@article {pmid40953740,
year = {2025},
author = {Wang, Q and Chen, Y and You, S and Li, Y and Li, J and Liu, C and Liang, X and Wang, X},
title = {Metagenomic insights revealing the stabilizing regulatory role of biochar in partial denitrification-anammox under carbon-limited conditions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133296},
doi = {10.1016/j.biortech.2025.133296},
pmid = {40953740},
issn = {1873-2976},
abstract = {Carbon utilization efficiency and microbial community stability critically constrain the nitrogen removal performance of partial denitrification/anammox (PD/A) processes. Although biochar can serve as an electron donor, its regulatory mechanisms governing microbial interactions within PD/A remain unclear. This study demonstrates that under carbon-limited conditions, biochar adaptively enhances both nitrogen removal performance and microbial community interactions in PD/A systems. Under mild carbon limitation (C/N = 2.5), the biochar-amended reactor significantly enriched denitrifiers such as Thauera (16.75 % vs. 6.72 % in the blank control reactor). It also promoted acetate metabolism to enhance electron generation and facilitated electron transfer through downstream components of the electron transport chain. Under severe carbon limitation (C/N = 2.0), the relative abundance of Candidatus Brocadia increased significantly from 2.11 % to 7.00 %, accompanied by marked upregulation of key TCA cycle enzymes and anammox-related genes, indicating a metabolic shift toward a more energy-efficient anammox pathway. The PD/A system stability was maintained, with ammonium and nitrate removal efficiencies of approximately 75.85 % and 73.11 %, respectively. Additionally, biochar stimulated extracellular polymeric substance secretion to alleviate environmental stress. These findings suggest that biochar acts as an effective niche-modulating medium, supporting the stable and efficient operation of PD/A processes under varying carbon source conditions.},
}

@article {pmid40953724,
year = {2025},
author = {Lan, T and Zhang, Y and Xie, R and Wu, Q and Wang, H and Du, J and Guo, W},
title = {Aromatic hydrocarbon exposure alters soil microbial communities and redox-driven carbon metabolism.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122845},
doi = {10.1016/j.envres.2025.122845},
pmid = {40953724},
issn = {1096-0953},
abstract = {The environmental behavior and toxicological impacts of benzene, toluene, ethylbenzene, and xylene (BTEX) have been widely studied. Yet their concentration-dependent effects on soil microbial structure, redox dynamics, and metabolism remain insufficiently understood, constraining predictions of ecosystem responses and the development of targeted bioremediation strategies. Here, we explored how exposure to different concentrations of BTEX reshaped microbial community structure and metabolic function by integrating phased amplicon sequencing, metagenomic analysis, and metabolite profiling. BTEX exposure did not significantly alter the overall microbial richness or diversity across treatment groups but substantially changed the taxonomic composition (Stress = 0.096, R = 0.2284, P = 0.0500). It reduced the dominance of Bacillus and enriched various Clostridium spp. closely associated with acetate and butyrate production. At higher BTEX concentrations, Sporolactobacillus was selectively enriched, directing carbon flow toward lactate production. Functionally, BTEX inhibited early reactions in the pentose phosphate pathway (PPP), while increasing the abundance of genes involved in downstream glycolysis and PPP, leading to rapid pyruvate and NADH accumulation. Meanwhile, inhibition of NADH: ubiquinone oxidoreductase indicated a reduced capacity for respiratory NADH turnover. At slight BTEX concentrations, the redox imbalance increased NADH availability, thereby enhancing alcohol synthesis by 38.03% (±29.18%) (P < 0.05). Conversely, high BTEX concentrations enhanced lactate biosynthesis, redirecting carbon and reducing equivalents away from alcohol and acid accumulation (P<0.05). These findings demonstrate that BTEX reshapes microbial redox dynamics and carbon allocation in a concentration-specific manner, providing mechanistic insights into soil microbiome responses to aromatic hydrocarbon pollution and a basis for designing and optimizing future bioremediation strategies.},
}

@article {pmid40953718,
year = {2025},
author = {Liu, H and Yang, C and Qin, S and Zhang, Q},
title = {Metagenomic insights into carbon-nitrogen metabolism of heterotrophic nitrification-aerobic denitrification bacteria utilizing different biodegradable polymers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122864},
doi = {10.1016/j.envres.2025.122864},
pmid = {40953718},
issn = {1096-0953},
abstract = {Nitrogen pollution poses a critical threat to aquatic ecosystems worldwide, and biodegradable polymers have recently gained increasing attention as effective carbon sources to enhance biological nitrogen removal. This study systematically evaluated the nitrogen removal performance of heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria using various biodegradable polymers. Among them, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV, 100 kDa) showed promising performance, with a sustained carbon release rate of 2.04 mg·g[-1]·h[-1] and a total nitrogen (TN) removal rate of 1.82 mg·L[-1]·h[-1]. Metagenomic analysis indicated that Acidovorax, a key degrader of PHBV granules, played a dominant role in the denitrification process with a relative abundance of 33.89%, contributing 31.8% and 48.23% to carbon and nitrogen metabolism, respectively. In the PHBV (100 kDa) system, Stappia was identified as the predominant genus, accounting for 52.35% of the microbial community and contributing 57.87% and 64.52% to carbon and nitrogen metabolism, respectively. Functional gene profiling further suggested that PHBV significantly upregulated key nitrogen metabolism genes and enzymes, including nirK, norB, and nosZ. These results provide valuable insights into microbial mechanisms supporting polymer-based nitrogen removal and highlight the potential of PHBV as a sustainable carbon source in wastewater treatment.},
}

@article {pmid40953560,
year = {2025},
author = {Zhang, F and Yang, A and Wu, Y and Li, W and Guo, J and He, F and Wang, M and Zhang, P and Li, J},
title = {Exploring sustainable fertility of live microalgal cells: Impacts on lettuce growth and soil microbial metabolic responses.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127235},
doi = {10.1016/j.jenvman.2025.127235},
pmid = {40953560},
issn = {1095-8630},
abstract = {The excessive dependency on chemical fertilizers presents significant challenges to agricultural sustainability, thereby necessitating the development of eco-friendly alternatives that can enhance nutrient efficiency. This study investigates live Chlorella sp. cells (OX) as biofertilizers in lettuce cultivation, comparing their effects with freeze-thaw disrupted algal biomass (OO), bead-milled disrupted algal biomass (OZ), and a water-only control (CK). OX significantly enhanced lettuce growth-stem length (+32.6 %), leaf count (+33.3 %), chlorophyll (+233.3 %), and protein content (+47.5 %)-by continuously releasing nitrogen-rich metabolites, phytohormones, and extracellular polymers. OX also improved soil health: total nitrogen (+53.2 %), ammonium-N (+85.2 %), catalase activity (+76.6 %), and available phosphorus (+11.1 %) increased, while pH decreased due to organic acids. Metagenomic analysis revealed OX enriched nutrient-cycling bacteria (e.g., Pseudomonadota, Bacteroidota, and phosphate-solubilizing Massilia) and upregulated genes that store nitrogen (NapAB) and reduce greenhouse gases (NosZ). Crucially, live cells sustained balanced root-microbe interactions via photosynthesis, whereas disrupted biomass (OO/OZ) caused transient nutrient pulses. These findings demonstrate that live microalgae reconcile crop productivity, soil health, and environmental sustainability, reducing dependence on chemical inputs while restoring degraded soils, offering a low-carbon alternative to synthetic fertilizers.},
}

@article {pmid40953197,
year = {2025},
author = {Ogarkov, O and Orlova, E and Suzdalnitsky, A and Mokrousov, I},
title = {Microbiota of the Lung Tuberculoma: Paucibacillary Bacterial Community.},
journal = {International journal of mycobacteriology},
volume = {14},
number = {3},
pages = {209-218},
pmid = {40953197},
issn = {2212-554X},
abstract = {Caseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-resistant persisting Mycobacterium tuberculosis (MTB). However, tubercle bacilli are not the only bacterial inhabitants of this necrosis. We discuss the available data on metagenomic and amplicon sequencing of 16S rRNA of caseous necrosis from surgically excised tuberculosis (TB) foci. This approach facilitated the characterization of the biodiversity and the potential biochemical pathways of these bacterial communities. We postulate that in terms of MTB content relative to satellite anaerobic lipophilic bacteria, caseum may present two distinct terminal states. "True" TB necrosis, containing 99.9% tubercle bacilli, and a polymicrobial community wherein anaerobic lipophilic bacteria predominate over MTB. Isolation from caseum and genomic characterization of several Corynebacterium and Staphylococcus species support this concept.},
}

@article {pmid40953082,
year = {2025},
author = {Kotaki, T and Kanai, Y and Onishi, M and Sakai, Y and Motooka, D and Chen, Z and Enoki, Y and Komatsu, S and Hirai, K and Minami, S and Kawagishi, T and Ushijima, H and Kobayashi, T},
title = {Single-round infectious rotaviruses with deletions of VP7 or VP4 genes, based on SA11 and WC3 strain backbones, and their potential use as viral vectors.},
journal = {PLoS pathogens},
volume = {21},
number = {9},
pages = {e1013484},
doi = {10.1371/journal.ppat.1013484},
pmid = {40953082},
issn = {1553-7374},
abstract = {Single-round infectious rotavirus, which lacks a gene essential for virion assembly, serves not only as a safe and effective rotavirus vaccine but also as an orally-administrable viral vector vaccine that induces mucosal immunity. Previously, we generated a single-round infectious rotavirus by partially deleting the viral VP6 gene, and demonstrated its potential as a promising vaccine platform. However, this system has several limitations; namely, low viral protein expression levels and safety concerns. Here, we addressed these challenges by introducing large deletions into the VP7 or VP4 genes, which are dispensable for viral protein expression but essential for virion assembly. These VP7- or VP4-defective viruses exhibited markedly higher protein expression in wild-type MA104 cells than the previously developed VP6-defective virus. In addition, the large deletions reduce the risk of viral reversion, thereby increasing both efficacy and safety. In a mouse model, these viruses induced neutralizing antibodies at levels comparable with those elicited by wild-type rotavirus, indicating their potential as rotavirus vaccines. Moreover, a VP4-defective rotavirus harboring a heterologous gene achieved high expression of heterologous proteins, warranting its application as a viral vector vaccine. To further increase safety, we established a reverse genetics system for the bovine rotavirus WC3 strain, a parental strain of the licensed live attenuated rotavirus vaccine, and successfully generated a single-round VP4-defective rotavirus based on the WC3 backbone. Taken together, these optimizations facilitate development of safe and effective single-round infectious rotavirus platforms suitable for human use.},
}

@article {pmid40953029,
year = {2025},
author = {Park, R and Chevalier, C and Kieser, S and Marizzoni, M and Paquis, A and Armand, S and Scheffler, M and Allali, G and Assal, F and Momjian, S and Frisoni, GB},
title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330251},
doi = {10.1371/journal.pone.0330251},
pmid = {40953029},
issn = {1932-6203},
abstract = {Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.},
}

@article {pmid40952163,
year = {2025},
author = {Nir, I and Armoza-Zvuloni, R and Barak, H and De Los Ríos, A and McKay, CP and Kushmaro, A},
title = {The Biology, Microclimate, and Geology of a Distinctive Ecosystem Within the Sandstone of Hyper-Arid Timna Valley, Israel.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70188},
doi = {10.1111/1758-2229.70188},
pmid = {40952163},
issn = {1758-2229},
support = {PID2023-147027NB-I00B//Agencia Estatal de Investigación. Write: Agencia Estatal de Investigacion (AEI), MICINN/ ; EXO-92-4//NASA AMES/ ; 3-17370//Minstry of Science and Technology (MOST), Israel/ ; },
abstract = {Microbial endolithic communities in the sandstone rocks of the southern Negev Desert, particularly in Timna Park, were initially discovered by Imre Friedmann and Roseli Ocampo-Friedmann in their pioneering study about 50 years ago. Nonetheless, this harsh microecosystem, dominated by cyanobacterial taxa, raises questions about the adaptive mechanisms that enable the survival of these microorganisms. The present study provides comprehensive data, including extensive precipitation records for the Timna Valley, and multi-year microclimatic data from a colonised site. It includes examinations of rock structure, as well as microscopic and metagenomic analysis. Our findings point to a distinct bacterial endolithic population dominated by the cyanobacterial genus Chroococcidiopsis. Although the taxa are well known, we show here how their exclusive persistence is driven by the sandstone's fine porosity and thermal properties, combined with rare, low-volume precipitation. This highly selective microenvironment highlights how specific rock and climate interactions can filter microbial diversity in hyper-arid deserts. Additionally, it demonstrates an adaptation strategy based on both short-term and decadal-scale dormancy. Thus, it offers new insights for the survival of these unique ecosystems and provides valuable perspectives for astrobiology and the search for evidence of microbial life on Mars.},
}

@article {pmid40952106,
year = {2025},
author = {Xu, Q and Huang, Y},
title = {Stringent response-mediated ferroptosis-like death resistance underlies Novosphingobium persistence during ciprofloxacin stress.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0147525},
doi = {10.1128/aem.01475-25},
pmid = {40952106},
issn = {1098-5336},
abstract = {Antibiotics, as emerging hazardous materials in the environment, pose significant risks to ecosystems and contribute to the spread of antibiotic-resistant bacteria. Although extensive knowledge has been accumulated on antibiotic-resistance mechanisms in individual bacteria, less is understood about how the bacterial communities respond to antibiotic exposure under natural environmental conditions, where nutrient supplies are often limited and fluctuating. Here, we report that Novosphingobium dominated in a wetland bacterial community under 1 µg/mL ciprofloxacin (CIP) exposure and persisted during DL-serine hydroxamate-induced starvation, where the stringent response alarmer (p)ppGpp was detected. Metagenome sequencing revealed that genes associated with siderophore transport, cytochrome c, and glutathione S-transferase were significantly enriched in Novosphingobium, linking its dominance under CIP stress to iron homeostasis and oxidative stress responses. Further study on the survival mechanism of Novosphingobium pentaromativorans US6-1 under 8 µg/mL CIP stress demonstrated that stringent response regulated the growth rate and maintained cell viability by suppressing the TCA cycle and oxidative phosphorylation, deterring the entry of CIP and siderophore into cells, reducing intracellular ferrous iron and malondialdehyde, and balancing cellular redox status, thereby protecting cells from ferroptosis-like death. This study is the first to report Novosphingobium's dominance and persistence in a bacterial community during CIP stress in natural environmental conditions and to propose the stringent response-mediated ferroptosis-like death resistance as one of its key survival mechanisms.IMPORTANCEAntibiotics in the environment are increasingly recognized as a new class of pollutants that accelerate the evolutionary selection of antibiotic-resistant bacteria. However, little is known about how this selection occurs under natural conditions, including how specific bacteria taxa and mechanisms respond to particular antibiotics. This study reveals for the first time the selection effect of CIP on Novosphingobium under nutrient-limited conditions, during which stringent response and iron homeostasis play important roles. An innovative linkage between stringent response and ferroptosis-like death resistance is proposed in N. pentaromativorans US6-1, which serves as the CIP resistance mechanism for Novosphingobium. These findings may help inform strategies to combat antimicrobial resistance in the natural environment.},
}

@article {pmid40952003,
year = {2025},
author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L},
title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002325},
doi = {10.1128/msystems.00023-25},
pmid = {40952003},
issn = {2379-5077},
abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.},
}

@article {pmid40952001,
year = {2025},
author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO},
title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0099125},
doi = {10.1128/msystems.00991-25},
pmid = {40952001},
issn = {2379-5077},
abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.

IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.},
}

@article {pmid40951842,
year = {2025},
author = {Fenibo, EO and Nkuna, R and Matambo, T},
title = {Metagenomic Insights Into Biopile Remediation of Petroleum-Contaminated Soil Using Chicken Droppings in Rivers State, Nigeria.},
journal = {Bioinformatics and biology insights},
volume = {19},
number = {},
pages = {11779322251371117},
pmid = {40951842},
issn = {1177-9322},
abstract = {Petroleum hydrocarbon pollution is an escalating global issue, particularly in developing countries, where it has attracted significant attention from researchers focusing on bioremediation, monitoring and sustainability. This study utilised metagenomics to investigate the bacterial community's response in polluted soil undergoing field-scale biopile treatment, with chicken droppings as a nutrient source. Hydrocarbon concentrations were monitored over a 90-day remediation period using the Fourier transform infrared (FTIR) spectrometry technique. Molecular and bioinformatic analyses were conducted to track the dynamics of bacterial species, their abundance and functional roles during the bioremediation process. The initial total petroleum hydrocarbon (TPH) concentration of 446 945 ppm was first reduced to 80 332 ppm through dilution. Following a 90-day bioremediation process using poultry waste, the level further decreased to 5326 ppm, representing a 93.37% reduction. In the metagenomic analysis, a total of 26 736 reads were obtained, averaging 6684 counts per sample. In addition, the study identified diverse bacterial metagenomes, including well-established hydrocarbon-degrading bacteria from Proteobacteria, Firmicutes, Acidobacteria and Actinobacteria phyla, and species previously not reported as hydrocarbon-degrading. Biomarkers associated with hydrocarbon metabolisms, such as aromatic dioxygenases, alkane-1-monooxygenase and methanol oxidation pathways, were identified. A significant decrease in the relative abundance of bacterial genera in heavily polluted soil was observed, alongside an increased presence of Caballeronia, Paraburkholderia and Fontibacillus genera. These findings indicate that chicken droppings contribute 0.30% to the reduction of TPH in the biopiling remediation technique used for treating heavily contaminated soil. A comparative assessment of hydrocarbon attenuation in nutrient-amended vs unamended soils indicates that a 3-month remediation timeframe is insufficient to achieve optimal bioremediation outcomes. However, the TPH reduction in unamended treatment highlights the intrinsic natural attenuation capacity of the impacted soil matrix, attributable to indigenous microbial consortia and prevailing environmental conditions.},
}

@article {pmid40951757,
year = {2025},
author = {Gupta, S and Angrup, A and Rana, SS and Batra, G and Rana, N and Ramola, M and Vashist, T and Bisht, K and Monga, N and Jolly, SS and Singla, M and Sareen, S and Goyal, A and Duseja, RN},
title = {Microbial overlap in dental plaque and tumor tissue of esophageal cancer patients: A pilot study.},
journal = {Journal of Indian Society of Periodontology},
volume = {29},
number = {2},
pages = {153-163},
pmid = {40951757},
issn = {0972-124X},
abstract = {INTRODUCTION: Microbial dysbiosis has been shown to be involved in various types of gastrointestinal cancers, but there is a dearth of strong studies linking the oral microbiome imbalance with esophageal cancer (EC).

OBJECTIVES: The main objective of the study was to identify the link between oral microbiome and EC.

MATERIALS AND METHODS: Twelve suspected EC and two healthy control patients were recruited. After the histological confirmation of EC, four confirmed EC patient samples and two healthy control samples were subjected to 16S metagenomics study using the Oxford Nanopore Technology sequencing platform.

RESULTS: Species richness of microbial community was higher in the healthy controls followed by diseased plaque, tumor tissue and adjacent tissue. Bacillota, Pseudomonata, Fusobacteriota, Bacteroidota, and Campylobacterota were the major phyla identified in all the groups. Majorly prevalent genera (core microbiome analysis) in all the groups were Streptococcus, Salmonella, Bacillus, Enterococcus, Veillonella, Klebsiella, Clostridioides, Prevotella, Gemella, Selenomonas, Firmicutes, and Proteobacteria followed by Bacteroidetes and Fusobacteria.

CONCLUSION: Our study suggests an association between oral microbiome and EC. The prevalence of same microbial genus in the oral cavity (dental plaque) and tumor tissue depicts a possible link. Our study opens the plausible microbe-based biomarker screening of EC.},
}

@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.

METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.

RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.

CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}

@article {pmid40951304,
year = {2025},
author = {Chen, J and Wang, Y and Aikebaier, R and Liu, H and Li, Y and Yang, L and Haiyilati, A and Wang, L and Fu, Q and Shi, H},
title = {RAA-CRISPR/Cas12a-based visual field detection system for rapid and sensitive diagnosis of major viral pathogens in calf diarrhea.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616161},
pmid = {40951304},
issn = {2235-2988},
abstract = {Calf diarrhea is a complex digestive disorder in cattle that imposes significant economic losses in terms of calf mortality, growth impairment, and treatment costs. Both infectious and non-infectious agents contribute to its aetiology; however, most of the infectious cases are caused by viruses, often accompanied by severe co-infections. To identify viral culprits, we performed viral metagenomic sequencing on three pooled samples from the 150 diarrheal samples from Xinjiang, China, which helped with identification of the following four predominant agents: bovine nepovirus (BNeV), bovine coronavirus (BCoV), bovine viral diarrhea virus (BVDV) and bovine enterovirus (BEV). Currently, the process of diagnosing these pathogens involves time-consuming workflows, limited sensitivity, poor portability, and lack of field applicability. Keeping these diagnostic shortcomings in mind, an integrated platform called RAA-CRISPR/Cas12a system was developed by combining recombinase-aided amplification (RAA) at 37°C with CRISPR/Cas12a-mediated fluorescence detection, which achieved 100-100,000 times higher sensitivity than conventional polymerase chain reaction (PCR) (detection limits: 1-10 copies/μL) and demonstrated 100% specificity against non-target pathogens. Clinical validation of sensitivity and specificity of 252 samples revealed 1.6-4.9 times higher detection rates (239 positives) than PCR (81 positives), which was consistent with PCR-confirmed cases. The assay's 40-min. workflow enables rapid on-site deployment without specialized instrumentation, as it requires only a portable heat block and blue LED transilluminator. Hence, with its laboratory accuracy and field applicability, this method helps in early identification of pathogens, outbreak containment and mitigation of economic loss in the global cattle industry.},
}

@article {pmid40950993,
year = {2025},
author = {Jin, L and Chen, C and Zhao, H and Chen, L and Wang, X and Wang, Q and Yuan, J and Li, J and Xu, S and Zhang, R and Chu, W and Ye, N and Zou, G and Ye, J},
title = {Fusobacterium nucleatum infection leading to rare hepatorenal abscess: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1540430},
pmid = {40950993},
issn = {2296-858X},
abstract = {Fusobacterium nucleatum is a gram-negative anaerobic bacterium commonly associated with periodontal disease. However, its role in extraoral infections, particularly in immunocompetent individuals, is increasingly recognized. We report a rare case of hepatorenal abscess caused by F. nucleatum in a previously healthy woman, initially suspected to have a malignant tumor based on PET-CT findings. Next-generation sequencing (NGS) of abscess aspirate confirmed the pathogen. The patient responded well to targeted antibiotic therapy. This case highlights the importance of considering anaerobic pathogens in deep-seated abscesses and the utility of NGS in achieving accurate microbial diagnosis.},
}

@article {pmid40950887,
year = {2025},
author = {Zhu, N and Sun, J and Wu, D and Xia, H and Fei, L},
title = {Pathogen distribution and prognostic risk factors in respiratory intensive care unit (RICU) patients of a large general hospital before and after COVID-19 pandemic.},
journal = {Journal of thoracic disease},
volume = {17},
number = {8},
pages = {6176-6188},
pmid = {40950887},
issn = {2072-1439},
abstract = {BACKGROUND: The evolving pathogen spectrum and prognosis of severe pulmonary infections in the respiratory intensive care unit (RICU) during the coronavirus disease 2019 (COVID-19) pandemic remain unclear. This study aimed to investigate shifts in the pathogen landscape of pulmonary infections among intensive care unit (ICU) patients following the regular prevention and control of COVID-19.

METHODS: A total of 132 patients with pulmonary infections admitted to the RICU of the First Affiliated Hospital of Anhui Medical University between January 2022 and March 2023 were included in the study. Patients were categorized into two cohorts: pre-strategy (n=65, Jan to Nov 2022) and post-strategy (n=67, Dec 2022 to Mar 2023), based on the implementation of regular COVID-19 prevention and control measures. Metagenomic next-generation sequencing (mNGS), and conventional tests using bronchoalveolar lavage fluid (BALF) and blood samples were used to detect pathogens. Retrospective data were obtained from the patients' medical records. The spectrum of pathogens was analyzed. Additionally, univariate and multivariate logistic regression models were employed to analyze the risk factors associated with adverse outcomes.

RESULTS: After the regular prevention and control of COVID-19 in December 2022, there was a significant shift in the pathogen landscape. The proportion of patients with severe acute respiratory coronavirus 2 (SARS-CoV-2) increased dramatically from 0% to 74.6%. This was accompanied by a significant rise in the incidence of Staphylococcus aureus (S. aureus) infections. Among the COVID-19 patients, a slight decrease in Gram-negative (G-) bacterial co-infections and a corresponding increase in Gram-positive (G+) bacterial co-infections was observed. The overall mortality rate among all enrolled patients was 30.3%, with 24.6% in the pre-strategy group and 35.8% in the post-strategy group. Additionally, there was a marked increase in the detection rates of Candida and herpes simplex virus 1 (HSV-1) in COVID-19 patients following the strategy change. The analysis of risk factors revealed that a poor prognosis was strongly associated with co-infections of SARS-CoV-2 with Candida [odds ratio (OR) =2.91, 95% confidence interval (CI): 1.01-8.41] or Aspergillus (OR =3.08, 95% CI: 0.89-10.66) species. Further, bacterial and fungal co-infections (OR =3.92, 95% CI: 1.41-10.86) were identified as significant risk factors for a poor prognosis in patients without COVID-19.

CONCLUSIONS: Our findings highlight the pathogen spectrum in RICU patients changed significantly after the shift in COVID-19 policy. Co-infections with fungi and G+ bacteria require increased clinical vigilance and early intervention to improve outcomes.},
}

@article {pmid40950593,
year = {2025},
author = {Silva, ACP and Migliaccio, F and Barosa, B and Gallucci, L and Yücel, M and Foustoukos, D and Le Bris, N and Bartlett, SJ and D'Alessandro, V and Vetriani, C and Giovannelli, D},
title = {Hydrodynamic flow and benthic boundary layer interactions shape the microbial community in Milos shallow water hydrothermal vents.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649514},
pmid = {40950593},
issn = {1664-302X},
abstract = {In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.},
}

@article {pmid40950589,
year = {2025},
author = {Li, YH and Yang, M and Wei, TS and Chen, HG and Gong, L and Wang, Y and Gao, ZM},
title = {Survival strategies for the microbiome in a vent-dwelling glass sponge from the middle Okinawa Trough.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1636046},
pmid = {40950589},
issn = {1664-302X},
abstract = {The adaptive mechanisms of sponge microbiomes to harsh deep-sea environments, including hydrothermal vents and cold seeps, remain unclear. Here, we used metagenomics to investigate the microbiome of an undescribed vent-dwelling glass sponge from the middle Okinawa Trough, probably representing a novel species within the family Bolosominae. Eleven high-quality prokaryotic metagenome-assembled genomes (MAGs) were retrieved, none assignable to known species, with two representing new genera. Dominant MAGs included sulfur-oxidizing bacteria (SOB) and ammonia-oxidizing archaea, followed by methane-oxidizing bacteria (MOB) and nitrite-oxidizing bacteria. Global distribution analysis suggested that most MAGs were sponge-specific symbionts. Comparative genomics revealed functional redundancy among SOB and early-stage genome reduction in a unique MOB lineage. Additionally, a total of 410 viral contigs were identified, most exhibiting a lytic lifestyle and forming distinct clades from known viruses. Our work expands understanding of the diversity and novelty of deep-sea sponge-associated prokaryotes and viromes, and suggests their niche adaptation to hydrothermal fluid environments.},
}

@article {pmid40950585,
year = {2025},
author = {Kardaras, FS and Siatravani, E and Tsilipounidaki, K and Petinaki, E and Hatzigeorgiou, AG and Miriagou, V},
title = {Identification of nasopharyngeal microbial dysbiosis in COVID-19 patients by 16S rRNA gene sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1631198},
pmid = {40950585},
issn = {1664-302X},
abstract = {BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted extensive research into factors influencing the onset and severity of the disease. Among these factors, the role of the nasopharyngeal microbiome, a vital ecosystem critical for respiratory health and immune modulation, remains incompletely understood. This study aimed to elucidate the relationship between the composition of nasopharyngeal microbiota and the clinical presentation of COVID-19 during the initial phase of infection.

MATERIALS AND METHODS: A total of 81 nasopharyngeal swab samples were collected from individuals in Central Greece between January and February 2021. Following quality control, 77 samples were selected for microbiome analysis. This selection included SARS-CoV-2-negative controls (NE, n = 26) and SARS-CoV-2-positive patients classified as asymptomatic (AS, n = 19), mild (MI, n = 16), or severe (SE, n = 16) based on clinical criteria. All COVID-19-positive samples were collected within 2 days of symptom onset, and participants with recent hospitalization or antibiotic use were excluded. Microbiome profiling was performed using 16S rRNA gene-targeted metagenomic sequencing, followed by comprehensive bioinformatics and statistical analyses.

RESULTS: Significant differences were observed in both alpha and beta diversity measures, with alpha diversity decreasing as the severity of COVID-19 increased. Three of the four individual study groups, namely NE, MI, and SE, exhibited distinct microbial profiles, while the asymptomatic group showed greater heterogeneity. Significant variations in the abundance of specific phyla, families, and genera were identified between the different study groups. When comparing the NE and SE groups, we observed a significant increase in the abundance of the Proteobacteria phylum in the SE group, while the abundance of Fusobacteria was significantly lower in the SE group. In symptomatic COVID-19 patients, we observed a significant reduction in the abundance of key family constituents of the nasopharyngeal microbiota, such as Fusobacteriaceae, Prevotellaceae, and Streptococcaceae, suggesting a disruption in microbial homeostasis during the infection. Conversely, we found an increased prevalence of families associated with pathogenic or opportunistic pathogenic bacteria, including Enterobacteriaceae and Bacillaceae, in the SE group, suggesting a potential role of these taxa in the disease progression of COVID-19.

CONCLUSION: These findings shed light on specific genera that undergo significant changes during COVID-19 infection and contribute to our understanding of the dynamic nature of the nasopharyngeal microbiome in relation to disease progression and severity.},
}

@article {pmid40950048,
year = {2025},
author = {Shaw, J and Marin, MG and Li, H},
title = {High-resolution metagenome assembly for modern long reads with myloasm.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.05.674543},
pmid = {40950048},
issn = {2692-8205},
abstract = {Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. We present myloasm, a metagenome assembler for PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi comparable for assembly: for a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm recovers previously inaccessible within-species diversity; we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with > 93% similarity from an oral metagenome. With this improved resolution, we resolved two 98% similar ermF antibiotic resistance genes spreading through distinct strain-specific mobile genetic elements in a human gut.},
}

@article {pmid40949832,
year = {2025},
author = {Guo, N and Ma, G and Liu, H and Qiu, J and Yu, Y and Gao, Y and Yi, Z and Wan, Z and Zhang, L and Wu, X},
title = {Metagenomic Next-Generation Sequencing Reveals Porphyromonas gingivalis in Geriatric Severe Pneumonia Complicated by Empyema: Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4811-4816},
pmid = {40949832},
issn = {1178-6973},
abstract = {BACKGROUND: Severe pneumonia with empyema in elderly patients presents diagnostic and therapeutic challenges. Traditional culture methods often fail to identify the causative pathogen, leading to delays in targeted treatment. Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for detecting rare and fastidious pathogens.

CASE PRESENTATION: We report a 77-year-old male with a history of chronic smoking and alcohol consumption who presented with a two-month history of cough, sputum production, and progressive dyspnea. His condition rapidly deteriorated with high fever and respiratory failure. Initial antibiotic therapy was ineffective, and multiple cultures of blood, sputum, and pleural fluid were negative. However, mNGS of blood and pleural fluid identified Porphyromonas gingivalis, a well-known periodontal pathogen rarely associated with pulmonary infections. The patient's treatment was adjusted to include targeted anaerobic coverage (imipenem plus vancomycin) alongside chest tube drainage, leading to significant clinical improvement.

CONCLUSION: This case highlights the clinical utility of mNGS in diagnosing culture-negative pulmonary infections. Porphyromonas gingivalis should be considered a potential pathogen in patients with severe pneumonia and empyema, particularly in those with poor oral hygiene or periodontal disease.},
}

@article {pmid40949821,
year = {2025},
author = {Hirose, E and Lopez, JV and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the photosymbiotic ascidian, Trididemnum clinides Kott, 1977 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {357},
pmid = {40949821},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Trididemnum clinides (photosymbiotic ascidian; Chordata; Ascidiacea; Aplousobranchia; Didemnidae). The T. clinides genome sequence has a total length of 906.92 megabases. Most of the assembly (97.83%) is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.98 kilobases in length. The host ascidian has multiple symbionts, including Prochloron, a bacterial genus that can also synthesise bioactive natural products of interest for potential therapeutic development. Biosynthesis of active compounds sometimes involves microbial associates.},
}

@article {pmid40949424,
year = {2025},
author = {Hall, N and Wong, WW and Lappan, R and Ricci, F and Jeppe, KJ and Glud, RN and Kawaichi, S and Rotaru, AE and Greening, C and Cook, PLM},
title = {Coastal methane emissions driven by aerotolerant methanogens using seaweed and seagrass metabolites.},
journal = {Nature geoscience},
volume = {18},
number = {9},
pages = {854-861},
pmid = {40949424},
issn = {1752-0894},
abstract = {Methanogenesis is thought to be limited to strictly anoxic environments. While oxygenated oceans are a known methane source, it is argued that methane production is driven by methylphosphonate-degrading bacteria and potentially other sources rather than by methanogenic archaea. Here we develop in situ monitoring and ex situ manipulation experiments, combined with biogeochemical, metagenomic and culture-based experiments, to show that methane is rapidly produced by archaea in frequently oxygenated sandy sediments. We show that methane emissions from sandy sediments are not inhibited by repeated oxygen exposure and suggest the activity is driven by aerotolerant methylotrophic methanogens (primarily Methanosarcinaceae) broadly distributed in the surface layers of sandy sediments. Moreover, we show that methane emissions are driven by methylated seaweed and seagrass metabolites, revealing a feedback loop between primary production and greenhouse gas emissions.},
}

@article {pmid40949051,
year = {2025},
author = {Guillemot, Q and Clemens, T and Inthasot, V and Mahadeb, B and Maillart, E and Clevenbergh, P},
title = {Community-Acquired Chlamydia psittaci Severe Pneumonia: A Case Report.},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {6627159},
pmid = {40949051},
issn = {2090-6625},
abstract = {Chlamydia psittaci, the causative agent of psittacosis, is an intracellular bacterium typically transmitted from birds to humans, leading to atypical pneumonia. We present a case of a 60-year-old man with no reported bird exposure but a history of working as a chief cook, potentially exposed to poultry. He presented with high fever, diffuse soreness, and left-sided pulmonary consolidation. Initial treatment with β-lactams was ineffective, but a multiplex PCR on bronchoalveolar lavage identified C. psittaci DNA. Therapy was switched to moxifloxacin, resulting in rapid clinical improvement. C. psittaci causes approximately 1% of community-acquired pneumonias, often underdiagnosed due to nonspecific symptoms and the need for advanced diagnostic tools like nucleic acid amplification tests (NAATs) or metagenomic next-generation sequencing (mNGS). The bacterium is endemic in birds and poultry, with human infections linked to occupational exposure or contact with infected animals. Diagnosis relies on NAAT and mNGS, as serology and culture are less practical. Treatment with tetracyclines, quinolones, or macrolides is effective, reducing mortality from 10%-20% to < 1%. Preventive measures, including protective equipment for high-risk individuals and treatment of infected birds, are crucial. Mandatory reporting of cases could improve understanding of the disease burden. This case highlights the importance of considering psittacosis in atypical pneumonia, even without direct bird exposure, and the role of NAAT or mNGS in accurate diagnosis.},
}

@article {pmid40948444,
year = {2025},
author = {Bryson, S and Sisson, Z and Nelson, B and Grove, J and Reister, E and Liachko, I and Auch, B and Graiziger, C and Khoruts, A},
title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559019},
doi = {10.1080/19490976.2025.2559019},
pmid = {40948444},
issn = {1949-0984},
abstract = {Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.},
}

@article {pmid40947719,
year = {2025},
author = {Wei, CR and Basharat, Z and Osama, M and Mah, K and Waheed, Y and Hassan, SS},
title = {An Overview of the Association of the Urinary Tract Microbiome with Various Diseases and Implications for Therapeutics.},
journal = {Mini reviews in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113895575398906250825113635},
pmid = {40947719},
issn = {1875-5607},
abstract = {The urinary tract (UT) was once considered sterile, but now it is known to host a diverse community of microorganisms, known as the urinary microbiome. The collective microbiota is made up of bacteria, fungi, and viruses, necessary for maintaining UT health. This review aims to synthesize current knowledge on the urinary microbiome and clarify its emerging role as a key modulator in both health and a wide spectrum of UT disorders. Dysbiosis within this microbial community has been linked to conditions such as urinary tract infections (UTIs), interstitial cystitis/ bladder pain syndrome (IC/BPS), urinary incontinence, urolithiasis, benign prostatic hyperplasia (BPH), and even urinary tract malignancies. Advances in methodologies, such as expanded quantitative urine culture and metagenomics, have provided valuable insights into microbial variability influenced by factors like age, sex, and disease conditions. Additionally, this review explores the therapeutic potential of probiotics and bacteriophages, as well as the association of urinary microbiota with autoimmune and inflammatory conditions. Special emphasis is placed on translational relevance, including emerging microbiome-targeted therapies and personalized interventions for UTIs. Ethical considerations allied with UT microbiome research, such as data privacy, informed consent, and equitable access to emerging therapies, are also discussed. Despite substantial progress, challenges such as methodological heterogeneity, a lack of longitudinal data, and unresolved causal relationships persist. The study concludes by identifying key knowledge gaps and proposing future directions for multidisciplinary research to advance therapeutic innovation in urological health.},
}

@article {pmid40946852,
year = {2025},
author = {Zheng, C and Song, J and Shan, M and Qiu, M and Cui, M and Huang, C and Chen, W and Wang, J and Zhang, L and Yu, Y and Fang, H},
title = {Nutrition cycling microbiomes drive the succession of antibiotic resistome in long-term manured soils.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.09.019},
pmid = {40946852},
issn = {2090-1224},
abstract = {INTRODUCTION: The spread of antibiotic resistance genes (ARGs) in the environment has received widespread attention. Nutrition cycling microbiomes specifically refer to microorganisms capable of mineralizing nitrogen and phosphorus, which dominate the microbial community in long-term manured soils. However, changes in nutrition cycling genes/microbiomes and the mechanisms by which these microbiomes mediate ARG transfer through vertical and horizontal gene transfer remain poorly understood.

OBJECTIVES: This study aimed to elucidate how nutrition cycling microbiomes mediate the dissemination and ecological risk of antibiotic resistance genes (ARGs) in long-term manure-amended soils.

METHODS: Here, we employed metagenomic assembly and binning to investigate the distribution of nutrition mineralization genes, nutrition cycling microbiomes, mobile genetic elements (MGEs), and ARGs in rapeseed cake, pig manure, duck manure and their corresponding long-term amended soils.

RESULTS: Long-term application of organic manures led to the dominance of nutrition cycling microbiomes associated with methanogenesis (pmoA and mmoX) and incomplete denitrification (norBC), thereby exacerbating soil nutrient loss. Nutrition cycling microbiomes, particularly Rhodanobacter and Pseudomonas, served as the primary host for ARGs and harbored multiple clinically relevant resistance genes, including MexF, ceoB, and mdtB. Notably, the abundance of ARGs in rapeseed cake and pig manure was 2.09-2.23-fold and 6.74-7.38-fold higher, respectively, than in duck manure, promoting the vertical transmission of ARGs via nutrition cycling microbiomes under long-term application. Furthermore, a significant positive correlation between nutrition mineralization genes and ARGs revealed a co-dispersal mechanism between nutrition cycling microbiomes and ARGs in long-term manured soils.

CONCLUSIONS: It is concluded that the nutrition cycling microbiome plays a more prominent role in shaping antibiotic resistome through vertical transfer in manured soils, compared to horizontal gene transfer mediated by MGEs.},
}

@article {pmid40946456,
year = {2025},
author = {Li, C and Yuan, Z and Liu, B and Sun, Y and Wang, Y and Quan, J and Shen, X and Guo, J},
title = {Comparative recovery of carbon, nitrogen, and phosphorus from food waste via anaerobic digestion and Black Soldier Fly Larvae.},
journal = {Water research},
volume = {288},
number = {Pt A},
pages = {124587},
doi = {10.1016/j.watres.2025.124587},
pmid = {40946456},
issn = {1879-2448},
abstract = {With rising global population and energy demands, efficient recovery of carbon (C), nitrogen (N), and phosphorus (P) from food waste has become increasingly critical for sustainable resource management. Although anaerobic digestion (AD) and Black Soldier Fly Larvae (BSFL) conversion have been separately investigated for food waste treatment, direct and systematic comparisons of their nutrient recovery potential across scales remain limited. This study evaluates and compares two treatment pathways, including conventional AD and the emerging BSFL conversion for their potential to recover C-N-P across lab-scale to pilot/full-scale implementations. A full-scale anaerobic system achieved a high methane yield of 667 mL/g VS, recovering 53.2 % of the food waste C with most N and P remained in digestate. In the BSFL system, increased larval density and feeding frequency significantly enhanced larval biomass production, with a peak yield of 309.2 g/kg dry food waste. Pilot-scale trials demonstrated that 29.1 % of C, 34.4 % of N, and 32.7 % of P were effectively converted into larval biomass, which holds value as protein-rich bioresource. Metagenomic analysis revealed that acetate-producing and syntrophic acetate-oxidizing bacteria, along with hydrogenotrophic methanogens, dominated microbial metabolism in AD systems. Meanwhile, a stable gut microbiota composed of Enterococcus, Actinomyces, and Morganella facilitated organic matter assimilation in BSFL conversion. Based on these findings, we propose an integrated technological framework to optimize full-spectrum resource recovery from food waste. This is the first study to systematically compare AD and BSFL technologies for nutrient recovery from food waste, providing a scientific foundation for the development of circular and sustainable food waste management strategies.},
}

@article {pmid40946204,
year = {2025},
author = {Burnett, J and Buckley, D and Grinstead, DA and Oliver, HF},
title = {Microbial Community Associations With Listeria monocytogenes in Food Processing Environments: A Systematic Review and Meta-Analysis.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {5},
pages = {e70277},
doi = {10.1111/1541-4337.70277},
pmid = {40946204},
issn = {1541-4337},
support = {//Diversey/ ; },
abstract = {Listeria monocytogenes persistence in food processing environments challenges current understanding of microbial community dynamics. This systematic review and meta-analysis examined peer-reviewed studies that screened for Listeria spp. and performed culture-independent metagenomics on FPE surface samples. Following PRISMA guidelines, we searched PubMed, Web of Science, and Food Science and Technology Abstracts databases, screening 464 studies, with 73 qualifying for full-text review. Seven studies met the inclusion criteria for final analysis, encompassing 1659 environmental samples from meat processing (n = 4 studies) and produce facilities (n = 3 studies). Meta-analysis using random effects models revealed no significant correlation between Listeria presence and overall microbial community alpha diversity (Shannon: z = -0.89, p = 0.40; inverse Simpson and Chao1 indices similarly non-significant). This finding challenges previous assumptions about the relationship between microbial diversity and pathogen persistence. Differential abundance analyses identified three genera most frequently associated with Listeria presence across multiple studies: Pseudomonas, Psychrobacter, and Acinetobacter. These Gammaproteobacteria are characterized as aerobic biofilm formers capable of growth at refrigeration temperatures. One study using rigorous mixed-effects modeling identified Veillonella as significantly associated with L. monocytogenes presence, suggesting potential anaerobic niche interactions within biofilm communities. Synthesis of metabolic capabilities reported in the literature suggests these associated genera may provide structural biofilm matrices and potentially complementary metabolic functions that could facilitate L. monocytogenes survival in FPE conditions. However, the genus-level resolution of 16S rRNA amplicon sequencing data and methodological variations across studies limit definitive conclusions about specific metabolic interactions. These findings indicate that L. monocytogenes persistence appears to be associated with specific microbial partners rather than overall community diversity metrics. Understanding these ecological relationships may inform targeted control strategies focusing on biofilm-forming genera that create favorable conditions for Listeria survival in food processing environments.},
}

@article {pmid40945449,
year = {2025},
author = {Wang, X and Wang, J and Li, Z and Yang, M and Rehman, A},
title = {Alginate-driven co-metabolic degradation mechanism of sulfamethoxazole by marine consortia.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139778},
doi = {10.1016/j.jhazmat.2025.139778},
pmid = {40945449},
issn = {1873-3336},
abstract = {Pharmaceuticals and personal care products (PPCPs), known for their severe ecological risks, are frequently detected in coastal waters worldwide. However, the environmental fate in marine systems remains poorly understood. This study investigated the co-metabolic degradation mechanism of a typical PPCP, sulfamethoxazole (SMX), by a marine consortium SAB using alginate-a natural organic matter-as a co-substrate, aiming to elucidate the biodegradation process of PPCPs in actual marine environments. An integrated approach, including metagenomic sequencing (with binning), RT-qPCR, molecular docking, metabolic modeling, and metabolomics, was employed. Results demonstrated that the SAB consortium efficiently degraded SMX at concentrations from 50 μg/L to 10 mg/L, achieving over 96 % removal within 24 h. SMX degradation was achieved through metabolic cross-feeding of alginate by key species within the SAB consortium. Specifically, alginate is initially converted by Vibrio into the central metabolite 2-keto-3-deoxy-D-gluconate (KDG). KDG is subsequently metabolized by Tritonibacter, Halopseudomonas, and Vibrio, generating key metabolites such as acetyl-CoA, serine, cysteine, and guanine. These metabolites support microbial growth and induce production of SMX-degrading enzymes, such as threonine dehydratase, cysteine S-conjugate β-lyase, and guanine deaminase, leading to SMX cleavage and mineralization. Additionally, acetyl-CoA provides acetyl groups for arylamine N-acetyltransferase-mediated SMX acetylation. These processes collectively drive the co-metabolic degradation of SMX. Overall, this study provides critical insights into PPCPs' fate in marine environments.},
}

@article {pmid40945361,
year = {2025},
author = {Zhang, M and Zhang, D and Zhou, B and Wu, Q and Liu, X and Wang, M and Liang, J and Zhou, L},
title = {Metagenomic insights into fungal enzyme-mediated propionic acid production from food waste via succinic acid pathway.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127243},
doi = {10.1016/j.jenvman.2025.127243},
pmid = {40945361},
issn = {1095-8630},
abstract = {Employing fungal enzyme additives as a pretreatment for propionic acid (PA) production from food waste is a promising approach to achieving sustainable waste management. This study explored the feasibility and underlying mechanisms of complex enzyme pretreatment in promoting PA-oriented metabolic via mixed cultures. PA-orienting fermentation was achieved under complex enzyme (CE) pretreatment at pH 7, with PA concentration and proportion of 12.6 ± 0.80 g·COD/L and 39.0 ± 1.10 % of total VFAs, respectively. CE addition significantly enhanced hydrolysis and acidogenesis, improving the simultaneous conversion of polysaccharides and proteins. Bacteroides, including B. ovatus, B. sp. M10, and B. xylanisolvens, P. saccharofermentans and E. coil significantly enriched as the dominant species in PA-type fermentation system. Succinic acid pathway emerged as the primary metabolic route for PA production. Functional genes associated with this pathway, including K01676, K01079, frdA, sdhAD, sucCD, MUT, and ACSS, were significantly upregulated with CE addition. The findings provide a practical strategy for designing and optimizing VFA production from food waste, advancing sustainable waste valorization.},
}

@article {pmid40945100,
year = {2025},
author = {Caley, A and Marzinelli, EM and Mayer-Pinto, M},
title = {Limited microbial community responses of marine macroalgae to artificial light at night and moderate warming conditions.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107536},
doi = {10.1016/j.marenvres.2025.107536},
pmid = {40945100},
issn = {1879-0291},
abstract = {Multiple stressors such as Artificial Light at Night (ALAN) and warming are increasingly common in marine systems and can interact in complex ways. Microbial communities play critical roles in the functioning of coastal habitat-forming species such as seaweeds, however the effects of ALAN on seaweed-associated microbial communities remain unknown. We tested the independent and combined effects of ALAN and warming on microbial communities associated with the habitat-forming seaweeds Ecklonia radiata and Sargassum sp. In Ecklonia, ALAN increased the relative abundance of two potentially light-responsive taxa: Dokdonia sp000212355 and an unidentified ASV from Pseudomonadales, whereas warming had the opposite effect. Warming increased microbial community dispersion in Ecklonia and resulted in non-significant increases in relative abundance of putative pathogenic and agarolytic taxa (microbes capable of degrading algal polysaccharides). However, further analyses using metagenomics are needed to confirm functional roles. In contrast, neither ALAN nor warming affected dominant taxa associated with Sargassum. Contrary to expectations, cyanobacteria relative abundance was unaffected by ALAN in either seaweed host, despite their photosynthetic capacity. We found limited evidence for interactive effects of ALAN and warming, and community composition remained unchanged in both seaweed species. Our findings highlight the importance of considering species-specific microbial responses to ALAN and warming, with implications for coastal management.},
}

@article {pmid40945093,
year = {2025},
author = {Niu, Y and Zhang, X and Jiao, M and Storey, KB and Shekhovtsov, SV},
title = {Metabolic plasticity and gut microbiome synergy underlie high-altitude adaptation in the plateau frog Rana kukunoris: A multi-omics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119050},
doi = {10.1016/j.ecoenv.2025.119050},
pmid = {40945093},
issn = {1090-2414},
abstract = {Life on the Qinghai-Tibet Plateau is exposed to extreme abiotic stressors, yet endemic frog species such as Rana kukunoris thrive due to specialized adaptations. However, the metabolic and gut microbial mechanisms that enable survival at high altitude remain unclear. Here, we used metabolomic analysis and metagenomic sequencing to compare metabolic profiles of liver and skeletal muscle, as well as gut microbial composition and function, between high- (3730 m) and low-altitude (1990 m) populations. Metabolomic profiling revealed significant altitude-driven shifts, including the down-regulation of glycolysis (fructose-1,6-bisphosphate and glyceraldehyde 3-phosphate decreased by 44.2 % and 40.7 %, respectively) and tricarboxylic acid (TCA) cycle intermediates (fumaric acid and malic acid reduced by 37.7 % and 35.9 %, respectively) in the liver, and enhanced oxidative phosphorylation efficiency via elevated flavins (flavin mononucleotide and flavin adenine dinucleotide increased 1.43- and 1.28-fold, respectively) in skeletal muscle. These findings suggest a conserved strategy of metabolic rate depression and tissue-specific metabolic regulation. Significantly differential metabolites were enriched in glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis, highlighting membrane remodeling as a key adaptive response to cold stress at high altitudes. Moreover, gut microbiomes of high-altitude frogs exhibited increased α-diversity and functional enrichment in the biosynthesis of secondary metabolites, cofactors, amino acids, and carbohydrate-active enzymes (GHs/GTs), all likely improving tolerance to stressful environments and maintaining homeostasis. Key microbial taxa, including Candidatus Udaeobacter, Desulfovibrio, Bradyrhizobium, and Akkermansia, showed a specific dominance in high-altitude frogs, which may support host energy homeostasis and fortify gut barrier function. Multi-omics data highlighted the convergence of protective mechanisms in high-altitude frogs, including autophagy and two-component/quorum sensing systems. This study reveals significant adaptive remodeling of metabolism and gut microbiota in high-altitude R. kukunoris, providing novel insights into host-microbe synergistic interactions under extreme environments.},
}

@article {pmid40945085,
year = {2025},
author = {Wang, J and Zhang, Q and Wang, M and Li, W and Zhuang, Y and Huang, T and Yang, Z and Huang, J},
title = {Integrated field-scale natural composite oxidation pond system for livestock wastewater treatment: Microbial insights and nutrient removal dynamics.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119026},
doi = {10.1016/j.ecoenv.2025.119026},
pmid = {40945085},
issn = {1090-2414},
abstract = {Livestock wastewater rich in organic matter, nitrogen, and phosphorus can cause eutrophication and degrade aquatic ecosystems. Current water management practices in rural areas are insufficient to meet environmental protection requirements, highlighting the urgent need for low-cost, low-energy, ecologically sustainable approaches to livestock wastewater management across diverse settings. However, current hybrid systems are often limited to lab-scale or pilot studies. Therefore, we developed a natural composite oxidation pond system, integrating biological contact, oxidation ponds, and artificial aeration, to treat piggery wastewater, while simultaneously supporting aquaculture. High-resolution in-situ monitoring, metagenomic sequencing, and partial least squares modelling were employed to assess the system's pollutant removal performance and to elucidate the underlying mechanisms. The natural composite oxidation pond systems achieved average removal efficiencies of 76.6 ± 9.5 %, 60.8 ± 23.1 %, 70.8 ± 10.4 %, 74.2 ± 11.6 %, 81.9 ± 13.0 %, and 78.9 ± 39.5 % for total phosphorus, soluble reactive phosphorus, total nitrogen, NH4[+]-N, NO3[-]-N, and NO2[-]-N, respectively (n = 72), improving water quality from inferior Class V (pond 1) to Class IV or V (pond 4 or pond 5). The removal efficiencies of soluble reactive phosphorus, NO3[-]-N, and NO2[-]-N showed significant variation with temperature (p ≤ 0.01). Proteobacteria dominated nitrogen removal through dissimilatory nitrate reduction and denitrification, with sediment microbes playing a more prominent role than water-column communities. Despite seasonal variability challenges, this closed-loop system provides a sustainable, dual-purpose approach to rural wastewater treatment and resource recovery.},
}

@article {pmid40944761,
year = {2025},
author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U},
title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.},
journal = {Neurosurgical review},
volume = {48},
number = {1},
pages = {641},
pmid = {40944761},
issn = {1437-2320},
abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.},
}

@article {pmid40943747,
year = {2025},
author = {Pasricha, ND and Larco, P and Miller, D and Altamirano, DS and Rose-Nussbaumer, JR and Alfonso, EC and Amescua, G},
title = {Infectious Keratitis Management: 10-Year Update.},
journal = {Journal of clinical medicine},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/jcm14175987},
pmid = {40943747},
issn = {2077-0383},
support = {1K08EY033859-05/NH/NIH HHS/United States ; Career Development Award//Research to Prevent Blindness/ ; Grant//All May See Foundation/ ; },
abstract = {Infectious keratitis (IK), including bacterial, fungal, parasitic, and viral etiologies, continues to represent a significant cause of ocular morbidity in the United States and around the world. Corneal scraping for smears and cultures remains the gold standard in diagnosing IK; however, molecular diagnoses, including metagenomic deep sequencing (MDS), are promising emerging diagnostic tools. Despite recent interest in procedural treatment such as riboflavin photoactivated chromophore corneal collagen cross-linking (PACK-CXL) and Rose Bengal photodynamic antimicrobial therapy (RB-PDAT), medical treatment advances have remained stagnant. Methods: This review highlights IK pathogens obtained from corneal cultures at Bascom Palmer Eye Institute (BPEI) from 2011 to 2021 and provides the current BPEI algorithms for initial management of IK or as a referred clinically worsening patient. The roles of corticosteroid therapy, PACK-CXL, and RB-PDAT for IK are also summarized. Results: A total of 9326 corneal cultures were performed at BPEI between 2011 and 2021, and only 3609 (38.7%) had a positive organism identified, of which bacteria were the most common (83.4%). Fortified vancomycin and tobramycin are recommended as first-line medical therapy for IK patients based on culture sensitivity data for the top Gram-negative (Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus) bacteria. PACK-CXL and RB-PDAT may benefit IK patients with corneal melting and fungal IK, respectively. Conclusions: Drug holidays, minimizing contamination, and optimizing sample order are crucial to maximizing corneal culture positivity. PACK-CXL and RB-PDAT are promising procedural advancements for IK therapy.},
}

@article {pmid40943646,
year = {2025},
author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A},
title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178724},
pmid = {40943646},
issn = {1422-0067},
support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.},
}

@article {pmid40943581,
year = {2025},
author = {Gałęcki, R and Nowak, A and Szulc, J},
title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178663},
pmid = {40943581},
issn = {1422-0067},
support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; },
abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.},
}

@article {pmid40943207,
year = {2025},
author = {Gilyazova, I and Korytina, G and Kochetova, O and Savelieva, O and Mikhaylova, E and Vershinina, Z and Chumakova, A and Markelov, V and Abdeeva, G and Karunas, A and Khusnutdinova, E and Gusev, O},
title = {Advances in Genomics and Postgenomics in Poultry Science: Current Achievements and Future Directions.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178285},
pmid = {40943207},
issn = {1422-0067},
support = {№ 075-15-2025-484//Government of Russian Federation/ ; },
abstract = {The poultry industry, a globally fast growing agricultural sector, provides affordable animal protein due to high efficiency. Gallus gallus domesticus are the most common domestic birds. Hybrid chicken breeds (crosses) are widely used to achieve high productivity. Maintaining industry competitiveness requires constant genetic selection of parent stock to improve performance traits. Genetic studies, which are essential in modern breeding programs, help identify genome variants linked to economically important traits and preserve population health. Next-generation sequencing (NGS) has identified millions of single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), enabling detection of genome-wide regions associated with selection traits. Recent studies have pinpointed such regions using broiler lines, laying hen lines, or pooled genomic data. This review discusses advances in chicken genomic and transcriptomic research focused on traits enhancing meat breed performance and reproductive abilities. Special attention is given to transcriptome studies revealing regulatory mechanisms and key signaling pathways involved in artificial molting, as well as metagenome studies investigating resistance to infectious diseases and climate adaptation. Finally, a dedicated section highlights CRISPR/Cas genomic editing techniques for targeted genome modification in chicken genomics.},
}

@article {pmid40943165,
year = {2025},
author = {Wang, R and Ren, W and Liu, S and Li, Z and Li, L and Ma, S and Yao, X and Meng, J and Zeng, Y and Wang, J},
title = {Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178239},
pmid = {40943165},
issn = {1422-0067},
support = {2022A02007-1 and ZYYD2025JD02.//Xinjiang Uygur Autonomous Region Major Science and Technology Special Project and the Central Guidance for Local Science and Technology Development Fund/ ; },
abstract = {This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods.},
}

@article {pmid40942030,
year = {2025},
author = {Wang, W and Wei, J and Guo, Z and Bai, X and Song, Y},
title = {Reduction in ARGs and Mobile Genetic Elements Using 2-Bromoethane Sulfonate in an MFC-Powered Fenton System.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {17},
pages = {},
doi = {10.3390/molecules30173502},
pmid = {40942030},
issn = {1420-3049},
support = {2025YSKY-20//Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China/ ; 2022-YRUC-01-050206-017//Joint Research Program for Ecological Conservation and High Quality Development of the Yellow River Basin/ ; },
abstract = {The integration of an MFC-powered Fenton (MFC-Fenton) system into the traditional anaerobic composting process can promote excess dewatered sludge (ES) decomposition. However, the antibiotic resistance gene (ARG) profiles in ES treated by MFC-Fenton systems remain poorly understood; in addition, the effect of adding 2-bromoethane sulfonate (BES, a methane inhibitor) during ES treatment using an MFC-Fenton system on ARG levels is largely unexplored. The present work focused on investigating the effects of BES and bioelectrochemical processes on ARG and MGE abundances and unraveling the ARG attenuation mechanism. According to our findings, adding BES promoted ARG reduction in ES in an MFC-Fenton system. The average ARG levels in the MFC-Fenton samples containing high BES contents (0.4 or 0.5 g BES/g VSS) markedly declined relative to those in samples containing lower BES levels. Moreover, macrolide transporter ATP-binding protein, macrolide-efflux protein, and macB levels markedly decreased as BES levels increased. BES supplementation and bioelectrochemical assistance were crucial for altering the ARG composition in the MFC-Fenton system. Changes in the microbial community composition had the greatest effect on the variation in ARG composition. Furthermore, the Actinobacteria and Firmicutes levels accounted for 52.8% of the overall ARG variation. Among MGEs, plasmids, insertion sequences, and integrons showed lower levels within the sludge metagenomes. Typically, sulI, sulII, tetG, and bla TEM levels were positively correlated with metal resistance genes (MRGs), and their levels markedly declined following the MFC-Fenton process. Thus, the collective evidence indicates that BES synergizes with bioelectrogenesis to reduce ARG abundance.},
}

@article {pmid40941824,
year = {2025},
author = {Fernández-Pastrana, VM and González-Reguero, D and Robas-Mora, M and Penalba-Iglesias, D and Alonso-Torreiro, P and Probanza, A and Jiménez-Gómez, PA},
title = {Biotechnological Test of Plant Growth-Promoting Bacteria Strains for Synthesis of Valorized Wastewater as Biofertilizer for Silvicultural Production of Holm Oak (Quercus ilex L.).},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172654},
pmid = {40941824},
issn = {2223-7747},
abstract = {The degradation of Mediterranean forest ecosystems, such as holm oak forests, has intensified in recent decades due to climate change, forest fires, and deforestation, compromising the natural regeneration of the soil. In this context, it is essential to apply sustainable strategies to restore soil and promote plant growth, thus helping the regeneration of the ecosystem. One of these strategies is the use of plant growth-promoting bacteria (PGPB) in combination with recovered organic waste, such as that from wastewater treatment plants (WWTPs). In this paper, the effects of a biofertilizer formulated from WWTP residue (with and without sterilization), supplemented with two PGPB strains (Bacillus pretiosus and Pseudomonas agronomica), on the growth of holm oak seedlings (Quercus ilex) were evaluated under field conditions. A study was carried out on its nutritional composition, the rhizospheric cenoantibiogram, and its functional and taxonomic microbial diversity. Nine combinations of chemical and biological treatments using irrigation with water as a control were compared. The results showed that treatments with WWTP, especially combined with PGPB strains, promoted greater plant development and a lower seedling mortality rate. The cenoantibiogram exhibited a reduction in the resistance profile in soils treated with biofertilizer, without affecting soil microbial diversity, which remained unaltered across treatments, as confirmed by metagenomic and functional diversity analyses. Overall, this research reinforces the viability of the use of biofertilizers recovered from WWTP as an ecological and effective strategy for the recovery of degraded holm oak forests.},
}

@article {pmid40941779,
year = {2025},
author = {Belevich, TA and Milyutina, IA and Demidov, AB and Vorob'eva, OV and Polukhin, AA and Shchuka, SA and Troitsky, AV},
title = {Distribution and Phylogenetic Diversity of Synechococcus-like Cyanobacteria in the Late Autumn Picophytoplankton of the Kara Sea: The Role of Atlantic and Riverine Water Masses.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172614},
pmid = {40941779},
issn = {2223-7747},
support = {24-24-00022//Russian Science Foundation/ ; },
abstract = {Increased Atlantic water transport and river discharge are more pronounced effects of global warming at high latitudes. Both phenomena may lead to changes in the species composition of small-celled algae populations in marine ecosystems, as well as to the emergence of new species. This study investigated the spatial distribution of picocyanobacterial (PC) abundance and the phylogenetic diversity of PC Synechococcus in the Kara Sea. PC abundance varied from 2 to 88 cells mL[-1] and increased with warming temperatures and decreasing salinity caused by river water influence. The contribution of Synechococcus to the total picophytoplankton biomass was low (<16%). The Synechococcus community was characterized at deep taxonomic level using amplicon sequencing targeting the petB gene. Diversity was low, revealing only Synechococcus subcluster 5.1 polar lineages I and IV, and euryhaline subcluster 5.2. Synechococcus subcluster 5.1.I represented on average 97% of the total reads assigned to cyanobacteria. For the first time, the presence of estuarine Synechococcus subcluster 5.2 was documented as far north as 82° N. Modified Atlantic water was the main source of cyanobacteria in the Kara Sea, followed by river discharge. Our study contributes to the understanding of PC sources in the Kara Sea and allows for the further monitoring of PC distribution and evolution.},
}

@article {pmid40941733,
year = {2025},
author = {Alatawi, AD and Hetta, HF and Ali, MAS and Ramadan, YN and Alaqyli, AB and Alansari, WK and Aldhaheri, NH and Bin Selim, TA and Merdad, SA and Alharbi, MO and Alatawi, WAH and Algammal, AM},
title = {Diagnostic Innovations to Combat Antibiotic Resistance in Critical Care: Tools for Targeted Therapy and Stewardship.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172244},
pmid = {40941733},
issn = {2075-4418},
abstract = {Antibiotic resistance is a growing global health threat, with critical care settings representing one of the most vulnerable arenas due to the high burden of infection and frequent empirical antibiotic use. Rapid and precise diagnosis of infectious pathogens is crucial for initiating appropriate therapy, minimizing unnecessary antimicrobial exposure, and supporting effective stewardship programs. This review explores how innovative diagnostic technologies are reshaping infection management and antimicrobial stewardship in critical care. We examine the clinical utility of molecular assays, multiplex PCR, MALDI-TOF mass spectrometry, metagenomic sequencing, point-of-care (POC) diagnostics, and emerging tools like biosensors and AI-powered predictive models. These platforms enable earlier pathogen identification and resistance profiling, facilitating timely and targeted therapy while minimizing unnecessary broad-spectrum antibiotic use. By integrating diagnostics into stewardship frameworks, clinicians can optimize antimicrobial regimens, improve patient outcomes, and reduce resistance selection pressure. Despite their promise, adoption is challenged by cost, infrastructure, interpretation complexity, and inequitable access, particularly in low-resource settings. Future perspectives emphasize the need for scalable, AI-enhanced, and globally accessible diagnostic solutions. In bridging innovation with clinical application, diagnostic advancements can serve as pivotal tools in the global effort to curb antimicrobial resistance in critical care environments.},
}

@article {pmid40941729,
year = {2025},
author = {Hu, L and Li, X and Liu, D and Yao, J and Li, X and Wang, Y},
title = {Beyond the Urogenital Tract, the Role of Ureaplasma parvum in Invasive Infection in Adults: A Case Series and Literature Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172242},
pmid = {40941729},
issn = {2075-4418},
abstract = {Background/Objectives: Ureaplasma parvum (Up) is an opportunistic pathogen associated with urogenital tract infections, pregnancy complications, and reproductive system diseases. Advances in molecular diagnostics have expanded its pathogenic spectrum to include invasive conditions such as arthritis, meningitis, and pneumonia. However, the pathogenic significance of Up remains controversial. Methods: This study retrospectively analyzed nine adult cases of Up detected by metagenomic next-generation sequencing (mNGS) between 2023 and 2024. Results: Patients, aged 21 to 70 years, predominantly had underlying immunosuppressive conditions (66.7%). Infections involved the urinary system (44.4%), respiratory system (33.3%), and peritoneal cavity (22.2%). Symptomatic relief was achieved in five cases following treatment with tetracyclines, quinolones or tigecycline. Conclusions: These findings highlight Up as a potential causative agent of invasive infections, particularly in immunocompromised patients. Up has potential pathogenic significance, whether it is detected as a single pathogen or as a coexisting pathogen.},
}

@article {pmid40941705,
year = {2025},
author = {Wang, Q and Ling, Y and Huang, Y and Zhao, L and Lou, Z and Fan, G and Xue, J},
title = {An Unveiling of the Misdiagnosis of Granulomatosis with Polyangiitis as Acute Sinusitis: A Case Report.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172218},
pmid = {40941705},
issn = {2075-4418},
abstract = {Background and Clinical Significance: Granulomatosis with polyangiitis (GPA), an immune-mediated systemic small-vessel vasculitis affecting the upper/lower respiratory tracts and kidneys, frequently presents with non-specific nasal symptoms that lead to misdiagnosis. Case Presentation: We report a case of a 55-year-old female with GPA complicated by Bartter syndrome. She presented with one month of left nasal congestion, rhinorrhea, epistaxis, and headache. Initial diagnosis was acute sinusitis. Computed tomography (CT) revealed left maxillary and ethmoid sinus inflammation with bone destruction, while metagenomic next-generation sequencing (mNGS) suggested conventional bacterial infection. Postoperative pathology demonstrated chronic mucosal inflammation with lymphoid tissue hyperplasia. GPA was ultimately diagnosed based on PR3-ANCA seropositivity and chest CT findings of cavitary pulmonary nodules. Postoperatively, severe hypokalemia and hypomagnesemia secondary to Bartter syndrome emerged. Following electrolyte correction, induction therapy with glucocorticoids and cyclophosphamide was initiated. Conclusions: This case underscores that GPA's head and neck manifestations are frequently misdiagnosed as infections or malignancies. Early diagnosis requires vigilance for GPA 'red flags', such as refractory nasal symptoms to conventional therapy (e.g., bloody rhinorrhea), characteristic CT findings (e.g., sinus opacification without ostiomeatal complex obstruction), and nasal endoscopy findings (e.g., ulcers/crusting). Otolaryngologists play a pivotal role in recognizing early disease onset and initiating timely treatment.},
}

@article {pmid40941662,
year = {2025},
author = {Papa Mze, N and Fernand-Laurent, C and Maxence, S and Zanzouri, O and Daugabel, S and Marque Juillet, S},
title = {Optimization of 16S RNA Sequencing and Evaluation of Metagenomic Analysis with Kraken 2 and KrakenUniq.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172175},
pmid = {40941662},
issn = {2075-4418},
abstract = {Background/Objectives: 16S ribosomal RNA sequencing has, for several years, been the main means of identifying bacterial and archaeal species. Low-throughput Sanger sequencing is often used for the detection and identification of microbial species, but this technique has several limitations. The use of high-throughput sequencers may be a good alternative to improve patient identification, especially for polyclonal infections and management. Kraken 2 and KrakenUniq are free, high-throughput tools providing a very rapid and accurate classification for metagenomic analyses. However, Kraken 2 can present false-positive results relative to KrakenUniq, which can be limiting in hospital settings requiring high levels of accuracy. The aim of this study was to establish an alternative next-generation sequencing technique to replace Sanger sequencing and to confirm that KrakenUniq is an excellent analysis tool that does not present false results relative to Kraken 2. Methods: DNA was extracted from reference bacterial samples for Laboratory Quality Controls (QCMDs) and the V2-V3 and V3-V4 regions of the 16S ribosomal gene were amplified. Amplified products were sequenced with the Illumina 16S Metagenomic Sequencing protocol with minor modifications to adapt and sequence an Illumina 16S library with a small 500-cycle nano-flow cell. The raw files (Fastq) were analyzed on a commercial Smartgene platform for comparison with Kraken 2 and KrakenUniq results. KrakenUniq was used with a standard bacterial database and with the 16S-specific Silva138, RDP11.5, and Greengenes 13.5 databases. Results: Seven of the eight (87.5%) QCMDs were correctly sequenced and identified by Sanger sequencing. The remaining QCMD, QCMD6, could not be identified through Sanger sequencing. All QCMDs were correctly sequenced and identified by MiSeq with the commercial Smartgene analysis platform. QCMD6 contained two bacteria, Acinetobacter and Klebsiella. KrakenUniq identification results were identical to those of Smartgene, whereas Kraken 2 yielded 25% false-positive results. Conclusions: If Sanger identification fails, MiSeq with a small nano-flow cell is a very good alternative for the identification of bacterial species. KrakenUniq is a free, fast, and easy-to-use tool for identifying and classifying bacterial infections.},
}

@article {pmid40941485,
year = {2025},
author = {Wright, SL and Slusanschi, O and Giura, AC and Părlătescu, I and Funieru, C and Gaidula, SM and Moore, NE and Weyrich, LS},
title = {SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
doi = {10.3390/healthcare13172133},
pmid = {40941485},
issn = {2227-9032},
abstract = {Periodontal disease is a widespread chronic condition linked to systemic illnesses such as cardiovascular disease, diabetes, and adverse pregnancy outcomes. Despite its global burden, population-specific studies on its risk factors remain limited, particularly in Central and Eastern Europe. The SANA-biome Project is a cross-sectional, community-based study designed to investigate the biological and social determinants of periodontal disease in Romania, a country with disproportionately high oral disease rates and minimal microbiome data. This protocol will integrate metagenomic, proteomic, and metabolomic data of the oral microbiome from saliva and dental calculus samples with detailed sociodemographic and lifestyle data collected through a structured 44-question survey. This study is grounded in two complementary frameworks: the IMPEDE model, which conceptualizes inflammation as both a driver and a consequence of microbial dysbiosis, and Ecosocial Theory, which situates disease within social and structural contexts. Our aims are as follows: (1) to identify lifestyle and behavioral predictors of periodontal disease; (2) to characterize the oral microbiome in individuals with and without periodontal disease; and (3) to evaluate the predictive value of combined microbial and sociodemographic features using statistical and machine learning approaches. Power calculations based on pilot data indicate a target enrollment of 120 participants. This integrative approach will help disentangle the complex interplay between microbiological and structural determinants of periodontal disease and inform culturally relevant prevention strategies. By focusing on an underrepresented population, this work contributes to a more equitable and interdisciplinary model of oral health research and supports the development of future precision public health interventions.},
}

@article {pmid40941346,
year = {2025},
author = {Ishii, PE and Teixeira, FA and Lin, CY and Naqvi, SA and Sardi, MI and Norton, SA and Jarett, JK and Khafipour, E and Frantz, N and Chakrabarti, A and Suchodolski, JS},
title = {Effects of a Saccharomyces cerevisiae Fermentation Product on Diet Palatability and Feline Intestinal Health, Immunity, and Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/ani15172551},
pmid = {40941346},
issn = {2076-2615},
abstract = {This study evaluated the effects of adding a Saccharomyces cerevisiae fermentation product (SCFP) to adult cat diets on palatability, intestinal health, nutrient digestibility, immune parameters, and the fecal microbiome over 42 days. Sixty-three healthy Domestic Short-hair cats were randomized to three diets: a control diet (CD) without SCFP, or the same diet containing 1.0% or 2.0% SCFP, targeting daily intakes of 150 or 300 mg/kg body weight, respectively. Body weight and blood parameters remained within reference ranges across all groups. Stool quality was largely not affected, although compared with controls, SCFP-supplemented cats had slightly firmer stools at day 21, and increased fecal pH. Shotgun metagenomic sequencing revealed that microbiome diversity remained steady in SCFP-fed cats, whereas diversity in the control group declined over time. Fecal immunoglobulin A concentrations were lower in cats supplemented with SCFP at 150 mg/kg BW by the end of the study, and positive shifts in the circulatory leukocyte profile were observed at both inclusion levels. Apparent total tract macronutrient digestibility did not differ among groups. Palatability tests showed diets with SCFP were generally preferred, indicating a potential benefit for commercial feline feeds, particularly at the 150 mg/kg BW level, which was preferred over 300 mg/kg BW. Overall, these findings suggest that SCFP can act as a functional ingredient in feline nutrition to maintain microbial diversity and enhance diet acceptance without compromising digestibility.},
}

@article {pmid40941237,
year = {2025},
author = {Xu, P and He, Y and Wang, J and Sheng, Y and Wang, J},
title = {Blueberry Anthocyanins Ameliorate Hepatic Dysfunction in High-Fat Diet-Fed Mice: Association with Altered Gut Microbiota and Bile Acid Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173121},
pmid = {40941237},
issn = {2304-8158},
support = {2021DG700024-KF202407//open project titled "Identification of Anti-Damage Functional Factors in Anoectochilus roxburghii and Their Mechanisms of Action"/ ; },
abstract = {The rapid rise in obesity has evolved into a critical global public health concern. Considering the potential adverse effects of current anti-obesity medications, the development of functional foods sourced from natural materials has emerged as a viable alternative. Blueberries, a category of berry fruits, exhibit potential anti-obesity characteristics. In this research, we assessed the impacts of Blueberry extract rich in anthocyanins (BE) on lipid metabolism and liver health in a high-fat diet (HFD)-induced obese mouse model. The findings indicated that BE notably diminished lipid accumulation in both serum and the liver, and mitigated hepatic steatosis and oxidative stress. Integrated proteomic, metagenomic, and metabolomic analyses further revealed the underlying mechanisms. Consumption of BE intake reconfigured the gut microbiota composition and reduced the microbial capacity for secondary bile acid metabolism, thereby interrupting bile acid recycling and facilitating fecal excretion. This process led to a reduction in systemic cholesterol levels and ultimately alleviated hepatic lipid accumulation, resulting in enhanced liver health.},
}

@article {pmid40941211,
year = {2025},
author = {Yu, Z and Zhao, H and Ma, T and Zhang, X and Yan, Y and Zhu, Y and Yu, Y},
title = {Insights into the Composition and Function of Virus Communities During Acetic Acid Fermentation of Shanxi Aged Vinegar.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173095},
pmid = {40941211},
issn = {2304-8158},
support = {2023M741438//China Postdoctoral Science Foundation/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; },
abstract = {Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems.},
}

@article {pmid40941207,
year = {2025},
author = {Kyoung, M and Lee, JI and Kim, SS},
title = {Effects of UVC Treatment on Biofilms of Escherichia coli Strains Formed at Different Temperatures and Maturation Periods.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173091},
pmid = {40941207},
issn = {2304-8158},
abstract = {In the present study, the biofilm formation and ultraviolet-C (UVC) resistance characteristics of Escherichia coli isolated from an occluded biliary stent were compared with those of four E. coli O157:H7 strains (ATCC 35150, 43889, 43890, and 43895). To evaluate biofilm formation, the E. coli isolated from a stent and four E. coli O157:H7 strains were incubated at 37, 25, and 15 °C for 7 days, revealing that peak biofilm formation occurred at 37 °C (day 1), 25 °C (day 3), and 15 °C (day 5), with the stent-isolated strain consistently exhibiting significantly higher biofilm cell counts than the others (p < 0.05). The UVC treatment was less effective at reducing viable biofilm cells as the formation temperature decreased, with the stent-isolated E. coli biofilm formed at 15 °C showing the lowest reduction levels. Exopolysaccharide quantification revealed that all E. coli strains produced more extracellular polymeric substances (EPSs) at lower temperatures, with the stent-isolated E. coli biofilm formed at 15 °C showing significantly higher EPS levels than the other strains (p < 0.05), potentially explaining its greater UVC resistance. Based on these results, it was confirmed that the biofilm formed by the E. coli isolated from the stent at 15 °C exhibited the highest resistance to UVC, which can be attributed to its elevated exopolysaccharide production. This study demonstrates that both temperature and maturation period significantly influence E. coli biofilm characteristics and provides valuable insights into E. coli isolated from the stent, which may pose a risk of cross-contamination in food-related environments.},
}

@article {pmid40941186,
year = {2025},
author = {Dissook, S and Thongkumkoon, P and Noisagul, P and Sriaporn, C and Suwannapat, S and Pramoonchakko, W and Suksawat, M and Kulthawatsiri, T and Phetcharaburanin, J and Chewonarin, T and Ruangsuriya, J},
title = {Insights into Microbial and Metabolite Profiles in Traditional Northern Thai Fermented Soybean (Tuanao) Fermentation Through Metagenomics and Metabolomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173070},
pmid = {40941186},
issn = {2304-8158},
support = {FF66/023//Fundamental Fund 2023, Chiang Mai University/ ; },
abstract = {Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside 1H-NMR and UHPLC-ESI-QTOF-MS/MS metabolomics. Bacillus spp. (phylum Bacilliota) quickly supplanted early Enterobacterales and dominated the mature microbiome. The rise of Bacillus coincided with genes for peptide and carbohydrate utilization and with the accumulation of acetate, free amino acids (glutamine, leucine, alanine, valine) and diverse oligopeptides, whereas citrate and glucose-1-phosphate were depleted. This Bacillus-linked metabolic shift indicates that Tuanao is a promising source of probiotics and bioactive compounds. Our study provides the first system-level view of Tuanao fermentation and offers molecular markers to guide starter-culture design and quality control.},
}

@article {pmid40940618,
year = {2025},
author = {Valiauga, B and Žulpaitė, D and Sharrock, AV and Ackerley, DF and Čėnas, N},
title = {Novel TdsD nitroreductase: characterization of kinetics and substrate specificity.},
journal = {Biotechnology letters},
volume = {47},
number = {5},
pages = {103},
pmid = {40940618},
issn = {1573-6776},
abstract = {The reduction of quinones and nitroaromatic compounds catalyzed by Type I nitroreductases is important due to its role in their potential cytotoxic effects and/or biodegradation. The main goal of this work was to investigate the mechanism of catalysis of a TdsD nitroreductase (NR) (TdsD1), a member from an understudied branch of the nitroreductase superfamily, derived from a soil metagenome study. Like the Type I NRs NfsA and NfsB, TdsD1 performed two-electron reduction of quinones and four-electron reduction of nitroaromatic compounds according to a "ping-pong" mechanism with a rate-limiting oxidative half-reaction. TdsD1 was also inhibited by the classical inhibitors of other NRs, dicoumarol and Cibacron blue. Despite sharing only a low degree of homology with the NfsA and NfsB subfamily enzymes, sequence comparisons and computer modelling point to the possibility of an analogous FMN isoalloxazine ring location within the intersubunit space of TdsD1. It also possesses similar specificity for nitroaromatic compounds and quinones, in particular the shared characteristic of being especially active with 2-hydroxy-1,4-naphthoquinone derivatives. It is possible that the similar character of binding of oxidants and other ligands relative to the NfsA and NfsB subfamily enzymes may be related to the conserved Arg27 and Ser53 residues in the active site of TdsD1.},
}

@article {pmid40940575,
year = {2025},
author = {Abenaim, L and Mercati, D and Mandoli, A and Carpentier, J and Noël, G and Conti, B and Caparros Megido, R and Dallai, R},
title = {Exploring the plastivorous activity of Hermetia illucens (Diptera Stratiomyidae) larvae.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40940575},
issn = {1614-7499},
abstract = {Hermetia illucens (Diptera Stratiomyidae), also known as Black Soldier Fly (BSF), is one of the insect species most investigated for biodegradation ability in its larvae. H. illucens larvae can biodegrade organic waste but also contaminants like pesticides, antibiotics, and mycotoxins. This study wants to investigate the ability of these larvae to degrade polystyrene (PS). Experiments evaluated the growth performance, survival rates, intestinal and intracellular morphological alterations, degradation by-product formation and intestinal microbiota alterations of larvae fed a PS-enriched diet. Despite the addition of PS microparticles, no significant differences in growth or survival were observed compared to the standard diet (p > 0.05). Confocal Laser Scanning Microscopy and Transmission Electron Microscopy confirmed the presence of PS microparticles in the larval gut, with potential signs of biodegradation. Metabolomic analyses identified styrene in the gut after 1 and 3 days of PS feeding, but its occurrence was likely due to thermal depolymerisation of the PS microparticles under GC-MS conditions. Metagenomic analysis revealed significant shifts in the intestinal microbiota. Notably, an enrichment of Corynebacterium, known for its role in aerobic PS degradation, and the abundance increase of other genera (Enterococcus, Enterobacteriaceae, Enterobacter, and Escherichia-Shigella) associated with synthetic polymer metabolism was observed. These results confirm the potential of BSF larvae to manage plastic waste through the interaction between their gut microbiota and synthetic materials. This study provides a foundation for future research focusing on isolating bacterial communities and enzymatic processes involved in polymer degradation, aiming to develop sustainable strategies for plastic waste management.},
}

@article {pmid40940533,
year = {2025},
author = {Burian, J and Boer, RE and Hernandez, Y and Morales-Amador, A and Jiang, L and Bhattacharjee, A and Panfil, C and Ternei, MA and Brady, SF},
title = {Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40940533},
issn = {1546-1696},
support = {R35GM122559//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Metagenomics provides access to the genetic diversity of uncultured bacteria through analysis of DNA extracted from whole microbial communities. Long-read sequencing is advancing metagenomic discovery by generating larger DNA assemblies than previously possible. However, harnessing the potential of long-read sequencing to access the vast diversity within soil microbiomes is hampered by the challenge of isolating high-quality DNA. Here we introduce a method that can liberate large, high-quality metagenomic DNA fragments from soil bacteria and pair them with optimized nanopore long-read sequencing to generate megabase-sized assemblies. Using this method, we uncover hundreds of complete circular metagenomic genomes from a single soil sample. Through a combination of bioinformatic prediction and chemical synthesis, we convert nonribosomal peptide biosynthetic gene clusters directly into bioactive molecules, identifying antibiotics with rare modes of action and activity against multidrug-resistant pathogens. Our approach advances metagenomic access to the vast genetic diversity of the uncultured bacterial majority and provides a means to convert it to bioactive molecules.},
}

@article {pmid40940504,
year = {2025},
author = {Ruiz-Malagón, AJ and Rodríguez-Sojo, MJ and García-García, J and Ho-Plagaro, A and García, F and Vezza, T and Redondo-Cerezo, E and Griñán-Lisón, C and Marchal, JA and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A and Gálvez, J},
title = {Tigecycline suppresses colon cancer stem cells and impairs tumor engraftment by targeting SNAI1-regulated epithelial-mesenchymal transition.},
journal = {Acta pharmacologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {40940504},
issn = {1745-7254},
abstract = {Cancer stem cells (CSCs) play a key role in the progression of colorectal cancer (CRC). The high heterogeneity of CSCs has hindered the clinical application of CSC-targeting therapies. Tetracyclines are drugs with therapeutic potentials beyond their antibiotic activity. We previously demonstrated the efficacy of tigecycline, a third-generation tetracycline, against a model of colitis-associated colorectal cancer, primarily focusing on its immunomodulatory role with a preliminary assessment of its impact on stemness. In this study we characterize the effects of tigecycline on colon CSCs in vitro and in a CRC xenograft model, with special attention on the signaling pathways involved and the modulation of the gut microbiota. We generated secondary colonospheres from two colon tumor cell lines HCT116 and CMT93, and evaluated the effect of tigecycline on CSCs properties. We showed that tigecycline (25, 50 μM) effectively reduced colon CD133[+]CD44[+]LGR5[+]ALDH[+] subpopulations and their viability, self-renewal and migratory capacity. Moreover, tigecycline treatment hindered epithelial-mesenchymal transition (EMT) process through targeting SNAI1 and β-catenin, resulting in an upregulation of epithelial markers (E-cadherin) and a downregulation of pluripotency and mesenchymal ones (Vimentin, N-cadherin, SOX2, NANOG, MIR155, MIR146). This effect was confirmed in two independent CRC-xenograft murine models in which tigecycline administration led to a reduction in tumor volume. Finally, CRC samples were taken from HCT116 xenograft model mice for analysis of CSCs-related signaling pathways and stools were collected for gut microbiome metagenomic analysis. We found that the antibiotic modulated gut dysbiosis by increasing the abundance of beneficial bacterial species such as Parabacteroides sp., which were involved in metabolic pathways that hindered SNAI1-Wnt-β-catenin signaling. These results reinforce the new role of tigecycline in the therapy of CRC and demonstrate for the first time the effect of tigecycline on colon CSCs and their malignancies.},
}

@article {pmid40940455,
year = {2025},
author = {He, P and Wang, S and Mao, R and Jiang, M and Siegel, S and Pedretti, G and Ignowski, J and Strachan, JP and Luo, R and Li, C},
title = {Real-time raw signal genomic analysis using fully integrated memristor hardware.},
journal = {Nature computational science},
volume = {},
number = {},
pages = {},
pmid = {40940455},
issn = {2662-8457},
support = {C7003-24Y, 17207925, 27210321, C1009-22GF, T45-701/22-R, GHKU707/23//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 62122005//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {Advances in third-generation sequencing have enabled portable and real-time genomic sequencing, but real-time data processing remains a bottleneck, hampering on-site genomic analysis. These technologies generate noisy analog signals that traditionally require basecalling and read mapping, both demanding costly data movement on von Neumann hardware. Here, to overcome this, we present a memristor-based hardware-software codesign that processes raw sequencer signals directly in analog memory, combining the two separated steps. By exploiting intrinsic device noise for locality-sensitive hashing and implementing parallel approximate searches in content-addressable memory, we experimentally showcase on-site applications, including infectious disease detection and metagenomic classification on a fully integrated memristor chip. Our experimentally validated analysis confirms the effectiveness of this approach on real-world tasks, achieving a 97.15% F1 score in virus raw signal mapping, with 51× speed-up and 477× energy saving over an application-specific integrated circuit. These results demonstrate that in-memory computing hardware provides a viable solution for integration with portable sequencers, enabling real-time and on-site genomic analysis.},
}

@article {pmid40940422,
year = {2025},
author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL},
title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40940422},
issn = {1460-2075},
support = {P30GM140963//HHS | National Institutes of Health (NIH)/ ; R35GM136390//HHS | National Institutes of Health (NIH)/ ; DBI-1828765//National Science Foundation (NSF)/ ; },
abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.},
}

@article {pmid40940010,
year = {2025},
author = {Ellis, EK and Ióca, LP and Liu, J and Chen, M and Bruner, SD and Ding, Y and Paul, VJ and Donia, MS and Luesch, H},
title = {Structure Determination and Biosynthesis of Dapalides A-C, Glycosylated Kahalalide F Analogues from the Marine Cyanobacterium Dapis sp.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c00757},
pmid = {40940010},
issn = {1520-6025},
abstract = {Kahalalides were originally isolated from the marine mollusk Elysia rufescens and its green algal diet Bryopsis sp., but the true producer was revealed as the obligate bacterial symbiont Candidatus Endobryopsis kahalalidefaciens, residing within Bryopsis sp. The most notable is kahalalide F, a broad-spectrum antitumor depsipeptide that entered the clinic but failed from lack of efficacy. We have isolated three new glycosylated analogues of kahalalide F, termed dapalides A-C (1-3), from a marine cyanobacterium, Dapis sp., collected from Guam. The planar structures were determined by extensive NMR coupled with mass spectrometry. Acid hydrolysis of 1 using amino acid analysis revealed the absolute configuration of singlet and a mixture of duplicate amino acids. Metagenomic analysis unveiled a biosynthetic gene cluster (BGC) with a nonribosomal peptide synthetase (NRPS) system and downstream glycosylation enzymes, which assisted the configurational assignment through epimerization domain analysis. The discovered BGC, termed dap, was assigned to a high-quality metagenome-assembled genome of the Dapis sp. Dapalide A (1) was subjected to phenotypic bioassays and exhibited weak anticancer cytotoxicity. This discovery expands the chemical diversity of the kahalalide F family, suggests their broad ecological role across diverse organisms, and presents an intriguing case of natural product biosynthesis evolution.},
}

@article {pmid40939728,
year = {2025},
author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB},
title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115102},
doi = {10.1016/j.physbeh.2025.115102},
pmid = {40939728},
issn = {1873-507X},
abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.

METHODOLOGY: Forty-four male rats were divided into four groups (n = 11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 minutes and progressing to 60 minutes. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.

RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.

CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.},
}

@article {pmid40939672,
year = {2025},
author = {Ai, C and He, Y and Cheng, Z and Wu, J and Liu, C and Wang, N and Yu, Z and Liao, H and Zhou, S},
title = {Unveiling of active bacteria associated with nutrient cycling during cattle manure composting.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122810},
doi = {10.1016/j.envres.2025.122810},
pmid = {40939672},
issn = {1096-0953},
abstract = {Bacteria play a pivotal role in nutrient turnover during the composting process. However, studies relying on total DNA analysis for bacterial community may be confounded by the presence of extracellular DNA from dead cells. In this study, ethidium monoazide (EMA) was employed to extract intracellular DNA from composting samples for amplicon and metagenomic sequencing, enabling the assessment of active bacterial community dynamics during cattle manure composting. The results revealed that total DNA-based 16S rRNA sequencing could only represent 36.9%-81.6% of the active bacterial communities. In contrast, EMA-based 16S rRNA sequencing identified Proteobacteria as the dominant active bacterial phylum throughout the composting process, with Actinobacteria exhibiting increased activity during the maturation phase. EMA-based metagenomic sequencing further showed that carbon and nitrogen metabolism genes showed the highest activity during the initial phase. Proteobacteria were identified as key functional bacteria in nutrient turnover, with its contribution reaching 55.4% and participating in 82.1% (23/28) of metabolic pathways. Meanwhile, Firmicutes (bin-23, g_Capillibacterium, bin-66, c_Bacilli) were the sole active nitrogen-fixing bacteria, harboring nitrogenase genes (nifH and nifD). This study offers novel understandings regarding the contribution of active bacteria in nutrient turnover and highlights the importance of distinguishing between active and total bacterial communities for a better understanding of microbial processes in composting systems.},
}

@article {pmid40939661,
year = {2025},
author = {Feng, F and Zhao, C and Chen, Y and Zhang, Y and Hu, X and Mu, H and Zhang, W},
title = {Mechanistic insights into sulfidated nanoscale zero-valent iron enhanced methanogenesis: Electron redistribution and direct interspecies electron transfer-driven metabolic reconfiguration.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133300},
doi = {10.1016/j.biortech.2025.133300},
pmid = {40939661},
issn = {1873-2976},
abstract = {Sulfidated nanoscale zero-valent iron (S-nZVI) enhances methanogenesis, yet the underlying mechanisms linking its interfacial structure to microbial metabolic responses remain unclear. This study elucidated S-nZVI's role via electron redistribution, microbial syntrophy enhancement, and metabolic pathway reconfiguration. Density functional theory revealed that sulfur-induced Fe-3d and S-3p orbital coupling, bandgap opening, and valence band shift collectively improved interfacial conductivity. At 5 g·L[-1], S-nZVI increased methane yield by 15 % and 68 % over nZVI and control, respectively. It also shortened lag phase, promoted extracellular polymeric substances secretion, and shifted electron transfer from cytochrome-based to abiotic pathways. Metagenomics confirmed enrichment of direct interspecies electron transfer (DIET)-associated genera and acetoclastic methanogenesis genes. Furthermore, the in-situ formation of conductive Fe3O4 and enhanced microbe colonization collectively reinforced DIET and methanogenesis. Overall, S-nZVI facilitated electron redistribution and drove the reconfiguration of syntrophic metabolism toward more efficient methanogenesis, offering mechanistic insights into material-microbe synergy for enhanced bioenergy recovery.},
}

@article {pmid40939657,
year = {2025},
author = {Tan, HT and Lei, Y and Chek, MF and He, M and Pow, KC and Gong, S and Hao, Q and Hakoshima, T and Sudesh, K and Liu, G},
title = {Engineering chimeric polyhydroxyalkanoate synthases for enhanced copolymerization of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate): A promising biotechnological approach.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133307},
doi = {10.1016/j.biortech.2025.133307},
pmid = {40939657},
issn = {1873-2976},
abstract = {The escalating health and environmental threats posed by microplastics and nanoplastics (MNPs) highlight the urgent need for sustainable alternatives like polyhydroxyalkanoates (PHAs), biodegradable polyesters synthesized by bacterial PHA synthases (PhaCs). However, natural PhaCs exhibit suboptimal substrate specificity and polymer heterogeneity, limiting industrial scalability. To address this, chimeric PhaCs were engineered by swapping N-terminal domains between PhaC from mangrove soil metagenome (PhaCBP-M-CPF4; low 3-hydroxyhexanoate [3HHx] content, fewer but larger granules) and PhaC2 of Rhodococcus aethirovorans I24 (PhaC2Ra; high 3HHx, numerous small granules). This strategy aimed to combine enhanced 3HHx incorporation with controlled granule morphology. Using structural predictions, chimeric enzymes were constructed and tested, revealing that the C-terminal domain retained compatibility with diverse N-terminal regions. The resulting chimeras exhibited improved PHA production, enhanced 3HHx incorporation, and optimized granule formation, overcoming historical challenges in chimeric enzyme design by avoiding β-strand interference. Among the chimeras, distinct strains achieved: (i) up to 200 % increase in PHA production; (ii) up to 45 mol% 3HHx incorporation; and (iii) optimized granule formation, approaching a single-granule-per-cell phenotype (mean count: 1.079) and a granule size increase of up to 7.2-fold (mean area: 1.272 µm[2]). This approach provides a robust framework for tailoring PhaCs to produce high-performance copolymers. By elucidating domain compatibility, the study advances strategies in synthetic biology for creating modular enzymes with tailored functionalities, offering transformative potential in sustainable materials, protein engineering, and innovation in biodegradable plastics.},
}

@article {pmid40939655,
year = {2025},
author = {Hu, F and Qin, J and Yang, H and Al-Dhabi, NA and Dong, Y and Bai, Z and Liu, L and Chai, F and Jin, B and Tang, W and Ji, J},
title = {An effective strategy for restoring the biofilm system of anammox/endogenous partial denitrification combined with continuous-flow partial nitration from deterioration.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133311},
doi = {10.1016/j.biortech.2025.133311},
pmid = {40939655},
issn = {1873-2976},
abstract = {Hydroxylamine supplementation has recently emerged as a potential strategy to persistent sustain partial nitration (PN), but its feasibility in the biofilm system of anammox/endogenous partial denitrification combined with continuous-flow partial nitration (SAEPD-CFPN) systems remains unexplored. Thus, this study assessed the feasibility of hydroxylamine dosing for restoring PN in continuous-flow biofilm reactor and investigated the impact of continuous-flow partial nitration (CFPN) deterioration on biofilm system of SAEPD-CFPN. Results showed that nitrogen removal efficiency (NRE) decreased from 88.86 % to 39.56 %, with the nitrite accumulation rate (NAR) dropping from 87.28 % to 34.33 % due to the deterioration of CFPN. After effective hydroxylamine dosing, the average NRE increased to 89.90 %, while the average NAR rose to 83.83 %. The SAEPD biofilm system could handle insufficient NO2[-]-N supply caused by CFPN performance insignificant deterioration; however, its effectiveness diminished when CFPN performance severely deteriorated over the long term due to lower influent COD concentrations. Metagenomic analysis revealed that CFPN recovery was attributed to the effective inhibition of Nitrobacter and NxrAB. The robustness of the SAEPD biofilm reactor against fluctuations in influent NO2[-]-N was attributable to its complex microbial community structure. Additionally, intermittent hydroxylamine dosing was proposed as a sustainable strategy to ensure stable SAEPD-CFPN biofilm process operation.},
}

@article {pmid40938427,
year = {2025},
author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D},
title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1112},
pmid = {40938427},
issn = {1573-2959},
support = {GSBTM/JD(R&D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; },
abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.},
}

@article {pmid40938103,
year = {2025},
author = {Desingu, PA and Arunkumar, S and Nagarajan, K and Saikumar, G},
title = {Metagenomic detection of the complete coding regions of Tanay virus from mosquitoes (Armigeres subalbatus) in India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0038925},
doi = {10.1128/mra.00389-25},
pmid = {40938103},
issn = {2576-098X},
abstract = {So far, the Tanay virus has only been detected in the Philippines and China. Here, we report that a complete coding region-wide virus with 3.7-16.7% nucleotide diversity to the Tanay viruses identified in China and 25.2% nucleotide diversity to those identified in the Philippines is circulating in mosquitoes (Armigeres subalbatus) in India.},
}

@article {pmid40937156,
year = {2025},
author = {Anselmi, S and Ni, Y and Tonoli, A and Wu, J and Wang, Y and Prout, L and Miodownik, M and Jeffries, JWE and Hailes, HC},
title = {The discovery of new metagenomic urethanases utilising a novel colorimetric assay for applications in the biodegradation of polyurethanes.},
journal = {Green chemistry : an international journal and green chemistry resource : GC},
volume = {},
number = {},
pages = {},
pmid = {40937156},
issn = {1463-9262},
abstract = {The enzymatic molecular recycling of plastics is of increasing interest, where polymers are converted into monomers for reuse or upcycled into value added chemicals. Polyurethanes are an important class of synthetic hydrolysable polymers found in textiles as an elastane component, also known as lycra and spandex, with most post-consumer waste currently disposed of in landfill. Here we have identified three active novel urethane hydrolytic enzymes from a drain metagenome able to breakdown methylenedianiline-based elastane model substrates. In addition, we have established a new colorimetric assay, suitable for high-throughput applications using tyrosinases. For the urethanases identified, the reaction conditions and substrate scope were explored. Finally, the urethanases and assay were used with commercial fabrics, demonstrating breakdown of the polymer.},
}

@article {pmid40936885,
year = {2025},
author = {Ye, X and Li, C and Zhou, Z and Yang, J and Jiang, H and Hu, L and Pan, H and Wei, X and Huang, Y and Lin, Y and Wang, L},
title = {Metagenomic Next-Generation Sequencing-Assisted Risk Prediction and Stratification of Infections After Kidney Transplantation: A Case Study of COVID-19.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4763-4776},
pmid = {40936885},
issn = {1178-6973},
abstract = {BACKGROUND: During the COVID-19 pandemic, COVID-19 infection has severely damaged the transplanted kidney function and health of kidney transplant patients. This study aims to investigate the clinical characteristics, risk factors and predictors of severe COVID-19 in patients after kidney transplantation.

MATERIAL AND METHODS: The clinical data of patients with COVID-19 after kidney transplantation were collected from December 2022 to January 2023 at the First Affiliated Hospital of Soochow University. Logistic regression analysis was performed to identify risk factors for severe disease and to construct a nomogram model. Concurrently, metagenomic next-generation sequencing (mNGS) was employed to detect the sputum microbiome.

RESULTS: A total of 58 patients were enrolled and were categorized into the common group (n=35) and the severe group (n=23) based on infection severity. The common group comprised 23 males with a mean age of 45.60 ± 9.11 years, while the severe group included 16 males with a mean age of 48.22 ± 9.95 years. Multivariate logistic analysis revealed that days of fever before hospitalization, C-reactive protein (CRP) and interleukin-10 (IL-10) on admission were significantly independent risk factors for severity, with an area under the ROC curve at 0.906. Comparison of the sputum microbiome revealed that there were no significant differences in α and β diversity between the two groups. Streptococcus parasanguinis was significantly more abundant in the specimens from the severe group, while Gemella sanguinis and Gemella haemolysans were significantly more abundant in the common group.

CONCLUSION: The severity of COVID-19 in kidney transplant patients is associated with days of fever before hospitalization, and the levels of CRP and IL-10 at admission, which also alter the abundance of certain species in the sputum microbiome. Therefore, it is necessary to actively monitor the clinical indicators of kidney transplant patients admitted with COVID-19 to reduce the risk of progression to severe disease.},
}

@article {pmid40936884,
year = {2025},
author = {Wu, Y and Yu, X and Zhang, Y and Liu, J and Chen, Y and Wang, R and Zhang, W},
title = {Challenges in Management of Disseminated Mucormycotic Infection with Endocarditis in an Adult Patient Receiving Liver Transplantation.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4711-4721},
pmid = {40936884},
issn = {1178-6973},
abstract = {Mucormycosis is a rare fungal infection. With the recent advancements in diagnostic technologies, including molecular diagnostic techniques, such as PCR and metagenomic next-generation sequencing, the detection rates of mucormycosis have increased. However, its mortality rates remain alarmingly high. Although post-liver transplantation mucormycosis cases are infrequently reported (less than 1%), their mortality rate ranges from 60% to 90%, while mucormycotic endocarditis is even rarer. This article summarizes the clinical manifestations of mucormycosis in a post-liver transplantation adult patient and reviews the existing literature on mucormycotic endocarditis, with the aim of outlining its clinical features, diagnostic challenges, and therapeutic strategies.},
}

@article {pmid40936227,
year = {2025},
author = {Liu, C and Long, J and Li, Y and Leng, X and Zhang, J and Chen, S and Fu, J and Li, C and Zhou, Y and Feng, C and Huang, B},
title = {The Comparison of Diagnostic Performance Between Next-Generation Sequencing of Blood and Tissues for Primary Spinal Infections.},
journal = {Global spine journal},
volume = {},
number = {},
pages = {21925682251375446},
doi = {10.1177/21925682251375446},
pmid = {40936227},
issn = {2192-5682},
abstract = {Study designprospective study.ObjectivesThe hematogenous spread of pathogens from a distant infected area is the main route of primary spinal infections. It is expected that blood metagenomic next-generation sequencing (mNGS) has potential in the pathogen detection of primary spinal infections. The aim of this study is to compare the diagnostic performance of blood and tissue mNGS in primary spinal infections.MethodsA total of 21 patients with primary spinal infections were analyzed. The results of mNGS and culture of blood and spinal specimens were used to calculate the diagnostic efficiency-related parameters.ResultsThe positive rate, sensitivity and specificity of blood mNGS were significantly lower than those of tissue mNGS (42.86% vs 90.48%, 9.52% vs 95%, 12.5% vs 100%). The positive rate and sensitivity of blood mNGS were higher (42.86% vs 4.76, 9.52% vs 5%) than those of blood pathogen culture. Also, the sensitivity and specificity of blood mNGS were lower than tissue pathogen culture (9.52% vs 45%, 12.5% vs 100%). Moreover, the specificity of blood mNGS was the lowest among the 4 pathogen identification techniques.ConclusionsThe diagnostic performance of blood mNGS is worse than tissue mNGS in primary spinal infections. The application prospects of blood mNGS in pathogen identification of primary spinal infections are limited. Further studies will be required to investigate the diagnostic values of blood mNGS in other types of spinal infections or in subpopulations of spinal infections.},
}

@article {pmid40935925,
year = {2025},
author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y},
title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40935925},
issn = {2058-5276},
support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.},
}

@article {pmid40935888,
year = {2025},
author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y},
title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40935888},
issn = {1435-5922},
support = {JP22K08040//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.

METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.

RESULTS: Microbiome analysis revealed significantly reduced α-diversity indices in patients with AIG when compared with the control group. β-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.

CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.},
}

@article {pmid40935532,
year = {2025},
author = {Webster, AM and Triumph, Z and Wei, B and Martin, RM and Smith, LE and Wilhelm, SW and Cleckner, LB and Razavi, NR and Boyer, GL},
title = {First report of nodularin production by Nostochopsis sp. in a temperate eutrophic lake.},
journal = {Harmful algae},
volume = {149},
number = {},
pages = {102956},
doi = {10.1016/j.hal.2025.102956},
pmid = {40935532},
issn = {1878-1470},
abstract = {Benthic cyanobacteria are understudied in comparison to their planktonic counterparts. Consequently, our understanding of cyanotoxin production in benthic mats remains limited. We detected nodularin-R (NOD-R) in a population of Nostochopsis from Honeoye Lake (New York, United States). Identification as Nostochopsis was supported by morphological (see section 3.1 for a detailed description) and metagenomic analyses. The first metagenome assembled genome of Nostochopsis was drafted and estimated at 99.28 % complete. Cyanotoxin testing of Nostochopsis biomass showed production of NOD-R but not microcystins, anatoxins, or cylindrospermopsins. The complete nodularin synthetase cluster was confirmed in the Nostochopsis genome. To our knowledge, this is the first report of nodularin production, or any cyanotoxin production, by the benthic cyanobacteria Nostochopsis. This is the fourth genus of cyanobacteria reported to produce nodularins.},
}

@article {pmid40935105,
year = {2025},
author = {Zhao, J and Guo, Z and Tang, L and Lu, X and Li, Y and Yang, K},
title = {Dynamic evolution of antibiotic resistance risk in sewage sludge-amended soil during crop growth: a field-based metagenomic perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122799},
doi = {10.1016/j.envres.2025.122799},
pmid = {40935105},
issn = {1096-0953},
abstract = {Sewage sludge, a ubiquitous by-product of wastewater treatment, accumulates globally. Land application, a prominent waste valorization strategy, inadvertently disseminates the sludge antibiotic resistome into ecosystems, threatening ecological security and public health. Risk assessment of antibiotic resistance (AR) during sludge land application is urgently needed. Herein, we conducted a field study by planting three crops in sludge-amended soil, and monitoring the dynamic evolution of AR risk throughout their growth cycles. Metagenomic sequencing assessed antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and their co-occurrence. Sludge amendment exerted persistent, yet largely recoverable, impacts on soil microbial community and the resistome. The resulting AR risk evolution was nonlinear and fluctuating, dominated by soil microbial community reconstruction. Given the differences in crop edible parts, growth periods of crops, complex AR risk dynamics, and external factors like weather, we propose a time-sensitive control strategy targeting critical risk windows. This strategy aims to mitigate AR risk under the "One Health" paradigm for sustainable sludge land application.},
}

@article {pmid40935093,
year = {2025},
author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F},
title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102901},
doi = {10.1016/j.tmaid.2025.102901},
pmid = {40935093},
issn = {1873-0442},
abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2 %) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5 %), followed by Giardia duodenalis (12.6 %), Dientamoeba fragilis (7.5 %), Cryptosporidium parvum (6.5 %), and Entamoeba histolytica (4 %). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.},
}

@article {pmid40934662,
year = {2025},
author = {Zhang, J and Zhao, J and Gao, Z and Ding, X and Li, Y and Shi, J and Zhao, D and Shi, L and Bi, X and Miao, Y},
title = {An effective method for enhancing metabolic activity of anammox bacteria: Accelerating heme biosynthesis by glutamate.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127301},
doi = {10.1016/j.jenvman.2025.127301},
pmid = {40934662},
issn = {1095-8630},
abstract = {Enhancing and maintaining anammox bacteria (AnAOB) activity is a major challenge for application of anammox process, which could be achieved by accelerating heme biosynthesis. Heme is crucial for electron transport and redox reaction and its biosynthesis may be promoted by glutamate. To explore the effect of glutamate on AnAOB activity, four parallel anammox systems (named R0, R1, R2, and R3) with different concentrations of glutamate (0, 0.125, 0.25, and 0.5 mM) were set up. The results showed that AnAOB activities and nitrogen removal efficiencies of R1 and R2 were about 58.3 % and 48.8 %, and 80.5 % and 64.1 % higher than that of R0, respectively, whereas excessive glutamate (0.5 mM) deteriorated the system performance. Moreover, heme content, activities of hydrazine synthase and hydrazine dehydrogenase, and sludge particle size in R1 and R2 were significantly higher than R0. Metagenomic sequencing analysis further revealed that the moderate amount of glutamate (0.125 mM, 0.25 mM) could effectively improve AnAOB activity by enhancing heme biosynthesis, accelerating electron transport and energy synthesis, and promoting the aggregation of microorganisms. This study provides an effective method for enhancing AnAOB metabolic activity and clarifies the underlying mechanism.},
}

@article {pmid40934587,
year = {2025},
author = {Wang, F and Xiong, J and Lin, L and Xu, W and Liu, L and Yang, S and Cao, W},
title = {Antibiotic resistance genes link to nitrogen removal potential via co-hosting preference for denitrification genes in a subtropical estuary.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139801},
doi = {10.1016/j.jhazmat.2025.139801},
pmid = {40934587},
issn = {1873-3336},
abstract = {Estuaries are important sinks for antibiotic resistance genes (ARGs) and hotspots of nitrogen cycling. However, the interactions between nitrogen cycling functional genes (NCGs) and ARGs in estuaries remain poorly understood. This study employed metagenomic sequencing to explore potential interactions between nitrogen, ARGs, and microbial-mediated nitrogen cycling processes in estuarine waters. Results showed beta-lactam was the predominant subtype of ARGs (407 species), and sul1 exhibited the highest relative abundance (4.11 %). Nitrogen was the important factor driving spatiotemporal variation of ARGs, promoting their proliferation and dispersal by enhancing microbial growth and reproduction. Network analysis revealed wide and complex correlations between ARGs and NCGs. Nitrate-reducing bacteria were the main hosts of ARGs, and the greatest number of potential hosts were those involved in assimilatory nitrate reduction to ammonium (17.44 %), dissimilatory nitrate reduction to nitrite (16.59 %), and denitrification (15.71 %). Compared with dissimilatory nitrite reduction to ammonium genes, ARGs prefer to form co-hosting relationships with denitrification genes, indicating that ARGs had a stronger effect on the nitrogen removal potential than on the nitrogen retention potential. This study highlights the complex interactions between ARGs and nitrogen cycling processes in subtropical estuaries, and will provide a scientific base for couple management strategies of nitrogen and antibiotic pollution.},
}

@article {pmid40934284,
year = {2025},
author = {Lucas, A and Schäffer, DE and Wickramasinghe, J and Auslander, N},
title = {kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013470},
doi = {10.1371/journal.pcbi.1013470},
pmid = {40934284},
issn = {1553-7358},
abstract = {Shotgun metagenomic sequencing can determine both the taxonomic and functional content of microbiomes. However, functional classification for metagenomic reads remains highly challenging as protein mapping tools require substantial computational resources and yield ambiguous classifications when short reads map to homologous proteins originating from different bacteria. Here we introduce kMermaid for the purpose of uniquely mapping bacterial short reads to taxa-agnostic clusters of homologous proteins, which can then be used for downstream analysis tasks such as read quantification and pathway or global functional analysis. Using a nested hash map containing amino acid k-mer profiles as a model for protein assignment, kMermaid achieves the sensitivity of popular existing protein mapping tools while remaining highly resource efficient. We evaluate kMermaid on simulated data and data from human fecal samples as well as demonstrate the utility of kMermaid for classifying reads originating from new, unseen proteins. kMermaid allows for highly accurate, unambiguous and ultrafast metagenomic read assignment into protein clusters, with a fixed memory usage, and can easily be employed on a typical computer.},
}

@article {pmid40933810,
year = {2025},
author = {Tigrero-Vaca, J and Villavicencio-Vásquez, M and Coronel, J and Cevallos-Cevallos, JM},
title = {Multi-platform metagenomic characterization of the microbial community during spontaneous cacao fermentation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1630515},
doi = {10.3389/fbioe.2025.1630515},
pmid = {40933810},
issn = {2296-4185},
abstract = {Cacao fermentation is a spontaneous process in which microorganisms play a key role in the development of distinctive chocolate flavors. The microbiota acting during cacao fermentation has been routinely characterized by culture-based techniques and next-generation sequencing using Illumina's platform. However, the potential of in situ sequencing technologies to monitor microbial dynamics during cacao fermentation has not been assessed. In this study, cacao bean samples were collected at 0, 24, 48, 72, and 96 h after the start of the fermentation. Total DNA was extracted, and sequencing libraries were prepared for further sequencing using Illumina's and Nanopore's MinION sequencing platforms. Additionally, microorganisms were isolated using traditional culture-based methods. At the order and family taxonomic levels, Illumina and MinION sequencing revealed similar microbial composition in the samples. However, discrepancies were observed at the genus and species levels. In this sense, Illumina sequencing revealed a predominance of Limosilactobacillus, Levilactobacillus, Lactiplantibacillus, Frauteria, Saccharomyces and Acetobacter, while MinION sequencing showed a prevalence of Escherichia, Salmonella, Liquorilactobacillus, Lentilactobacillus, Acetobacter and Komagataeibacter during fermentation. The three methods were consistent in detecting the major yeast (Saccharomyces cerevisiae), lactic acid bacteria (Lactiplantibacillus plantarum, Leuconostoc pseudomesenteroides, Levilactobacillus brevis, Liquorilactobacillus mali, and Lentilactobacillus hilgardii) and acetic acid bacteria (Acetobacter pasteurianus) species during fermentation. Functional analysis based on a hybrid assembly of Illumina and MinION data revealed the roles of lactic acid bacteria and acetic acid bacteria in the metabolism of carbohydrates, amino acids, and secondary metabolites such as polyphenols and theobromine. This study represents the first report assessing the applicability of MinION sequencing for the characterization of microbial populations during cacao fermentation, demonstrating its potential as a complementary tool to established sequencing platforms.},
}

@article {pmid40933579,
year = {2025},
author = {Lin, B and Zhong, D and Qin, L and Liu, Q and Wu, L and Wang, B and Wang, K and Lu, X and Deng, S and Pan, L},
title = {Application of metagenomics sequencing to diagnose paralytic rabies with stroke-like onset: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1639262},
doi = {10.3389/fmed.2025.1639262},
pmid = {40933579},
issn = {2296-858X},
abstract = {BACKGROUND: Rabies is an acute zoonotic infectious disease caused by infection with a virus of the genus Lyssavirus. We report a case of paralytic rabies with a stroke-like onset, which was diagnosed using metagenomics next-generation sequencing (mNGS).

CASE PRESENTATION: A 58-year-old man was admitted to the hospital with "numbness and weakness in the right upper extremity for 2 days, aggravated for 1 day." Twenty-five days before his admission, the patient was bitten on the back of right hand by an unvaccinated domestic dog, resulting in a penetrating injury, classified as grade III according to the rabies exposure classification method. Following admission, the patient exhibited rapidly progressive stroke symptoms, and on the second day, he suffered a sudden respiratory arrest accompanied by a weakened heartbeat and a decreased heart rate. He was treated with emergency tracheal intubation, cardiopulmonary resuscitation, and dehydration to lower cranial pressure.

RESULTS: The patient's condition deteriorated rapidly after admission. A lumbar puncture was conducted on the morning of the second day of admission, and cerebrospinal fluid (CSF) was sent to Weiyuan Genetic Laboratories (Guangzhou, China) for rabies virus identification. The patient died on the third day of admission. Pathogen capture macro-genomics was performed on CSF using an Illumina NextSeq second-generation sequencer, and nine rabies virus sequences, which shared more than 99% nucleotide homology with the genome sequence of the rabies virus Rabies lyssavirus (NCBI accession no. MN175989.1), were detected. The Q30 ratio of this test was 98.3%.

CONCLUSION: Compared to polymerase chain reaction (PCR) and direct fluorescent antibody (DFA) test, mNGS shortens the diagnostic window and improves sensitivity to low-virus or seronegative manifestations by simultaneously capturing and sequencing the entire pathogen genome. The mNGS technology can effectively aid in the diagnosis of paralytic rabies.},
}

@article {pmid40933366,
year = {2025},
author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR},
title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.},
journal = {PNAS nexus},
volume = {4},
number = {9},
pages = {pgaf260},
doi = {10.1093/pnasnexus/pgaf260},
pmid = {40933366},
issn = {2752-6542},
abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.},
}

@article {pmid40933132,
year = {2025},
author = {Li, X and Lu, H},
title = {Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626002},
doi = {10.3389/fmicb.2025.1626002},
pmid = {40933132},
issn = {1664-302X},
abstract = {The human gastrointestinal tract (GIT) is inhabited by a heterogeneous and dynamic microbial community that influences host health at multiple levels both metabolically, immunologically and via neurological pathways. Though the gut microbiota-overwhelmingly Bacteroidetes and Firmicutes-has essential functions in nutrient metabolism, immune regulation, and resistance to pathogens, its dysbiosis is likewise associated with pathologies, such as inflammatory bowel disease (IBD), obesity, type 2 diabetes (T2D), and neurodegenerative diseases. While conventional metagenomic techniques laid the groundwork for understanding microbial composition, next-generation enhanced metagenomic techniques permit an unprecedented resolution in exploring the functional and spatial complexity of gut communities. Advanced frameworks such as high-throughput sequencing, bioinformatic and multi-omics technologies are expanding the understanding of microbial gene regulation, metagenomic pathways, and host-microbe communication. Beyond taxonomic profiling, they map niche-specific activities of gut microbiota along a dichotomy of facultative mutualism, evidenced by relations of beneficial symbionts, represented here by Enterobacteriaceae. In this review, we critically consider the latest approaches (e.g., long-read sequencing, single-cell metagenomics and AI-guided annotation) that mitigate biases stemming from DNA extraction, sequencing depth and functional inference.},
}

@article {pmid40933127,
year = {2025},
author = {Akhtar, MF and Wenqiong, C and Umar, M and Changfa, W},
title = {Biochemical properties of lactic acid bacteria for efficient silage production: an update.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581430},
doi = {10.3389/fmicb.2025.1581430},
pmid = {40933127},
issn = {1664-302X},
abstract = {Ensiling, a microbial-driven process employed for preserving fresh forage in both bio-refineries and animal production, triggers significant biochemical transformations. These changes have spurred the exploration of novel silage additives, with a particular emphasis on the potential of microbial strains that exhibit superior biopreservation capabilities. Lactic acid bacteria (LAB) species have gained widespread recognition for their diverse applications as additives in the fermentation of crops and forage biomasses during ensiling. Nonetheless, recent variations in silage quality might be attributed to a lack of comprehensive information on the gene expression and molecular mechanisms of the microbiota involved in silage production. Contemporary research efforts have been directed toward uncovering nutrient-rich animal feed solutions through enhanced LAB inoculants. This review aims to shed light on the role of LAB inoculants in silage production and the modern biotechnological methods, including metabolomics, proteomics, metagenomics, genomics, transcriptomics, and genetic manipulation. These powerful tools are instrumental in the identification, enhancement, and development of high-performance LAB strains. Additionally, the review outlines emerging trends and prospective developments in LAB advancement for the enhancement of silage, which holds significant promise for breakthroughs in sustainable agriculture and improved animal feed production.},
}

@article {pmid40933007,
year = {2025},
author = {Le, J and Hakimjavadi, H and Parsana, R and Chamala, S and Michail, S},
title = {Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study.},
journal = {Gastro hep advances},
volume = {4},
number = {10},
pages = {100741},
doi = {10.1016/j.gastha.2025.100741},
pmid = {40933007},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising tool to modulate the gut microbiome in pediatric ulcerative colitis (UC). We investigated the long-term impact of FMT on the gut microbiome and identified microbial signatures associated with disease severity and clinical outcomes.

METHODS: This study combined a randomized, double-blind trial comparing FMT to autologous placebo with an open-label extension to assess FMT's effects on the gut microbiome in pediatric UC patients over 48 weeks. Stool samples were collected at baseline and postintervention, and clinical response was evaluated using the Pediatric Ulcerative Colitis Activity Index. Shotgun metagenomic sequencing characterized the fecal microbiome's composition and functional potential. Taxon set enrichment analysis identified microbial taxon sets associated with UC and FMT.

RESULTS: FMT induced significant, sustained increases in gut microbial diversity over 48 weeks. Key changes included decreases in Klebsiella oxytoca and increases in Coprobacter fastidiosus post-FMT. Microbial signatures were associated with disease severity, including increased indole producers and decreased mucin degraders in mild UC compared to remission. Patients with clinical improvement post-FMT showed decreased Fusobacterium nucleatum and Veillonella parvula. Klebsiella pneumoniae and Klebsiella variicola decreased after open-label FMT.

CONCLUSION: FMT induces sustained changes in the pediatric UC gut microbiome, with distinct microbial signatures associated with disease severity and clinical outcomes. However, the high autologous placebo response rate underscores the need for further research to elucidate the mechanisms underlying FMT and placebo responses. Our study provides insights into the gut microbiome's role in pediatric UC, laying the foundation for developing personalized microbiome-targeted therapies. ClinicalTrials.gov number, NCT02291523.},
}

@article {pmid40932661,
year = {2025},
author = {Sachdeva, S and Sarethy, IP},
title = {Antibiotic resistance profiling in an ancient Indian sulfur-rich stepwell: a case study of Gandhak-ki-Baoli.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {895},
pmid = {40932661},
issn = {1573-4978},
mesh = {India ; *Sulfur/analysis ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, increasingly recognized to emerge not only from clinical and agricultural sources but also from natural and historical environments. Despite their ecological and cultural significance, ancient water bodies such as stepwells remain largely unexplored in the context of environmental resistomes.

METHOD: This study investigates AMR in Gandhak-ki-Baoli, an ancient sulfur-rich stepwell located in Delhi, India. A combined methodological approach involving culture-based microbial isolation and metagenomics sequencing was used to identify bacterial taxa and associated antibiotic resistance genes (ARGs).

RESULTS: The analysis revealed a diverse microbial community harboring ARGs, including those conferring multidrug resistance. Several genes showed evidence of co-selection mechanisms with heavy metals and biocides. The stepwell's unique environmental conditions characterized by stagnant water, low light, variable moisture, and limited nutrients that likely contribute to the persistence and potential horizontal transfer of resistance traits.

CONCLUSIONS: This is the first study to profile AMR in a historical stepwell, revealing the presence of a complex environmental resistome. The findings suggest that ancient water structures like stepwells can act as hidden reservoirs of AMR. These insights highlight the need to include such environments in future AMR surveillance efforts to better understand the broader ecological landscape of resistance.},
}

India
*Sulfur/analysis
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Metagenomics/methods
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Water Microbiology
Metagenome

@article {pmid40932534,
year = {2025},
author = {Wang, F and Xia, J and Sun, J},
title = {Microbiological diagnostics and their impact on hematology nursing.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40932534},
issn = {1874-9356},
abstract = {Microbiological diagnostics have become a foundational element in hematology nursing, where early and accurate infection detection is vital for immunocompromised patients. This review explores how both traditional techniques, such as microscopy, culture, and antigen detection, and emerging technologies, including polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and MALDI-TOF mass spectrometry, contribute to clinical decision-making and infection control. These tools not only accelerate pathogen identification and resistance profiling but also support precision medicine approaches tailored to hematologic patient needs. The expanding role of hematology nurses is emphasized, particularly in diagnostic stewardship, specimen collection, result interpretation, and coordination of infection management strategies. Educational interventions have proven effective in reducing contamination rates and improving antimicrobial targeting. Furthermore, novel point-of-care platforms, such as CRISPR-based diagnostics and AI-enhanced digital PCR, are shifting diagnostic capabilities closer to the bedside, redefining nursing workflows and responsibilities. These innovations empower nurses to engage in real-time clinical decisions, monitor therapy responses, and enhance patient education regarding diagnostic procedures and infection risks. However, gaps remain in microbiology-related training and confidence among nurses, highlighting the need for integrated educational curricula and interdisciplinary collaboration. By aligning technological advancements with frontline nursing practice, microbiological diagnostics not only optimize patient outcomes but also elevate the role of nurses as key stakeholders in infection prevention, antimicrobial stewardship, and evidence-based care. This review underscores the urgent need to equip hematology nurses with the skills and tools necessary to adapt to the rapidly evolving diagnostic landscape in order to support safe, timely, and personalized healthcare delivery.},
}

@article {pmid40932289,
year = {2025},
author = {Zhao, Y and Du, L and Song, J and Sun, W and Chen, Y and Yu, X and Huang, H and Huang, G and Huang, E and Wang, N and An, S and Ai, L and Chen, P},
title = {Hierarchical integration of mNGS, PCR, and other conventional methods for precision TB diagnostics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0193125},
doi = {10.1128/spectrum.01931-25},
pmid = {40932289},
issn = {2165-0497},
abstract = {UNLABELLED: This study systematically compared the diagnostic accuracy of seven assays for detecting the Mycobacterium tuberculosis complex, including metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction, real-time quantitative polymerase chain reaction, EasyNAT MTC, GeneXpert MTB/RIF, interferon-gamma release assay (IGRA), and acid‒fast staining (AFS). We try to select appropriate combinations of tuberculosis (TB) detection methods for regions with varying levels of medical resources, based on sensitivity, cost-effectiveness, and operational feasibility. A retrospective analysis was conducted on 141 samples collected from patients with suspected active TB at The First Affiliated Hospital of Sun Yat-sen University between April 2022 and April 2024. Among these samples, there were 100 cases assigned to the case group and 41 cases to the control group, based on the tuberculosis diagnostic criteria. Historical data for Xpert, IGRA, and AFS were collected, and parallel experiments using mNGS, droplet digital PCR (ddPCR), real-time quantitative polymerase chain reaction (RT-qPCR), and EasyNAT were conducted on all samples. Diagnostic performance was evaluated by comparing it with the final clinical diagnoses. Sensitivity, specificity, positive predictive value, negative predictive value, and receiver operating characteristic (ROC) curve analysis were conducted, along with DeLong tests for statistical comparison. Compared with the final clinical diagnosis, mNGS demonstrated the highest sensitivity (100%), followed by IGRA (79.2%), EasyNAT (79.1%), RT-qPCR (78.0%), ddPCR (75.8%), Xpert (75.3%), and AFS (16.7%). The specificity was 100% for both Xpert and AFS, followed by ddPCR (97.6%), RT-qPCR (95.1%), EasyNAT (92.7%), IGRA (72.7%), and mNGS (75.6%). ROC analysis revealed a significantly greater area under the ROC curve for mNGS (0.878) than for ddPCR (0.817, P = 0.031). DeLong tests revealed statistically significant differences in diagnostic performance between mNGS and ddPCR (P < 0.05) and between IGRA and AFS (P < 0.01). mNGS uniquely identified the pathogens involved in co-infection and quantified pathogen-specific sequencing reads. Through a comprehensive evaluation of the diagnostic efficacy, cost-effectiveness, and timeliness of tuberculosis detection methods, we propose corresponding combinations of TB testing approaches for regions with different healthcare resources. For undeveloped regions with limited resources, a combination of AFS +EasyNAT + chest X-ray is recommended. Primary care facilities may additionally employ IGRA + RT-qPCR. Intermediate-level hospitals can incorporate Xpert MTB/RIF for drug resistance testing, while tertiary hospitals or specialized centers should, on the basis of these fundamental tests, utilize mNGS for diagnosis and ddPCR for therapeutic monitoring in patients with complex mixed infections.

IMPORTANCE: This study is the first to comprehensively evaluate the diagnostic efficacy, cost-effectiveness, and timeliness of seven TB detection methods in a single-center cohort. Our findings provide actionable solutions for optimizing TB diagnostics in diverse healthcare ecosystems, aligning with the WHO's End TB Strategy to ensure equitable access to rapid diagnostics.},
}

@article {pmid40931802,
year = {2025},
author = {Gernert, JA and Klein, M and Schöberl, F and Müller, KJ and Schmidbauer, ML and Forbrig, R and Roeber, S and Herms, J and Terpolilli, N and Milakovic Obradovic, M and Graf, A and Dächert, C and Keppler, OT and Münchhoff, M and Dimitriadis, K},
title = {Severe course of tick-borne encephalitis (TBE) in a patient with relapsing multiple sclerosis (MS) treated with ocrelizumab.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585251369425},
doi = {10.1177/13524585251369425},
pmid = {40931802},
issn = {1477-0970},
abstract = {Description of a patient with multiple sclerosis (MS) who underwent immunotherapy with ocrelizumab and suffered a severe course of tick-borne encephalitis (TBE): A 33-year-old man presented with acute cerebellitis with tonsillar herniation. The initial suspected diagnosis of TBE was confirmed after a significant diagnostic delay, likely caused by negative serological testing due to B-cell depletion from ocrelizumab treatment for underlying MS. TBE diagnosis was made using polymerase chain reaction (PCR) and oligo-hybrid capture metagenomic next-generation sequencing (mNGS) of cerebral spinal fluid and brain biopsy samples which yielded a near-full length TBE Virus (TBEV) genome.},
}

@article {pmid40931531,
year = {2025},
author = {Gasparini, J},
title = {Targeted 'infectiosome' for disease ecology: A new tool to answer old questions.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70130},
pmid = {40931531},
issn = {1365-2656},
abstract = {Research Highlight: Bralet, T., Aaziz, R., Tornos, J., Gamble, A., Clessin, A., Lejeune, M., Galon, C., Michelet, L., Lesage, C., Jeanniard du Dot, T., Desoubeaux, G., Guyard, M., Delannoy, S., Moutailler, S., Laroucau, K. and Boulinier, T. (2025). High-throughput microfluidic real-time PCR as a promising tool in disease ecology. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.70088. Disease ecology aims to understand the causes and consequences of the maintenance and transmission of pathogenic infectious agents. A crucial step in studying disease ecology is identifying the 'infectiosome', which I define as all infectious agents circulating among individuals, populations and the community of a given ecosystem. In a recent study, Bralet et al. (2025) propose a new, cheap and adaptable toolkit for determining a targeted 'infectiosome', which appears very useful in disease ecology approaches: high-throughput microfluidic real-time PCR (Htrt PCR). This method is a good alternative to costly metagenomic approaches and consists of running several dozen PCRs from a single tissue sample. This technique enables screening, from a single sample, the presence of dozens of targeted infectious agents: the targeted 'infectiosome', allowing one to answer several questions. For example, Bralet et al. (2025) applied this method to 274 seabirds and 80 mammals samples collected from the Southern Ocean islands and detected pathogenic infectious agents in new locations. The results also show that some species are potential 'reservoirs' of several infectious agents in this ecosystem. This method is really promising and can be easily adapted and used to test different hypotheses in disease ecology at the scales of the population and the community in other ecosystems, such as the urban ecosystem.},
}

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

*Metagenome
*Metagenomics/methods
*Databases, Genetic
*Microbiota

@article {pmid40931024,
year = {2025},
author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP},
title = {Metagenomic complexity of high, seasonal transmission of Plasmodium spp. in asymptomatic carriers in Northern Sahelian Ghana.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {386},
pmid = {40931024},
issn = {2730-664X},
support = {R01-AI149779//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01-AI149779//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {BACKGROUND: Mixed-species, mixed-strain plasmodia infections are known to occur in humans in malaria endemic areas. It may be surprising that to date, the extent of this complexity has not been systematically explored in high-burden countries of sub-Saharan Africa, especially in the reservoir of asymptomatic infections in all ages, which sustains transmission.

METHODS: Here we take a metagenomic lens to these infections by sampling variable blood volumes from 188 afebrile residents living in high, seasonal transmission in Northern Sahelian Ghana. We estimated multiplicity of infection for different Plasmodium spp. through genotyping of antigens and microsatellites. We further defined 'metagenomic complexity' as a measure of overall within-host complexity across the combination of species and strains.

RESULTS: We show that prevalence of Plasmodium spp. and inter-/intra-species complexity is significantly higher in larger blood volumes from these individuals. Overall, malaria infections display high levels of metagenomic complexity comprising single-, double-, and triple-species infections with varying levels of intra-species complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We also report a subset of individuals with highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in northern Ghana.

CONCLUSIONS: Our metagenomic investigation underscores the need to more sensitively measure within-host Plasmodium spp. complexity in asymptomatic carriers of infection. This will optimise strategies for malaria surveillance and control.},
}

@article {pmid40930091,
year = {2025},
author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP},
title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.020},
pmid = {40930091},
issn = {1097-4172},
abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.},
}

@article {pmid40929977,
year = {2025},
author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W},
title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139749},
doi = {10.1016/j.jhazmat.2025.139749},
pmid = {40929977},
issn = {1873-3336},
abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.},
}

@article {pmid40929972,
year = {2025},
author = {Liu, K and Wang, X and Li, F and Tao, J and Weng, CH and Hu, Q and Kang, D and Luo, Z and Tang, Z and Liu, N and Qiu, J},
title = {Metagenomic characterization of antibiotic resistance genes and human bacterial pathogens in groundwater from agricultural, landfill, and hazardous waste disposal sites (HWDS) sources: Drivers, risks, and source tracking.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139803},
doi = {10.1016/j.jhazmat.2025.139803},
pmid = {40929972},
issn = {1873-3336},
abstract = {Agricultural sources, landfills, and hazardous waste disposal sites (HWDS) are major hotspots for the spread of groundwater antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, there is a lack of systematic understanding regarding the environmental behavior of groundwater ARGs, the pathogenic risks of HBPs, and the relative contribution mechanisms of different sources, presenting critical scientific challenges for developing targeted groundwater pollution control strategies. To address this, this study collected 26 groundwater metagenomic samples to characterize the composition, influencing factors, and health risks of ARGs and HBPs near key ARG reservoirs, and constructed a source-tracking indicator system. The research identified 16 clinically critical high-risk ARGs (e.g., tetM, sul1) and 14 priority HBPs (e.g., Escherichia coli, Klebsiella pneumoniae) associated with severe human diseases and high transmissibility. Screening ARG source-specific indicators demonstrated high accuracy in predicting contributions from artificially mixed sources (prediction errors < 4 %). Validation with real groundwater samples showed that landfills contributed more significantly to groundwater ARGs pollution than other sources. This study deepens our understanding of antibiotic resistance risks in groundwater near key ARG reservoirs and provides a robust framework for tracing ARGs in complex groundwater environments by integrating microbe-gene-environment interactions across multiple pollution sources.},
}

@article {pmid40929881,
year = {2025},
author = {Liu, Y and Li, K and Xu, J and Shen, W and Li, Y and Ma, J and Wang, T and Liu, J and Li, T and Zhang, X and Tian, W and Tian, J and Wang, H and Zhang, X},
title = {Alpha-linolenic acid ameliorates T2DM via reshaping gut-liver axis and inflammatory GPR120-NF-κB/NLRP3 pathway in mouse and rat models.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157214},
doi = {10.1016/j.phymed.2025.157214},
pmid = {40929881},
issn = {1618-095X},
abstract = {BACKGROUND: The gut-liver axis, pivotal in managing glucose balance and insulin responsiveness, is central to the development of type 2 diabetes mellitus (T2DM). Research has highlighted the regulatory effects of dietary alpha-linolenic acid (ALA), but it remains unclear how ALA modulates gut microbiota and liver inflammation in T2DM.

PURPOSE: This study aimed to systematically investigate ALA's influence on liver inflammation, intestinal barrier integrity, gut microbial composition, and metabolic homeostasis in T2DM, with a focus on the underlying molecular mechanisms.

STUDY DESIGN: A dual-model approach was employed using both db/db mouse model and the SCZ/NA-induced T2DM rat model to ensure robust species and model validation.

METHODS: Animals received oral ALA supplementation, followed by assessments of glucose tolerance, insulin sensitivity, hepatic histology, and inflammatory markers. Intestinal barrier function, permeability, and systemic LPS levels were evaluated. Mechanistic analysis focused on the GPR120-NF-κB/NLRP3 signaling pathway. Multi-omics profiling including fecal metagenomics, SCFA quantification, and plasma metabolomics were conducted to assess gut microbiota and host metabolic responses.

RESULTS: Our results revealed that ALA therapy significantly mitigated insulin resistance and glucose intolerance in db/db mice. Histopathological analysis revealed a decrease in hepatic steatosis following ALA administration, alongside a reduction in inflammatory markers indicative of T2DM. Importantly, our findings demonstrated that ALA mitigates liver inflammation by inhibiting the NF-κB/NLRP3 pathway, possibly via its interaction with GPR120. Beyond this, augmenting ALA bolstered intestinal integrity, minimized permeability, curbed lipopolysaccharide leakage, and suppressed pro-inflammatory cytokine expression within the intestines. Significantly, an integrated multi-omics investigation, encompassing fecal metagenomic sequencing, SCFA evaluation, and plasma non-targeted metabolomics, disclosed a potent correlation between ALA's hypoglycemic efficacy and the modulation of gut microbial community structure, elevation of SCFA synthesis, and enhancement of metabolic signatures.

CONCLUSION: Our study's initial insights indicated that dietary ALA modulates inflammation and metabolism in T2DM via the gut-liver axis, specifically through the GPR120-NF-κB/NLRP3 pathway. This elucidates ALA's dual function in reshaping the gut microbiota and combating systemic inflammation, positioning it as a potentially efficacious dietary component for managing T2DM.},
}

@article {pmid40929831,
year = {2025},
author = {Liu, F and Yang, B and Han, T and Li, F and Wang, L and Xu, H},
title = {Metagenomic and Micro-CT insights into Fe(III)-modulated extracellular polymeric substances driving anammox granulation and enhancement of nitrogen removal.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127283},
doi = {10.1016/j.jenvman.2025.127283},
pmid = {40929831},
issn = {1095-8630},
abstract = {Multivalent cations are commonly employed to accelerate sludge aggregation and granulation, yet they often compromise intragranular mass transfer and diminish microbial activity. Here, the effect of Fe(III) dosing on granule formation and anammox-driven nitrogen removal over a 110-day continuous operation was investigated. Fe(III) supplementation enhanced interactions with extracellular polymeric substances (EPS), transforming flocculent biomass into highly porous granules and yielding a 67.9 % increase in specific anammox activity (SAA). During the first 30 days of Fe(III) dosing, the Zeta potential shifted from -12.0 to -9.3 mV and EPS content surged from 32.8 mg/g VSS to 49.0 mg/g VSS, accelerating primary floc aggregation. Subsequently, the protein-to-polysaccharide ratio of EPS escalated from 1.7 to 5.3, reflecting a transition from a carbohydrate-rich, hydrophilic gel to a protein-dominated, hydrophobic network that facilitated granulation. Micro-computed tomography revealed that smaller (1.5 mm) granules exhibited dense architectures, whereas larger (2.5 mm) granules developed internal cavities as a result of mass transfer limitations, approaching structural fragmentation. Metagenomic analysis showed that Fe(III) upregulated pathways for hydrophobic amino acids (e.g., isoleucine, leucine, valine) synthesis and downregulated polysaccharide biosynthesis, thereby increasing EPS hydrophobicity and promoting granulation. The observed SAA enhancement was linked to Fe(III)-dependent activation of iron-containing enzymes (e.g., hzs ABC), cytochrome c maturation, and Fe-S cluster assembly. Concurrently, the relative abundance of Ca. Kuenenia rose from 14.1 % during aggregation to 18.6 % after sludge granulation. This work elucidates the mechanism of Fe(III)-EPS-mediated granulation and offers a sustainable strategy to reconcile structural integrity with metabolic efficiency in metal-driven anammox wastewater treatment processes.},
}

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40929468,
year = {2025},
author = {Xiang, Y and Man, X and Zhang, H and Chen, M and Yang, R},
title = {Nitrogen removal efficiency and pathways of the simultaneous nitrification and denitrification process under ultra-low oxygen conditions.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/09593330.2025.2556497},
pmid = {40929468},
issn = {1479-487X},
abstract = {To explore strategies for further reducing aeration energy consumption in the simultaneous nitrification and denitrification (SND) process, an SND reactor was constructed to treat low carbon-to-nitrogen (C/N) ratio domestic wastewater under ultra-low dissolved oxygen (DO) conditions (DO < 0.05 mg·L[-][1]). The effects of hydraulic retention time (HRT) and C/N ratio on nitrogen removal performance were systematically evaluated, and batch experiments were conducted to determine nitrification and denitrification rates. Under influent condition of 50.0 mg·L[-][1] ammonia and a C/N ratio of 2.2, the reactor maintained stable ultra-low DO levels, achieved effluent ammonia concentrations below 5.0 mg·L[-][1], and attained optimal SND efficiencies exceeding 80.0%. Although a shortened HRT destabilised performance, increasing the C/N ratio successfully restored nitrogen removal stability. Nitrification and denitrification rates ranged from 4.20-30.89 mg·L[-][1]·h[-][1] and 1.57-21.92 mg·L[-][1]·h[-][1], respectively, under C/N ratios from 2.2-8.0. High-throughput sequencing and metagenomic analysis revealed that heterotrophic nitrification and aerobic denitrification dominated nitrogen transformation, with microorganisms utilising low-energy nap and nirK enzymes to adapt to the ultra-low DO environment. These findings provide novel insights into energy-efficient nitrogen removal pathways under ultra-low oxygen conditions.},
}