualization and navigational technologies, minimally invasive techniques, and other advanced tools have enabled the surgeon to perform both standard and novel procedures in unique ways.},
}

@article {pmid40836244,
year = {2025},
author = {Yu, LC and Wei, SC and Li, YH and Huang, CY and Pai, YC and Hung, YM and Lai, LC and Ni, YH},
title = {Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {63},
pmid = {40836244},
issn = {1757-4749},
support = {NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NHRI-EX111/112/113-11108BI//National Health Research Institute, Taiwan/ ; NSTC 113-2320-B002-062-MY3, MoST 110-2320-B-002-011-MY3//National Science and Technology Council, Taiwan/ ; },
abstract = {BACKGROUND: Symbiotic microbes benefit the host, but the emergence of pathobionts leads to disease. An invasive Escherichia coli LI60C3, isolated from mouse colonocytes, shows colitogenic and tumorigenic properties. Despite extensive research on the role of microbiota in colorectal cancer (CRC) development, the genetic markers associated with this pathobiont remain elusive. The objective is to characterize the tumorigenic E. coli through whole-genome sequencing (WGS) and phenotypic assays, and validate their presence in human CRC.

METHODS: The intracellular bacterial counts and proliferation rates of human intestinal epithelial cells were evaluated after exposure to various E. coli strains. Tumor burden was assessed in mice orally administered LI60C3. WGS of LI60C3 was performed on a PacBio Sequel II platform, and the long reads were assembled de novo for gene annotation and detection of virulence factors and antibiotic resistance. Bacteria-specific genes were assessed in CRC specimens by qPCR analysis.

RESULTS: A 100-fold increase in intracellular bacterial count was observed in epithelial cells exposed to LI60C3 compared to commensal E. coli strains. LI60C3 resulted in a threefold increase in epithelial cell cycle rate and a fourfold rise in mouse tumor numbers. WGS revealed a circular chromosome of 4,863,930 bases for LI60C3, demonstrating a high sequence homology to adherent-invasive E. coli LF82 (91%) and NC101 (87%) and to uropathogenic E. coli 536 (88%). Two extrachromosomal plasmids, pTra and pCoMb, were identified. While pTra exhibits sequence homology with other commensal E. coli plasmids, pCoMb has partial matches with those found in pathogenic bacteria. LI60C3 is classified as phylogroup B2 and expresses virulence factors, including Type 1 and P fimbriae, contact-dependent growth inhibition system, iron acquisition system, and hemolysin. Unique gene clusters, named Epm and Phz islands, were identified in the LI60C3 genome. The emergence of LI60C3-specific genes was observed in mouse tumors induced by chemicals and gene mutation, and higher levels of LI60C3 markers were validated in human CRC specimens compared with healthy mucosal samples.

CONCLUSION: Genetic signatures of LI60C3 were detected in mouse and human CRC. The comparative genome analysis for LI60C3 helps identify pathobionts and may be used as cancer predictors.},
}

@article {pmid40836206,
year = {2025},
author = {Xiong, Q and Zheng, L and Zhang, Q and Li, T and Zheng, L and Song, L},
title = {Comparative genomic insights into ecological adaptations and evolutionary dynamics of Trebouxiophyceae algae.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {764},
pmid = {40836206},
issn = {1471-2164},
support = {Grant No.2021xjkk0600//Supported by the Third Xinjiang Scientific Expedition Program/ ; },
mesh = {Phylogeny ; *Genomics/methods ; *Evolution, Molecular ; *Chlorophyta/genetics/classification ; *Adaptation, Physiological/genetics ; },
abstract = {BACKGROUND: The Trebouxiophyceae is a diverse and species-rich class within the Chlorophyta, exhibiting a wide array of lineages and remarkable variations in morphology and ecology. This group encompasses various lifestyles, including photobionts in symbiotic relationships, free-living forms, and parasitic heterotrophs lacking photosynthetic capacity. Trebouxiophycean algae have attracted considerable scientific interest due to their fundamental biological significance and their promising applications in biotechnology. This study presents a comprehensive genomic analysis of six newly sequenced strains of Trebouxiophyceae, expanding upon a foundation of 25 previously reported high-quality genomes to conduct comparative genomics and evolutionary assessments.

RESULTS: Molecular phylogenetic analyses based on 18 S rDNA and single-copy orthologues confirmed the accurate identification of species. The analyzed strains exhibited variable genome sizes ranging from 2.37 Mb to 106.45 Mb, with GC content varying between 46.19% and 67.20%, and repeat content ranging from 1.67 to 19.73%. Gene family expansion and contraction analyses revealed that the subaerial species Apatococcus exhibited the most extensive expansions, while Picochlorum, along with the ancestors of the parasitic genera (Auxenochlorella, Helicosporidium, and Prototheca) experienced pronounced contractions. Evolutionary analyses using the branch model and branch-site model in PAML indicated that genera with the most marked gene family expansion and contraction also contained orthogroups undergoing positive selection and rapid evolution. Comparative assessments of biosynthetic gene clusters (BGCs), nitrogen transport and assimilation proteins, hexose-proton symporter-like genes (HUP1, HUP2, and HUP3), and C4-related enzymes across 31 Trebouxiophyceae genomes revealed further patterns of adaptation. Coccomyxa was the only genus containing all the ten types of BGCs, while most other genera exhibited relatively fewer BGCs. The nitrate transporter and the urea active transporter were both absent in the three parasitic genera, and urease, the urease accessory proteins and arginase were nearly universally missing in all the species. All the species possessed the HUP1, HUP2, and HUP3 genes, except that HUP2 was absent in Prototheca and Picochlorum, and the relative abundances of the three genes varied among genera. The NAD-ME, and PCK subtypes of C4-related genes were widely distributed in all the samples, while the malate dehydrogenase (NADP+) was identified only in the four freshwater strains belonging to Chlorella and Coccomyxa.

CONCLUSIONS: Expanded gene families, along with the rapid evolution and positive selection genes, likely played important roles in environmental adaption across terrestrial and marine habitat. Conversely, genome streamlining due to widespread gene families likely contributed to the parasitic heterotrophic lifestyles. Additionally, the distribution of BGCs, nitrogen transport proteins and HUP-like genes, and the types of C4-related enzymes perhaps highlighted the potential of Trebouxiophyceae to adapt to complex and varied environmental conditions.},
}

Phylogeny
*Genomics/methods
*Evolution, Molecular
*Chlorophyta/genetics/classification
*Adaptation, Physiological/genetics

@article {pmid40835991,
year = {2025},
author = {Guo, M and Yuan, T and Jiang, L and Zhou, G and Huang, H},
title = {Acclimation mechanisms of reef-building coral Acropora gemmifera juveniles to long-term CO2-driven ocean acidification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30655},
pmid = {40835991},
issn = {2045-2322},
support = {2018A0303130173//Natural Science Foundation of Guangdong Province, China/ ; 2023B1212060047//Science and Technology Planning Project of Guangdong Province, China/ ; 2021YFC3100500//National Key Research and Development Project of China/ ; U23A2035//National Natural Science Foundation of China/ ; },
abstract = {Ocean acidification (OA) is a major threat to the sexual recruitment of reef-building corals. Acclimation mechanisms are critical but poorly understood in reef-building corals to OA during early life stages. Here, Acropora gemmifera, a common Indo-Pacific coral cultured in in situ seawater from Luhuitou reef at three levels of pCO2 (pH 8.14, 7.83, 7.54), showed significantly delayed larval metamorphosis and juvenile growth, but adapted to long-term high pCO2. Differentially expressed genes (DEGs) emerged as a time- and dose-dependent mode of short-term response (3 days post settlement, d p.s.) and long-term acclimation (40 d p.s.), with more DEGs responding to high pCO2 (pH 7.54) than to medium pCO2 (pH 7.83). High pCO2, a presumed threatening seawater baseline for A. gemmifera juveniles, activated DNA repair, macroautophagy, microautophagy and mitophagy mechanisms to maintain cellular homeostasis, recycle cytosolic proteins and damaged organelles, and scavenge reactive oxygen species (ROS) and H[+], but at the cost of delayed development through cell cycle arrest associated with epigenetic and genetic regulation at 3 d p.s.. However, A.gemmifera juveniles acclimated to high pCO2 by up-regulating cell cycle, transcription, translation, cell proliferation, cell-extracellular matrix, cell adhesion, cell communication, signal transduction, transport, binding, Symbiodiniaceae symbiosis, development and calcification from 3 d p.s. to 40 d p.s., when energy reallocation and metabolic suppression occurred for high demand but short-term energy limitation in coral cells undergoing flexible symbiosis. All results indicate that acclimation mechanisms of complicated gene expression improve larval and juvenile resilience to OA for coral population recovery and reef restoration.},
}

@article {pmid40834857,
year = {2025},
author = {Teyssendier de la Serve, J and Gautrat, P and Laffont, C and Lesterps, Z and Huault, E and Guerard, F and San Clemente, H and Aguilar, M and Bensmihen, S and Gakière, B and Frei-Dit-Frey, N and Frugier, F},
title = {The sTDIF signaling peptide modulates the root stele diameter and primary metabolism to accommodate symbiotic nodulation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.056},
pmid = {40834857},
issn = {1879-0445},
abstract = {Legume plants form specific organs on their root system, the nitrogen-fixing nodules, thanks to a symbiotic interaction with soil bacteria collectively named rhizobia. Rhizobia, however, do not only induce the formation of these nodule organs but also modulate root system architecture. We identified in Medicago truncatula a previously unnoticed increase in the root stele diameter occurring upon rhizobium inoculation. This symbiotic root response, similarly observed in another crop legume, pea, occurs rapidly and locally after rhizobium inoculation, leading to an increased number of vascular cells. Interestingly, this root stele diameter symbiotic response requires tracheary element differentiation inhibitory factor (TDIF) signaling peptides and, notably, the MtCLE37 TDIF-encoding gene whose expression is increased during nodulation, thus being referred to as symbiotic nodulation TDIF (sTDIF). Indeed, a cle37/stdif mutant is not responsive to rhizobium regarding its root stele diameter increase and has a reduced nodule number. Combined transcriptomic and metabolomic analyses revealed that stdif has a defective primary metabolism, notably affecting carbohydrate/sugar accumulation in both roots and nodules. Remarkably, a sucrose or a malate exogenous treatment is able to rescue the rhizobium-induced stele diameter symbiotic response in stdif. This metabolic deregulation is thus instrumental in explaining the altered symbiotic response of the mutant. Overall, this study highlights a novel function of TDIF signaling peptides in legumes plants, which, beyond regulating stele development, also modulates the root primary metabolism adaptations required for symbiotic nodule development.},
}

@article {pmid40834321,
year = {2025},
author = {Busenitz, K and Lundgren, JG},
title = {No effects of human-grade probiotics on Apis mellifera (Hymenoptera: Apidae) health metrics.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf210},
pmid = {40834321},
issn = {1938-291X},
abstract = {Dietary-administered probiotics may address poor health and performance in honey bees (Apis mellifera L. [Hymenoptera: Apidae]). Human-grade probiotics are an affordable source of general probiotics. We examined the effects of human-grade probiotics by comparing colony and individual level health and performance between colonies administered a probiotic every other week, and those not given probiotic supplementation (control treatment group). We found that probiotics did not statistically increase individual honey bee health and performance as measured by body lipid level, tibial length, and weight of bees, nor colony performance as measured by monthly assessments of brood area, colony weight, and Varroa destructor Anderson and Trueman (Mesostigmata: Varroidae) mite infestation rate.},
}

@article {pmid40833415,
year = {2025},
author = {Khan, F and Liu, Y and Whitfield, D and Pang, L and Ali, H and Huang, Y and Zhou, F and Hagan, RS and Frenis, K and Rowe, RG and Chen, P},
title = {Macrophage TBK1 signaling drives the development and outgrowth of breast cancer brain metastasis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {34},
pages = {e2420793122},
doi = {10.1073/pnas.2420793122},
pmid = {40833415},
issn = {1091-6490},
support = {R01 NS124594/NS/NINDS NIH HHS/United States ; R01NS127824//HHS | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; W81XWH-21-1-0380//U.S. Department of Defense (DOD)/ ; P30CA043703//HHS | NIH | NCI | Center for Cancer Research (CCR)/ ; },
mesh = {*Protein Serine-Threonine Kinases/metabolism/genetics ; *Breast Neoplasms/pathology/metabolism/genetics ; Humans ; Female ; *Brain Neoplasms/secondary/metabolism/pathology/genetics ; *Signal Transduction ; Animals ; Mice ; Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; Tumor Microenvironment ; Cell Line, Tumor ; *Macrophages/metabolism/pathology ; *Tumor-Associated Macrophages/metabolism/pathology ; Epithelial-Mesenchymal Transition ; Cell Movement ; NF-kappa B/metabolism ; },
abstract = {Tumor-associated macrophages (TAMs) are the predominant immune cells in the tumor microenvironment that promote breast cancer brain metastasis (BCBM). Here, we identify TANK-binding kinase (TBK1) as a critical signaling molecule enriched and activated in TAMs of BCBM tumors, playing an indispensable role in BCBM development and metastatic outgrowth in the brain. Mechanistically, BCBM cell-secreted matrix metalloproteinase 1 binds to protease-activated receptor 1 and integrin αVβ5 on macrophages, leading to TBK1 activation mediated by the nuclear factor-kappa B pathway. Reciprocally, TBK1-regulated TAMs produce granulocyte-macrophage colony-stimulating factor (GM-CSF) to drive breast cancer cell epithelial-mesenchymal transition, migration, and invasion, ultimately contributing to BCBM development and brain metastatic outgrowth. Inhibition of TBK1 signaling in TAMs or GM-CSF receptor in cancer cells impedes BCBM development and brain metastatic outgrowth. Correspondingly, the TBK1-GM-CSF signaling axis correlates with lower overall survival in patients with BCBM. Thus, TBK1-mediated tumor-TAM symbiotic interaction provides a promising therapeutic target for patients with BCBM.},
}

*Protein Serine-Threonine Kinases/metabolism/genetics
*Breast Neoplasms/pathology/metabolism/genetics
Humans
Female
*Brain Neoplasms/secondary/metabolism/pathology/genetics
*Signal Transduction
Animals
Mice
Granulocyte-Macrophage Colony-Stimulating Factor/metabolism
Tumor Microenvironment
Cell Line, Tumor
*Macrophages/metabolism/pathology
*Tumor-Associated Macrophages/metabolism/pathology
Epithelial-Mesenchymal Transition
Cell Movement
NF-kappa B/metabolism

@article {pmid40833097,
year = {2025},
author = {Staehelin, C and Forsberg, LS and D'Haeze, W and Gao, M-Y and Carlson, RW and Xie, Z-P and Pellock, BJ and Jones, KM and Walker, GC and Streit, WR and Broughton, WJ},
title = {Correction for Staehelin et al., "Exo-Oligosaccharides of Rhizobium sp. Strain NGR234 Are Required for Symbiosis with Various Legumes".},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0015725},
doi = {10.1128/jb.00157-25},
pmid = {40833097},
issn = {1098-5530},
}

@article {pmid40833026,
year = {2025},
author = {Li, Z and Lu, Y and Du, P and Zhang, M and Li, D and Xie, F and Chen, D and Lin, H and Li, Y},
title = {A Lipopolysaccharide Lipid A Acyltransferase Gene msbB Is Involved in Soybean Rhizobial Intracellular Colonization and Symbiotic Nitrogen Fixation.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-02-25-0018-R},
pmid = {40833026},
issn = {0894-0282},
abstract = {Three major components of lipopolysaccharide (LPS) in rhizobia, namely core polysaccharide, o-antigen, and lipid A, act as microbe-associated molecular patterns (MAMPs) to participate in the symbiosis between rhizobia and legume. Rhizobia have a different lipid A structure from other Gram-negative bacteria. The 3-hydroxy group on the 2' or 3' myristate acyl chain of its lipid A is substituted by a unique very long chain fatty acid (VLCFA). VLCFAs are transferred to lipid A by an acyltransferase MsbB. In this research, we constructed the msbB deletion mutant, complementary, and overexpression strains of Sinorhizobium fredii HH103, and investigated their free-living and symbiotic phenotypes. The findings revealed that deletion of msbB had no impact on the autonomous growth of HH103, yet significantly reduced the resistance of rhizobia to abiotic stresses. The promoter-GUS assays revealed that msbB was mainly expressed at the early stage of nodulation. Quantitative analysis of early infection revealed that the mutation of msbB significantly reduced root hair curling, infection threads, and nodule primordia, suggesting impairment of the symbiotic infection process. The nodulation assay and transmission electron microscopy analysis of nodule ultrastructure showed that msbB deletion led to the formation of ineffective root nodules without colonization of rhizobia, thereby causing a loss of nitrogen fixation capacity. RNA-seq analysis indicated that HH103ΩmsbB inoculation trigger a localized defense response in the soybean root to result in symbiotic deficiencies. Taken together, these results reveal the important role of VLCFAs in soybean rhizobia in the establishment of effective symbiosis and nodule nitrogen fixation.},
}

@article {pmid40832871,
year = {2025},
author = {Fu, J and Liu, Y and Yoshioka, T and Igai, K and Mabuchi, T and Kihara, K and Murakami, T and Lo, N and Ohkuma, M and Hongoh, Y},
title = {Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf178},
pmid = {40832871},
issn = {1751-7370},
abstract = {Mixotricha paradoxa is a large, cellulolytic flagellate present in the hindgut of the termite Mastotermes darwiniensis. This parabasalid flagellate is unique in its reliance on ectosymbiotic spirochetes for motility. We analyzed the transcriptome of M. paradoxa and the genomes of the ectosymbiotic spirochete Propulsinema mixotrichae ("Treponematales"), the rod-shaped ectosymbiont Synergitannerella mixotrichae (Bacteroidales), and the endosymbiont Endomicrobiellum mixotrichae (Endomicrobiales), all of which are obligately associated with M. paradoxa and were taxonomically described in this study. Mixotricha paradoxa highly expressed genes for diverse glycoside hydrolases (GHs) and likely ferments sugars to H2, CO2, acetate, ethanol, and glycerol. Similar to the case for parasitic parabasalids such as Trichomonas vaginalis, transcripts for biosynthesis of nucleotides and many amino acids were not detected in our analyses of M. paradoxa. Propulsinema mixotrichae possesses genes encoding proteins for the assembly of flagella and for those in pathways associated with chemotaxis and dinitrogen fixation. Such genes are absent in Syn. mixotrichae, which instead possesses numerous genes encoding GH enzymes, which are largely complementary to the GH repertoire of M. paradoxa. Endomicrobiellum mixotrichae appears to provide nucleotides and nine amino acids to its host, which in turn likely supplies three amino acids, including tryptophan, to Endo. mixotrichae. Because bacterial cells, in addition to wood particles, were observed in food vacuoles of M. paradoxa, these ecto- and endosymbionts may be digested by the flagellate host. Overall, the distinct roles of each symbiont highlight the efficient functional division of labor that has evolved in this holobiont.},
}

@article {pmid40832279,
year = {2025},
author = {Selmoni, O and Cleves, PA and Exposito-Alonso, M},
title = {Global coral genomic vulnerability explains recent reef losses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.25.586253},
pmid = {40832279},
issn = {2692-8205},
abstract = {The dramatic decline of reef-building corals calls for a better understanding of coral adaptation to ocean warming. Here, we characterized genetic diversity of the widespread genus Acropora by building a genomic database of 595 coral samples from different oceanic regions-from the Great Barrier Reef to the Persian Gulf. Through genome-environment associations, we found that different Acropora species showed parallel evolutionary signals of heat-adaptation in the same genomic regions, pointing to genes associated with molecular heat shock responses and symbiosis. We then projected the present and the predicted future distribution of heat-adapted genotypes across reefs worldwide. Reefs projected with low frequency of heat-adapted genotypes display higher rates of Acropora decline, indicating a potential genomic vulnerability to heat exposure. Our projections also suggest a transition where heat-adapted genotypes will spread at least until 2040. However, this transition will likely involve mass mortality of entire non-adapted populations and a consequent erosion of Acropora genetic diversity. This genetic diversity loss could hinder the capacity of Acropora to adapt to the more extreme heatwaves projected beyond 2040. Genomic vulnerability and genetic diversity loss estimates can be used to reassess which coral reefs are at risk and their conservation.},
}

@article {pmid40830815,
year = {2025},
author = {Monzón-Ramos, A and Pérez-González, S and Pulido-Suárez, L and Díaz-Peña, F and Rodríguez-Pérez, A and Reyes-Betancort, JA and León-Barrios, M},
title = {Efficient but Elusive Rhizobia Fix Nitrogen in the Wild Legumes Bituminaria bituminosa and Coronilla Viminalis.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70095},
doi = {10.1002/jobm.70095},
pmid = {40830815},
issn = {1521-4028},
support = {//This study was financed by the Consejería de Transición Ecológica, Lucha contra el Cambio Climático y Planificación Territorial of the Gobierno de Canarias within the framework of the FEDER Operational Program (2014-2020)./ ; },
abstract = {In ecological restoration of degraded natural habitats, revegetation with wild native plants is a priority. Legumes play a key role in this process through nitrogen (N)-fixing symbiosis with rhizobia, obtaining N for their growth and improving soil fertility, which benefits other nonleguminous plants in the environment. This study explores the rhizobia of two wild legumes, Coronilla viminalis and Bituminaria bituminosa, found in a degraded habitat in Lanzarote (Canary Islands). We found these legumes nodulated by highly efficient N-fixing mesorhizobia harboring the symbiovars canariensis and hedysari in Mesorhizobium species distinct from those originally reported to carry these symbiovars. However, isolating these rhizobia was challenging. Despite the good plant development and the pink color of root nodules indicating effective N-fixation, these rhizobia could not be cultured in most cases. This suggests the presence of unculturable or "fastidious" rhizobia in the nodules, with requirements poorly mimicked in conventional rhizobial media. Additionally, the presence of fast-growing non-rhizobial endophytes in the nodules complicates the isolation of slower-growing rhizobia, which requires special care during the isolation protocol to avoid endophytes and extend incubation times. The difficulty of cultivating the rhizobia of these two wild legumes suggests that their diversity may be greater than described here.},
}

@article {pmid40830270,
year = {2025},
author = {Yang, Q and Guo, B and Lu, M and Liu, Y and Kardol, P and Reich, PB and Bardgett, RD and Cornelissen, JHC and Kraft, NJB and Díaz, S and Wright, IJ and He, N and Hogan, JA and Pei, Y and Han, Q and Li, Z and Wang, Z and Yang, W and Ding, J and Yang, Z and Wu, H and Carmona, CP and Valverde-Barrantes, OJ and Li, D and Cai, J and Zeng, H and Zhang, Y and Ren, W and Zhao, Y and Yang, X and Fan, G and Wang, J and Li, G and Kong, D},
title = {Arbuscular mycorrhizal association regulates global root-seed coordination.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40830270},
issn = {2055-0278},
abstract = {Terrestrial plants exhibit immense variation in their form and function among species. Coordination between resource acquisition by roots and reproduction through seeds could promote the fitness of plant populations. How root and seed traits covary has remained unclear until our analysis of the largest-ever compiled joint global dataset of root traits and seed mass. Here we demonstrate that seed mass and seed phosphorus mass scale positively with root diameter in arbuscular mycorrhizal (AM) plants, depending on variation in root cortical thickness instead of root vessel size. These findings suggest a dual role of AM association in phosphorus uptake and pathogen resistance which drives the global root-seed coordination, instead of initially expected resource transport via root vessels as the main driver. In contrast, we found no relationship between root traits and seed mass in ectomycorrhizal plants. Overall, our study reveals coordination between roots and seeds in AM plants, which is probably regulated by root-mycorrhizal symbiosis, and may be crucial in shaping global plant diversity and species distributions.},
}

@article {pmid40829788,
year = {2025},
author = {Hadfield, MG and Freckelton, M and Nedved, BT},
title = {Marine Bacterial Biofilms: Shaping Surface Communities.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-051524-024455},
pmid = {40829788},
issn = {1545-3251},
abstract = {The assembly of marine benthic communities has become a focal point in marine ecology. We address how the bottom layers of benthic communities (i.e., the microbes inhabiting the basal biofilm) influence the complex accumulation of eukaryotes that grow on top of them. Specifically, we discuss (a) what organisms make up benthic biofilms, what brings about their attachment to surfaces, and how they vary in space and time; (b) what eukaryotic organisms are in marine benthic communities, how they vary in space and time, and the nature of microbial cues that bring about their recruitment to particular benthic sites; (c) the roles of bacterial-animal symbiosis in the composition of benthic communities; (d) what is happening to biofilms and their roles as habitat engineers in the rapidly changing world; and (e) how the geological history of bacteria and microbial mats on the ocean floor powerfully influenced the evolution of larval-bacterial interactions.},
}

@article {pmid40829558,
year = {2025},
author = {Huang, WC and Spang, A},
title = {DPANN archaea.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R791-R794},
doi = {10.1016/j.cub.2025.06.038},
pmid = {40829558},
issn = {1879-0445},
mesh = {*Archaea/genetics/physiology/classification/metabolism ; *Symbiosis ; Phylogeny ; *Genome, Archaeal ; Biological Evolution ; },
abstract = {Archaea are one of the two primary domains of life alongside Bacteria. Extant archaea play an important role in global nutrient cycles and comprise members that were crucial for the evolution of life on Earth including the origin of eukaryotic cells through a symbiotic integration of an archaeal and bacterial partner. Despite their importance in ecology and evolution, our knowledge of archaeal diversity and function remains limited in part because it has proven challenging to cultivate archaea in the laboratory. Over the last two decades, the use of novel cultivation-independent approaches such as metagenomics has not only led to the discovery of a vast diversity of previously unknown archaeal lineages but also provided a window into their genomic content, allowing researchers to make predictions about metabolic functions and lifestyles. For example, by combining genomics approaches with phylogenetic analyses (that is, the reconstruction of species trees) researchers have uncovered several phylum-level lineages of putative genome-reduced archaea referred to as the 'DPANN' archaea, whose members were shown to have limited metabolic capabilities, indicating their dependency on symbiotic partners. These findings are consistent with observations from cultivation-based studies that have succeeded in enriching some of these small-cell symbionts in co-cultures with their hosts. Although they were initially discovered in extreme environments, DPANN archaea have now been shown to be widespread across a variety of environments and may thus play an important role in not only host evolution but also ecology. Herein, we aim to highlight DPANN archaea by providing an overview of their diversity, genomic and metabolic features, unique cell biology and interactions, and evolutionary origins. We also underscore several fascinating topics that remain underexplored.},
}

*Archaea/genetics/physiology/classification/metabolism
*Symbiosis
Phylogeny
*Genome, Archaeal
Biological Evolution

@article {pmid40829389,
year = {2025},
author = {Qin, T and Yang, Z and Dou, Y and Wang, J and Wang, L and Tang, L and Wu, Z and Qiu, R},
title = {Effects of artificial humic acid on rhizosphere ecology and microbial regulation in a ryegrass-Bacillus cereus symbiotic system for remediating Cr(VI)-contaminated soil.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139566},
doi = {10.1016/j.jhazmat.2025.139566},
pmid = {40829389},
issn = {1873-3336},
abstract = {Pollution by heavy metals, particularly hexavalent chromium (Cr(VI)), has become a significant environmental threat. This study aimed to evaluate the synergistic effects of artificial humic acid (A-HA) and Bacillus cereus Q-0 on Cr(VI) remediation in a ryegrass-soil system. A-HA was synthesized, and B. cereus Q-0 was labeled with gfp to enable tracking of its colonization in the soil-plant environment. The results showed that compared with the control group, combined treatment with A-HA and B. cereus Q-0-gfp significantly improved Cr(VI) reduction efficiency, decreasing soil Cr(VI) content from 69.8 mg kg[-1] to 17.07 mg kg[-1]. Simultaneously, the total Cr content in plants increased by 37.2 %, indicating enhanced hyperaccumulation capacity in ryegrass. A-HA promoted the enrichment of functional microbial communities associated with heavy metal resistance, such as Proteobacteria and Firmicutes, reflecting an optimized soil microbial structure. In terms of plant growth, the combined treatment increased ryegrass biomass by up to 790.3 %, root length by 310.0 %, soil organic matter content by 650.12 %, and soil enzyme activity. Additionally, A-HA significantly enhanced the colonization ability of B. cereus Q-0 in both the rhizosphere and endophytic compartments of plants. This study highlights the unique potential of combining A-HA and B. cereus for effective and eco-friendly Cr(VI) remediation, offering a novel strategy to enhance phytoremediation efficiency in contaminated soils.},
}

@article {pmid40829280,
year = {2025},
author = {Papadopoulos, C and Roshanfekrrad, M and Tsikou, D and Papadopoulou, KK and Calonne-Salmon, M and Declerck, S and Karpouzas, DG},
title = {Developing a toolbox of Tier I tests to assess pesticides toxicity on the asymbiotic and symbiotic phases of arbuscular mycorrhizal fungi.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118892},
doi = {10.1016/j.ecoenv.2025.118892},
pmid = {40829280},
issn = {1090-2414},
abstract = {Soil microorganisms are a key protection goal in the European Union (EU) pesticide regulatory framework. Arbuscular mycorrhizal fungi (AMF) were identified as good proxies for assessing pesticides toxicity on the soil microbiota. This could involve ecotoxicity testing at the different life stages of AMF. We evaluated the effects of five pesticides (pyraclostrobin, fludioxonil, hymexazol, etridiazole, glyphosate) and a transformation product (AMPA), with distinct mode of action, on the development and functionality of Rhizophagus irregularis at the asymbiotic and symbiotic phase using a spore germination assay and a gnotobiotic AMF-host plant system (AMF-sandwich test), respectively. Based on arbuscular colonization in the AMF-sandwich test, fludioxonil was the most toxic (EC50 0.085 mg/L) followed by glyphosate (EC50 2.58 mg/L) and pyraclostrobin (EC50 9.22 mg/L), while etridiazole, hymexazol, and AMPA showed EC50 values higher than the highest tested concentration. However, for glyphosate and pyraclostrobin negative effects on symbiosis functioning were observed at lower concentrations than for colonization, as depicted by the expression of plant marker genes and/or P-uptake, suggesting the establishment of non-functional arbuscular symbiosis. The high toxicity of fludioxonil (EC50 0.03 mg/L) and the low toxicity of AMPA (EC50 > 432 mg/L) on R. irregularis was verified also for the asymbiotic phase via spore germination assay. Comparative tests showed differences in the toxicity of pure active substances and commercial formulations of fludioxonil and pyraclostrobin on the AMF-sandwich test. We propose that the AMF-sandwich system together with the spore germination test could be used as a toolbox for Tier-I assessment of pesticides toxicity on AMF.},
}

@article {pmid40829219,
year = {2025},
author = {Jing, J and Wang, T and Guo, X and Huang, P and Li, C and Qu, Y},
title = {Continuous exogenous bioaugmented remediation of petroleum-contaminated soil: Ecological effects, microbial communities, and mechanisms.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127007},
doi = {10.1016/j.jenvman.2025.127007},
pmid = {40829219},
issn = {1095-8630},
abstract = {The exogenous bioaugmentation technique is a widely employed strategy for remediating petroleum-contaminated soil. However, sustaining exogenous functional bacteria over extended periods in complex petroleum-contaminated environments is challenging, leading to reduced efficacy, and the interaction mechanisms with indigenous microorganisms remain poorly understood. This study utilized the previously developed petroleum-degrading bacterial agent ECT in a continuous bioaugmentation (C-Bio) approach for soil remediation. The outcomes were compared with those from a disposable bioaugmentation (D-Bio) and a control group (CG). After a 200-day remediation period, the C-Bio approach achieved a simulated petroleum degradation rate of 99.42 %. Concurrently, assessments of soil physicochemical properties, enzyme activities, and plant growth demonstrated that C-Bio resulted in favorable ecological restoration. Metagenomic analysis confirmed the successful colonization of the three exogenous bacteria in the C-Bio system. Network analysis revealed that this approach facilitated the directional succession of soil microbial communities, with the newly dominant indigenous bacteria forming cooperative or symbiotic relationships with the exogenous strains. Together, they synergistically degrade alkanes via terminal oxidation pathways and aromatic hydrocarbons through salicylic acid and phthalic acid pathways, leading to effective remediation of petroleum-contaminated soil. This study offers theoretical insights and empirical evidence supporting the development of continuous bioaugmentation processes for the remediation of petroleum-contaminated soils.},
}

@article {pmid40828971,
year = {2025},
author = {Singh, J},
title = {Metabolic Detour, Symbiotic Delay: Insights from Sinorhizobium meliloti Suppressor Mutants.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {38},
number = {4},
pages = {490},
doi = {10.1094/MPMI-07-25-0078-CM},
pmid = {40828971},
issn = {0894-0282},
}

@article {pmid40828281,
year = {2025},
author = {Enciso Garcia, JS and Chignola, M and Ragionieri, L and Rey, F and Fluch, M and Borruso, L and Corretto, E and Schuler, H},
title = {High-Throughput Amplicon Sequencing for Analyzing Microbial Communities of Insects.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {237-258},
pmid = {40828281},
issn = {1940-6029},
abstract = {Insects represent more than 80% of all described species on the planet. This diversity is a result of millions of years of evolution, during which insects have colonized nearly every habitat. Their success is partly due to their ability to form symbiotic relationships with a wide variety of other organisms, especially microorganisms. Identifying and characterizing associated microorganisms are crucial to understanding the complexity and dynamics of these symbiotic relationships. To date, advancements in sequencing technologies that provide large sequence data sets have become ideal tools for characterizing insect microbiomes, including information about non-cultivable microorganisms commonly found in insects. Despite the growing number of studies focused on insect microbiome characterization, there are few protocols detailing methodological procedures for fieldwork, DNA extraction, and data processing. Here, we present an overview of the characterization of insect-associated bacterial communities. We cover best practices for data interpretation and visualization, including alpha and beta diversity analyses, community composition profiling, and statistical testing to identify microbial associations of insects.},
}

@article {pmid40827673,
year = {2025},
author = {Ninzatti, L and Sana, TG and Acar, T and Moreau, S and Jardinaud, MF and Marti, G and Coen, O and Carlier, AL},
title = {Artificial symbiont replacement in a vertically transmitted plant symbiosis reveals a role for microbe-microbe interactions in enforcing specificity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf177},
pmid = {40827673},
issn = {1751-7370},
abstract = {Some plants engage in permanent, vertically transmitted symbioses with bacteria. Often, these bacteria are hosted extracellularly within structures on the leaves, where they produce specialized bioactive metabolites that benefit their host. These associations are highly specific, with one plant species associating with a single bacterial species, but little is known about how these symbioses originate and how specificity is maintained. In this study, we show that the symbiotic association between a wild yam and a bacterium can be manipulated experimentally, and that bacteria-free plants are open to colonization by environmental bacteria. Through metabolic profiling, we show that the endophytic niche is rich in organic acids and intermediates of the TCA cycle. Environmental bacteria capable of utilizing these acids, such as the soil bacterium Pseudomonas putida, readily colonize aposymbiotic plants. However, successful colonization is contingent upon the absence of the vertically transmitted symbiont or the impairment of its type VI secretion system. Unexpectedly for a vertically transmitted symbiosis, these findings suggest that microbe-microbe interactions, including antagonism, may play a crucial role in maintaining the specificity of an association. However, low transmission rates of synthetic symbionts provide evidence that transmission barriers or bottlenecks may still occur, further enforcing partner fidelity. Together, these results highlight the complexity of mechanisms underlying mutualistic associations, and provide insights into the evolution of bacterial leaf symbiosis.},
}

@article {pmid40826837,
year = {2025},
author = {Hill, RA and Plett, KL and Wong-Bajracharya, JW and Wang, M and Lipzen, A and Ng, V and Grigoriev, IV and Martin, F and Anderson, IC and Jeffries, TC and Plett, JM},
title = {Eucalyptus grandis MYB-Like and RAN-Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70454},
doi = {10.1111/ppl.70454},
pmid = {40826837},
issn = {1399-3054},
support = {ANR-11- LABX-0002-01//Agence Nationale de la Recherche/ ; DP160102684//Australian Research Council/ ; DP220103325//Australian Research Council/ ; CSP1953//U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; },
abstract = {Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.},
}

@article {pmid40825678,
year = {2025},
author = {Nam, Y and Lee, J and Kim, SR and Kim, JN},
title = {Isolation and Purification of Antibacterial Compound from Kombucha of SCOBY.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2504012},
doi = {10.4014/jmb.2504.04012},
pmid = {40825678},
issn = {1738-8872},
abstract = {The misuse of antibiotics has contributed to the widespread emergence of antimicrobial resistance (AMR), emphasizing the need for alternative antimicrobial agents. Kombucha, a fermented beverage containing a symbiotic culture of bacteria and yeast (SCOBY), has gained attention for its antibacterial activity and potential health benefits. This study investigated the antibacterial properties of kombucha and SCOBY, isolating and characterizing the active compounds responsible for these effects. Both kombucha broth and dried SCOBY effectively inhibited Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Salmonella Typhimurium, with dried SCOBY demonstrating stronger activity. Instrumental analyses identified 5-hydroxymethylfurfural (HMF) as the primary antibacterial compound in the SCOBY extracts. HMF significantly inhibited L. monocytogenes and S. aureus, with its antibacterial inhibition surpassing that of chloramphenicol in these two bacterial species. Previous studies have shown that, in addition to its antibacterial effects, HMF has potential applications in the production of polymers and pharmaceuticals, and as a fuel additive, suggesting its potential in the chemical and biofuel industries. This study highlights the antibacterial activity of HMF and underscores the need for further research to evaluate its safety and applicability in various fields.},
}

@article {pmid40810324,
year = {2025},
author = {Aniski, BF},
title = {School Nursing and SchoolYard Gardening: A Tale of Mutual Symbiosis.},
journal = {NASN school nurse (Print)},
volume = {},
number = {},
pages = {1942602X251360002},
doi = {10.1177/1942602X251360002},
pmid = {40810324},
issn = {1942-6038},
abstract = {Working within NASN's School Nursing Practice Framework, this author proposes schoolyard gardening as an action oriented approach found in the "Leadership" principle of the Framework. Leadership references "activities related to the mind-set of leadership, not a position." The author suggests that schoolyard gardening is an emerging topic with student health being the desired outcome, as well as, proposing a schoolyard garden is needed in every school. A basic overview of School Nurse Certification in New Jersey is shared along with a 15 year outline of an award-winning schoolyard garden and how a schoolyard garden relates to wellness and teaching health within the New Jersey Student Learning Standards.},
}

@article {pmid40803112,
year = {2025},
author = {Ma, S and Guo, R and Wang, Y and Yan, Y and Chu, Q and Cui, N and Zhang, Y and Zhang, L and Jiang, L and Shi, L and Guo, J and Gao, Y and Xing, F and Zhang, T},
title = {Nitrogen and phosphorus addition affected soil organic carbon storage and arbuscular mycorrhizal fungi contributions.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126904},
doi = {10.1016/j.jenvman.2025.126904},
pmid = {40803112},
issn = {1095-8630},
abstract = {Substantial quantities of nitrogen (N) and phosphorus (P) released by human activities, enter terrestrial ecosystems, thereby affecting the carbon cycling within these ecosystems. Previous studies found that arbuscular mycorrhizal fungi (AMF) could affect soil organic carbon (SOC) storage, the impacts of AMF on SOC under nutrients enrichment have yet to be well understood. Here, we conducted an 8-year field experiment involving N and P addition, and a[13]C labeled microcosm experiment labeled with AMF inoculation, to explore how SOC respond to nutrients enrichment, as well as AMF-induced changes in SOC. N addition increased particulate organic carbon (POC) content by 5.03 % by promoting plant primary productivity. Phosphorus (P) addition reduced the mineral-bound organic carbon (MAOC) by 16.0 % by facilitating the microbial degradation process. Correlation analysis showed that AMF intraradical infection intensity (IRII) was positively correlated with both nitrate nitrogen (NO3[-]-N) and MAOC, but negatively correlated with available phosphorus (AP) and total phosphorus (TP). This result suggested that nutrients enrichment potentially modulate MAOC accumulation via affecting AMF-plant symbiosis. Furthermore, Structural equation modeling (SEM) results also showed that AMF are crucial in regulating plant and soil microbial contributions to SOC. [13]C stable isotope labelling experiment results further showed that AMF inoculation increased the [13]C content in the soil by 4.75 % and simultaneously increased plant N uptake by 6.32 %. Therefore, we speculated that AMF could promote the accumulation of SOC by facilitating the exchange of carbon and nitrogen between plants and soil. These findings suggest that global nutrient eutrophication could significantly affect the stability of SOC, highlighting the critical role of AMF in mediating the responses of SOC stability to environmental changes.},
}

@article {pmid40792181,
year = {2025},
author = {You, YH and Bae, HJ and Park, JM and Ku, YB and Nam, GH and Kwak, TW and Bang, YJ and Jeong, TY and Hong, JW},
title = {Fungal and Bacterial Community Dynamics in the Rhizosphere and Rhizoplane of Diabelia spathulata in Relation to Soil Properties.},
journal = {Mycobiology},
volume = {53},
number = {5},
pages = {605-619},
pmid = {40792181},
issn = {1229-8093},
abstract = {Diabelia spathulata, a rare deciduous shrub native to East Asia, is critically endangered in Korea, yet little is known about its interactions with soil fungal communities. This study presents the first comprehensive analysis of fungal and bacterial communities in the rhizoplane (RP), rhizosphere (RS), and surrounding soil (SS) of D. spathulata in its natural habitat on Mt. Cheonseong, South Korea. High-throughput sequencing of the ITS and 16S rRNA gene regions revealed distinct microbial assemblages across soil compartments. Fungal taxa such as Russula, Trechispora, and Capronia were enriched in RP and RS, highlighting their potential roles in nutrient cycling, organic matter (OM) decomposition, and symbiosis. In contrast, the SS exhibited greater fungal richness but lower specialization. Among bacteria, root-associated compartments were enriched with plant-beneficial genera such as Bacillus and Bradyrhizobium, while bulk soil hosted more generalist taxa. Soil physicochemical analyses showed higher OM and total nitrogen in RS compared to SS, indicating root-driven enrichment. Correlation and network analyses identified strong links between specific fungal and bacterial taxa and key soil properties including pH, OM, and cation exchange capacity. These results suggest that D. spathulata modulates its RS microbiome to enhance nutrient availability and stress tolerance. This study highlights the ecological significance of fungal communities in root-associated microhabitats and provides foundational knowledge for incorporating soil microbiota into conservation and habitat restoration efforts for endangered plant species.},
}

@article {pmid40749791,
year = {2025},
author = {Li, M and Zhao, G and Li, MM},
title = {Regulatory mechanisms of quorum sensing in microbial communities and their potential applications in ruminant livestock production.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.055},
pmid = {40749791},
issn = {2090-1224},
abstract = {BACKGROUND: Quorum sensing (QS) is a cell-to-cell communication system that enables microbial communities to dynamically regulate their metabolism and physiological activities according to the surrounding cell density. The rumen's diverse microbial ecosystem represents a classic example of host-microbiome symbiosis. Despite significant progress in understanding the composition and function of ruminal microbial communities, the underlying communication mechanisms in the rumen ecosystem remain largely enigmatic. Gaining insight into these regulatory mechanisms is crucial for developing knowledge-based strategies to improve animal productivity, health, and sustainability in ruminant livestock production.

AIM OF REVIEW: This review aims to provide an overview of microbial QS communication systems mediated by diverse signaling molecules, including bacterial intraspecies and interspecies QS, fungal QS, and archaeal QS. We conducted a structured review by searching multiple scientific databases, synthesizing data from relevant studies, and critically evaluating the roles of QS systems in microbial communities. This approach ensures a comprehensive analysis of the current understanding of QS mechanisms and their implications for ruminant livestock. Specifically, we elucidate the identification and potential mechanisms of the QS system facilitated by three prevalent signaling molecules (N-acyl homoserine lactones, autoinducing peptides, and autoinducer 2) in ruminants. Recent advances in understanding the effects of QS on microbial fermentation, immune function, biofilm formation, and virulence factor production are summarized in detail, providing a scientific basis for applying QS in ruminant livestock production.

The rumen harbors various QS signaling molecules that modulate microbial community dynamics, impacting composition, structure, and function. The versatility of QS allows it to regulate ruminal fermentation and inhibit pathogen growth, thereby improving productivity and reducing disease risk in ruminants. This review synthesizes recent advances in QS mechanisms, crucial for disease prevention, combating antibiotic resistance, and promoting sustainable livestock production. Future research should investigate QS pathways and networks in the rumen microbiome through in vivo experiments and multi-omics analyses to gain a deeper understanding of microbial community regulation.},
}

@article {pmid40695816,
year = {2025},
author = {Xu, X and Wang, Q and Sun, T and Gao, H and Gu, R and Yang, J and Zhou, J and Fu, P and Wen, H and Yang, G},
title = {Structural basis for the activity regulation of Medicago calcium channel CNGC15.},
journal = {Cell discovery},
volume = {11},
number = {1},
pages = {63},
pmid = {40695816},
issn = {2056-5968},
support = {32422038//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Cyclic nucleotide-gated ion channels (CNGCs) in plants mediate Ca[2+] influx in response to environmental changes. Among numerous plant CNGCs, Medicago truncatula CNGC15a/b/c (MtCNGC15) is localized to the nuclear envelope. The opening and closing cycle of MtCNGC15 is tightly associated with the Ca[2+] oscillation in symbiosis. However, the molecular mechanism underlying MtCNGC15 activity regulation remains unclear. In this study, we present the structures of MtCNGC15 in its apo form and in the presence of CaM. The apo MtCNGC15b exhibits a flexible cytoplasmic domain (CPD), whereas binding of the MtCaM inhibits Ca[2+] currents and stabilizes the highly dynamic CPD. Furthermore, the activity of MtCNGC15b seems to be independent of cGMP. The hypothetical binding pocket for cGMP is occupied by an arginine residue. These findings elucidate the structural basis for the activity regulation of nuclear localized MtCNGC15.},
}

@article {pmid40691349,
year = {2025},
author = {Nobu, MK},
title = {A model 'organism' split to uncover microbial symbiosis.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {9},
pages = {548},
pmid = {40691349},
issn = {1740-1534},
}

@article {pmid40559014,
year = {2025},
author = {Jia, J and Liang, M and Zhao, Z and Huang, W and Feng, Q and Lin, Z and Ji, X},
title = {Effects of Periodic Short-Term Heat Stress on Biological Characteristics and Gut Bacteria of Spodoptera frugiperda.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
pmid = {40559014},
issn = {2075-4450},
support = {FW20230002//This work was supported by the technical innovation project of the provincial scientific research institute of the Hainan Academy of Agricultural Sciences, China/ ; },
abstract = {In this study, the migratory agricultural pest Spodoptera frugiperda was exposed to three periodic short-term heat stress regimes at 37 °C, 40 °C, and 43 °C (2 h daily), with a constant 26 °C control. We systematically evaluated the effects of periodic thermal stress on developmental traits across all life stages. Combined with 16S rRNA high-throughput sequencing, we analyzed the structural and functional characteristics of the gut bacterial community in adults under heat stress. The results demonstrated that 37 °C exposure accelerated egg-to-adult development, whereas 43 °C markedly extended it. Additionally, 43 °C heat stress suppressed pupation and eclosion rates. Increasing stress temperatures were negatively correlated with pupal weight and body size in both sexes. Notably, 43 °C heat stress caused complete loss of hatching ability in offspring eggs, thereby rendering population reproduction unattainable. 16S rRNA sequencing revealed that Proteobacteria (>90%) dominated the gut bacterial community at the phylum level across all treatments. Under 43 °C heat stress, although female and male adults exhibited an increase in specific bacterial species within their gut bacteria, Alpha diversity analysis revealed no significant differences in the diversity (Shannon index) and richness (Chao index) of gut bacterial communities between sexes under temperature treatments. PICRUSt2 functional prediction indicated that metabolic pathways, biosynthesis of secondary metabolites, and microbial metabolism in diverse environments constituted the dominant functions of gut bacteria in both sexes, while heat stress exerted minimal effects on the functional profiles of gut bacteria in S. frugiperda. These findings not only provide a theoretical basis for predicting summer population dynamics and formulating ecological control strategies for S. frugiperda but also offer critical insights into the adaptive interactions between this pest and its gut bacterial community under heat stress. The results lay a foundation for further exploring the interactions between insect environmental adaptability and bacterial symbiosis.},
}

@article {pmid40456416,
year = {2025},
author = {Han, X and Zhou, Y and Feng, X and Wang, Y and Zhang, H},
title = {Potassium uptake function of LbKT1 and LbSKOR from Lycium barbarum and their influence on the arbuscular mycorrhizal symbiosis.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {359},
number = {},
pages = {112587},
doi = {10.1016/j.plantsci.2025.112587},
pmid = {40456416},
issn = {1873-2259},
mesh = {*Mycorrhizae/physiology ; *Potassium/metabolism ; *Symbiosis ; *Lycium/metabolism/genetics/microbiology/physiology ; Nicotiana/microbiology/metabolism/genetics/growth & development ; *Plant Proteins/metabolism/genetics ; Plant Roots/metabolism/microbiology ; *Potassium Channels/metabolism/genetics ; },
abstract = {Potassium participates in a variety of plant physiological processes and has great impact on plant growth and stress adaptation. The absorption of potassium by Plant is mediated by potassium channels and transporters, and the Shaker potassium channel gene family plays an important role in potassium uptake. Arbuscular mycorrhizal (AM) fungi form ubiquitous symbioses with plants and increase plants' potassium uptake. However, few studies have focused on the interaction of plant potassium channels from the Shaker gene family with AM fungi. In this study, the potassium uptake function of LbKT1 and LbSKOR (homologs of AKT1 and SKOR in Arabidopsis) from the Shaker gene family in Lycium barbarum was verified by the complementary assay using a yeast potassium uptake mutant. LbKT1 and LbSKOR were also overexpressed in tobacco to assess their influence on AM fungi under low and normal potassium conditions in a pot experiment. LbKT1 could rescue the phenotype of the yeast mutant, while LbSKOR could not. Overexpression of LbKT1 increased tobacco plant growth and potassium uptake and promoted the colonization of AM fungi. Meanwhile, overexpression of LbSKOR promoted potassium translocation from root to shoot and showed no obvious influence on the colonization of AM fungi. Our results suggested that the AM fungi could promote tobacco growth and potassium uptake, while the plant potassium status and the AM fungal colonization may form positive feedback in promoting tobacco potassium uptake and growth.},
}

*Mycorrhizae/physiology
*Potassium/metabolism
*Symbiosis
*Lycium/metabolism/genetics/microbiology/physiology
Nicotiana/microbiology/metabolism/genetics/growth & development
*Plant Proteins/metabolism/genetics
Plant Roots/metabolism/microbiology
*Potassium Channels/metabolism/genetics

@article {pmid40080223,
year = {2025},
author = {Dondero, L and De Negri Atanasio, G and Tardanico, F and Lertora, E and Boggia, R and Capra, V and Cometto, A and Costamagna, M and Fi L S E, and Feletti, M and Garibaldi, F and Grasso, F and Jenssen, M and Lanteri, L and Lian, K and Monti, M and Perucca, M and Pinto, C and Poncini, I and Robino, F and Rombi, JV and Ahsan, SS and Shirmohammadi, N and Tiso, M and Turrini, F and Zaccone, M and Zanotti-Russo, M and Demori, I and Ferrari, PF and Grasselli, E},
title = {Unlocking the Potential of Marine Sidestreams in the Blue Economy: Lessons Learned from the EcoeFISHent Project on Fish Collagen.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {2},
pages = {63},
pmid = {40080223},
issn = {1436-2236},
support = {EcoeFISHent-101036428//European Commission/ ; Research for Programma Operativo Nazionale (PON) Ricerca e Innovazione, FSE REACT-EU: D31B21008650007//Ministero dell'Università e della Ricerca/ ; },
mesh = {Animals ; *Collagen/chemistry/biosynthesis ; *Fishes/metabolism ; Fisheries/economics ; Aquaculture/economics ; Conservation of Natural Resources ; },
abstract = {This review provides a general overview of collagen structure, biosynthesis, and biological properties, with a particular focus on marine collagen sources, especially fisheries discards and by-catches. Additionally, well-documented applications of collagen are presented, with special emphasis not only on its final use but also on the processes enabling sustainable and safe recovery from materials that would otherwise go to waste. Particular attention is given to the extraction process, highlighting key aspects essential for the industrialization of fish sidestreams, such as hygiene standards, adherence to good manufacturing practices, and ensuring minimal environmental impact. In this context, the EcoeFISHent projects have provided valuable insights, aiming to create replicable, systemic, and sustainable territorial clusters based on a multi-circular economy and industrial symbiosis. The main goal of this project is to increase the monetary income of certain categories, such as fishery and aquaculture activities, through the valorization of underutilized biomass.},
}

Animals
*Collagen/chemistry/biosynthesis
*Fishes/metabolism
Fisheries/economics
Aquaculture/economics
Conservation of Natural Resources

@article {pmid39574446,
year = {2024},
author = {El-Sappah, AH and Li, J and Yan, K and Zhu, C and Huang, Q and Zhu, Y and Chen, Y and El-Tarabily, KA and AbuQamar, SF},
title = {Fibrillin gene family and its role in plant growth, development, and abiotic stress.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1453974},
pmid = {39574446},
issn = {1664-462X},
abstract = {Fibrillins (FBNs), highly conserved plastid lipid-associated proteins (PAPs), play a crucial role in plant physiology. These proteins, encoded by nuclear genes, are prevalent in the plastoglobules (PGs) of chloroplasts. FBNs are indispensable for maintaining plastid stability, promoting plant growth and development, and enhancing stress responses. The conserved PAP domain of FBNs was found across a wide range of photosynthetic organisms, from plants and cyanobacteria. FBN families are classified into 12 distinct groups/clades, with the 12th group uniquely present in algal-fungal symbiosis. This mini review delves into the structural attributes, phylogenetic classification, genomic features, protein-protein interactions, and functional roles of FBNs in plants, with a special focus on their effectiveness in mitigating abiotic stresses, particularly drought stress.},
}

@article {pmid38150088,
year = {2024},
author = {Wang, XM and Fan, L and Meng, CC and Wang, YJ and Deng, LE and Yuan, Z and Zhang, JP and Li, YY and Lv, SC},
title = {Gut microbiota influence frailty syndrome in older adults: mechanisms and therapeutic strategies.},
journal = {Biogerontology},
volume = {25},
number = {1},
pages = {107-129},
pmid = {38150088},
issn = {1573-6768},
support = {National Traditional Chinese Medicine People's Education Letter[2021] No. 203//the QI HUANG Scholars (Junping Zhang) Special Funding/ ; Jin Wei Zhong[2020]No.732//the Tianjin Famous Traditional Chinese Medicine (Junping Zhang) Inheritance Studio Special Funding/ ; No. CACM-2018-QNRC2-B04//the Young Talent Lifting Project of China Association of Chinese Medicine/ ; },
mesh = {Humans ; Aged ; *Gastrointestinal Microbiome ; *Frailty/therapy ; Frail Elderly ; *Probiotics/therapeutic use ; Prebiotics ; },
abstract = {Frailty syndrome denotes a decreased capacity of the body to maintain the homeostasis and stress of the internal environment, which simultaneously increases the risk of adverse health outcomes in older adults, including disability, hospitalization, falls, and death. To promote healthy aging, we should find strategies to cope with frailty. However, the pathogenesis of frailty syndrome is not yet clear. Recent studies have shown that the diversity, composition, and metabolites of gut microbiota significantly changed in older adults with frailty. In addition, several frailty symptoms were alleviated by adjusting gut microbiota with prebiotics, probiotics, and symbiosis. Therefore, we attempt to explore the pathogenesis of frailty syndrome in older people from gut microbiota and summarize the existing interventions for frailty syndrome targeting gut microbiota, with the aim of providing timely and necessary interventions and assistance for older adults with frailty.},
}

Humans
Aged
*Gastrointestinal Microbiome
*Frailty/therapy
Frail Elderly
*Probiotics/therapeutic use
Prebiotics

@article {pmid23291051,
year = {2013},
author = {Edge, SE and Shearer, TL and Morgan, MB and Snell, TW},
title = {Sub-lethal coral stress: detecting molecular responses of coral populations to environmental conditions over space and time.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {128-129},
number = {},
pages = {135-146},
doi = {10.1016/j.aquatox.2012.11.014},
pmid = {23291051},
issn = {1879-1514},
mesh = {Alveolata/physiology ; Analysis of Variance ; Animals ; Anthozoa/*genetics/*metabolism ; *Ecosystem ; Environmental Monitoring ; Gene Expression Profiling ; *Gene Expression Regulation ; *Stress, Physiological ; Time Factors ; },
abstract = {In order for sessile organisms to survive environmental fluctuations and exposures to pollutants, molecular mechanisms (i.e. stress responses) are elicited. Previously, detrimental effects of natural and anthropogenic stressors on coral health could not be ascertained until significant physiological responses resulted in visible signs of stress (e.g. tissue necrosis, bleaching). In this study, a focused anthozoan holobiont microarray was used to detect early and sub-lethal effects of spatial and temporal environmental changes on gene expression patterns in the scleractinian coral, Montastraea cavernosa, on south Florida reefs. Although all colonies appeared healthy (i.e. no visible tissue necrosis or bleaching), corals were differentially physiologically compensating for exposure to stressors that varied over time. Corals near the Port of Miami inlet experienced significant changes in expression of stress responsive and symbiont (zooxanthella)-specific genes after periods of heavy precipitation. In contrast, coral populations did not demonstrate stress responses during periods of increased water temperature (up to 29°C). Specific acute and long-term localized responses to other stressors were also evident. A correlation between stress response genes and symbiont-specific genes was also observed, possibly indicating early processes involved in the maintenance or disruption of the coral-zooxanthella symbiosis. This is the first study to reveal spatially- and temporally-related variation in gene expression in response to different stressors of in situ coral populations, and demonstrates that microarray technology can be used to detect specific sub-lethal physiological responses to specific environmental conditions that are not visually detectable.},
}

Alveolata/physiology
Analysis of Variance
Animals
Anthozoa/*genetics/*metabolism
*Ecosystem
Environmental Monitoring
Gene Expression Profiling
*Gene Expression Regulation
*Stress, Physiological
Time Factors

@article {pmid13483498,
year = {1957},
author = {NETTESHEIM, F and PILLAR, W},
title = {Nil nocere!: tuberculostatics & appendicitis; a contribution on interference with intestinal symbiosis.},
journal = {Munchener medizinische Wochenschrift (1950)},
volume = {99},
number = {38},
pages = {1366-1367},
pmid = {13483498},
issn = {0027-2973},
mesh = {Anti-Bacterial Agents/*adverse effects ; *Antibiotics, Antitubercular ; Appendicitis/*etiology ; *Aviation ; *Dermatologic Agents ; Humans ; *Intestines ; *Symbiosis ; Tuberculosis/*therapy ; },
}

Anti-Bacterial Agents/*adverse effects
*Antibiotics, Antitubercular
Appendicitis/*etiology
*Aviation
*Dermatologic Agents
Humans
*Intestines
*Symbiosis
Tuberculosis/*therapy

@article {pmid40824823,
year = {2025},
author = {Sunal, E and Castro-Rodriguez, V and Sadoine, M},
title = {Fluorophore-based Genetically Encoded Biosensors for Ratiometric Fluorescence Imaging in Microbes.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {222},
pages = {},
doi = {10.3791/68339},
pmid = {40824823},
issn = {1940-087X},
abstract = {Investigating small-molecule dynamics within microbes is essential for comprehensive studies of microbial function. Both intra-organism and inter-organism small molecule dynamics play critical roles in microbial physiology, symbiosis, and disease. However, monitoring these dynamics remains highly challenging using most existing techniques. Fluorophore-based genetically encoded biosensors are powerful tools for tracking small-molecule dynamics in vivo and hold high potential for driving new discoveries. These biosensors are most commonly used in fluorescence imaging, often in combination with perfusion devices that allow precise control over environmental conditions. When integrated with advanced imaging techniques, this approach provides high-resolution, spatially and temporally resolved data, enabling insights into single-cell microbial responses. Despite their promise, implementing such biosensors remains technically challenging. Understanding the key steps is crucial for broader adoption. Here, we present a protocol designed to support the effective deployment of newly engineered biosensors into microbes for quantitative ratiometric fluorescence imaging under controlled conditions.},
}

@article {pmid40824068,
year = {2025},
author = {Sather, LM and Fazeli, N and Kearsley, JVS and Jones, K and Finan, TM},
title = {Unexpected modulation of Hna phage defense activity by the symbiotic regulator NolR.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0018225},
doi = {10.1128/jb.00182-25},
pmid = {40824068},
issn = {1098-5530},
abstract = {The Hna phage defense system is one of many systems that protect bacteria against bacterial viruses (phages). Hna was first discovered in the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, which forms root nodules on leguminous plants. We report that the efficacy of the Hna system depends on NolR, a transcriptional regulator known to regulate expression of nodulation genes. Strains carrying a mutant nolR gene (e.g., the widely used laboratory strain Rm1021) display dramatically reduced Hna-mediated phage resistance compared to those with the wild-type nolR gene. hna expression is approximately doubled in nolR[+] (wild-type) compared to nolR[-] strains. Integration of a second copy of hna increased phage resistance in a nolR[-] strain >1,000-fold, indicating that a moderate hna expression difference is sufficient to affect the Hna phage resistance phenotype. NolR does not appear to directly regulate hna,as there is no predicted NolR binding site upstream of hna, and purified NolR protein does not bind to the hna upstream sequence. Other genes whose transcription is regulated by NolR were identified through RNA-seq experiments. These include the lipopolysaccharide sulfotransferase gene lpsS, which is located downstream of a NolR binding site. This work illustrates how modest differences in expression between strains can dramatically alter the protective phenotype of a defense system.IMPORTANCEThe ability of a bacterial culture to survive phage infection is significant in both medical (phage therapy) and industrial (e.g., cheese production) contexts. This study describes a factor that influences the efficacy of a recently discovered phage defense system (Hna) in the agriculturally relevant soil bacterium Sinorhizobium meliloti. Like other phage defense systems, Hna systems undergo extensive horizontal transfer and must be able to maintain functionality across different genetic backgrounds. Our work demonstrates that host factor differences can significantly impact the performance of phage defense systems.},
}

@article {pmid40823834,
year = {2025},
author = {Sarasa-Buisán, C and Nieves-Morión, M and Lindblad, P and Nierzwicki-Bauer, S and Schluepmann, H and Flores, E},
title = {Intercellular communication in the fern endosymbiotic cyanobacterium Nostoc azollae.},
journal = {mBio},
volume = {},
number = {},
pages = {e0118725},
doi = {10.1128/mbio.01187-25},
pmid = {40823834},
issn = {2150-7511},
abstract = {The water fern Azolla spp. harbors as an endobiont the N2-fixing, filamentous, heterocyst-forming cyanobacterium Nostoc azollae. N. azollae provides the fern with fixed nitrogen permitting its growth in nitrogen-poor environments. In the diazotrophic filaments of heterocyst-forming cyanobacteria, intercellular molecular exchange occurs in which heterocysts provide vegetative cells with fixed nitrogen and vegetative cells provide heterocysts with reduced carbon. Intercellular molecular exchange takes place by diffusion through septal junctions and can be probed by fluorescence recovery after photobleaching (FRAP) analysis with fluorescent markers such as calcein and 5-carboxyfluorescein. The septal junctions traverse the septal peptidoglycan (PG) through nanopores that can be visualized in isolated septal PG disks by electron microscopy. Here, we obtained from Azolla plants material containing the symbiotic cyanobacterium in a viable state and with different morphologies, including heterocyst-containing filaments. FRAP analysis showed effective transfer of the fluorescent markers between vegetative cells, as well as from vegetative cells to heterocysts. Interestingly, communicating and noncommunicating vegetative cells and heterocysts could be distinguished, showing conservation in the endobiont of a mechanism regulating the septal junctions. PG sacculi were also isolated and showed septal disks with arrays of nanopores that conform to those visualized in other heterocyst-forming cyanobacteria. However, a wider range of septal disk size was observed in N. azollae. In spite of its eroded genome, N. azollae maintains the intercellular communication system that is key for its growth as a multicellular organism. Additionally, labeling with the fluorescent sucrose analog esculin suggests sucrose as a source of reduced carbon for the endobiont.IMPORTANCEThe water fern Azolla constitutes a unique symbiotic system in which cyanobacterial endobionts capable of fixing atmospheric nitrogen provide the plant with the nitrogen needed for growth. This symbiosis is an important fertilizer for rice crops worldwide, thereby reducing the reliance on fossil fuel-derived nitrogen fertilizers. The symbiotic cyanobacterium, Nostoc azollae, is a heterocyst-forming strain in which a filament of cells is the organismic unit of growth. Here, we show that the intercellular molecular exchange function necessary for the multicellular behavior of the organism is conserved in the endobiotic N. azollae.},
}

@article {pmid40823765,
year = {2025},
author = {Shan, Y and Zhu, X and Wang, T and Zhang, L and Qi, Y and Hu, Z and Jiang, Z and Zhu, Y and Lu, Y and Yao, J and Xiong, H},
title = {Mitochondria-Targeted Ferroptosis Nanodrug for Triple-Negative Breast Cancer Therapy via Fatty Acid Metabolism Remodeling and Tumor Bacterial Symbiosis Inhibition.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e06443},
doi = {10.1002/smll.202506443},
pmid = {40823765},
issn = {1613-6829},
support = {2018Z063//Post-doctoral support of Jiangsu Province/ ; },
abstract = {Triple-negative breast cancer (TNBC) is considered one of the most aggressive subtypes of breast cancer, due to its pronounced propensity for metastasis. This challenge is amplified by the critical role of mitochondria in metastasis, regulating processes like fatty acid metabolism that drive tumor cell migration. Moreover, emerging evidence suggests that bacterial infiltration, particularly Staphylococcus xylosus (S. xylosus), could further exacerbate TNBC metastasis. To address both metabolic dysregulation and bacterial involvement, a mitochondria-targeted ferroptosis-activated nanosystem is developed, named ICM, which is integrated the mitochondrial membrane (MM) for mitochondrial targeting, the FeCl3 for ferroptosis therapy, the photosensitizer indocyanine green, and cytochrome c (CytC) through self-assembly technology. During assembly, CytC interacted with cardiolipin on the MM, endowing ICM with peroxidase-like and catalase-like activities. Dual enzymatic activities, combined with phototherapy, enhance FeCl3-induced ferroptosis in tumor cell mitochondria, thereby reprogramming fatty acid metabolism and inhibiting metastasis. Additionally, the amplified ferroptosis effects also effectively inhibit S. xylosus, disrupting the tumor-bacteria symbiosis and further preventing metastatic spread. Finally, ICM nanoparticles significantly suppress TNBC metastasis by modulating lipid metabolism and inhibiting bacterial-mediated metastasis. These findings suggest that ICM offer a multifaceted therapeutic approach for combating TNBC metastasis, providing a potential strategy for cancer treatments.},
}

@article {pmid40822732,
year = {2025},
author = {Daud, M and Qiao, H and Xu, S and Hui, X and Adil, M and Lu, Y},
title = {Understanding abiotic stress in alfalfa: physiological and molecular perspectives on salinity, drought, and heavy metal toxicity.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1627599},
doi = {10.3389/fpls.2025.1627599},
pmid = {40822732},
issn = {1664-462X},
abstract = {Alfalfa (Medicago sativa L.), a vital perennial legume forage, has been widely cultivated owing to a variety of favorable characteristics, including comprehensive ecological resilience, superior nutritive value, digestibility, and nitrogen fixation capacity. The productivity traits of alfalfa, particularly its biomass yield and forage quality, are profoundly influenced by a range of abiotic stress conditions. As a common abiotic stress, drought adversely impacts growth and photosynthetic efficiency, accompanied by increased oxidative damage and stomatal closure as a mechanism to minimize water loss; meanwhile, transgenic approaches have been employed to enhance drought resilience by improving antioxidant activity and water-use efficiency. Salinity stress disturbs ionic balance, resulting in sodium (Na[+]) toxicity and the generation of oxidative damage; however, alfalfa cultivars exhibit salinity tolerance through mechanisms such as Na[+] exclusion, K[+] retention, activation of antioxidant defenses, hormonal regulation, and the upregulation of stress-responsive genes. In addition, heavy metals pose a significant challenge to alfalfa production, as they impair plant development and disrupt symbiotic nitrogen fixation, but recent studies have highlighted the potential of microbial-assisted phytoremediation in mitigating these detrimental effects. By integrating recent findings, this review highlights the intricate physiological, biochemical, and molecular mechanisms involved in alfalfa's responses to key abiotic stressors specifically drought, salinity, and heavy metal toxicity. Breakthroughs in genetic modification, notably the development of transgenic lines exhibiting altered expression of stress-responsive genes, offer valuable potential for improving stress resilience. Future research should employ omics approaches, advanced gene-editing and de novo gene synthesis to target key regulatory elements responsible for stress adaptation.},
}

@article {pmid40822399,
year = {2025},
author = {Luo, C and Song, Y and Meng, L and Cheng, Y and Dai, H and Qiao, Y and Xie, X},
title = {Transcriptomic insights into the molecular mechanism of abietic acid promoting growth and branching in Armillaria gallica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632512},
doi = {10.3389/fmicb.2025.1632512},
pmid = {40822399},
issn = {1664-302X},
abstract = {Armillaria gallica, a valuable edible and medicinal fungus, is essential for the symbiotic cultivation of the traditional Chinese medicinal herb Gastrodia elata. Abietic acid, a plant-derived secondary metabolite, modulates microbial growth and metabolism. This study investigates the effects of abietic acid on A. gallica growth and branching using phenotypic analysis and transcriptomic approaches to uncover underlying molecular mechanisms. The experiment compared an abietic acid treatment group (0.6 g/L) with a control group, assessing growth over several days via biomass measurements, rhizomorph counting, and RNA sequencing for transcriptomic profiling. Abietic acid significantly promoted A. gallica growth and branching, with the most pronounced effects on the third day: dry biomass weight increased by 302% and total rhizomorphs by 378.4% (p < 0.01). Transcriptomic analysis showed upregulation of GH5, GH16, MFS, and NAD(P)-binding protein genes in the treatment group, optimizing carbon utilization, cell wall remodeling, and nutrient transport. These findings elucidate abietic acid's role in regulating A. gallica development and provide a theoretical foundation for enhancing the symbiotic cultivation of G. elata and A. gallica.},
}

@article {pmid40822337,
year = {2025},
author = {Xin Yee Tan, K and Shigenobu, S},
title = {Targeted disruption of the cls gene in Buchnera aphidicola impairs membrane integrity and host symbiont dynamics.},
journal = {iScience},
volume = {28},
number = {8},
pages = {113178},
doi = {10.1016/j.isci.2025.113178},
pmid = {40822337},
issn = {2589-0042},
abstract = {The obligate symbiosis between pea aphids (Acyrthosiphon pisum) and Buchnera aphidicola represents metabolic interdependence between the host insect and its bacterial symbiont. Buchnera has a highly reduced genome that has lost nearly all phospholipid synthesis genes except cls, encoding a cardiolipin synthase homologue. We employed in vivo antisense, cell-penetrating peptide (CPP)-conjugated synthetic peptide nucleic acids (PNAs) to knock down cls in Buchnera. This intervention resulted in significant downregulation of cls expression, lowered Buchnera titers, pronounced morphological distortions, and reduced aphid reproduction. Notably, Buchnera cells were often detected in the aphid gut following anti-cls PNAs treatment, deviating from their typical intracellular niche within bacteriocytes. Collectively, the cls gene is critical for maintaining Buchnera integrity, proper cellular localization, and symbiont-host interactions. Given that the retention of cls is a common feature among many obligate endosymbionts despite massive gene loss, our findings offer key insights into the evolutionary principles shaping symbiotic relationships involving membrane biology.},
}

@article {pmid40819100,
year = {2025},
author = {Shin, MS and Yang, I and Wang, W and Kim, H},
title = {Diversity and composition of sponge-associated microbiomes from Korean sponges revealed by full-length 16S rRNA analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30021},
pmid = {40819100},
issn = {2045-2322},
support = {NRF-2021R1F1A1063787//Ministry of Science and ICT/ ; RS-2022-NR071935//Ministry of Science and ICT/ ; RS-2023-NR076615//Ministry of Science and ICT/ ; RS-2022-NR072431//Ministry of Science and ICT/ ; },
abstract = {Marine sponges host diverse and specialized microbial communities that serve essential functions in nutrient cycling, ecosystem stability, and biotechnological applications. This study investigates the diversity and composition of sponge-associated microbiomes from eight sponge species collected in Chuksan Harbor, South Korea, using full-length 16S rRNA sequencing and amplicon sequence variant (ASV)-based methods. Our results demonstrate that each sponge species harbors distinct and highly structured microbial communities. Proteobacteria, and especially Alpha- and Gammaproteobacteria, were generally dominant; however, unique dominance patterns, such as the near-exclusive presence of an uncharacterized Gammaproteobacterial lineage in Cliona celata, suggest strong host-symbiont specificity and possible coevolution. Notably, no ASVs were shared between seawater and sponge samples, confirming that sponge hosts select and maintain unique sets of microbial partners. In several Halichondria species, we detected the presence of Entotheonella, a symbiont with high biosynthetic gene cluster diversity that may contribute to host chemical defense and metabolic versatility. Depth-driven differences in microbial community composition were exemplified by Geodia reniformis, whose microbiome was dominated by deep-sea adapted and metabolically versatile lineages such as SAR202, PAUC34f, and Dadabacteriales. This study establishes a new baseline for understanding sponge-microbe partnerships in Korean marine environments. Our integrative, high-resolution approach not only uncovers remarkable taxonomic and functional diversity, but also provides a valuable genetic resource for future marine natural-product discovery and advances ecological restoration efforts.},
}

@article {pmid40818932,
year = {2025},
author = {Ansari, BK and Shukla, AK and Sinam, G and Upreti, DK},
title = {Active transplantation study of nickel uptake by Pyxine cocoes (Sw.) Nyl.: prospection for atmospheric nickel biomonitoring.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/09593330.2025.2545633},
pmid = {40818932},
issn = {1479-487X},
abstract = {The prevalence of nickel pollution is anticipated to rise due to the advent of novel low-carbon technologies and electric vehicles. Biomonitoring, which is increasingly overlooked in favour of technology-driven methods, remains a cost-effective approach and enables the monitoring of extensive spatial areas. In the present study, Pyxine cocoes (P. cocoes), a symbiotic lichen, was examined for the first time for its capacity to uptake sprayed nickel (Ni) in vivo and the subsequent effects on its physicochemical parameters. Transplanted P. cocoes was treated with different concentrations of Ni solutions (5 µM, 50 µM, 100 µM, 150 µM, 200 µM). The lichen, P. cocoes, had the capacity to accumulate Ni linearly in a dose- and time-dependent manner. The effect of Ni on photosynthetic parameters, cell membrane integrity, antioxidants and protein content was quantified corresponding to concentrations and durations of treatment. At a low dose (5 µM), a beneficial effect was observed on chlorophyll-a, chlorophyll-b, total chlorophyll and protein content in P. cocoes. At higher doses of Ni (150 µM, 200 µM), it exhibited an inhibitory effect as observed by reduced photosynthetic parameters and antioxidant activity. Cell membrane integrity (CMI) deteriorated in response to increasing Ni exposure, as indicated by increased electrolyte conductivity. Using the linear regression coefficient, it was determined that at lower Ni concentrations, the adsorption kinetics followed pseudo-second-order (chemisorption) and, at higher concentrations, it followed pseudo-first-order kinetics (physisorption). This active (transplant) monitoring method is a novel endeavour in monitoring Ni stress and utilising the physicochemical parameters as a bioindicator for Ni pollution.},
}

@article {pmid40816675,
year = {2025},
author = {Li, J and Song, Y and Qiu, Y and Liu, G and Feng, Y},
title = {Simultaneous carbon, nitrogen, and phosphorus removal and energy recovery from wastewater in a zero-energy microbial electrochemical system with algal-bacterial biocathode.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122607},
doi = {10.1016/j.envres.2025.122607},
pmid = {40816675},
issn = {1096-0953},
abstract = {Addressing the challenge of high energy consumption in conventional wastewater treatment, this study develops a zero-energy microbial electrochemical system (MES) featuring an algal-bacterial symbiotic biocathode. Under simulated day-night cycles, this configuration achieves simultaneous and efficient removal of carbon, nitrogen, and phosphorus pollutants while recovering electrical energy. During the illuminated phase, algal photosynthesis generates oxygen to sustain a stable voltage output (∼600 mV) without external aeration. In the dark phase, the system promotes denitrification, thereby enabling effective nitrogen removal. A petal-like NiO-modified carbon felt biocathode was fabricated, significantly enhancing the cathode's specific surface area and active sites, thereby effectively promoting the formation of a microbial-algal composite biofilm and cathodic reduction reaction. This innovative design and operational strategy enable zero-energy wastewater treatment coupled with resource recovery, offering a promising pathway toward energy self-sufficiency and carbon neutrality in practical wastewater treatment applications.},
}

@article {pmid40815476,
year = {2025},
author = {Papaleo, S and Panelli, S and Bitar, I and Sterzi, L and Nodari, R and Comandatore, F},
title = {Nucleotide composition shapes gene expression in Wolbachia pipientis: a role for MidA methyltransferase?.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0077925},
doi = {10.1128/msystems.00779-25},
pmid = {40815476},
issn = {2379-5077},
abstract = {UNLABELLED: Wolbachia pipientis is an obligate intracellular bacterium, associated with several arthropods and filarial nematodes. Wolbachia establishes a variety of symbiotic relationships with its hosts, with consequent genomic rearrangements, variation in gene content, and loss of regulatory regions. Despite this, experimental studies show that Wolbachia gene expression is coordinated with host developmental stages, but the mechanism is still unknown. In this work, we analyzed published RNA-seq data of four Wolbachia strains, finding a correlation between gene nucleotide composition and gene expression. The strength and direction of this phenomenon changed with the expression of the S-adenosyl-methionine-dependent methyltransferase midA. Specifically, when midA is overexpressed, there is a negative relationship between gene adenine content and gene expression, while downregulation of midA reverses this trend. MidA is known to methylate protein arginine, with potential effect on protein affinity for substrates, including nucleic acids. To expand our understanding of this poorly characterized enzyme, we investigated its ability to methylate DNA expressing it in Escherichia coli. The experiment revealed that the Wolbachia MidA can methylate both adenine and cytosine. Lastly, we found upstream the midA gene, a conserved binding site for the Ccka/CtrA signaling transduction system, and we hypothesize that this mechanism could be involved in the communication between the host and the bacterium. Overall, these findings suggest a cascade mechanism in which the host activates the bacterium Ccka/CtrA signaling system, thus inducing the expression of the midA gene, with subsequent effect on the expression of several Wolbachia genes on the basis of their nucleotide composition.

IMPORTANCE: Wolbachia pipientis is one of the most common intracellular bacteria in insects, and it is currently utilized as a tool for the control of vector-borne diseases. As for many other endosymbiont bacteria, Wolbachia experienced important genome rearrangements, gene content changes, and the loss of several regulatory sequences, affecting the integrity of operons and promoters. Nevertheless, experimental studies have shown that Wolbachia gene expression is coordinated with the host physiology (e.g., developmental stages), although the underlying mechanism remains unclear. In this work, based on in silico analyses and an experimental study on wOo methyltransferase, we propose that bacterial DNA methylation could be a key mechanism regulating Wolbachia gene expression. Additionally, we found evidence suggesting that the DNA methylation process in Wolbachia can be activated by the host.},
}

@article {pmid40815469,
year = {2025},
author = {Dai, M and Zhao, F and Shi, X and Tian, C and Lin, Y and Bai, L and Li, T and Jin, X and Xiao, L and Kristiansen, K and Li, X and Zhang, Z},
title = {Cultivation and sequencing of microbiota members unveil the functional potential of yak gut microbiota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0036725},
doi = {10.1128/msystems.00367-25},
pmid = {40815469},
issn = {2379-5077},
abstract = {The animal gut microbiota exhibits extensive taxonomic diversity, yet cultivated isolates and complete genomes from animal hosts remain scarce, hindering functional and ecological insights. We present a cultivated Yak (Bos grunniens) Fecal bacteria genome Reference (YFR), comprising 548 high-quality genomes based on aerobic and anaerobic cultivation. Notably, 216 strains represented novel taxa, classified into 29 species-level clusters spanning 4 phyla and 14 genera. The YFR increased the proportion of cultured ruminant gut bacterial species by 19.39%, significantly expanding the reference database for this ecosystem. Among these, 11 species harbor abundant CAZymes Gene Clusters (CGCs), indicating a high capacity for digesting complex polysaccharides. Biosynthetic Gene Clusters (BGCs) are predicted and demonstrated to possess distinct novelty in YFR genomes, demonstrating a potential for future applications. We demonstrated that the symbiotic relationship between host bacterial strains and bacteriophages can be effectively studied using cultured strains by enabling precise mapping of viral genes to host metabolic adaptations. Culturing animal gut bacterial species not only expands the resources of culturable strains but also provides a basis for subsequent functional mining.IMPORTANCEAs a representative species in high-altitude extreme environments, yaks rely on their gut microbiota to support critical physiological functions and adapt to harsh conditions. This study established a comprehensive pipeline by integrating innovative single-bacterium culture conditions with optimized strategies for the yak gut microbiota. The resulting genomic repository not only expands the culturable microbial resources for extremophile mammals but also reveals unique metabolic traits, including polysaccharide-digesting CAZyme clusters, novel BGCs, and phage-host interactions. This approach provides essential microbial resources for advancing our understanding of host-microbial adaptations to extreme environments and offers tangible tools for industrial enzyme discovery and synthetic biology applications.},
}

@article {pmid40814858,
year = {2025},
author = {DelPercio, R and McGregor, M and Morley, S and Nikaeen, N and Meyers, B and Baldrich, P},
title = {Transcriptional Dynamics of Nitrogen Fixation and Senescence in Soybean Nodules: A Dual Perspective on Host and Bradyrhizobium Regulation.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-04-25-0037-R},
pmid = {40814858},
issn = {0894-0282},
abstract = {The Soybean-Bradyrhizobium symbiosis enables symbiotic nitrogen fixation (SNF) within root nodules, reducing reliance on synthetic N-fertilizers. However, nitrogen fixation is transient, peaking several weeks after Bradyrhizobium colonization and declining as nodules senesce in coordination with host development. To investigate the regulatory mechanisms governing SNF and senescence, we conducted a temporal transcriptomic analysis of soybean nodules colonized with Bradyrhizobium diazoefficiens USDA110. Weekly nodule samples (2-10 weeks post-inoculation, wpi) were analyzed using RNA and small RNA sequencing, while acetylene reduction assays assessed nitrogenase activity from 4 to 7 wpi. We identified three major nodule developmental phases: early development (2-3 wpi), nitrogen fixation (3-8 wpi), and senescence (8-10 wpi). Soybean showed extensive transcriptional reprogramming during senescence, whereas Bradyrhizobium underwent major transcriptional shifts early in development before stabilizing during nitrogen fixation. We identified seven soybean genes and several microRNAs as candidate biomarkers of nitrogen fixation, including lipoxygenases (Lox), suggesting roles for oxylipin metabolism. Soy hemoglobin-2 (Hb2), previously classified as non-symbiotic, was upregulated during senescence, implicating oxidative stress responses within aging nodules. Upregulation of the Bradyrhizobium paa operon and rpoH during senescence suggested metabolic adaptation for survival beyond symbiosis. Additionally, Bradyrhizobium NIF gene expression showed stage-specific regulation, with nifK peaking at 2 wpi, nifD and nifA at 2 and 10 wpi, and nifH, nifW, and nifS at 10 wpi. These findings provide insights into SNF regulation and nodule aging, revealing temporal gene expression patterns that could inform breeding or genetic engineering strategies to enhance nitrogen fixation in soybeans and other legume crops.},
}

@article {pmid40812734,
year = {2025},
author = {Pu, D and Jin, Y and Wang, L and Wang, R and Li, L and Song, Y and Han, X},
title = {Combined supplementation of short-chain fatty acids reduces hyperphosphorylation of Tau at T181,T231 and S396 sites and improves cognitive impairment in a chemically induced AD mouse model via regulation of HDAC and Keap1.},
journal = {Neurochemistry international},
volume = {189},
number = {},
pages = {106034},
doi = {10.1016/j.neuint.2025.106034},
pmid = {40812734},
issn = {1872-9754},
abstract = {Alzheimer's disease (AD) is characterized by the pathological hallmarks of β-amyloid deposition and Tau protein hyperphosphorylation, with memory loss and cognitive dysfunction as its primary clinical manifestations. The incidence of AD has been progressively increasing in recent years. Short-chain fatty acids (SCFAs), key effector molecules in host-gut microbial interactions, play a crucial role in maintaining central nervous system homeostasis. In this study, AD mouse model was established via AlCl3/D-gal induction. The effects of mixed SCFA intervention on spatial learning and memory in AD model mice were assessed using behavioral tests, including the Morris Water Maze. Levels of pro-inflammatory cytokines and activities of oxidative stress-related enzymes in brain and colon tissues were quantified using ELISA and commercial kits. Key protein expression levels were analyzed by Western blot, immunohistochemistry, and immunofluorescence. Results demonstrated that SCFAs significantly alleviated cognitive dysfunction in AD model, reduced Tau hyperphosphorylation at T181, T231 and S396 sites, suppressed pro-inflammatory cytokine release, and enhanced antioxidant capacity, but with no reversal in elevated Aβ levels in AD model. Mechanistically, SCFAs inhibited glial cell activation, upregulated MCT-1 and tight junction proteins in the blood-brain barrier and strengthened gut-brain barrier integrity, potentially regulating small molecule trans-barrier transport. Furthermore, examination of relevant protein expressions revealed that SCFAs activated HDAC1 and inhibited overexpressed HDAC3 and Keap-1 in AD mice model. These findings suggest that SCFAs may regulate epigenetic modifications in the brain of AD to exert neuroprotective effects. This study provides novel evidence supporting the potential of symbiotic microbe-derived SCFAs in alleviating AD.},
}

@article {pmid40812177,
year = {2025},
author = {Zhang, X and Tan, X and Wang, E},
title = {Networks of the symbiosis-immunity continuum in plants.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1256-1275},
doi = {10.1016/j.chom.2025.06.009},
pmid = {40812177},
issn = {1934-6069},
abstract = {Plants continuously interact with diverse microbes. Forming essential symbiotic relationships promotes plant growth, while defending against harmful microbes prevents disease. Plants resist pathogens by detecting molecules released from microbes. Beneficial microbes distinguish themselves from harmful pathogens before establishing symbiosis by releasing molecules and suppressing plant defenses during the infection and colonization stages. Despite their distinct outcomes, symbiotic and immune responses lie on a continuum and share key features, including dynamic cellular remodeling, metabolite rearrangement, and the maintenance of defenses against pathogens. This review explores the regulatory networks governing these processes, highlighting the shared and unique molecular mechanisms underlying symbiotic and immune responses. Understanding how plants integrate environmental signals to balance symbiotic compatibility and defense will provide valuable insights into optimizing plant health and productivity in changing ecosystems.},
}

@article {pmid40812045,
year = {2025},
author = {Zhou, Y and Zhang, C and Deng, Y and Lei, L and Hu, T},
title = {Oral microecological community- Streptococcus mutans dysbiosis and interaction provide therapeutic perspectives for dental caries.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106367},
doi = {10.1016/j.archoralbio.2025.106367},
pmid = {40812045},
issn = {1879-1506},
abstract = {OBJECTIVE: This review aims to provide an overview of the dysbiosis and interaction between Streptococcus mutans (S. mutans) and other Streptococci, Veillonella spp., Lactobacillus spp., and Candida albicans in the oral cavity, which is a major driver of cariogenicity.

DESIGN: The search for this narrative review was conducted in databases including PubMed, Web of Science, and Google Scholar, employing keywords like "Dental caries," "Streptococcus mutans," "Commensal Streptococci," "Veillonella," "Lactobacillus," "Candida albicans," and "Interaction" while manually retrieving the reference lists of journal articles.

RESULTS: Dental caries has a high prevalence and low treatment rate in the population, which poses a great burden to public health and the social economy. The etiology of dental caries is closely linked to the imbalance of oral microbial communities. S. mutans is the major pathogen of dental caries. The cariogenic mechanism of S. mutans is primarily related to acid production and acid resistance, as well as polysaccharide production, adhesion, colonization, and the formation of cariogenic biofilm. However, there are complex interactions between S. mutans and other symbiotic microorganisms in the oral cavity, which synergistically or antagonistically affect the pathogenicity of microorganisms.

CONCLUSION: The interactions between S. mutans and oral commensal microorganisms on the microecology provide an in-depth understanding of the etiology of cariogenicity and new pathways for multiple caries prevention and treatment, such as hydrogen peroxide, arginine, farnesol, and probiotics.},
}

@article {pmid40811611,
year = {2025},
author = {Araújo, NH and Landry, D and Quilbé, J and Pervent, M and Nouwen, N and Klopp, C and Cullimore, J and Gully, D and Vicedo, C and Gasciolli, V and Brottier, L and Pichereaux, C and Racoupeau, M and Rios, M and Gressent, F and Chaintreuil, C and Gough, C and Giraud, E and Lefebvre, B and Arrighi, JF},
title = {The receptor-like cytoplasmic kinase AeRLCK2 mediates Nod-independent rhizobial symbiosis in Aeschynomene legumes.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf201},
pmid = {40811611},
issn = {1532-298X},
abstract = {Many plants interact symbiotically with arbuscular mycorrhizal fungi to enhance inorganic phosphorus uptake, and legumes also develop a nodule symbiosis with rhizobia for nitrogen acquisition. The establishment and functioning of both symbioses rely on a common plant signaling pathway activated by structurally related Myc and Nod factors. Recently, a SPARK receptor-like kinase (RLK)/receptor-like cytoplasmic kinase (RLCK) complex was shown to be essential for arbuscular mycorrhiza formation in both monocot and dicot plants. Here, we show that in Aeschynomene legumes, the RLCK component of this receptor complex has undergone a gene duplication event and mediates a unique nodule symbiosis that is independent of rhizobial Nod factors. In Aeschynomene evenia, AeRLCK2 is crucial for nodule initiation but not for arbuscular mycorrhiza symbiosis. Additionally, AeRLCK2 physically interacts with and is phosphorylated by the cysteine-rich RLK, AeCRK, which is also required for nodulation. This finding uncovers an important molecular mechanism that controls the establishment of nodulation and is associated with Nod-independent symbiosis.},
}

@article {pmid40811509,
year = {2025},
author = {Pen, IAM and Benedict, C and Broe, MB and Delgado, A and Glon, H and Zhang, M and Daly, M},
title = {Resolving Acuticulata (Metridioidea: Enthemonae: Actiniaria), a clade containing many invasive species of sea anemones.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0328544},
pmid = {40811509},
issn = {1932-6203},
abstract = {Acuticulata is a globally distributed group in the actiniarian superfamily Metridioidea comprised of taxa with ecological, economic, and scientific significance. Prominent members such as Exaiptasia diaphana and Diadumene lineata serve as model organisms for studying coral symbiosis, bleaching phenomena, and ecological invasions. Despite their importance, unresolved phylogenetic relationships and outdated taxonomic frameworks hinder a full understanding of the diversity and evolution of the taxa in this clade. In this study, we employ a targeted sequence-capture approach to construct a robust phylogeny for Acuticulata, addressing long-standing questions about familial monophyly and comparing the results to results from a more conventional five-gene dataset. Specimens from previously underrepresented families and global regions, including the Falkland Islands, were included to elucidate evolutionary interrelationships and improve resolution. Our results support the monophyly of Aliciidae, Boloceroididae, Diadumenidae, Gonactiniidae, and Metridiidae. Our results reiterate the need for taxonomic revision within the family Sagartiidae, as the specimens we included from this family were recovered in four distinct clades. Based on our results, we transfer Paraiptasia from Aiptasiidae to Sagartiidae. These findings emphasize the utility of genome-scale data for resolving phylogenetic ambiguities for morphologically problematic taxa and suggest a framework for future integrative taxonomic and ecological studies within Acuticulata.},
}

@article {pmid40811445,
year = {2025},
author = {Gebre, KY and Demissie, AG and Tesema, AA and Belay, HZ and Akalye, MW and Friew, AB and Baye, FG and Felatie, HB and Yohannes, MA and Eshetu, MA and Shiferaw, WA},
title = {Isolation, biochemical characterization, and greenhouse authentication of chickpea (Cicer arietinum L.) rhizobia collected from some major chickpea growing areas of Woldia, North Wollo, Ethiopia.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330169},
pmid = {40811445},
issn = {1932-6203},
abstract = {Chickpea (Cicer arietinum L.) is a vital legume crop worldwide, valued for its high nutritional content and significant contribution to food security and soil fertility through biological nitrogen fixation. Despite its importance, chickpea yields remain suboptimal in many regions, including Ethiopia, primarily due to constraints such as poor soil fertility and inadequate use of effective rhizobia inoculants. This study aimed to isolate and characterize native Rhizobium strains from chickpea root nodules collected from fields in the Woldia region and to assess their potential to promote plant growth. A total of 41 bacterial isolates were obtained, of which 12 were presumptively identified as Rhizobium based on growth characteristics on Congo red and bromothymol blue media. These isolates were further characterized morphologically and biochemically. Five biochemically promising isolates were selected for evaluation in a controlled 45-day greenhouse experiment under sterile conditions. Inoculation with these isolates significantly enhanced seed germination and early seedling growth compared to uninoculated controls. The symbiotic effectiveness of the isolates ranged from 74.3% to 121.9%, with isolates WUSFDG-23, WUSFMC-31, and WUSFMC-23 demonstrating high effectiveness, isolate WUSFDG-23 markedly increased nodulation and biomass accumulation. This study highlights the potential of native Rhizobium isolates from Woldia chickpea fields, especially WUSFDG-23, as effective bio-inoculants to promote sustainable chickpea production and reduce dependence on chemical fertilizers.},
}

@article {pmid40811300,
year = {2025},
author = {Zheng, J and Nishida, Y and Okrasinska, A and Bonito, GM and Heath-Heckman, EAC and Liu, KJ},
title = {The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {4},
pages = {1265-1277},
doi = {10.1109/TCBBIO.2025.3553405},
pmid = {40811300},
issn = {2998-4165},
abstract = {Just as a phylogeny encodes the evolutionary relationships among a group of organisms, a cophylogeny represents the coevolutionary relationships among symbiotic partners. Both are primarily reconstructed using computational analysis of biomolecular sequence data. The most widely used cophylogenetic reconstruction methods utilize an important simplifying assumption: species phylogenies for each set of coevolved taxa are required as input and assumed to be correct. Many studies have shown that this assumption is rarely - if ever - satisfied, and the consequences for cophylogenetic studies are poorly understood. To address this gap, we conduct a comprehensive performance study that quantifies the relationship between species tree estimation error and downstream cophylogenetic estimation accuracy. We study the performance of state-of-the-art methods for cophylogenetic reconstruction using in silico model-based simulations. Our investigation also assessed cophylogenetic reproducibility using genomic sequence data from two important models of symbiosis: soil-associated fungi and their endosymbiotic bacteria, and bobtail squid and their bioluminescent bacterial symbionts. Our findings conclusively demonstrate the major impact that upstream phylogenetic estimation error has on downstream cophylogenetic reconstruction. Relative to other experimental factors such as cophylogenetic estimation method choice and coevolutionary event costs, phylogenetic estimation error ranked highest in importance based on a random forest-based variable importance assessment. We conclude with practical guidance and future research directions. Among the many considerations needed for accurate cophylogenetic reconstruction - choice of computational method, method settings, sampling design, and others - just as much attention must be paid to careful species phylogeny estimation using modern best practices.},
}

@article {pmid40810521,
year = {2025},
author = {Kruasuwan, W and Arigul, T and Munnoch, JT and Nutaratat, P and Songvorawit, N},
title = {Gut-associated bacteria and their roles in wood digestion of saproxylic insects: The case study of flower chafer larvae.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70010},
pmid = {40810521},
issn = {1365-2583},
support = {FF-2567A10512010//National Science, Research and Innovation Fund (NSRF), Thaksin University (Research Project Grant) Fiscal Year 2024/ ; CUFRB65_bcg(20)_088_23_18//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; R016841017//Mahidol University (Fundamental Fund: Fiscal Year 2025)/ ; B13F660073//Program Management Unit for Human Resources & Institutional Development, Research Innovation/ ; },
abstract = {Protaetia acuminata (Fabricius, 1775) (Coleoptera: Scarabaeidae) is widely distributed throughout Southeast Asia and plays a significant role in nutrient cycling by facilitating the decomposition of woody materials, a process that likely relies heavily on the contribution of symbiotic bacteria within their digestive system. However, their gut bacteria have not been thoroughly studied. By using V3-V4 amplicon sequencing, it was revealed that the midgut (MG) of Pr. acuminata larvae and fermented sawdust after rearing (FSD) share a similar microbial community, predominantly composed of Proteobacteria and Actinobacteriota, as well as functional genes associated with cellulolysis, nitrogen respiration, nitrate reduction and aerobic chemoheterotrophy. In contrast, the bacterial community in the hindgut (HG) was distinctly different, with anaerobic respiration being the dominant metabolic process. Agromyces, Altererythrobacter, Bacillus, Cellulomonas, Lysinibacillus, Pseudoxanthomonas and the family Promicromonosporaceae were the most common genera in MG, HG and FSD samples. The culture-based isolation method yielded 67 isolates from the larvae, with gram-positive bacteria predominating in HG and MG, whereas gram-negative bacteria were primarily found in the FSD. These microorganisms produce a range of lignocellulolytic enzymes including β-endoglucanase, laccase and xylanase that enable the beetles to digest their plant-based diet efficiently and also involve many biochemical pathways relating to biogeochemical cycling. Our results provide valuable insights into the gut-associated Pr. acuminata flower chafer larvae and could serve as a basis and reservoir for future studies on lignocellulolytic enzyme-producing bacteria.},
}

@article {pmid40810464,
year = {2025},
author = {González-López, AM and Quiñones-Aguilar, EE and Guizar-González, C and Rincón-Enríquez, G},
title = {Annonacin accumulation in leaves of Annona muricata L. induced by mycorrhizal colonization.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf085},
pmid = {40810464},
issn = {1574-6968},
abstract = {Annona muricata L. is a tropical tree known for its secondary metabolites, particularly acetogenins, which have cytotoxic and antitumor properties. Research has shown that arbuscular mycorrhizal fungi (AMF) symbiosis and drought stress can increase the production of terpenoids, alkaloids, and phenolic compounds in plants. Our objective was to assess whether AMF symbiosis (both species and consortia) and two irrigation regimens enhanced foliar annonacin concentration, the primary acetogenin in A. muricata leaves. Two irrigation levels were used: normal irrigation (NI) and low irrigation (LI). Trees were inoculated with two AMF consortia: Cerro del Metate (CM) and Agua Duce (AD); and two AMF species: Rhizophagus intraradices (RI) and Funneliformis mosseae (FM). Results showed that annonacin concentration was 83% lower in leaves under LI compared to NI. However, AMF symbiosis increased annonacin concentration, especially under LI conditions. Dry leaf weight was higher in mycorrhizal plants under the LI level than in controls. No growth promotion due to AMF symbiosis was observed under NI. In conclusion, AMF symbiosis promotes foliar annonacin concentration in A. muricata leaves in the two irrigation levels. FM treatment promotes higher annonacin concentration in the NI condition while AD, CM, and FM treatments promotes annonacin concentration in the LI condition.},
}

@article {pmid40810459,
year = {2025},
author = {Boo, KH and Oh, YK and Møller, C and Lee, D and Jeon, GL and Kim, D and Burow, M and Großkinsky, DK and Kim, J and Ryu, MY and Lee, B and Suh, J and Ha, CM and Roitsch, T and Lim, PO and Berger, F and Suh, JW and Kim, SI and Oh, TR and Cho, SK and Kim, W and Kim, S and Riu, KZ and Yang, SW},
title = {Dasineura asteriae Reprograms the Flower Gene Expressions of Vegetative Organs to Create Flower-Like Gall in Aster scaber.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70127},
pmid = {40810459},
issn = {1365-3040},
support = {//This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean Ministry of Science and ICT (No. 2017R1A2B4010255) and by Samsung Science and Technology Foundation Project SSTF-BA1801-09 to S.W.Y. and was also supported by the Basic Science Research Program of the NRF funded by the Korean Ministry of Education (2016R1A6A1A03012862) and (2017R1D1A1B03034952) to K.Z.R and S.K., respectively. The "Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01319101)" funded by the Korean Rural Development Administration and a grant (715003-07) from the Research Center for Production Management and Technical Development for High Quality Livestock Products through Agriculture, Food and Rural Affairs Research Center Support Program, Ministry of Agriculture, Food and Rural Affairs to K.Z.R. Lastly, this study was supported by the National Sustainability Program I (NPU w, grant number LO1415) funded by the Ministry of Education, Youth, and Sports of the Czech Republic to T.R. F.B. was supported by core funding from GMI./ ; },
abstract = {Plant galls are abnormal growing tissues induced by various parasitic organisms, exhibiting diverse and complex morphologies. Typically, these galls differ significantly in appearance from their host plants. Here, we report that larvae of a parasitic fly generate unique, rosette galls on Aster scaber, a perennial herb. These galls develop from vegetative organs after the larvae reprogram floral gene expression. To investigate the underlying mechanisms, we conducted whole-genome sequencing and transcriptome analysis. Our findings reveal that the larvae induce host organ dedifferentiation into an amorphous callus, activate floral genes, and selectively suppress genes associated with carpel development. As a result, the pseudoflowers consist solely of tepal-like leaflets and a specialized chamber, and the larvae influence pigment biosynthesis. Hijacking plants developmental gene networks by insects to sequentially mediate dedifferentiation, cytokinin regulation, and tepal-like leaflets formation provides a framework to study highly elaborate forms of parasitism and symbiosis between plants and insects.},
}

@article {pmid40809550,
year = {2025},
author = {Gallardo Salamanca, MLÁ and Asorey, C and Macpherson, E},
title = {A new species of Galathea (Decapoda, Galatheidae) from the seamounts of the Easter Island area (Southeast Pacific Ocean Ridge) associated with a sea urchin.},
journal = {ZooKeys},
volume = {1248},
number = {},
pages = {111-123},
pmid = {40809550},
issn = {1313-2989},
abstract = {Galatheatukitukimea sp. nov. is described from the seamounts near Rapa Nui (Easter Island) and represents the first record of the genus for this region of the Pacific Ocean and for Chilean territory. The new species belongs to the group of species having the carapace with median protogastric and cardiac spines. G.tukitukimea has always been observed associated with the sea urchin Stereocidarisnascaensis. This potential mimicry-based association is uncommon in squat lobsters, which warrants further study.},
}

@article {pmid40809039,
year = {2025},
author = {Strzelecki, P and Nowicki, D},
title = {Tools to study microbial iron homeostasis and oxidative stress: current techniques and methodological gaps.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1628725},
pmid = {40809039},
issn = {2296-889X},
abstract = {Iron is a vital nutrient for both microbial pathogens and their eukaryotic hosts, playing essential roles in stress adaptation, symbiotic interactions, virulence expression, and chronic inflammatory diseases. This review discusses current laboratory methods for iron detection and quantification in microbial cultures, host-pathogen models, and environmental samples. Microbial pathogens have evolved sophisticated specialized transport systems, iron acquisition strategies to overcome its limitation, including siderophore production, uptake of heme and host iron-binding. These iron-scavenging systems are closely linked to the regulation of virulence traits such as adhesion, motility, toxin secretion, and biofilm formation. In ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli), iron limitation enhances biofilm development, which protects bacteria from antibiotics and immune responses and promotes persistent infections. Even worse, pathogens can also manipulate host iron metabolism, exacerbating inflammation and disease progression. Although iron is indispensable for microbial growth, excessive intracellular iron promotes reactive oxygen species generation, causing oxidative damage and ferroptosis-like cell death. Understanding the dual role of iron as both a nutrient and a toxic agent highlights its importance in infection dynamics. We provide a critical overview of existing analytical techniques and emphasize the need for careful selection of methods to improve our understanding of microbial iron metabolism, host-pathogen interactions, and to support the development of new therapeutic and environmental monitoring strategies.},
}

@article {pmid40808256,
year = {2025},
author = {Kumar, A and Gao, JP and Murray, JD},
title = {How Plants Discriminate Mutualistic Symbiosis from Immunity.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.08.005},
pmid = {40808256},
issn = {1752-9867},
}

@article {pmid40808187,
year = {2025},
author = {Asan, G and Arslan, O},
title = {Multifunctional, Biocompatible Hybrid Surface Coatings Combining Antibacterial, Hydrophobic and Fluorescent Applications.},
journal = {Polymers},
volume = {17},
number = {15},
pages = {},
pmid = {40808187},
issn = {2073-4360},
abstract = {The hybrid inorganic-organic material concept plays a bold role in multifunctional materials, combining different features on one platform. Once varying properties coexist without cancelling each other on one matrix, a new type of supermaterial can be formed. This concept showed that silver nanoparticles can be embedded together with inorganic and organic surface coatings and silicon quantum dots for symbiotic antibacterial character and UV-excited visible light fluorescent features. Additionally, fluorosilane material can be coupled with this prepolymeric structure to add the hydrophobic feature, showing water contact angles around 120°, providing self-cleaning features. Optical properties of the components and the final material were investigated by UV-Vis spectroscopy and PL analysis. Atomic investigations and structural variations were detected by XPS, SEM, and EDX atomic mapping methods, correcting the atomic entities inside the coating. FT-IR tracked surface features, and statistical analysis of the quantum dots and nanoparticles was conducted. Multifunctional final materials showed antibacterial properties against E. coli and S. aureus, exhibiting self-cleaning features with high surface contact angles and visible light fluorescence due to the silicon quantum dot incorporation into the sol-gel-produced nanocomposite hybrid structure.},
}

@article {pmid40807545,
year = {2025},
author = {Guzińska, N and Castillo, MDD and Kordialik-Bogacka, E},
title = {Fermentation to Increase the Value of Roasted Coffee Silverskin as a Functional Food Ingredient.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40807545},
issn = {2304-8158},
support = {PID2019-11510RB-I00/AEI/10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {Roasted coffee silverskin (RCSS) is a by-product of coffee production characterized by its content of phenolic compounds, both free and bound to macromolecules. In this study, RCSS was fermented to release these compounds and consequently increase its value as a functional food ingredient. Fermentation was carried out using yeast, acetic acid bacteria, and lactic acid bacteria, either as single strains or as a designed microbial consortium. The latter included Saccharomycodes ludwigii, Gluconobacter oxydans, and Levilactobacillus brevis, mimicking a symbiotic culture of bacteria and yeast commonly used in kombucha fermentation (SCOBY). This symbiotic microbial culture consortium demonstrated notable efficacy, significantly enhancing the total phenolic content in RCSS, with values reaching 14.15 mg GAE/g as determined by the Folin-Ciocalteu assay and 7.12 mg GAE/g according to the Fast Blue BB method. Antioxidant capacity improved by approximately 28% (ABTS) and 20% (DPPH). Moreover, the fermented RCSS supported the viability of probiotic strains (Saccharomyces boulardii SB01 and Levilactobacillus brevis ŁOCK 1152) under simulated intestinal conditions. These results suggest that RCSS, particularly after fermentation with a full symbiotic microbial culture consortium, has strong potential as a clean label, zero-waste functional food ingredient.},
}

@article {pmid40807366,
year = {2025},
author = {Ziemlewska, A and Zagórska-Dziok, M and Nowak, A and Muzykiewicz-Szymańska, A and Wójciak, M and Sowa, I and Szczepanek, D and Nizioł-Łukaszewska, Z},
title = {Enhancing the Cosmetic Potential of Aloe Vera Gel by Kombucha-Mediated Fermentation: Phytochemical Analysis and Evaluation of Antioxidant, Anti-Aging and Moisturizing Properties.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {15},
pages = {},
pmid = {40807366},
issn = {1420-3049},
abstract = {Aloe vera gel is a valuable raw material used in the cosmetic industry for its skin care properties. The present study analyzed the effects of the fermentation of aloe vera gel with a tea fungus kombucha, which is a symbiotic consortium of bacteria and yeast, carried out for 10 and 20 days (samples F10 and F20, respectively). The resulting ferments and unfermented gel were subjected to chromatographic analysis to determine the content of biologically active compounds. The permeability and accumulation of these compounds in pig skin were evaluated. In addition, the methods of DPPH, ABTS and the determination of intracellular free radical levels in keratinocytes (HaCaT) and fibroblasts (HDF) cell lines were used to determine antioxidant potential. The results showed a higher content of phenolic acids and flavonoids and better antioxidant properties of the ferments, especially after 20 days of fermentation. Cytotoxicity tests against HaCaT and HDF cells confirmed the absence of toxic effects; moreover, samples at the concentrations tested (mainly 10 and 25 mg/mL) showed cytoprotective effects. The analysis of enzymatic activity (collagenase, elastase and hyaluronidase) by the ELISA technique showed higher levels of inhibition for F10 and F20. The kombucha ferments also exhibited better moisturizing properties and lower levels of transepidermal water loss (TEWL), confirming their cosmetic potential.},
}

@article {pmid40806669,
year = {2025},
author = {Colby, L and Preskitt, C and Ho, JS and Balsara, K and Wu, D},
title = {Brain Metastasis: A Literary Review of the Possible Relationship Between Hypoxia and Angiogenesis in the Growth of Metastatic Brain Tumors.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
pmid = {40806669},
issn = {1422-0067},
abstract = {Brain metastases are a common and deadly complication of many primary tumors. The progression of these tumors is poorly understood, and treatment options are limited. Two important components of tumor growth are hypoxia and angiogenesis. We conducted a review to look at the possibility of a symbiotic relationship between two transcription factors, Hypoxia-Inducible Factor 1α (HIF1α) and Vascular Endothelial Growth Factor (VEGF), and the role they play in metastasis to the brain. We delve further into this possible relationship by examining commonly used chemotherapeutic agents and their targets. Through an extensive literature review, we identified articles that provided evidence of a strong connection between these transcription factors and the growth of brain metastases, many highlighting a symbiotic relationship. Further supporting this, combinations of chemotherapeutic drugs with varying targets have increased the efficacy of treatment. Angiogenesis and hypoxia have long been known to play a large role in the invasion, growth, and poor outcomes of tumors. However, it is not fully understood how these factors influence one another during metastases. While prior studies have investigated the effects separately, we specifically delve into the synergistic and compounding effects that may exist between them. Our findings underscore the need for greater research allocation to investigate the possible symbiotic relationship between angiogenesis and hypoxia in brain metastasis.},
}

@article {pmid40806290,
year = {2025},
author = {Sonkodi, B},
title = {It Is Time to Consider the Lost Battle of Microdamaged Piezo2 in the Context of E. coli and Early-Onset Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
pmid = {40806290},
issn = {1422-0067},
abstract = {The recent identification of early-onset mutational signatures with geographic variations by Diaz-Gay et al. is a significant finding, since early-onset colorectal cancer has emerged as an alarming public health challenge in the past two decades, and the pathomechanism remains unclear. Environmental risk factors, including lifestyle and diet, are highly suspected. The identification of colibactin from Escherichia coli as a potential pathogenic source is a major step forward in addressing this public health challenge. Therefore, the following opinion manuscript aims to outline the likely onset of the pathomechanism and the critical role of acquired Piezo2 channelopathy in early-onset colorectal cancer, which skews proton availability and proton motive force regulation toward E. coli within the microbiota-host symbiotic relationship. In addition, the colibactin produced by the pks island of E. coli induces host DNA damage, which likely interacts at the level of Wnt signaling with Piezo2 channelopathy-induced pathological remodeling. This transcriptional dysregulation eventually leads to tumorigenesis of colorectal cancer. Mechanotransduction converts external physical cues to inner chemical and biological ones. Correspondingly, the proposed quantum mechanical free-energy-stimulated ultrafast proton-coupled tunneling, initiated by Piezo2, seems to be the principal and essential underlying novel oscillatory signaling that could be lost in colorectal cancer onset. Hence, Piezo2 channelopathy not only contributes to cancer initiation and impaired circadian regulation, including the proposed hippocampal ultradian clock, but also to proliferation and metastasis.},
}

@article {pmid40806090,
year = {2025},
author = {Shremo Msdi, A and Wang, EM and Garey, KW},
title = {Prebiotics Improve Blood Pressure Control by Modulating Gut Microbiome Composition and Function: A Systematic Review and Meta-Analysis.},
journal = {Nutrients},
volume = {17},
number = {15},
pages = {},
pmid = {40806090},
issn = {2072-6643},
abstract = {Background: Ingestion of dietary fibers (DFs) is a safe and accessible intervention associated with reductions in blood pressure (BP) and cardiovascular mortality. However, the mechanisms underlying the antihypertensive effects of DFs remain poorly defined. This systematic review and meta-analysis evaluates how DFs influence BP regulation by modulating gut microbial composition and enhancing short-chain fatty acid (SCFA) production. Methods: MEDLINE and EMBASE were systematically searched for interventional studies published between January 2014 and December 2024. Eligible studies assessed the effects of DFs or other prebiotics on systolic BP (SBP) and diastolic BP (DBP) in addition to changes in gut microbial or SCFA composition. Results: Of the 3010 records screened, nineteen studies met the inclusion criteria (seven human, twelve animal). A random-effects meta-analysis was conducted on six human trials reporting post-intervention BP values. Prebiotics were the primary intervention. In hypertensive cohorts, prebiotics significantly reduced SBP (-8.5 mmHg; 95% CI: -13.9, -3.1) and DBP (-5.2 mmHg; 95% CI: -8.5, -2.0). A pooled analysis of hypertensive and non-hypertensive patients showed non-significant reductions in SBP (-4.5 mmHg; 95% CI: -9.3, 0.3) and DBP (-2.5 mmHg; 95% CI: -5.4, 0.4). Animal studies consistently showed BP-lowering effects across diverse etiologies. Prebiotic interventions restored bacterial genera known to metabolize DFs to SCFAs (e.g., Bifidobacteria, Akkermansia, and Coprococcus) and increased SCFA levels. Mechanistically, SCFAs act along gut-organ axes to modulate immune, vascular, and neurohormonal pathways involved in BP regulation. Conclusions: Prebiotic supplementation is a promising strategy to reestablish BP homeostasis in hypertensive patients. Benefits are likely mediated through modulation of the gut microbiota and enhanced SCFA production.},
}

@article {pmid40806005,
year = {2025},
author = {Thompson, RS and Hopkins, S and Kelley, T and Wilson, CG and Pecaut, MJ and Fleshner, M},
title = {A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Attenuates Hypergravity-Induced Disruptions to the Microbiome in Female Mice.},
journal = {Nutrients},
volume = {17},
number = {15},
pages = {},
pmid = {40806005},
issn = {2072-6643},
support = {80NSSC19K1038, 16-ROSBFP_PI-0079/NASA/NASA/United States ; },
abstract = {BACKGROUND/OBJECTIVES: Environmental stressors, including spaceflight and altered gravity, can negatively affect the symbiotic relationship between the gut microbiome and host health. Dietary prebiotics, which alter components of the gut microbiome, show promise as an effective way to mitigate the negative impacts of stressor exposure. It remains unknown, however, if the stress-protective effects of consuming dietary prebiotics will extend to chronic altered-gravity exposure.

METHODS: Forty female C57BL/6 mice consumed either a control diet or a prebiotic diet containing galactooligosaccharides (GOS) and polydextrose (PDX) for 4 weeks, after which half of the mice were exposed to 3 times the gravitational force of Earth (3g) for an additional 4 weeks. Fecal microbiome samples were collected weekly for 8 weeks, sequenced, and analyzed using 16S rRNA gene sequencing. Terminal physiological endpoints, including immune and red blood cell characteristics, were collected at the end of the study.

RESULTS: The results demonstrate that dietary prebiotic consumption altered the gut microbial community structure through changes to β-diversity and multiple genera across time. In addition, consuming dietary prebiotics reduced the neutrophil-to-lymphocyte ratio (NLR) and increased red blood cell distribution width (RDW-CV). Importantly, the prebiotic diet prevented the impacts of altered-gravity on β-diversity and the bloom of problematic genera, such as Clostridium_sensu_stricto_1 and Turicibacter. Furthermore, several prebiotic diet-induced genera-level changes were significantly associated with several host physiological changes induced by 3g exposure.

CONCLUSIONS: These data demonstrate that the stress-protective potential of consuming dietary prebiotics extends to environmental stressors such as altered gravity, and, potentially, spaceflight.},
}

@article {pmid40805780,
year = {2025},
author = {Xue, DY and Chen, WF and Yang, GP and Li, YG and Zhang, JJ},
title = {Screening and Application of Highly Efficient Rhizobia for Leguminous Green Manure Astragalus sinicus in Lyophilized Inoculants and Seed Coating.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805780},
issn = {2223-7747},
support = {2021YFD1700200//National Key Research and Development Program of China/ ; 2024-2027//Professor Workstation of Anhui WeiHua Biotechnology Co., Ltd./ ; },
abstract = {Astragalus sinicus, a key leguminous green manure widely cultivated in Southern China's rice-based cropping systems, plays a pivotal role in sustainable agriculture by enhancing soil organic matter sequestration, improving rice yield, and elevating grain quality. The symbiotic nitrogen-fixing association between A. sinicus and its matching rhizobia is fundamental to its agronomic value; however, suboptimal inoculant efficiency and field application methodologies constrain its full potential. To address these limitations, we conducted a multi-phase study involving (1) rhizobial strain screening under controlled greenhouse conditions, (2) an optimized lyophilization protocol evaluating cryoprotectant (trehalose, skimmed milk powder and others), and (3) seed pelleting trails with rhizobial viability and nodulation assessments over different storage periods. Our results demonstrate that Mesorhizobium huakuii CCBAU 33470 exhibits a superior nitrogen-fixing efficacy, significantly enhancing key traits in A. sinicus, including leaf chlorophyll content, tiller number, and aboveground biomass. Lyophilized inoculants prepared with cryoprotectants (20% trehalose or 20% skimmed milk powder) maintained >90% bacterial viability for 60 days and markedly improved nodulation capacity relative to unprotected formulations. The optimized seed pellets sustained high rhizobial loads (5.5 × 10[3] cells/seed) with an undiminished viability after 15 days of storage and nodulation ability after 40 days of storage. This integrated approach of rhizobial selection, inoculant formulation, and seed coating overcomes cultivation bottlenecks, boosting symbiotic nitrogen fixation for A. sinicus cultivation.},
}

@article {pmid40804293,
year = {2025},
author = {Zhang, M and Zhai, R and Niu, G and Chen, J and Tan, B and Wu, D and Meng, G and Wei, M},
title = {Telomere-to-telomere genome assembly uncovers Wolbachia-driven recurrent male bottleneck effect and selection in a sawfly.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1211},
pmid = {40804293},
issn = {2399-3642},
support = {20232BAB215017//Natural Science Foundation of Jiangxi Province (Jiangxi Province Natural Science Foundation)/ ; },
abstract = {Wolbachia, a widespread endosymbiotic bacterium, profoundly impacts insect hosts by distorting reproduction and population dynamics. Despite extensive laboratory research, its long-term effects on host evolution in nature remain poorly understood, especially the genomic consequences linked to disruptions in sex determination and reproductive processes. We present the first telomere-to-telomere (T2T) genome assembly of the sawfly Analcellicampa danfengensis and the complete genome of its symbiotic Wolbachia. Comparative population genomics across six Analcellicampa species revealed that Wolbachia-infected populations show starkly different demographic signals. While uninfected populations show similar demographic signals for both sexes, infected populations exhibit a lower apparent effective population size (Ne) in males, which may reflect a recurrent male bottleneck effect driven by Wolbachia-induced male scarcity. Genomic scans identified positively selected genes associated with reproductive functions, sensory perception, neural development, and longevity, suggesting that Wolbachia likely manipulates critical host pathways to promote its transmission. These findings provide direct genomic insights into Wolbachia as an evolutionary force, highlighting specific host genes and regions under selection resulting from these altered evolutionary dynamics. This work provides deeper insights into host-endosymbiont coevolution and has important implications for evolutionary theory and pest management strategies.},
}

@article {pmid40804160,
year = {2025},
author = {Majerová, E and Steinle, C and Drury, C},
title = {BAK knockdown delays bleaching and alleviates oxidative DNA damage in a reef-building coral.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1216},
pmid = {40804160},
issn = {2399-3642},
abstract = {As climate change threatens marine ecosystems, efforts to restore coral reefs using resilient corals are increasing. This conservation approach remains limited by our understanding of cellular mechanisms of resilience and trade-offs. Here, we demonstrate that downregulation of pa-BAK stabilizes the coral-algal endosymbiosis and slows bleaching during acute heat stress in Pocillopora acuta through coordinated expression of gene clusters. The improvement in thermal tolerance was closely related to the downregulation efficiency in individual corals. Oxidative DNA damage, a hallmark of thermal stress response, was prevented in corals with stabilized symbiosis, likely through a decrease in mitochondrial ROS release. We hypothesize that this manipulation causes a cascading molecular response, which may impact other traits such as oxidative mitochondrial damage, proving detrimental over the longer term. Developing our understanding of heat-stress defense mechanisms that promote stability in the coral-algal symbiosis is fundamental for effective modern coral reef restoration practices based on improving ecosystem resilience.},
}

@article {pmid40803427,
year = {2025},
author = {Li, XG and Zhao, X and Zheng, J and Xian, C and Liu, Z and Chen, H},
title = {The potential and underlying mechanisms of punicalagin in mitigating enterotoxigenic Escherichia coli-induced diarrhea.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.002},
pmid = {40803427},
issn = {1541-6100},
abstract = {Punicalagin is a well-studied polyphenolic compound with a wide array of pharmacological effects. This review summarizes its potential mechanisms of action along with the pathogenic implications and molecular pathways associated with Enterotoxigenic Escherichia coli (ETEC). One primary mechanism by which punicalagin exerts its effects is through antibacterial activity that suppresses ETEC proliferation and mitigates intestinal infections. It further promotes the growth of beneficial microbiota, including bifidobacteria and lactic acid-producing bacteria, thereby improving the symbiotic balance of the gut microbiome and bolstering resistance to ETEC colonization. In addition, punicalagin has been shown to inhibit the activity of ETEC, thereby enhancing intestinal mucosal integrity and fortifying the intestinal barrier. This action reduces the permeability of harmful substances, ultimately protecting gut health. Moreover, punicalagin has the potential to chelate metals, leading to various biological activities and applications. This positions it as a candidate for further exploration as a novel therapeutic agent or a raw material in health products. In conclusion, this study offers preliminary insights into the potential application of punicalagin in managing ETEC-induced diarrhea, highlighting its pharmacological efficacy. However, it should be emphasized that current clinical evidence supporting its effectiveness for this specific use remains limited and preliminary, requiring validation through rigorous clinical trials.},
}

@article {pmid40802030,
year = {2025},
author = {Gaye, M and Zinai, AZR and Armstrong, N and Herbette, G and Monnier, V and Bassene, H and Diatta, G and Sambou, M and Sokhna, C and Raoult, D and Fenollar, F and Mediannikov, O},
title = {Antibacterial activity of fungus comb extracts from Senegalese fungus-farming termites.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {117},
pmid = {40802030},
issn = {2191-0855},
support = {10-IAHU-03//Fondation Méditerranée Infection/ ; },
abstract = {Fungus-farming termites (Macrotermitinae), predominantly found in Africa, are eusocial insects with significant ecological roles. Historically, they have been valued in traditional medicine, human diets, and livestock feed. These termites share a long-standing symbiotic relationship with Termitomyces fungi, which has evolved over millions of years and is critical to their survival and ecological impact. This mutualism promotes a unique monoculture of Termitomyces in the fungus comb while suppressing fungal and bacterial antagonists, likely due to the comb's structural or chemical properties, sparking interest among researchers. In this study, we conducted an extensive examination of 11 fungus combs associated with five termite species collected in Senegal. Our analysis revealed significant antibacterial properties in the crude extracts of the combs, notably against multidrug-resistant strains. Chemical analyses led to the identification of dicrotalic acid (Meglutol) in the active fractions of two combs from agricultural areas. This compound, likely of plant origin, suggests a link between termite feeding habits and the antimicrobial potential of the combs. Although the exact bioactive compounds responsible for the antimicrobial activity have not yet been fully identified, the presence of various metabolites may explain the maintenance of Termitomyces monocultures and the suppression of pathogens. This also illustrates the complex ecological relationship between Termitomyces and termites, which may work together to produce natural bioactive compounds that suppress pathogens.},
}

@article {pmid40801964,
year = {2025},
author = {Neves, AS and van Galen, LG and Vohník, M and Peter, M and Martino, E and Crowther, TW and Delavaux, CS},
title = {Ericoid mycorrhizal growth response is influenced by host plant phylogeny.},
journal = {Mycorrhiza},
volume = {35},
number = {4},
pages = {51},
pmid = {40801964},
issn = {1432-1890},
abstract = {Ericoid mycorrhizal (ErM) fungi (ErMF) are crucial for the establishment of thousands of ericaceous species in heathlands and wetlands by increasing their tolerance to harsh conditions and improving nutrient uptake. However, ErM research has largely focused on a limited number of host species and four ErMF species (especially Hyaloscypha hepaticicola and Oidiodendron maius, to a lesser extent H. bicolor/H. finlandica and H. variabilis). Therefore, the degree to which other ericaceous plants and ErMF form functional associations, and corresponding benefits for plant growth, are not well understood. As such, we lack a clear understanding of how changes in fungal partners may influence plant fitness. To address this gap, we conducted a greenhouse experiment with nine ericaceous plant species and eight ErMF isolates to expand baseline knowledge regarding the effects of the ErM symbiosis on host plant growth. By analyzing ErM root colonization and host plant growth response, we observed that the mycorrhizal growth response (MGR) was variable and depended on plant and fungal identity. Moreover, overall inoculation effects on plant growth were independent from colonization levels. Finally, we found evidence that MGR was influenced by plant phylogeny. These results expand our basic understanding of the ErM symbiosis and provide valuable information for future restoration and conservation efforts.},
}

@article {pmid40801536,
year = {2025},
author = {Yang, JL and Zhu, H and Sadh, P and Aumiller, K and Guvener, ZT and Ludington, WB},
title = {Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0070725},
doi = {10.1128/aem.00707-25},
pmid = {40801536},
issn = {1098-5336},
abstract = {The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In Drosophila melanogaster, Lactiplantibacillus plantarum has been shown to protect against enteric pathogens. However, the strains of L. plantarum studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild fly-derived strain of L. plantarum that stably colonizes the fly gut in conjunction with a common enteric pathogen, Serratia marcescens. Flies stably associated with the L. plantarum strain were more resilient to oral Serratia marcescens infection as seen by longer life span and lower S. marcescens load in the gut. Through in vitro experiments, we found that L. plantarum inhibits S. marcescens growth due to acidification. We used gut imaging with pH indicator dyes to show that L. plantarum reduces the gut pH to levels that restrict S. marcescens growth in vivo. In flies colonized with L. plantarum prior to S. marcescens infection, L. plantarum and S. marcescens are spatially segregated in the gut, and S. marcescens is less abundant where L. plantarum heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.IMPORTANCEThe gut microbiomes of animals harbor an incredible diversity of bacteria, some of which can protect their hosts from invasion by enteric pathogens. Understanding the mechanisms behind this protection is essential for developing precision probiotics to support human and animal health. This study used Drosophila melanogaster as a model system due to its low cost, experimentally tractable gut microbiome, and overlap with bacterial species found in mammals. While resident microbes can protect hosts through various means, including toxin production and immune stimulation, we found that acidification was sufficient to limit a pathogen that normally reduces life span. Remarkably, specific gut regions are acidified either by host mechanisms or by the resident bacterium, Lactiplantibacillus plantarum, highlighting joint microbial and host control of gut chemistry. These findings are broadly relevant to microbiology and gut health, providing insight into how hosts may manage pathogens through their symbiotic microbiota.},
}

@article {pmid40801187,
year = {2025},
author = {Wang, L and Mai, C and He, S and Niu, B and Jia, G and Yang, T and Xu, Y and Ren, M and Zhao, X and Liu, X and Kong, Z},
title = {Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70007},
pmid = {40801187},
issn = {1744-7909},
support = {2021xG003//Scientific research fund for talents of Shanxi Agricultural University/ ; 2022xG0014//Scientific research fund for talents of Shanxi Agricultural University/ ; 202204051002013//Science and Technology Innovation Talent Team of Shanxi Province/ ; 202204051001020//Science and Technology Innovation Talent Team of Shanxi Province/ ; 32241045//National Natural Science Foundation of China/ ; 32241046//National Natural Science Foundation of China/ ; 20210302123365//Fundamental Research Program of Shanxi Province/ ; 202103021224146//Fundamental Research Program of Shanxi Province/ ; },
abstract = {Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.},
}

@article {pmid40797046,
year = {2025},
author = {Wei, L and Chen, S and Qin, Z and Pan, N and Lan, M and Zhang, T and He, R and Liang, H and Deng, W and Mo, C and Yu, K},
title = {Responses of the Coral Symbiont Cladocopium goreaui to Extreme Temperature Stress in Relatively High-Latitude Reefs, South China Sea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {88},
pmid = {40797046},
issn = {1432-184X},
abstract = {Global climate change has led to frequent extreme temperature events in oceans. Corals are susceptible to extreme high-temperature stress in summer and extreme low-temperature stress in winter in the relatively high-latitude reef areas of the South China Sea (SCS). The most abundant symbiotic coral Symbiodiniaceae in the higher-latitude reefs of the SCS is Cladocopium goreaui, predominantly associating with dominant coral hosts such as Acropora and Porites. However, to date, relatively few studies have focused on the response and mechanism of C. goreaui to the extreme high- and low-temperature stress. In this study, the responses and regulatory mechanisms of the dominant C. goreaui to extreme high- and low-temperature stress were investigated based on physiological indexes, transmission electron microscopy (TEM), and transcriptome analysis. The results showed that (1) under 34 °C heat stress, the disintegration of thylakoids triggered photosynthetic collapse in C. goreaui; survival is enabled through metabolic reprogramming that upregulates five protective pathways and redirects energy via pentose/glucuronate shunting to sustain ATP homeostasis, revealing a trade-off between damage containment and precision energy governance under thermal extremes. (2) Low temperature exposure induced suppression of maximum quantum yield (Fv/Fm), compounded by glutathione pathway inhibition, crippling ROS scavenging. The transcriptome results revealed that C. goreaui prioritizes gene fidelity maintenance under low temperature stress. These findings reveal that energy allocation trade-offs constitute the core strategy of C. goreaui temperature response: prioritizing energy maintenance under high-temperature stress, while safeguarding genetic fidelity at the expense of antioxidant defense under low-temperature stress.},
}

@article {pmid40796904,
year = {2025},
author = {Nowak, KH and Hartop, E and Prus-Frankowska, M and Buczek, M and Kolasa, MR and Roslin, T and Ovaskainen, O and Łukasik, P},
title = {What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {186},
pmid = {40796904},
issn = {2049-2618},
support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; 856506//Horizon 2020/ ; 336212//Research Council of Finland/ ; PPN/PPO/2018/1/00015//Narodowa Agencja Wymiany Akademickiej/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in 'dark taxa'-hyperdiverse yet understudied clades.

RESULTS: Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities. It combines four methodological innovations: (1) To establish a host taxonomic framework, we sequenced amplicons of the host marker gene (COI) and reconstructed barcodes alongside microbiota characterisation using 16S-V4 rRNA bacterial gene amplicons. (2) To assess microbiota abundance, we incorporated spike-in-based quantification. (3) To improve the phylogenetic resolution for the dominant endosymbiont, Wolbachia, we analysed bycatch data from the COI amplicon sequencing. (4) To investigate the primary drivers of host-microbe associations in massive multi-dimensional datasets, we performed Hierarchical Modelling of Species Communities (HMSC). Applying this approach to 1842 wild-caught scuttle flies (Diptera: Phoridae) from northern Sweden, we organised them into 480 genotypes and 186 species and gained unprecedented insights into their microbiota. We found orders-of-magnitude differences in bacterial abundance and massive within-population variation in microbiota composition. Patterns and drivers differed among microbial functional categories: the distribution and abundance of facultative endosymbionts (Wolbachia, Rickettsia, Spiroplasma) were shaped by host species, genotype, and sex. In contrast, many other bacterial taxa were broadly distributed across species and sites.

CONCLUSIONS: This study highlights facultative endosymbionts as key players in insect microbiota and reveals striking variations in distributional patterns of microbial clades. It also demonstrates the power of integrative sequencing approaches in uncovering the ecological complexity and significance of symbiotic microorganisms in multi-species natural communities. Video Abstract.},
}

@article {pmid40796359,
year = {2025},
author = {Szuba, A and Żukowska, WB and Mucha, J and Strugała, A and Marczak, Ł},
title = {Low Temperature Enhances N-Metabolism in Paxillus involutus Mycelia In Vitro: Evidence From an Untargeted Metabolomic Study.},
journal = {Environmental microbiology},
volume = {27},
number = {8},
pages = {e70162},
pmid = {40796359},
issn = {1462-2920},
support = {DEC-2011/03/D/NZ9/05500//National Science Centre (Poland)/ ; 2022/03/ZB/FBW/00006//Institute of Dendrology/ ; },
abstract = {This metabolomic study investigates, using GC MS/MS analysis, the molecular response of Paxillus involutus mycelia to prolonged low temperature (4°C) exposure. Alongside reduced growth, decreased overall nutrient levels, and increased oxidative stress indicators, analyses revealed a significant increase in nitrogen (N) concentration and enhanced N metabolism, particularly via the GS-GOGAT pathway, which was associated with elevated concentrations of numerous amino acids. In contrast, carbon (C) metabolism was not intensified but largely reprogrammed, with varying changes in carbohydrate abundance but higher levels of several stress-related metabolites, such as trehalose and inositol family members, indicating activation of tolerance mechanisms, all with unchanged C (%). These changes suggest enhanced NH4 [+] uptake and a redirection of glycolysis-derived C skeletons towards N-compound biosynthesis. The lack of massive upregulation of typical anti-stress compounds under low temperature exposure indicates either acclimatisation or mild stress. Mycelial restructuring, including increased dry mass (%) and accumulation of chitin precursors, implies cell wall remodelling and cold acclimatisation, supported by changes in membrane components. All these findings suggest that low temperatures may enhance N metabolism in ECM fungi even without additional carbon supply, potentially affecting symbiotic balance under climate change. Further studies are needed to validate these mechanisms and ecological implications.},
}

@article {pmid40796349,
year = {2025},
author = {Huang, WC and Probst, M and Hua, ZS and Szánthó, LL and Szöllősi, GJ and Ettema, TJG and Rinke, C and Williams, TA and Spang, A},
title = {Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf201},
pmid = {40796349},
issn = {1537-1719},
abstract = {The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focused on characterising the diversity of Asgard archaea in an effort to identify the closest extant relatives of eukaryotes. However, resolving archaeal phylogeny is challenging, and the positions of two recently-described lineages - Njordarchaeales and Panguiarchaeales - are uncertain, in ways that directly bear on hypotheses of early evolution. In initial phylogenetic analyses, these lineages branched either with Asgards or with the distantly-related Korarchaeota, and it has been suggested that their genomes may be affected by metagenomic contamination. Resolving this debate is important because these clades include genome-reduced lineages that may help inform our understanding of the evolution of symbiosis within Asgard archaea. Here, we performed phylogenetic analyses revealing that the Njordarchaeales and Pangiuarchaeales constitute the new class Njordarchaeia within Asgard archaea. We found no evidence of metagenomic contamination affecting phylogenetic analyses. Njordarchaeia exhibit hallmarks of adaptations to (hyper-)thermophilic lifestyles, including biased sequence compositions that can induce phylogenetic artifacts unless adequately modelled. Panguiarchaeum is metabolically distinct from its relatives, with reduced metabolic potential and various auxotrophies. Phylogenetic reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood-Ljungdahl pathway. The subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle potentially based on H2-syntrophy. Thus, Panguiarchaeum may contain the first obligate symbionts within Asgard archaea.},
}

@article {pmid40795952,
year = {2025},
author = {Pluer, BD and Travis, J},
title = {The Digestive Microbiome Diversity of the Least Killifish, Heterandria formosa, and Its Implications for Host Adaptability to Varying Trophic Levels.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70164},
pmid = {40795952},
issn = {1758-2229},
support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; },
abstract = {Symbiotic microbes, in associations with aquatic hosts, aid in the acquisition of nutrients, breakdown xenobiotics, and contribute to immune system function. If associations with microbial communities facilitate host adaptation to different ecosystems, understanding the important ecological factors that act as drivers of differences among conspecific populations' microbiomes can help conservation efforts to promote beneficial interactions between fish and their microbiome for freshwater fish species facing rapid environmental changes. Here we describe the microbial communities in the gut of a freshwater fish, Heterandria formosa, in spring habitats using 16S rRNA sequencing. We quantified microbiota composition and diversity among springs ranging from oligotrophic to near eutrophic to determine the extent to which the microbiota are associated with different environmental conditions. We found higher microbial richness at sites with lower nutrient load stress. At more eutrophic sites, we detected the potential for increased metabolic capacity for pollutant degradation in the associated microbiota. We noted greater phylogenetic similarity between more environmentally similar sites, supporting previous evidence that the microbiota of freshwater fish is influenced by site water chemistry. Our findings bring to light microbial taxa and pathways that might play critical roles in the bioremediation of stressful environmental conditions.},
}

@article {pmid40795928,
year = {2025},
author = {Moore, LD and Ballinger, MJ},
title = {Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf174},
pmid = {40795928},
issn = {1751-7370},
abstract = {Bacteria commonly deploy toxic proteins that act with specificity on target molecules to support invasion and improve survival in competitive environments. Many toxin-encoding bacteria have evolved into host-associated defensive partnerships, in which they use toxins to improve host survival during infection. The stability of these relationships requires that symbiont toxins target diverse parasites while minimizing damage to the host. We investigate the specificity of a group of ribosome-targeting toxins (RIPs) encoded by heritable Spiroplasma symbionts that contribute to defense against parasite infection in fruit fly hosts. Using E. coli to express five divergent copies of this toxin, we show that distantly related members of the family all retain the ability to inactivate ribosomes by adenine cleavage at the α-sarcin/ricin loop, the enzymatic hallmark of RIPs. However, when exposed to live insect and fungal cells, ribosome inactivation varies across the five toxins, suggesting cellular recognition or localization play a role in target specificity. To identify toxin domains required for specificity, we removed rapidly evolving "accessory" domains from two toxins. Both truncated toxins exhibit significantly increased activity on purified ribosomes in vitro, suggesting one role of accessory domains is to reduce toxicity, which may help protect hosts from collateral damage. One of the truncated toxins also showed significantly reduced inactivation of cellular ribosomes in vivo, indicating a role for accessory domains in cell specificity. Together, these data reveal a mechanism for symbiont discrimination between hosts and parasites and highlight how dynamic toxin evolution can contribute to stability and novelty in defensive symbiosis.},
}

@article {pmid40795033,
year = {2025},
author = {Friar, L and Keepers, K and Garber, AI and McCutcheon, JP and Wing, B and Kane, NC},
title = {Selection maintains photosynthesis in a symbiotic cyanobacterium despite redundancy with its fern host.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf181},
pmid = {40795033},
issn = {1537-1719},
abstract = {Vertically inherited symbionts experience different physical, chemical, and population genetic environments than free-living organisms. As a result, they can experience long-term reductions in effective population size (Ne) and weaker purifying selection on genes that are less important in the host-associated environment. Over time, these forces result in gene loss. A comparative genomic approach using independently evolved symbiotic bacteria and free-living relatives can reveal which genes are important in the symbiotic state. We apply this approach to understand why some diazotrophic cyanobacteria evolving as vertically inherited symbionts of photosynthetic eukaryotic hosts have lost their ancestral capacity for photosynthesis while others have retained that capacity. We look specifically at Trichormus azollae, a diazotrophic cyanobacterium that remains photosynthetic after 50-90Ma as a vertically inherited symbiont of Azolla ferns. We show that gene loss is ongoing, with different genes lost across the eight T. azollae strains examined. We apply molecular evolutionary models to genomes of T. azollae and free-living relatives, finding genome-wide signatures of drift in T. azollae consistent with long-term reductions in Ne. Ribosomal proteins and proteins from the energy-capturing photosynthetic light reactions are under stronger purifying selection than genes from other pathways, including nitrogen fixation and photosynthetic carbon fixation. Strong purifying selection is expected for the ribosome given its extraordinary levels of conservation, even in ancient vertically inherited symbionts. That genes in the light reactions are under strong purifying selection and never lost in any strain suggests that energy capture, likely required for energy-intensive nitrogen fixation, remains important to this symbiont.},
}

@article {pmid40794807,
year = {2025},
author = {Méndez, SG and Mertens, S and Temmerman, A and Van den Eynde, H and Vermeersch, M and Vlaminck, L and Berteloot, O and Van Dingenen, J and Clarysse, A and De Keyser, A and Beullens, S and de Baenst, I and Roy, N and De Paepe, Q and Michiels, J and Roldan-Ruiz, I and Pannecoucque, J and Willems, A and Maere, S and Goormachtig, S},
title = {Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf152},
pmid = {40794807},
issn = {1751-7370},
abstract = {Soybean serves as a crucial source of plant-based protein for human diets. Recently, there is a growing incentive to extend the range of this crop to more northern latitudes, in order to enable profitable soybean production in Europe. To reach economic yields, soybean requires inoculation with symbiotic, diazotrophic rhizobial bacteria. However, the performance of commercial inocula is often variable under local conditions. Here, we present the citizen science project "Soy in 1,000 Gardens", a large-scale trapping experiment for isolating local soybean-nodulating rhizobia in Flanders, Belgium. We identified two locally isolated Bradyrhizobium strains performing at least as well as commercial strain B. diazoefficiens G49 in local field trials. Additionally, we found that nutrient content, microbial alpha diversity, and the presence of arbuscular mycorrhizal fungi in the soil were correlated with nodulation. Finally, we report a correlation between low bacterial alpha diversity and red nodule interior, and identified Tardiphaga as a dominant colonizer of red nodules.},
}

@article {pmid40794795,
year = {2025},
author = {Garfias-Gallegos, D and Pardo-De la Hoz, CJ and Haughland, DL and Magain, N and Aguero, B and Miadlikowska, J and Lutzoni, F},
title = {Central metabolism and development are rewired in lichenized cyanobacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf166},
pmid = {40794795},
issn = {1751-7370},
abstract = {Nostoc cyanobacteria are among the few organisms capable of fixing both carbon and nitrogen. These metabolic features are essential for the cyanolichen symbiosis, where Nostoc supplies both carbon (as glucose) and nitrogen (as ammonium) to a cyanolichen-forming fungal partner. This nutrient flow was established by seminal biochemical studies published in the 20th century. Since then, cyanolichen metabolism has received little attention, and the molecular mechanisms that underlie the physiology of lichenized Nostoc remain mostly unknown. Here, we aimed to elucidate the genomic and transcriptional changes that enable Nostoc's metabolic role in cyanolichens. We used comparative genomics across 243 genomes of Nostoc s. lat. Coupled with metatranscriptomic experiments using Peltigera cyanolichens. We found that genes for photoautotrophic carbon fixation are upregulated in lichenized Nostoc. This likely results in a higher rate of carbon fixation that allows Nostoc to provide carbon to the fungal partner while meeting its own metabolic needs. We also found that the transfer of ammonium from Nostoc to the lichen-forming fungus is facilitated by two molecular mechanisms: (i) transcriptional downregulation of glutamine synthetase, the key enzyme responsible for ammonium assimilation in Nostoc; and (ii) frequent losses of a putative high-affinity ammonium permease, which likely reduces Nostoc's capacity to recapture leaked ammonium. Finally, we found that the development of motile hormogonia is downregulated in lichenized Nostoc, which resembles the repression of motility in Nostoc symbionts after they colonize symbiotic cavities of their plant hosts. Our results pave the way for a revival of cyanolichen ecophysiology in the omics era.},
}

@article {pmid40794723,
year = {2025},
author = {Muffett, KM and Labonté, JM and Miglietta, MP},
title = {Florida Keys Cassiopea host benthos-like external microbiomes and a gut dominated by Vibrio, Endozoicomonas and Mycoplasma.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330180},
pmid = {40794723},
issn = {1932-6203},
mesh = {Animals ; Florida ; RNA, Ribosomal, 16S/genetics ; *Mycoplasma/genetics/isolation & purification/classification ; *Vibrio/genetics/isolation & purification ; *Scyphozoa/microbiology ; *Microbiota ; Phylogeny ; *Gastrointestinal Microbiome ; Symbiosis ; },
abstract = {Interactions with microbial communities fundamentally shape metazoans' physiology, development, and health across marine ecosystems. This is especially true in zooxanthellate (symbiotic algae-containing) cnidarians. In photosymbiotic anthozoans (e.g., shallow water anemones and corals), the key members of the associated microbiota are increasingly well studied, however there is limited data on photosymbiotic scyphozoans (true jellyfish). Using 16S rRNA barcoding, we sampled the internal and external mucus of the zooxanthellate Upside-Down Jellyfish, Cassiopea xamachana during August throughout eight sites covering the full length of the Florida Keys. We find that across sites, these medusae have low-diversity internal microbiomes distinct from the communities of their external surfaces and their environment. These internal communities are dominated by only three taxa: Endozoicomonas cf. atrinae, an uncultured novel Mycoplasma, and Vibrio cf. coralliilyticus. In addition, we find that Cassiopea bell mucosal samples were high diversity and conform largely to the communities of surrounding sediment with the addition of Endozoicomonas cf. atrinae. The microbial taxa we identify associated with wild Florida Keys Cassiopea bear a strong resemblance to those found within photosymbiotic anthozoans, increasing the known links in ecological position between these groups.},
}

Animals
Florida
RNA, Ribosomal, 16S/genetics
*Mycoplasma/genetics/isolation & purification/classification
*Vibrio/genetics/isolation & purification
*Scyphozoa/microbiology
*Microbiota
Phylogeny
*Gastrointestinal Microbiome
Symbiosis

@article {pmid40794385,
year = {2025},
author = {Rousk, K},
title = {Moss-cyanobacteria associations: A model for studying symbiotic interactions and evolutionary strategies.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70086},
doi = {10.1002/ajb2.70086},
pmid = {40794385},
issn = {1537-2197},
}

@article {pmid40794121,
year = {2025},
author = {Abdalla, MA and Waqas, K and Neugart, S and Mühling, KH},
title = {Flavonol glycosides accumulation in faba bean grown under combined selenium and sulfur application.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {5},
pages = {113},
pmid = {40794121},
issn = {1573-3890},
mesh = {*Vicia faba/metabolism/growth & development ; *Flavonols/metabolism/analysis ; *Selenium/metabolism/pharmacology ; *Sulfur/metabolism ; *Glycosides/metabolism/analysis ; Plant Leaves/metabolism ; Chromatography, High Pressure Liquid ; Tandem Mass Spectrometry ; Metabolomics/methods ; },
abstract = {INTRODUCTION: Faba bean (Vicia faba L.) leaves are edible; hence, they are primarily used as animal feed in agriculture. Additionally, seed pods and other plant tissues are considered edible and are used as green vegetables in many parts of the world.

OBJECTIVES: Flavonol glycosides are well-known in faba bean leaves; accordingly, in this study, we followed a targeted metabolomic approach to explore glycosylated flavonols and their concentrations in response to contrasting levels of selenium (Se) and sulfur (S) enrichment under faba bean-Rhizobium symbiosis.

METHODS: Faba bean plants were cultivated under growth chamber conditions and enriched with different levels of selenium and sulfur under Rhizobium inoculation. Their leaves were extracted using 70% methanol to quantify glycosylated flavonoids. Sample leaves were analyzed through a targeted method using high-performance liquid chromatography combined with a diode array detector (HPLC-DAD) and electrospray ionization-quadrupole-time-of-flight tandem mass spectrometry detection (HPLC-ESI-Q-ToF-MS/MS).

RESULTS: The analysis led to semi-quantifying 11 flavonol glycosides. Analysis of the metabolites of the different faba bean leaf extracts confirmed that selenium has a considerable impact on the accumulation of flavonol glycosides, especially under sulfur availability, possibly because it induces chalcone synthase and other enzymes for flavonols' biosynthesis.

CONCLUSION: To the best of our knowledge, this is the first report to investigate the impact of selenium and sulfur enrichment on the accumulation of faba bean flavonols under atmospheric nitrogen (N2) fixation conditions. This study highlights the medicinal and nutritional benefits of legumes as an essential source of protein in plant-based foods.},
}

*Vicia faba/metabolism/growth & development
*Flavonols/metabolism/analysis
*Selenium/metabolism/pharmacology
*Sulfur/metabolism
*Glycosides/metabolism/analysis
Plant Leaves/metabolism
Chromatography, High Pressure Liquid
Tandem Mass Spectrometry
Metabolomics/methods

@article {pmid40792658,
year = {2025},
author = {Rocha, AP and Palmeiras, MA and deOliveira, MA and Florentino, LH and Cataldi, TR and de C Bittencourt, DM and Labate, CA and Rosinha, GMS and Rech, EL},
title = {Cell-Free Production of Soybean Leghemoglobins and Nonsymbiotic Hemoglobin.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00197},
pmid = {40792658},
issn = {2161-5063},
abstract = {Hemoglobins are heme proteins and are present in certain microorganisms, higher plants, and mammals. Two types of hemoglobin are found in legume nodules: leghemoglobin (LegH) or symbiotic and nonsymbiotic (nsHb). LegHs occur in high amounts in legume roots, and together with bacteroides, are responsible for the nitrogen fixation process. nsHb Class 1 proteins have very high affinity for O2 and are found in monocotyledons and legumes. LegH has attracted great interest in the vegetable meat industry owing to its organoleptic and nutritional properties. In this study, soybean LegHs A, C1, C2 and C3 and nsHb were produced via Escherichia coli-based cell-free systems (CFS) and their amino acid sequences were correctly synthesized. In addition, certain post-translational modifications were made, which were confirmed using liquid chromatography-mass spectrometry analysis. All LegHs produced in this system exhibited peroxidase activity and heme binding, which were correlated with their concentrations in the assays. Furthermore, all proteins were readily digested by pepsin within 1 min under analog digestion conditions. Thus, LegHs and nsHb proteins were produced in this study using cell-free systems, maintaining their functionality and digestibility. These findings suggest that they could serve as viable alternative food additives for plant-based meat.},
}

@article {pmid40791400,
year = {2025},
author = {Gajigan, AP and Schvarcz, CR and Laughlin, AB and Weatherby, TM and Culley, AI and Edwards, KF and Steward, GF},
title = {A dinoflagellate-infecting giant virus with a micron-length tail.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.19.665647},
pmid = {40791400},
issn = {2692-8205},
abstract = {UNLABELLED: Viral infection is a ubiquitous source of marine plankton mortality, but relatively few viruses that infect phytoplankton have been characterized. Here we describe a virus, PelV-1, with unusual morphological and genomic features that infects a dinoflagellate, Pelagodinium sp. Both host and virus were isolated from the epipelagic zone in the North Pacific Subtropical Gyre. PelV-1 has a ∼200 nm capsid size, and the virion variably exhibits two appendages, the presence and length of which may reflect different stages of virion maturity or artifacts of sample preparation. The appendages are a thinner 30 nm-wide tail-like structure that can extend to 2.3 µm - the longest virus appendage described to date- and a shorter, thicker (>40-70 nm) protrusion, which appears to emerge from a star-shaped capsid opening directly opposite the attachment point of the long, thin tail. Sequencing and assembly of material in a purified lysate generated a high-coverage (> 4,000×) genome of 459 kb (33.8% GC). A second, distinct genome of 504 kb (25.8% GC) was also assembled, but had low read coverage (< 24×), suggesting the presence of a low-abundance, co-cultured virus (co-PelV). Phylogenetic analysis indicates that both PelV-1 and co-PelV are members of Mesomimiviridae . They contain various genes for the metabolism of amino acids (e.g., asparagine synthase), carbohydrates (e.g., epimerase, glycosyl hydrolase, aconitate hydratase, succinate dehydrogenase of the TCA cycle), and lipids (e.g., phospholipases), as well as other noteworthy genes (e.g., light-harvesting complex, rhodopsin, ion channel, sugar transporters, aquaporin). PelV-1 also has ORFs most similar to tail fiber genes of Synechococcus phage and other tail domain-containing protein homologs. The ecological advantages that might be conferred by the extraordinarily long tail and metabolic genes of PelV-1 is unknown, but this isolate expands the scope of morphological and metabolic diversity of viruses and suggests many more unusual marine viruses await discovery.

AUTHOR SUMMARY: Giant viruses challenged our traditional views of virology due to their large size and the presence of hundreds of auxiliary metabolic genes. But despite the immense giant virus diversity discovered through sequencing, few isolates were described, and those were primarily viruses that infect amoeba host and rarely from phytoplankton. This hampers our understanding of marine host-virus interaction and thus the impact of viruses on the ocean ecosystem. Here we provide genomic and morphological characterization of a novel dinoflagellate giant virus (PelV-1) and a second co-occurring, albeit low abundance, virus (co-PelV). Dinoflagellates are vital in marine symbiosis and algal blooms but only two giant virus isolates have been described with no available genomic resources to date. Thus, this is a significant contribution to the literature on dinoflagellate viruses. Among the notable features of PelV-1 are its unique micron-length tail appendage, phagocytosis-like entry mechanism and its varied auxiliary metabolic genes including photosynthesis and energy generating genes.},
}

@article {pmid40790863,
year = {2025},
author = {Alders, RG},
title = {The broader symbiotic relationships between animals and humans in low-, middle- and high-income countries.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-4},
doi = {10.1017/S0029665125101201},
pmid = {40790863},
issn = {1475-2719},
abstract = {BACKGROUND: Human-animal relationships have evolved over millennia, shaping societies, economies, and ecosystems. Domestic animals play critical roles in food and nutrition security, livelihoods, and cultural practices, with livestock systems varying by region and purpose. Since the 1950s, rising demand for animal products, urbanization, and technological advances have transformed some livestock production systems. Globally, animals support household well-being by contributing to social, spiritual, and physical health, particularly in resource-limited settings. Livestock offer vital services, such as manure production, draft power, and employment, while also supporting agroecosystems through regenerative practices that promote biodiversity and soil health.

BENEFITS AND ACCESSIBILITY: Animal-source foods (ASF)-including meat, milk, eggs, and offal-are rich in essential nutrients such as vitamin B12, iron, omega-3 fatty acids, and high-quality protein. They are especially important for vulnerable groups such as children and the elderly. ASF also provide year-round nutritional support in rainfed systems and offer economic security through barter or sale during crises. However, policies must consider local contexts to promote sustainable consumption and production, ensuring equitable access to ASF.

UTILISATION: Nose-to-tail eating is a traditional, sustainable approach that maximizes resource use, reduces waste, and enhances nutrition by utilizing all edible parts of animals. Organ meats and bone products are nutrient-dense and cost-effective, benefiting low-income communities and honouring ethical consumption values.

CONCLUSIONS: This review explores the diverse roles animals play in human societies, with a focus on the contribution of ASF to sustainable human nutrition through the integrated perspectives of One Health and One Welfare. It also provides policy recommendations to foster ethical and responsible human-animal relationships.},
}

@article {pmid40788120,
year = {2025},
author = {Takagi, T and Aoyama, K},
title = {Complete genome sequence of Maribacter sp. strain C-4077, isolated from the cell surface of a symbiotic dinoflagellate of the bivalve Fragum sp.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0035825},
doi = {10.1128/mra.00358-25},
pmid = {40788120},
issn = {2576-098X},
abstract = {A Maribacter sp. strain C-4077 was isolated from an endosymbiotic dinoflagellate of a bivalve and the genome was sequenced using a PacBio Sequel IIe system. The genome consists of a circular 4,085,762 bp chromosome and is predicted to harbor 6 rRNA genes, 39 tRNA genes, and 3,473 coding sequences.},
}

@article {pmid40785991,
year = {2025},
author = {Takeuchi, H and Matsuishi, TF and Hayakawa, T},
title = {Metagenomic Insights Into the Role of Gut Microbes in the Defensive Ink "Tsunabi" of Physeteroid Whales.},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71910},
pmid = {40785991},
issn = {2045-7758},
abstract = {Whales of the superfamily Physeteroidea, which includes the genera Physeter and Kogia, exhibit a unique visual defense mechanism involving the release of dark reddish-brown feces (locally called "tsunabi-ink" in Japan) into the water to obscure themselves from predators and other threats. However, the mechanism underlying pigmentation remains unknown. Because physeteroids possess an enlarged distal colon that retains fecal material, a possible explanation is that symbiont microbial metabolism contributes to the feces pigmentation. To investigate this, we provided a shotgun metagenomic catalog of gut microbiomes from the intestinal tracts of eight cetacean species, including two physeteroids: a sperm whale (Physeter macrocephalus) and a pygmy sperm whale (Kogia breviceps). The colonic microbiome of physeteroids exhibited relatively high abundances of tryptophan metabolism genes, particularly indolepyruvate ferredoxin oxidoreductases (iorA and iorB), suggesting that physeteroids accumulate indole-3-pyruvate-derived pigments in their colons. Furthermore, bacterial members of the phyla Bacillota and Bacteroidota were identified in the physeteroid colon as primary taxa conferring heavy-metal resistance, which may be related to the primary predation of physeteroids on cephalopods, which bioaccumulate high levels of heavy metals. Prolonged fecal retention can expose gut microbes to chronic heavy-metal stress and colonize them as heavy metal-tolerant microbial communities, some of which may produce pigments to reduce their toxicity. Thus, we propose that tsunabi-ink is a metabolic byproduct of shifts in the gut microbial community, influenced by the host's digestive physiology and foraging behavior through sustained ecological interactions with gut symbionts. Moreover, we believe that further empirical investigation would validate this hypothesis.},
}

@article {pmid40785172,
year = {2025},
author = {Mocci, G and Orrù, G and Elisei, W and Usai Satta, P and Onidi, FM and Tursi, A},
title = {Efficacy of a Preparation based on Symbiotic Association Between Inulin, FOS, L. rhamnosus GG, Bromelin, Boswellia, Vitamin D3, Quercetin and L-tryptophan in Mild-to-Moderate Ulcerative Colitis: A Pilot Retrospective Multicenter Study.},
journal = {Reviews on recent clinical trials},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115748871318114250725082904},
pmid = {40785172},
issn = {1876-1038},
abstract = {BACKGROUND AND OBJECTIVES: Several compounds based on short-chain fatty acids and/or probiotics/prebiotics have shown promising results in the therapy of mild-to-moderate ulcerative colitis (UC). The aim of the present study is to investigate the effectiveness of a preparation based on symbiotic association between inulin, fructooligosaccharides (FOS), Lactobacillus rhamnosus GG, bromelin, Boswellia, vitamin D3, quercetin and L-tryptophanon in patients with active mild-to-moderate UC.

MATERIALS: andMethods: This was a multicentre, retrospective, observational cohort study between January 2023 and June 2023. Disease activity was assessed using the partial Mayo score. Patients were assessed at baseline, at 8-week, and 16-week follow-up (FU). The primary endopoint was clinical response, defined as a partial Mayo score reduction of at least 2 points, whereas C-reactive protein (CRP) and fecal calprotectin (FC) reduction at weeks 8 and 16 were secondary endpoints.

RESULTS: Data were collected at baseline from 17 UC patients (M 8, F 9). Median age at diagnosis was 48 years (IQR 20-80), and median disease duration was 10 years (IQR: 2-23). The clinical response at 8 and 16 weeks was observed in 9/17 (52%) and 11/17 (64%) patients, respectively (p =0.697). No difference was observed regarding CRP values, neither at week 8 nor at week 16. Concerning FC levels, we observed a significant decrease from baseline to week 8, from baseline values of 252 (76-359) μg/g to values of 98 (20-448) μg/g at week 8 (p <0.02); no difference was observed from baseline to week 16. Finally, no adverse events were observed during the study period.

CONCLUSION: In this preliminary study, the supplementation with the symbiotic association between inulin, fructooligosaccharides (FOS), Lactobacillus rhamnosus GG, bromelin, Boswellia, vitamin D3, quercetin and L-tryptophanon offers real-world potential in controlling disease activity in patients with mild-to-moderate UC. Further multicentre, placebo-controlled, double-blind clinical trials are needed to validate our results on larger cohorts of patients with UC.},
}

@article {pmid40784505,
year = {2025},
author = {Peng, L and Shu, M and Fang, L and Xu, Y},
title = {Revealing roles of immobilization in microalgae-bacteria symbiosis system for nutrient removal from wastewater.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133136},
doi = {10.1016/j.biortech.2025.133136},
pmid = {40784505},
issn = {1873-2976},
abstract = {Limited information is available on immobilization roles in the microalgae-bacteria system for pollutant removal. In this work, nutrient removal performances and pathways were investigated in suspended microalgae-bacteria, immobilized microalgae-bacteria and co-immobilized microalgae-bacteria systems. Alginate immobilization enabled efficient biomass recovery with remarkable settling velocity at 1.88 cm s[-1]. Co-immobilization achieved the highest total nitrogen (TN) removal (50 %) despite the lowest ammonium removal (84 %). Bacterial nitrification dominated ammonium removal, despite contribution variations from 58 % in suspended group to 70 % in immobilized microalgae-bacteria due to decreasing microalgal assimilation, and to 51 % in co-immobilized group ascribed to encapsulation-induced mass transfer limitation. Co-immobilization enhanced bacterial denitrification (17 %) for TN removal. All systems achieved complete phosphorus removal via microalgal assimilation (>90 %), despite slight chemical oxygen demand increase in co-immobilized group originating from polymer hydrolysis. Considering lower separation cost ($0.47 m[-3]) and comparable stability, immobilization would provide alternatives realizing efficient wastewater treatment and resource recovery simultaneously.},
}