@article {pmid41052966,
year = {2025},
author = {Tang, W and Hexter, C and Dai, R and Fortin, SG and Tracey, JC and Intrator, N and Kunes, MA and Wan, XS and Jayakumar, A and Shi, D and Ward, BB},
title = {Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70187},
doi = {10.1111/1462-2920.70187},
pmid = {41052966},
issn = {1462-2920},
support = {OCE-1946516//National Science Foundation/ ; 675459//Simons Foundation/ ; //University of South Florida/ ; },
mesh = {*Nitrification ; *Nitrous Oxide/metabolism ; *Urea/metabolism ; *Archaea/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ammonia/metabolism ; Nitrites/metabolism ; },
abstract = {Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N2O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the ammonia-oxidising archaea (AOA), are also capable of oxidising urea, providing a previously ignored source of nitrite. Here, we show that the relative magnitude of urea and ammonia oxidation rates, and the relative rates of N2O production from the two substrates, is correlated with the ratio of the substrate concentrations. By examining all reported measurements of urea and ammonium concentrations and the paired urea and ammonia oxidation rates, we show that this relationship likely holds across the global ocean. Examination of newly acquired and previously published metagenomic data shows that the fraction of AOA with the genetic capability for urea oxidation increases with the urea:ammonium ratio, rather than depending on the urea or ammonium concentration alone. These results corroborate the correlation between substrate ratios and oxidation rate ratios, and extend it to N2O production. This may help explain the distribution of nitrification rates and N2O production in the ocean.},
}

*Nitrification
*Nitrous Oxide/metabolism
*Urea/metabolism
*Archaea/metabolism/genetics
*Ammonium Compounds/metabolism
Oxidation-Reduction
*Seawater/microbiology/chemistry
Ammonia/metabolism
Nitrites/metabolism

@article {pmid41052412,
year = {2025},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}

@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
doi = {10.1073/pnas.2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}

Animals
*Methane/metabolism/biosynthesis
*Fermentation/drug effects
*Rumen/microbiology/metabolism
Cattle
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Animal Feed
*Ruminants/microbiology/metabolism
Microbiota/drug effects
Fatty Acids, Volatile/metabolism

@article {pmid41052251,
year = {2025},
author = {Qin, Z and Yang, Z and Zhang, Y and Qi, L and Peng, Y and Deng, S and Wang, Y},
title = {Biotin Limitation Attenuates Streptococcus mutans Cariogenicity by Disrupting Metabolic Flux and Virulence Pathways.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000548822},
pmid = {41052251},
issn = {1421-976X},
abstract = {INTRODUCTION: Our previous metagenomic analysis revealed higher frequencies of biotin-related genes (i.e., bioY, bioM, bccP) in caries-active children, indicating a potential role of biotin in caries pathogenesis. This study investigated a biotin limitation strategy against the primary cariogenic bacterium Streptococcus mutans (S. mutans), including its effects on cariogenic phenotypes, gene expression, and metabolomics.

METHODS: S. mutans UA159 was cultured in biotin-free medium supplemented with different biotin concentrations. The cariogenic phenotypes of the strain, including growth kinetics, biofilm formation, exopolysaccharide (EPS) production, lactate synthesis, acid/oxidative tolerance, and membrane fluidity, were measured and compared across biotin concentrations. Biofilm architecture was visualized via confocal laser-scanning microscopy (CLSM) and scanning electron microscopy (SEM). Quantitative real-time polymerase chain reaction (RT-qPCR) was employed to analyze the expression of genes associated with virulence and biotin metabolism. Metabolomic analysis was performed to characterize metabolic perturbations induced by biotin limitation in S. mutans.

RESULTS: Under biotin limitation, S. mutans exhibited significantly reduced cariogenic phenotypes, accompanied by cell elongation and reduced membrane fluidity. At the molecular level, biotin limitation suppressed the expression of key virulence-associated genes and induced a compensatory upregulation of genes involved in biotin uptake and biotin-dependent carboxylases. Metabolomic analysis under biotin-limited conditions in S. mutans revealed perturbed pathways in central carbon metabolism and nucleotide metabolism.

CONCLUSION: Biotin limitation significantly reduced the cariogenic potential of S. mutans by disrupting metabolic flux and virulence gene expression, highlighting biotin uptake and metabolism as potential targets for anti-caries therapies.},
}

@article {pmid41051042,
year = {2025},
author = {Nancy, and Lakhawat, SS and Kumar, R and Sharma, PK},
title = {Cloning, Expression, Purification, and Characterization of Superoxide Dismutase from the Soil Metagenome.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665415743250926072254},
pmid = {41051042},
issn = {1875-5305},
abstract = {INTRODUCTION: Superoxide Dismutases (SODs) are enzymes that catalyze the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.

MATERIALS AND METHODS: Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector and subcloned into an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.

RESULTS: The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40°C and pH 8, respectively. The enzyme remains completely stable at 40°C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50°C and 60°C for 3 h. The biophysical investigation revealed stable confirmation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi- Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.

DISCUSSION: The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn2+ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.

CONCLUSION: The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, which include its therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.},
}

@article {pmid41050906,
year = {2025},
author = {Wiese, M and Klaassens, ES and Hatt, V and Kreikamp, A and Baak, ML and Heerikhuisen, M and Van Der Vossen, JMBM},
title = {Demonstration of phage inhibitory action against Clostridium perfringens LMG 11264 within a complex chicken cecal microbiota in vitro.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1599939},
pmid = {41050906},
issn = {2813-2467},
abstract = {INTRODUCTION: Clostridium perfringens strains may cause foodborne illness, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection may cause necrotic enteritis, and infections are associated with high mortality rates partially due to antibiotic resistance, which hampers efficient treatment. In-vitro screening approaches of alternative treatment options, for instance, specific phages, represent a promising strategy for the selection of novel interventions to combat infections.

MATERIAL AND METHODS: In this study, we explored the application of a C. perfringens strain LMG 11264-specific phage #7 introduced at 10[4] pfu/mL to inhibit the growth of C. perfringens at 10[6] cfu/mL compared to two antibiotics (amoxicillin at 10 µg/mL and clindamycin at 10 µg/mL) within complex chicken cecal microbiota in vitro. Samples for gDNA isolation, qPCR, and metagenome sequencing were taken at the beginning and after 24 and 48 h of incubation.

RESULTS: The C. perfringens strain LMG 11264 proliferated within the untreated complex microbiota and reached levels of approximately 10[8] and 10[9] genome equivalents per mL after 24 and 48 h of incubation, respectively. The phage intervention with phage #7 inhibited the growth of C. perfringens LMG 11264 significantly; the inhibitory effects were similar to those exerted by the antibiotic intervention with amoxicillin and stronger than the inhibitory effects with clindamycin. In the absence of the C. perfringens challenge, we found a significant effect of amoxicillin (p = 0.040) or clindamycin (p = 0.000017) compared to the untreated control after 24 h of incubation, and the phage addition did not affect the alpha diversity expressed as Chao index significantly (p = 1). In addition, the endogenous C. perfringens in the chicken microbiota appeared insensitive to phage #7. The phage titer of phage #7 only increased in the presence of the inoculated C. perfringens strain LMG 11264. In conclusion, the i-screen model can be implemented to test the efficacy and specificity of phage therapy in vitro.},
}

@article {pmid41050878,
year = {2025},
author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D},
title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101554},
pmid = {41050878},
issn = {2451-8654},
abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.

METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6 L. crispatus strains (LC106) or 15 L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of ≥ Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance ≥5 % of any LBP strain or ≥10 % of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.

CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.

TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).

PROTOCOL VERSION: 2.0 dated October 03, 2023.},
}

@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation & purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}

Humans
*Mucormycosis/diagnosis/microbiology/drug therapy
*Mucorales/genetics/isolation & purification/classification
Male
Female
Middle Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Aged
Adult
ROC Curve
Antifungal Agents/therapeutic use
Microbiota

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41050203,
year = {2026},
author = {Wang, Q and Shan, S and Sun, Q and Zhao, X and Yuan, C and Mou, Y and Wang, J and Yan, C and Wang, Q and Rui, Q and Li, C},
title = {The coupling effect of Penicillium baileys W2 in the Aspergillus flavus inhibition and peanut growth promotion.},
journal = {Synthetic and systems biotechnology},
volume = {11},
number = {},
pages = {127-140},
pmid = {41050203},
issn = {2405-805X},
abstract = {Aspergillus flavus is a significant plant pathogen, and peanut crops are particularly vulnerable to aflatoxin contamination. This vulnerability underscores the need for more effective control methods. In this study, the strain Penicillium baileys W2 was isolated from the rhizosphere soils of healthy peanut seedlings. The fermentation extract exhibited concentration-dependent inhibition of pathogenic A. flavus growth, with a minimum inhibitory concentration (MIC) of 55 % and a minimum fungicidal concentration (MFC) of 60 %. Physiological data and transcriptome analysis demonstrated that the W2 fermentation supernatant inhibited A. flavus growth by disrupting membrane permeability. Metabolomics analysis identified active compounds, including propylparaben, taxifolin, and phloretin, which exhibited significant antagonistic effects against A. flavus. Additionally, we evaluated the impact of the W2 fermentation broth on peanut growth promotion and on rhizosphere microbial community structure using metagenomic sequencing. The reduction of harmful soil microorganisms contributed to the maintenance of soil health, whereas the increased abundance of beneficial microorganisms enhanced peanut seedling growth by facilitating soil nutrient cycling. These findings indicate that the development and application of P. baileys strain W2 or its fermentation extract aligns with sustainable agricultural principles and offers a promising biological control approach.},
}

@article {pmid41049781,
year = {2025},
author = {Wang, B and He, T and Cheng, Y and Chen, H and Hu, Y and Liu, Y and Wang, F and Chen, L},
title = {Targeted enhancement strategies for Sojae Semen Praeparatum: Impact of Aspergillus oryzae and Bacillus subtilis on microbial communities, flavor substances, and functional components.},
journal = {Food chemistry: X},
volume = {30},
number = {},
pages = {102931},
pmid = {41049781},
issn = {2590-1575},
abstract = {Sojae Semen Praeparatum (SSP), a traditional Chinese fermented soybean product, was optimized through novel single/double enhancement fermentation using Aspergillus oryzae and Bacillus subtilis. Enhanced fermentation significantly increases the production of flavor amino acids. Using headspace solid-phase extraction microextraction gas chromatography-mass spectrometry (HS-SPEM-GC-MS) technology, 51 critical flavor substances were identified, confirming that enhanced fermentation improves the flavor profile of SSP. Isoflavone quantification revealed that enhancement strategies promoted isoflavone conversion. Enzyme inhibition and antioxidant activities were superior in the double enhancement fermentation group. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated a significant increase in SSP's enrichment in the flavone and flavonol biosynthesis pathway. Screening identified 19 key flavonoid components strongly correlated with bioactivity, and enhancement fermentation notably enhancing their accumulation. Metagenomic sequencing revealed 14 key differential microorganisms, essential to flavor development and activity enhancement in SSP. This study offers valuable insights for optimizing fermentation processes to enhance product quality.},
}

@article {pmid41049190,
year = {2025},
author = {Liu, C and Li, B and Wu, Q and Chen, D and Zhou, W and Ao, J},
title = {The effects and mechanism of urease inhibitor and its combination with nitrification inhibitor on nitrous oxide emission across four soil types.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1663261},
pmid = {41049190},
issn = {1664-462X},
abstract = {Nitrogen (N) fertilization is essential for ensuring crop productivity, while excessive N application significantly increases greenhouse gases (GHGs) emissions, particularly nitrous oxide (N2O). Urease inhibitors (UI) and combined urease and nitrification inhibitors (UN) have demonstrated potential in mitigating GHGs emission, though their efficiency with great variation across different soils types. In this study, controlled incubation experiments were conducted using four types of agricultural soils to evaluate the mitigation potential of UI and UN application and to investigate their underlying mechanisms. N fertilization significantly increased N2O emissions by 5.1~99.9-fold and elevated CO2 emissions by 13.6~65.4% across all soil types. The UI treatment decreased the peak of NO2 [-] concentrations in two alkaline soils, while the UN treatment decreased both NO2 [-] and NO3 [-] concentrations in all four soils. In terms of GHG mitigation, UI treatment reduced N2O emissions by 16.5~57.4% in alkaline soils and reduced CO2 emissions by 6.5~49.3% across four soil types. The UN treatment demonstrated superior efficacy, reducing N2O emissions by 52.5~92.4% and CO2 emissions by 4.2~87.2% across all soils. Metagenomic sequencing revealed that both UI and UN significantly inhibited the relative abundances of key functional genes associated with nitrification (hao and nxrAB), dissimilatory nitrate reduction (narGHI/napAB), nitrite reduction (nirS/nirK), and nitric oxide reduction (norBC). Random forest identified key factors influencing the N2O mitigation efficiency of UI and UN. These included soil properties such as soil pH, total nitrogen, organic matter, available potassium, water-filled pore space, texture. Additionally, partial functional genes related to nitrification, denitrification, carbon and methane metabolism, sulfur and phosphorus cycling were also identified as key contributors. Overall, these findings provide valuable insights for the region-specific application of UI and UN to effectively mitigate GHGs emissions. The identification of key soil abiotic and biotic factors offers a theoretical foundation for optimizing inhibitors application and enhancing their mitigation efficiency.},
}

@article {pmid41049022,
year = {2025},
author = {Cohodes, M and Fernandez, A and Ashkin, D and Reed, C and Park, S and Banaei, N and Fung, M and Jacobson, K and Goswami, ND},
title = {Curated cases from the TB expert network: Unplugged! Series: Use of plasma microbial cell-free DNA metagenomic sequencing to diagnose Mycobacterium tuberculosis.},
journal = {Journal of clinical tuberculosis and other mycobacterial diseases},
volume = {41},
number = {},
pages = {100563},
pmid = {41049022},
issn = {2405-5794},
abstract = {A 52-year-old U.S.-born man with diabetes and a kidney transplant 3 months prior presented with fever of unknown origin and left-sided weakness. On admission, he was found to have right internal carotid artery thrombus and cerebral infarct. He developed respiratory failure and underwent treatment for Pseudomonas bacteremia. Fevers continued through hospital day 30 and computed tomography (CT) scans demonstrated an esophageal mass, hepatic lesions, and pulmonary nodules, which were new compared to pre-transplant imaging 2 years prior. While awaiting results from acid-fast bacilli (AFB) cultures from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). Based on the results of mcfDNA sequencing, clinical presentation, and radiographic findings, a diagnosis of tuberculosis disease was made, and anti-tuberculosis treatment was initiated. While awaiting results from acid-fast bacilli (AFB) cultures and molecular studies from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). The patient was discharged on hospital day 60; 27 days after discharge, 58 days after the Mtb PCR resulted positive from tissue biopsy, and 60 days after the positive mcfDNA, sputum cultures returned positive for Mycobacterium tuberculosis.},
}

@article {pmid41048510,
year = {2025},
author = {Mieremet, A and van der Wurff, M and Pagan, L and Ferrer-González, E and Seo, J and Schuren, FHJ},
title = {Taxonomic and functional profiling of the vulvar microbiome indicates variations related to ecological signatures, aging, and health status.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633147},
pmid = {41048510},
issn = {1664-302X},
abstract = {INTRODUCTION: The vulvar microbiome is adjacent to that of the skin and the vagina and connects microbiomes present on a stratified epithelial barrier to that of a mucosal barrier. Yet, the characterization of the microbiome in the vulvar region of the body is understudied, although dysbiosis in the microbiome of the skin or vagina have been linked to impairments in women's health.

METHODS: To better understand the role of the vulvar microbiome during healthy aging or during presentation of vulvar diseases, we analyzed the vulvar microbiome by shotgun metagenomic sequencing on composition at species level and for functional capacity. This was performed in a large population enrolled in the Vulvar Microbiome Leiden Cohort (VMLC), including a total of 58 healthy women in a broad age range (22-82 years). Moreover, we analyzed vulvar microbiome derived from 9 participants presenting a vulvar disease, including vulvar lichen sclerosus (LS; N = 6), or high-grade squamous intraepithelial lesion (HSIL; N = 3).

RESULTS: Compositional analyses showed a skin-, vagina-, or multispecies mixture- dominant bacterial signature, which revealed differences in the alpha diversity and functional capacity of the microbiome. Upon aging the presence of Lactobacillus iners, L. crispatus, and L. gasseri in the vulvar microbiome shifted toward reduction. In the microbiome of individuals with a vulvar disease, higher abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium amycolatum, and Corynebacterium simulans was detected, and an altered functional capacity for the L-histidine pathway.

DISCUSSION: In conclusion, we identified variations in microbial taxa and functional capacities in the vulvar microbiome that are associated with age and disease (LS and HSIL), which can be targeted to develop microbiome-based vulvar therapies promoting women's health.},
}

@article {pmid41048504,
year = {2025},
author = {Ai, X and Huang, C and Liu, Q and Duan, R and Ma, X and Li, L and Shu, Z and Miao, Y and Shen, H and Lv, Y and Jiang, Z and Luo, H and Long, Z},
title = {Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629811},
pmid = {41048504},
issn = {1664-302X},
abstract = {INTRODUCTION: Population aging represents a significant challenge in contemporary society. The gut microbiome plays a critical role in maintaining host health and physiological functions, and its alterations with advancing age are closely associated with the process of healthy aging.

METHODS: This study conducted a comprehensive analysis of the gut microbiome in hundred healthy elderly individuals (aged ≥60) residing in Changshou Town, Zhongxiang City, Hubei Province, utilizing metagenomic sequencing technology. The primary objective was to investigate the changes in the gut microbiome and its potential functions during the latter stages of life. Participants were categorized into three distinct age groups: the Young-Old group (YO, ages 60-74), the Middle-Old group (MO, ages 75-89), and the Long-Lived Old group (LO, ages 90-99).

RESULTS: The findings indicate that the diversity of the gut microbiome tends to diminish with age. However, a significant reversal was observed among healthy longevity elderly individuals. Our analysis specifically focused on the trends in the alterations of gut microbiome species and their potential functions as age increases, revealing that the changes in major differential functions closely align with the trends in major differential species, demonstrating a strong positive correlation. The YO group exhibited a more diverse array of differential microbial characteristics and functional traits. Notably, there was a significant enrichment of Bacteroides stercoris in the YO group, which displayed a continuous decline with age, alongside a marked enrichment of pathways associated with xenobiotic biodegradation and metabolism. Furthermore, species significantly linked to aging-related pathways, such as oxidative phosphorylation, were identified through species functional correlation analysis. Specifically, Collinsella bouchesdurhonensis and Prevotella stercorea were enriched in the LO and YO groups, respectively. In total, we successfully obtained two hundred and thirty eight high-quality bins through metagenomic assembly, which included the identification of four species with 100% completeness, as well as the genomic information of the Methanobrevibacter smithii A across all groups.

DISCUSSION: This study characterizes the age-associated trends in gut microbiome composition and function during later-life healthy aging, providing exploratory insights that may inform future microecological intervention strategies, pending validation in longitudinal studies.},
}

@article {pmid41048502,
year = {2025},
author = {Peng, X and Wei, Y and Zhou, X},
title = {Enhancing pathogen identification through AI-assisted metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634194},
pmid = {41048502},
issn = {1664-302X},
abstract = {INTRODUCTION: To address the limitations of current metagenomic identification approaches, we proposed a principled AI-assisted architecture that enhances accuracy, scalability, and biological interpretability through three core innovations.

METHODS: Firstly, we developed a structured probabilistic model that formulates pathogen detection as a hierarchical and compositional inference task under taxonomic and ecological constraints. This framework enables the integration of phylogenetic priors and sparsity-aware mechanisms, reducing noise and ambiguity. By modeling taxonomic structure and ecological dependencies, the approach ensures more accurate identification, especially in complex or low-abundance microbial communities. Secondly, we introduced the Taxon-aware Compositional Inference Network (TCINet), a deep learning model that processes sequencing reads to produce taxonomic embeddings. TCINet estimates abundance distributions via masked neural activations that enforce sparsity and interpretability, while also propagating uncertainty through log-normal variance modeling. Designed to respect microbial phylogeny and co-occurrence patterns, TCINet enables scalable, biologically plausible inference across diverse clinical and environmental datasets. Thirdly, we presented the Hierarchical Taxonomic Reasoning Strategy (HTRS), a post-inference module that refines predictions by enforcing compositional constraints, propagating evidence across taxonomic hierarchies, and calibrating confidence using entropy and variance-based metrics. HTRS includes context-aware thresholding and co-occurrence priors to adaptively optimize performance based on dataset characteristics.

RESULTS: Together, these innovations create a unified framework for metagenomic identification that combines probabilistic modeling, deep learning, and structured reasoning.

DISCUSSION: The architecture delivers robust and interpretable results, making it suitable for applications in clinical diagnostics, environmental monitoring, and ecological research.},
}

@article {pmid41048492,
year = {2025},
author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J},
title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633379},
pmid = {41048492},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.

METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.

RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.

DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.},
}

@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}

New York City
*Metagenome
*Parks, Recreational
Metagenomics
Humans
*Seawater/microbiology
Microbiota/genetics
*Water Microbiology

@article {pmid41048206,
year = {2025},
author = {Tao, H and Zheng, W},
title = {Non-Tuberculous Mycobacterial Infections of the Skin and Soft Tissue in a Chinese Population: A Retrospective Analysis of 15 Cases.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5139-5147},
pmid = {41048206},
issn = {1178-6973},
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) skin and soft tissue infections (SSTIs) are increasingly recognized but underdiagnosed in China.

METHODS: This retrospective study analyzed 15 confirmed cases of NTM SSTIs treated at a southern Chinese hospital from 2012 to 2022. Clinical data, including demographics, clinical presentations, comorbidities, diagnostic methods, treatment regimens, and outcomes, were collected and analyzed. Diagnostic efficacy of conventional culture and metagenomic next-generation sequencing (mNGS) was compared.

RESULTS: The median age of patients was 57 years, and 66.7% were farmers. Pathogens identified included Mycobacterium abscessus (20.0%), M. marinum (13.3%), and rapidly growing mycobacteria (13.3%). Immunocompromised states, such as anti-interferon-gamma autoantibody positivity, were present in 40.0%. mNGS demonstrated superior diagnostic performance, achieving a detection rate of 86.7% (13/15 cases), compared to 26.7% for culture. Treatment regimens, including clarithromycin, rifampin, ethambutol, and moxifloxacin, lasted 1-24 months. Outcomes showed cure in 8 patients (53.3%), improvement in 6 (40.0%), and 1 lost to follow-up.

CONCLUSION: NTM SSTIs present significant diagnostic and therapeutic challenges, with clinical variability and frequent association with immunocompromised states. M. abscessus, M. marinum, and M. avium were the predominant pathogens. mNGS improves detection but still should complement culture. Precise pathogen identification and tailored therapy are essential for achieving optimal outcomes, and further studies are needed to refine diagnostics and treatment strategies.},
}

@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70054},
doi = {10.1111/1755-0998.70054},
pmid = {41048034},
issn = {1755-0998},
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}

@article {pmid41046791,
year = {2025},
author = {Wang, H and Chen, H and Ruan, C and Liao, J and Schwarz, C and Shi, B and Alvarez, PJJ and Yu, P},
title = {Nanoplastics induce prophage activation and quorum sensing to enhance biofilm mechanical and chemical resilience.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124712},
doi = {10.1016/j.watres.2025.124712},
pmid = {41046791},
issn = {1879-2448},
abstract = {Despite the prevalence of nanoplastics (NPs) in natural and engineered water systems and their association with microbial risks, bacterium-phage interactions have been largely overlooked in the context of biofilm formation. Here, we investigated the effects of positively (PS-NH2) and negatively (PS-COOH) charged polystyrene nanoplastics (PS-NPs) on dual-species biofilms composed of Escherichia coli (λ+) and Pseudomonas aeruginosa. PS-NPs promoted biofilm formation and stability at environmentally relevant concentrations (e.g., 100-1000 ng/L), with PS-NH2 exhibiting higher influence. The cellular internalization of PS-NPs increased the reactive oxygen species (ROS) levels by 2.18-2.25 folds, triggered prophage λ activation followed by lysis of E. coli (λ+) after exposure to PS-NPs. Transcriptomic analyses revealed that PS-NPs, especially PS-NH2, activated the SOS response (2.35-2.63-fold), λ phage replication (2.68-3.97-fold), and interspecies quorum sensing (2.24-5.13-fold), which was verified by the proteomic analyses. Therefore, PS-NPs stimulated protective extracellular polymeric substances (EPS) secretion with eDNA content increased to 325.8-433.8 μg/cm[2]. Enhanced EPS production contributed to improved biofilm mechanical properties (1.46-1.57-fold as measured by atomic force microscopy) and increased resistance to chlorine disinfection. Metagenomic analysis of pipeline biofilm demonstrated that PS-NPs promoted bacterium-phage interactions and enhanced bacterial antiviral defense systems, which stimulated multi-species biofilm formation and enhanced environmental resilience. Overall, our findings provide novel insights into the interplay between nanoplastics and bacterium-phage dynamics, highlighting increased microbial risks associated with waterborne nanoplastics.},
}

@article {pmid41046720,
year = {2025},
author = {Yang, J and Wang, S and Heal, KV and Chen, L and Zhou, C},
title = {Microbial functional groups activate insoluble rhizosphere phosphorus to mitigate P limitation of Chinese fir plantations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127503},
doi = {10.1016/j.jenvman.2025.127503},
pmid = {41046720},
issn = {1095-8630},
abstract = {The decline in soil phosphorus (P) reserves and its low solubility pose significant challenges in long-term plantation cultivation. In P-limited subtropical environments, the rhizosphere microbial community and associated genes play a crucial role in driving P cycling and availability during the long-term development of forest plantations. Using the space-for-time substitution method, we investigated rhizosphere P cycling in Chinese fir (Cunninghamia lanceolata) plantations at different growth stages in Fujian Province, southern China. We utilized the modified Hedley fractionation method and metagenomic sequencing for rhizosphere soil samples from stand ages of 6, 26, 45, and 102 years. The results revealed that, with stand development, rhizospheric concentrations of total, stable and moderately labile P decreased significantly, whereas labile P became progressively enriched (P < 0.05). Genes involved in organic P mineralization and P transport were positively correlated with labile P concentrations in the rhizosphere (P < 0.05), whereas P metabolism regulatory genes were negatively correlated with moderately labile P (P < 0.05). Additionally, the dominant P-solubilizing bacteria-Bacteroidetes and Rudaea-exerted significant positive effects on labile P and negative effects on stable P, respectively (P < 0.05). Overall, rhizospheric P reserves were significantly depleted in the Chinese fir plantations during their developmental progression. However, this unsustainable trend in P reserves was mitigated through synergistic interactions between P-solubilizing bacteria and P metabolism genes, which catalyzed the conversion of insoluble P into labile P, while enhancing plant P uptake efficiency. Consequently, we propose science-informed management practices-such as optimizing P fertilization management, inoculating P-solubilizing microbial agents, utilizing organic fertilizers, and introducing native broadleaf species-to sustain functional stability and long-term productivity of subtropical plantation ecosystems.},
}

@article {pmid41000811,
year = {2025},
author = {Konnaris, MA and Saxena, M and Lazar, N and Silverman, JD},
title = {Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41000811},
issn = {2692-8205},
abstract = {Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.},
}

@article {pmid41046693,
year = {2025},
author = {Theysgeur, S and Dugardin, C and Louvel, B and Lemière, S and Muchembled, J and Taminiau, B and Daube, G and Siah, A and Ravallec, R and Hilbert, JL and Lucau-Danila, A},
title = {Assessment of health effects of potato crop phytopharmaceuticals and storage products in a murine model.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180630},
doi = {10.1016/j.scitotenv.2025.180630},
pmid = {41046693},
issn = {1879-1026},
abstract = {Potatoes are among the most widely consumed staple foods worldwide, but their cultivation and storage frequently involve multiple phytopharmaceutical products (PPPs), raising concerns about the health risks of dietary pesticide residues. The health effects of multi-residue PPPs used in potato cultivation were assessed in an in vivo murine model, involving 36 mice, and evaluated through omics analyses. Two field cultivation methods (conventional and organic) and two post-harvest storage conditions (using 1,4-dimethylnaphthalene and mint essential oil as sprout inhibitor treatments) were considered. Potato tubers were processed into flour and administered to the animals at a moderate daily dose for 20 consecutive days. Nutrigenomic analyses revealed significant gene deregulations, with 70 genes affected in the liver, 56 in the jejunum, and 52 in the brain, suggesting disturbances in cellular proliferation, nervous system functions, lipid and carbohydrate metabolism, reproductive health, and immune responses. Metagenomic analyses indicated microbiota imbalances, including a shift in the Firmicutes/Bacteroidota ratio and changes in 2 bacterial genera with potentially adverse effects. The main residues suspected of producing these effects include propamocarb, carfentrazone, 1,4-dimethylnaphthalene, copper derivatives, and peppermint essential oil. These findings highlight the importance of large-scale omics approaches in uncovering potential biological disruptions, underscore the health risks associated with chronic dietary exposure to pesticide residues, particularly in mixtures, and emphasize the need to reassess regulatory standards to promote agricultural practices that minimize pesticide residues to better protect the environment and human health.},
}

@article {pmid41046691,
year = {2025},
author = {Zhang, N and Li, W and Wang, H and Lv, G},
title = {Metabolomic insights into rhizosphere microbial dynamics in desert plants under drought stress.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180653},
doi = {10.1016/j.scitotenv.2025.180653},
pmid = {41046691},
issn = {1879-1026},
abstract = {Drought hinders plant growth and development. However, studies on rhizospheric metabolism and microbial composition of desert plants under drought stress are limited. This study used untargeted metabolomics to detect that the differential metabolites included mainly alkaloids and their derivatives, benzenoids, lipids, and lipid molecules under drought stress. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the differences between drought stress in the rhizosphere environment were usually reflected in microbial metabolism, plant hormone biosynthesis, and secondary metabolite biosynthesis in different environments. Metagenomic analysis showed that the relative abundances of Chloroflexi, Firmicutes, and Gemmatimonadetes in the mild drought rhizosphere group (MiR) were significantly higher than those in the severe drought rhizospheric soil group (SR) in the phylum of the microorganisms; the relative abundance of Proteobacteria in the SR group was also significantly higher. Through the analysis of the correlation network, it is found that there is a significant correlation between microorganisms and differential metabolites. During drought stress, plants can indirectly influence the support of soil microbes by modifying the structure and concentration of metabolites, which helps to enhance drought tolerance. This study provides a theoretical basis for exploring new stress adaptation strategies and protecting soil microecology.},
}

@article {pmid41046678,
year = {2025},
author = {Alhaboub, A and Deschenes, NM and Li, XX and Williams, VR and Katz, KC and Park, SY and Aftanas, P and Wong, H and Sjaarda, C and Tozer, K and Maguire, F and Leis, J and Sheth, P and Kozak, R},
title = {Some assembly required: Comparison of bioinformatic pipelines for analysis of viral metagenomic sequencing from nosocomial respiratory virus outbreaks.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {181},
number = {},
pages = {105877},
doi = {10.1016/j.jcv.2025.105877},
pmid = {41046678},
issn = {1873-5967},
abstract = {INTRODUCTION: Metagenomic sequencing (mGS) is a useful tool for identifying pathogens in patient samples. During nosocomial outbreaks of respiratory viruses, mGS allows for the identification of viral strains and provides insight into their genetic relatedness. Multiple bioinformatics analysis assembler are available for processing data, but a comprehensive comparison of their performance in for respiratory virus outbreaks has not been conducted.

METHODS: This study sequenced samples from five separate nosocomial outbreaks of RNA respiratory viruses. RNA was extracted from the samples, and cDNA was synthesized using random hexamers, and then sequenced on an Illumina Miniseq following Nextera DNA Flex library preparation. The data from each outbreak were analyzed using four different assemblers: MEGAHIT, rnaSPAdes, rnaviralSPAdes, and coronaSPAdes, to evaluate their analytical performance.

RESULTS: The mGS confirmed the viral identification and provided accurate strain identification for both coronavirus and parainfluenza virus samples. However, differences were observed between the assemblers in terms of the largest contigs produced and the proportion of the viral genome aligned with reference genomes. Notably, coronaSpades outperformed the other pipelines for analyzing seasonal coronaviruses, generating more complete data and covering a higher percentage of the viral genome.

CONCLUSION: Achieving a higher percentage of the viral genome sequence is crucial for a more detailed characterization, which is especially valuable for outbreak analysis where viral strains may only differ by a few genetic changes. Comparison of assemblers will allow for clinical laboratories to determine the bioinformatic pipeline that is optimal for helping clinicians better manage outbreaks.},
}

@article {pmid41046586,
year = {2025},
author = {Kwiatkowska, AM and Guzmán, JA and Lafaurie, GI and Castillo, DM and Cardona, AF},
title = {Exploring the role of the oral microbiome in saliva, sputum, bronchoalveolar fluid, and lung cancer tumor tissue: A systematic review.},
journal = {Translational oncology},
volume = {62},
number = {},
pages = {102557},
doi = {10.1016/j.tranon.2025.102557},
pmid = {41046586},
issn = {1936-5233},
abstract = {OBJECTIVE: To explore the association between the oral microbiome and the presence or progression of lung cancer (LC) using metagenomic sequencing techniques.

METHODS: Databases, including PubMed and EMBASE, were reviewed. Eligible studies included the study of oral microorganisms via genomic sequencing and molecular mechanisms associated with LC in saliva, sputum, bronchoalveolar lavage fluid (BALF), or tumor tissue from LC patients. A quality analysis of the studies was carried out, and a qualitative synthesis was performed according to the localization and sample type. Meta-analysis was performed on alpha diversity indexes.

RESULTS: Of the 1880 scrutinized articles, 50 studies were selected, comprising 29 cross-sectional, 7 case-control, and 14 cohort studies. The quality analysis sheds light on potential biases. The findings revealed a conspicuous overgrowth of specific microbial taxa in LC patients' saliva BALF samples of Veillonella and Streptococcus. Conversely, the Bacteroides genus, related to periodontal disease, exhibited no significant correlation with LC. Microorganisms in tumoral tissue were associated with poor prognosis. Veillonella was associated with a better response to ICIs therapy. Oral microorganisms were related to metabolic reprogramming with xenobiotic biodegradation, amino acid, sugar, sucrose, and lipidic metabolism, immune modulation, and proinflammatory responses.

CONCLUSION: Overgrowth of specific oral microorganisms in the saliva and BALF is associated with diagnosis, poor prognosis, and low response to immunotherapy. Veillonella could be a marker for response to ICIs therapy. Further well-designed studies should evaluate the impact of the oral microbiome on the response to ICIs.},
}

@article {pmid41045990,
year = {2025},
author = {Liu, Y and Zheng, Y and Wang, L and Guo, Y and Huang, G and Yuan, Z and Wang, F and Gai, W and Xing, J},
title = {Bacteriophage combined with mNGS enhances the specificity of bacterial infection diagnosis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106618},
doi = {10.1016/j.jinf.2025.106618},
pmid = {41045990},
issn = {1532-2742},
abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) is an important tool for enhancing pathogen detection in infected patients. However, distinguishing between specimens that are infected or colonized is still a major challenge.

OBJECTIVES: To explore the composition of bacteriophages in the blood and respiratory tract of the human body, the association between bacteriophage detection and bacterial infections, and whether bacteriophages can assist in differentiating infectious pathogens according to mNGS results.

METHODS: Clinical samples from hospitalized patients were collected between January 2023 and February 2024. DNA and cell-free DNA were extracted from BALF and plasma retrospectively to identify the pathogens present, and bacteriophage annotations were conducted.

RESULTS: A total of 299 samples, comprising 136 blood samples and 163 BALF samples, were obtained from 218 patients. Compared with the samples negative for bacteria, both blood and bronchoalveolar lavage fluid (BALF) samples infected with Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and S. aureus showed a corresponding increase in the proportions of phages related to these pathogens. In BALF samples with Acinetobacter baumannii infection, the proportions of Autographiviridae, Siphoviridae, and Myoviridae were significantly greater than those in the Acinetobacter baumannii colonization group. The sensitivity of Myoviridae for differentiating between infection and colonization was 86.36%, and the specificity was 52.94%.

CONCLUSION: In sepsis, compared with conventional mNGS methods alone, the use of bacteriophages combined with mNGS was more effective in identifying causative pathogens and had higher specificity. These findings may provide new ideas and tools for improving clinical infection diagnosis.},
}

@article {pmid41045972,
year = {2025},
author = {Song, X and Meng, H and Yang, T and Li, Y and Zheng, F and Yan, X},
title = {Female accessory reproductive glands of Paederus fuscipes serve as a reservoir of symbiotic pederin-producing bacteria.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104408},
doi = {10.1016/j.ibmb.2025.104408},
pmid = {41045972},
issn = {1879-0240},
abstract = {Paederus fuscipes, an ecologically and medically important species, is known for its blistering toxin pederin in hemolymph. Evidence demonstrates that the toxin is synthesized by the uncultured symbiotic pederin-producing bacteria (PPB) in P. fuscipes, but the biological characteristics of PPB within the beetle host remain poorly characterized. Here, we investigated PPB abundance variations in P. fuscipes across different factors (sexes, life stages, habitats, and organs), along with their colonization sites and metabolic potentials. The findings revealed that the PPB abundance in female P. fuscipes at the level of individuals and tissues exhibited stable colonization patterns, independent of habitat and time changes. Notably, PPB dominated the bacterial community in females (relative abundance ≥ 66.08%) and nearly occupied reproductive organs (relative abundance ≥ 96.31%). Moreover, our results indicated that PPB were predominantly enriched in the accessory glands of female reproductive organs, which could serve as a reservoir for PPB proliferation. Although PPB were not cultured in this study, metagenomic binning yielded the draft genome of PPB (CheckM completeness = 85.14%, contamination = 0), in which genes related to pederin biosynthesis were identified. Phylogenetic analyses revealed that PPB formed a sister clade to Pseudomonas aeruginosa rather than nesting within the P. aeruginosa lineage. Metabolic module prediction analysis revealed specific deficiencies in PPB's energy metabolism and amino acid biosynthesis pathways, suggesting limited free-living potential for PPB. Collectively, this study provides insights into PPB biological characteristics within their beetle host and paves the way for biotechnological exploitation related to pederin production.},
}

@article {pmid41045941,
year = {2025},
author = {Alcolea-Medina, A and Snell, LB and Humayun, G and Al-Yaakoubi, N and Ward, D and Alder, C and Patel, V and Vivian, F and Meadows, CIS and Wyncoll, D and Paul, R and Barratt, N and Batra, R and Edgeworth, J and Nebbia, G and Whitehorn, J},
title = {Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101174},
doi = {10.1016/j.lanmic.2025.101174},
pmid = {41045941},
issn = {2666-5247},
abstract = {BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs).

METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation.

FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae.

INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies.

FUNDING: None.},
}

@article {pmid41045876,
year = {2025},
author = {Gebert, J and Böhnke-Brandt, S and Zander, F and Indenbirken, D and Bergmann, L and Krohn, I and Perner, M},
title = {Linking microbial community composition, microbial biomass and extracellular polymeric substances to organic matter lability gradients in sediments of the tidal Elbe River.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180614},
doi = {10.1016/j.scitotenv.2025.180614},
pmid = {41045876},
issn = {1879-1026},
abstract = {The port of Hamburg represents a transition zone between upstream, shallow regions of high net primary production and downstream deep and more turbulent waters in the tidal Elbe River in northwestern Germany. Correspondingly, strong gradients of degradable organic matter (OM) on a distance of a few river kilometers had been identified. This study links microbial community composition using 16S metagenomic amplicons and extracellular polymeric substances (EPS) composition to the observed gradients of sediment OM lability. It was hypothesized that lability gradients caused by higher concentrations of biogenic, autochthonous OM upstream and greater share of already stabilized OM downstream reflect in gradients of microbial community composition, diversity and EPS characteristics. Indeed, available OM was found to act as key driver regulating syntrophic microbial community composition and associated metabolic features, with location-specific overriding the effect of seasonal variations. Upstream sites with high available OM featuring lower bacterial but increased archaeal diversity and elevated methane and carbon dioxide fluxes, whereas lower OM lability downstream fostered a more diverse bacterial but decreased archaeal diversity. The ratio between microbial taxon richness and biomass correlated inversely with OM transformation rates. These patterns also reflected in increased EPS concentration produced in response to metabolic needs (i.e. polysaccharides and proteins), whereas structural components such as lipids, which can be more resistant under the prevailing anoxic conditions, remained more evenly distributed along the transect. Although bacterial relative abundances exceeded archaeal abundances (<1 %) by far, archaeal functional significance remained pivotal for the final release of carbon as methane and carbon dioxide under the mostly reducing conditions in the deposited sediment.},
}

@article {pmid41045656,
year = {2025},
author = {Tuffou, R and Windal, L and Delmotte, S and Skorski, G and Metton, I and Voisin, SN and Surribas, A and Beytur, S and Leborgne, M and Blanquart, H and Salducci, X and Feugier, A},
title = {Combining fermentation and vermicomposting for sustainable pet food waste management: Effects of waste profile and inoculum source.},
journal = {Waste management (New York, N.Y.)},
volume = {208},
number = {},
pages = {115176},
doi = {10.1016/j.wasman.2025.115176},
pmid = {41045656},
issn = {1879-2456},
abstract = {Ingredient production is the main driver of pet-food GHGs and land use. Indeed, the pet food industry uses nearly 495,000 km[2] of land annually. Yet, waste streams from production and declassified products remain underexplored as resources to produce high quality soil amendment. This study proposes an integrated approach to valorise such organic wastes through microbial fermentation prior to vermicomposting. Two experiments were conducted. (1) the effects of kibble incorporation ratio (15 % vs. 30 %), fibre source (spruce flakes, SF vs. beech sawdust, BS), and container size (50 L vs. 500 L) on fermentation dynamics, worm preference, and vermicompost properties were assessed. (2) the functional equivalence of commercial inoculum (EM®) and locally sourced indigenous microorganisms (IMO) was evaluated. Results showed that fibre type significantly influenced fermentation outcomes at low kibble incorporation, with BS lowering pH (from 9 in SF30% to 5.2 in BS15%, P < 0.001) and increasing redox potential (+213 %, P < 0.001). Electroconductivity was strongly affected by both kibble ratio (+110 %, P < 0.001) and fibre source (+130 %, P < 0.001). Worms displayed strong preference for BS-based substrates (+493 % density in 7 days, P < 0.001). Vermicompost derived from SF exhibited slower nitrogen and carbon mineralisation than BS. Container size had no effect on fermentation. EM® and IMO performed equivalently in fermentation efficiency, worm attraction, and functional microbial activity (metagenomic/metaproteomic analyses). This work demonstrates that combining microbial pre-digestion with vermicomposting can upcycle pet food waste into valuable soil amendments, while supporting local circular bioeconomy and sustainable waste management.},
}

@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}

*Bioreactors/microbiology
Anaerobiosis
*Sewage/microbiology
Methane/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Temperature
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics

@article {pmid41044758,
year = {2025},
author = {Pérez-Pérez, L and Galisteo, C and Sanjuán, JMO and Cobo-Díaz, JF and Puente, H and Rubio, P and Carvajal, A and Arguello, H},
title = {Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {105},
pmid = {41044758},
issn = {2524-4671},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
abstract = {BACKGROUND: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.

RESULTS: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.

CONCLUSIONS: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.},
}

@article {pmid41044750,
year = {2025},
author = {Kang, L and Li, Y and Wang, J and Fu, J and Li, Q and Jiang, Q and Zhou, H and Xiao, H and Zhang, Z and Hong, M},
title = {Seasonal dynamics, dietary patterns, and bamboo leaf nutrition shape the phyllosphere-associated gut microbiota of red pandas.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {104},
pmid = {41044750},
issn = {2524-4671},
support = {grant no. 32470516//National Natural Science Foundation of China/ ; grant no. KCXTD2022-7//Innovation Team Funds of China West Normal University/ ; grant no. 2024NSFSC2082//Sichuan Natural Science Foundation/ ; },
abstract = {BACKGROUND: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.

RESULTS: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.

CONCLUSIONS: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.},
}

@article {pmid41044404,
year = {2025},
author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL},
title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34482},
pmid = {41044404},
issn = {2045-2322},
mesh = {*Fresh Water/microbiology ; Metagenome ; *Genome, Bacterial ; Genome Size ; Ecosystem ; *Bacteria/genetics/classification ; },
abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.},
}

*Fresh Water/microbiology
Metagenome
*Genome, Bacterial
Genome Size
Ecosystem
*Bacteria/genetics/classification

@article {pmid41044010,
year = {2025},
author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L},
title = {The untapped potential of short-read sequencing in biodiversity research.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.09.001},
pmid = {41044010},
issn = {0168-9525},
abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.},
}

@article {pmid41043962,
year = {2025},
author = {Sessions, AL and Magnabosco, C and Barton, HA and Burkhardt, C and Dworkin, JP and Freissinet, C and French, KL and Glavin, DP and Leys, N and Maixner, F and Olsson-Francis, K and Probst, AJ and Quitté, G and Rampe, E and Steele, A and Carrier, BL and Hays, LE and Thiessen, F and Paardekooper, D and Hutzler, A and Harrington, AD and Teece, BL},
title = {Planning Considerations Related to Contamination Control for the Return and Analysis of Martian Samples.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15311074251382157},
pmid = {41043962},
issn = {1557-8070},
abstract = {The joint National Aeronautics and Space Administration and European Space Agency Mars Sample Return (MSR) Campaign is a proposed multi-mission effort to bring selected geological samples from Mars to Earth for the purpose of scientific investigation. Significant parts of these investigations could be affected by Earth-sourced contamination that is either misinterpreted as having a martian origin or that masks a martian signal. The Mars 2020 Perseverance rover implemented strict contamination control requirements to limit contamination of the samples during sample collection. Contamination control and contamination knowledge requirements have not yet been established for the samples after they arrive on Earth. The MSR Sample Receiving Facility (SRF) Contamination Panel (SCP) was tasked with defining the terrestrial biological, organic, and inorganic contamination limits for martian samples during their residence inside the SRF. To reach our recommendations, the SCP studied (i) the previously proposed limits and rationale of the Organic Contamination Panel, (ii) cleanliness levels achieved for sampling hardware by the M2020 mission, (iii) recent improvements in analytical technology and detection limits, (iv) updated information regarding the organic content of martian samples (e.g., from the Sample Analysis at Mars instrument on the Curiosity rover and laboratory analyses of martian meteorites), and (v) information about the composition and geologic context of samples being collected by the Perseverance rover for return to Earth.},
}

@article {pmid41039216,
year = {2025},
author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X},
title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {591},
pmid = {41039216},
issn = {1471-2180},
support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure.

RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-α (TNF-α)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype.

CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04245-4.},
}

@article {pmid41043636,
year = {2025},
author = {Ba, XQ and Wang, MF and Huang, WL and Ye, XF and Xu, YY and Li, MM and Jiang, RF and Chen, CN},
title = {Talaromyces Marneffei Infection Involving the Central Nervous System in a Patient with Acquired Immunodeficiency Syndrome: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108096},
doi = {10.1016/j.ijid.2025.108096},
pmid = {41043636},
issn = {1878-3511},
abstract = {BACKGROUND: Talaromycosis, an opportunistic deep invasive mycosis, is caused by the fungus Talaromyces marneffei and is predominantly observed in individuals with acquired immunodeficiency syndrome (AIDS). Involvement of the central nervous system (CNS) is exceedingly rare and presents significant diagnostic challenges, often associated with high mortality rates.

CASE PRESENTATION: This report details a case of CNS Talaromyces marneffei infection in an AIDS patient who initially presented with epileptic seizures. Neuroimaging identified a ring-enhancing lesion within the right frontal lobe, concurrent with a marked elevation in serum β-D-glucan levels. The diagnosis was confirmed through a multimodal approach, including histopathological examination and metagenomic next-generation sequencing (mNGS). Postoperative management involved a sequential regimen of amphotericin B followed by voriconazole, leading to a favorable recovery. The patient is currently on a maintenance elvitegravir-based antiretroviral therapy regimen.

CONCLUSIONS: CNS Talaromyces marneffei infection in AIDS patients often lacks specific clinical manifestations, which complicates diagnosis and treatment. This case report contributes to the existing body of knowledge by presenting a successfully managed case, thereby enhancing the understanding of diagnostic and therapeutic strategies for similar future presentations.},
}

@article {pmid41043345,
year = {2025},
author = {Yu, C and Zhu, H and He, Y and Weng, R},
title = {Comparison of sulfur cyclings coupled with anaerobic ammonium oxidation in response to different river remediations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127523},
doi = {10.1016/j.jenvman.2025.127523},
pmid = {41043345},
issn = {1095-8630},
abstract = {The evolution from 'malodor' to 'algae bloom' in remediated urban rivers has received an ever-increasing attention due to relatively high nitrogen (N) loadings. As pivotal autotrophic processes, anaerobic ammonium oxidation (anammox) and sulfur-driven denitrification (SDD) represent promising candidates for N removal in remediated rivers with low C/N ratios. However, how and to what extent SDD is coupled with anammox remained largely unknown. Our investigations of four remediated urban rivers revealed that SDD was more prevalent than anammox, with Thiobacillus (0.13 %-2.51 %) dominating over Candidatus_Brocadia (0-0.02 %). The injection of Ca(NO3)2 greatly enhanced the coupling of SDD and anammox (SDDA) in anaerobic environments, achieving a maximum total nitrogen (TN) removal of 93.89 %. Metagenomic and metatranscriptomic analyses identified Thiobacillus, Thermomonas, and Candidatus_Brocadia as key microbial players, with their activities increased by 0.060 %, 0.015 %, and 0.498 %, respectively. Differently, Sulfurisoma, Dechloromonas, and Candidatus_Scalindua emerged as key players in Na2S2O3-group, while Sulfurisoma, Sulfurimonas, and Candidatus_Scalindua played pivotal roles in FeS2-group. Additionally, river simulations revealed that Na2S2O3-group showed the strongest SDDA coupling, supported by the highest abundances of soxB (0.14 %), narG (0.05 %), nirS (5.92 %), and hzsB (6.14 %). The FeS2-group demonstrated moderate coupling, whereas the Ca(NO3)2-group displayed the weakest performance. Moreover, Na2S2O3-group also exhibited excellent TN removal (87.58 %) in real river scenarios, indicating its potential as one promising N removal strategy for practical application. This study contributes to the understanding of S-N cyclings in river ecosystems and provides insights into manipulating N-reduction for possible application in remediated urban rivers.},
}

@article {pmid41043307,
year = {2025},
author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q},
title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103929},
doi = {10.1016/j.identj.2025.103929},
pmid = {41043307},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.

METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-α) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.

RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.

CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.

CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.},
}

@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}

@article {pmid41042849,
year = {2025},
author = {Shen, LQ and Lin, D and Ye, YQ and Liu, Y and Ni, B and Wu, D and Wang, L and Zhu, D},
title = {Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {40},
pages = {e2516722122},
doi = {10.1073/pnas.2516722122},
pmid = {41042849},
issn = {1091-6490},
support = {2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 42207013//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {*Bacteriophages/genetics ; *Nitrogen ; *Soil Microbiology ; *Pesticides/toxicity ; Soil/chemistry ; Bacteria/genetics/virology/drug effects ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Phage-mediated dissemination of antibiotic resistance genes (ARGs) intensifies health threat in the environment. Increasing amounts of pesticides are entering the soil ecosystem, yet their potential influence on phage-mediated ARG spread, particularly under conditions of global change, remains poorly understood. In this study, we performed a long-term field experiment simulating pesticide contamination under nitrogen deposition and examined the role of soil phages in ARG spread and host adaptation using metagenomic and viromic sequencing. Combined pesticide markedly elevated the abundance of phage-encoded ARGs under nitrogen deposition. By enhancing phage-host interactions and increasing the co-occurrence of auxiliary metabolic genes with ARGs, phages may further facilitate the transfer of ARGs to bacterial hosts, conferring hosts a competitive edge in intensified microbial competition driven by combined pesticide exposure under nitrogen deposition. The phage-driven mechanism was supported by in vitro cultivation experiments, demonstrating that phages harboring ARGs, shaped by long-term combined pesticide exposure under nitrogen deposition, can infect bacterial hosts and confer resistance. Collectively, our findings underscore the pivotal role of phages in ARG mobilization under environmental stressors, reinforcing the importance of accounting for phage activity in ARG risk assessments under global change.},
}

*Bacteriophages/genetics
*Nitrogen
*Soil Microbiology
*Pesticides/toxicity
Soil/chemistry
Bacteria/genetics/virology/drug effects
*Drug Resistance, Microbial/genetics
*Soil Pollutants
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics

@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}

*Ice Cover/microbiology/virology
*Bacteria/genetics/virology/classification
*Microbiota/genetics
*Viruses/genetics/classification/isolation & purification
Switzerland
Metagenomics/methods
Ecosystem
Host Specificity

@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Soil Microbiology
Metagenomics
*Amorphophallus/microbiology
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification

@article {pmid41041976,
year = {2025},
author = {Breusing, C and Hauer, MA and Hughes, IV and Becker, JS and Casagrande, D and Phillips, BT and Girguis, PR and Beinart, RA},
title = {Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/mec.70126},
pmid = {41041976},
issn = {1365-294X},
support = {//Schmidt Ocean Institute/ ; EPSCoR Cooperative Agreement OIA-#1655221//National Science Foundation/ ; OCE-0732369//Division of Ocean Sciences/ ; OCE-1536331//Division of Ocean Sciences/ ; OCE-1736932//Division of Ocean Sciences/ ; 1747454//National Science Foundation Graduate Research Fellowship Program/ ; //Argonne National Laboratory/ ; },
abstract = {Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.},
}

@article {pmid41041810,
year = {2025},
author = {Oskolkov, N and Jin, C and Clinton, SL and Guinet, B and Wijnands, F and Johnson, E and Kutschera, VE and Kinsella, CM and Heintzman, PD and van der Valk, T},
title = {Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf108},
pmid = {41041810},
issn = {2047-217X},
support = {KAW 2021.0048 [P.D.H., F.W.]//Knut and Alice Wallenberg Foundation/ ; KAW 2022.0033 [P.D.H.]//Knut and Alice Wallenberg Foundation/ ; //National Bioinformatics Infrastructure Sweden at SciLifeLab/ ; VR 2020-04808//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab and Wallenberg Data Driven Life Science Program/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *DNA, Ancient/analysis ; Animals ; Phylogeny ; Archaea/genetics/classification ; },
abstract = {Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.},
}

*Metagenome
*Metagenomics/methods
*DNA, Ancient/analysis
Animals
Phylogeny
Archaea/genetics/classification

@article {pmid41041613,
year = {2025},
author = {Ma, R and Xu, B and Chen, X and Sun, Q and Li, Y and Zheng, Q and Jiao, N and Zhang, R},
title = {Prophages in marine Citromicrobium: diversity, activity, and interaction with the host.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf148},
pmid = {41041613},
issn = {2730-6151},
abstract = {Lysogeny was frequently detected in marine ecosystems, while how temperate phage genomes (prophages) impact marine microbial population or individual dynamics remained poorly understood. Using marine Citromicrobium strain collection as a model system, we revealed that 58% (22/38) were lysogens harboring 31 prophages that can be grouped into five novel genera (φA-φE). Prophage-encoded genes constituted 9% of host accessory genome, significantly expanding the microdiversity among citromicrobial clonal strains. Metagenomic abundance correlations indirectly supported the "Piggyback-the-Winner" dynamics for φA/φE, evidenced by their sublinear growth pattern with increasing host abundance. Most prophages were capable of spontaneous induction and exhibited high lytic activity when triggered by mitomycin C. Importantly, host-range profiling revealed these prophages deployed a dual "Kill-the-Relatives" and "Colonize-the-Relatives" strategy, and meanwhile, they protected parental host strains through superinfection immunity and enhanced phage resistance with greater prophage carriage. Sequencing data showed the dominance of Mu-like phages over non-Mu-like partners upon induced from the double lysogens. Our analysis further hinted at a unique Mu-type within-host competitive strategy: selectively targeting genes of co-resident prophages and host hypothetical genes, while avoiding self-damage and host metabolic genes potentially essential for phage lytic growth or progeny release. Collectively, this work establishes prophages as key architects of bacterial adaptation and provides new perspectives for prophage-driven evolution in marine bacterial hosts.},
}

@article {pmid41041524,
year = {2025},
author = {Happi, A and Sijuwola, A and Omah, IF and Ogunsanya, O and Saibu, F and Ayinla, A and Adedokun, O and Fadele, J and Nwofoke, C and Adelabu, A and Ogundana, E and Lawal, O and Elias, O and Okokoh, E and Colquhoun, R and Achonduh-Atijegbe, O and Nta, H and Onimajesin, A and Momoh, F and Mari-Saez, A and Redding, D and Murray, K and Hanefeld, J and Sesay, AK and Rambaut, A and Happi, C},
title = {Metagenomics reveals cryptic circulation of zoonotic viruses in Nigeria.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7630852/v1},
pmid = {41041524},
issn = {2693-5015},
abstract = {Zoonotic spillover events pose an ongoing threat to global health, with historic and recent viral diseases of international concern emerging from animal reservoirs 1-6. In Nigeria, limited surveillance of animal hosts at the human and animal interface continues to hinder our understanding of viruses that are cryptically circulating in animals near human dwellings with potential for consequential spillover events. We performed unbiased metagenomic next‑generation sequencing (mNGS) on tissue and swab samples collected from 240 individual animals across 11 taxa (rodents, shrews, bats, goats, sheep, pigs, dogs, cats, chickens, cattle egrets, and lizards) in two Lassa‑affected Nigerian states (Ondo and Ebonyi). Host‑depleted sequencing reads were assembled into contigs, taxonomically classified, and subjected to phylogenetic analyses to characterize viral diversity, host associations, and evidence of cross‑species transmission. Across all samples, we identified 214 distinct viral taxa spanning 33 families, of which 41% (n = 83) represent novel species by ICTV criteria. Positive‑sense RNA viruses dominated (Coronaviridae, Picornaviridae, Astroviridae), followed by negative‑sense RNA, single‑ and double‑stranded DNA, and double‑stranded RNA viruses. Notably, human‑associated enteroviruses-including Hepatitis A virus (genotype 1b), echoviruses, coxsackieviruses, and noroviruses-were detected in goats, pigs, dogs, and chickens, indicating cryptic circulation of human pathogens in peridomestic and domesticated animals. Phylogenetic reconstructions revealed multiple cross‑species viral sharing events, particularly among rodents, goats, sheep, and pigs, and extensive recombination within Nigerian Betacoronavirus 1 lineages. Interestingly we found a putative novel avian like coronavirus in rodents, goats and sheep. Ecological modelling demonstrated that host species identity, sample type, and sampling effort were primary drivers of viral richness and abundance, and that higher overall viral diversity strongly predicted cross‑species transmission potential. Our integrated mNGS approach uncovered a rich and dynamic virome within animals inhabiting human‑dominated environments in Nigeria, including undetected circulation of human enteric viruses. These findings underscore the importance of broad‑taxonomic, real‑time surveillance at human-animal interfaces to inform early‑warning systems and pandemic preparedness, particularly in low‑resource settings.},
}

@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.

METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.

RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p = 0.016) showing both a potentially sex-dependent responses to dietary intervention.

CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}

@article {pmid41040987,
year = {2025},
author = {Li, Y and Zhang, L and Ma, G and Li, C and Hu, W and Ren, R and Zang, Y and Ying, D and Qiu, S and Jin, S and Qiu, C and Cao, X},
title = {Optimization of decision thresholds for Mycobacterium tuberculosis can effectively improve the performance of mNGS in tuberculosis diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1646194},
pmid = {41040987},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis (TB) diagnosis remains challenging due to limitations in traditional methods. This study aimed to optimize the metagenomic next-generation sequencing (mNGS) threshold for Mycobacterium tuberculosis complex (MTBC) detection and evaluate its efficacy compared to standard diagnostic approaches.

METHODS: A total of 264 bronchoalveolar lavage fluid (BALF) samples were collected from patients with suspected pulmonary TB at Yongkang First People's Hospital between January 2022 and June 2023. After excluding patients with incomplete data, 59 clinically confirmed TB patients and 111 with non-tuberculous conditions were enrolled. mNGS data were analyzed to calculate reads per million (RPM) for MTBC, and thresholds of 0.02, 0.05, and 0.10 RPM were evaluated for diagnostic efficacy using clinical diagnosis as the gold standard.

RESULTS: The area under the receiver operating characteristic (ROC) curve (AUC) for mNGS in diagnosing TB at RPM thresholds of ≥0.02, ≥0.05, and ≥0.10 were 0.881, 0.873, and 0.814, respectively. The optimal detection threshold was found at RPM ≥ 0.05. Comparative analysis showed mNGS (AUC = 0.873) outperformed routine culture (0.718), PCR (0.741), and Xpert (0.763). Combining mNGS with these methods improved AUC values to 0.837, 0.868, and 0.873, respectively.

CONCLUSION: Optimizing the mNGS threshold to ≥0.05 significantly enhances MTBC detection in pulmonary TB. Combining mNGS with traditional methods further improves diagnostic efficacy, suggesting a potential role for mNGS in clinical TB management.},
}

Humans
*Mycobacterium tuberculosis/genetics/isolation & purification
Female
*Tuberculosis, Pulmonary/diagnosis/microbiology
Male
Middle Aged
Adult
*High-Throughput Nucleotide Sequencing/methods
ROC Curve
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity
*Metagenomics/methods
Aged
Young Adult

@article {pmid41040929,
year = {2025},
author = {Cho, HY and Park, HJ and Choi, JS and Kim, SH and Ryu, MO and Seo, KW},
title = {Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1571107},
pmid = {41040929},
issn = {2297-1769},
abstract = {BACKGROUND: The gut microbiome is a vital component of an organism's health, influencing metabolism, immune function, and overall homeostasis. In this study, we aimed to characterize the gut microbiota of healthy domestic short-hair cats in South Korea and evaluate the effects of age, body condition score (BCS), sex, and diet on microbial composition.

METHODS: From August to December 2023, 40 healthy cats aged 1-14 years with a body condition score (BCS) of 5-9 were selected. Cats were excluded if they had taken probiotics or antibiotics, exhibited gastrointestinal symptoms within the last 6 months, or had blood work abnormalities. DNA quantification was performed, and libraries targeting the V3 and V4 regions were prepared according to the Illumina 16S metagenomic sequencing protocol with a read length of 2 × 300 bp. The relative abundance of bacteria at the phylum, genus, and species levels was assessed according to the age, sex, diet, and BCS of the cats, with major bacterial groups selected for chart analysis.

RESULTS: Examination of the fecal samples from 40 healthy cats (aged 0.5-14 years) using 16S rRNA gene sequencing revealed 2,721 bacterial amplicon sequence variants. The predominant phyla were Bacillota, Bacteroidota, and Actinomycetota. Although age did not significantly affect alpha diversity, a trend toward increased diversity was observed in cats aged 7-14 years. Phocaeicola was more abundant in older cats, suggesting a possible association with age-related conditions. Furthermore, Verrucomicrobiota was enriched in cats with a BCS of 8-9, and Ruminococcus torque was positively correlated with higher BCS. Sex-based differences indicated increased levels of Pseudomonadota, Finegoldia magna, and Sutterella massiliensis in neutered males, potentially linked to inflammatory pathways. Dietary analysis revealed an increased abundance of Blautia and Lachnoclostridium following a combination of dry and wet food.

CONCLUSION: Our findings provide critical insights into the core microbiota of domestic short-hair cats in South Korea, emphasizing the influence of geographic, physiological, and environmental factors on gut microbial diversity. The results offer a valuable foundation for advancing feline gut health research and enhancing health management strategies for felines, particularly in South Korea.},
}

@article {pmid41040912,
year = {2025},
author = {Matsumura, M and Mitsui, H and Woo, T and Suzuki, T and Arai, H and Koike, C and Kataoka, T and Motooka, D and Fukushima, K and Okudela, K},
title = {Identification of key molecules in micropapillary progression of lung adenocarcinoma: A comprehensive gene expression analysis study using the spatial gene expression solution methodology.},
journal = {Oncology letters},
volume = {30},
number = {5},
pages = {533},
pmid = {41040912},
issn = {1792-1082},
abstract = {The micropapillary histological subtype is a high-grade element and a poor prognostic marker in lung adenocarcinoma (LUAD). This subtype develops through the lepidic-filigree micropapillary (filigree)-conventional/overt micropapillary (mPAP) pathway. The present study aimed to identify key molecules that promote this progression. To this end, gene expression profiles specific to lepidic, filigree and mPAP elements were investigated in histological sections obtained from 4 different LUAD cases. The 10× Genomics Visium Spatial Gene Expression Solution was used due to its superior resolution compared with conventional microdissection techniques. Cellular retinoic acid binding protein 2 (CRABP2), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) and mucin 21 (MUC21) were identified as common molecules with significantly elevated levels along the lepidic-filigree-mPAP pathway. Furthermore, the present findings indicated that CRABP2 may serve an important role in the early stage of this process, as its level significantly increases during the transition from the lepidic to the filigree substage. Immunohistochemical analysis of the expression of CRABP2, CEACAM5 and MUC21 proteins in 207 surgically resected LUAD samples (expanded sample size) was performed. The present study revealed an increase in the expression levels of CRABP2 between the lepidic and filigree elements, and between filigree and mPAP for CEACAM5 and MUC21. Thus, these three proteins were demonstrated to serve roles in the lepidic-filigree-mPAP pathway at different stages. Notably, these molecules were associated with poor prognosis, characterized by an elevated recurrence rate and poor survival rate. In conclusion, crucial molecules that promote the lepidic-filigree-mPAP pathway, and exhibit potential clinical utility as prognostic markers and molecular therapeutic targets, were identified.},
}

@article {pmid41040880,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Li, B and Zhang, M and Jiang, F and Song, P and Liang, C and Fan, Q and Xu, Y and Zhang, R},
title = {Developmental dynamics and functional adaptation of gut microbiota in Mongolian wild asses (Equus hemionus hemionus) across ontogenetic stages in arid desert ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659661},
pmid = {41040880},
issn = {1664-302X},
abstract = {Understanding the composition and function of gut microbiota is essential for elucidating how wild animals adapt to arid environments. The Mongolian wild ass (Equus hemionus hemionus), which inhabits harsh desert ecosystems, offers an ideal model for such investigations. This study employed metagenomic sequencing of fecal samples to characterize the composition and structure of the gut microbiota in adult, subadult, and juvenile Mongolian wild asses, with functional annotation based on the KEGG, CARD, and CAZy databases. Our study revealed that Bacillota and Bacteroidota were the dominant phyla, together accounting for over 85% of relative abundance, with their ratio (B/B value) showing clear age-dependent shifts. Juveniles were dominated by Bacillota (high B/B value), consistent with adaptation to a milk-based, protein- and lactose-rich diet, whereas adults shifted toward Bacteroidota dominance (low B/B value), with relative abundance increasing from 39.53% to 64.92%, reflecting enhanced polysaccharide and fiber degradation, thereby providing microecological support for adaptation to low-energy, high-fiber desert vegetation resources. Alongside this transition, α-diversity significantly increased with age, while β-diversity patterns shifted from dispersed to clustered, indicating a more complex, stable, and mature gut community. Over 58% of predicted genes were assigned to metabolic pathways, highlighting the essential contribution of gut microbes to herbivore digestion. Polysaccharide lyases, enriched in adults and subadults, were positively correlated with Bacteroidota abundance, highlighting their central role in fiber degradation and stable energy supply, thereby supporting adaptation to arid desert habitats. In contrast, juveniles were characterized by enrichment of the galactose metabolism pathway, high abundance of Pseudomonadota (LEfSe LDA > 4), and the largest number of antibiotic resistance genes (AROs), including 17 potential key AROs, reflecting greater microbial plasticity and higher environmental exposure risks during early development. This study provides the first systematic characterization of age-related gut microbiome dynamics and functional adaptations in the endangered Mongolian wild ass, offering novel insights into microbial contributions to host energy optimization and resilience in arid ecosystems, with implications for conservation strategies.},
}

@article {pmid41040879,
year = {2025},
author = {Hoepfner, C and Guzmán, D and Vidal-Veuthey, B and Foronda, V and Beggs, A and Cárdenas, JP and Vargas, VA and Alfaro, FD},
title = {Functional stratification and enzymatic arrangement in microbial communities across a hypersaline depth gradient.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1624058},
pmid = {41040879},
issn = {1664-302X},
abstract = {Extreme environments comprise a significant portion of Earth's terrestrial surface, posing challenges, such as extreme temperatures, pressure, pH extremes, oxygen and nutrient scarcity, and high salinity. Hypersaline ecosystems, such as those in the Andean Cold Deserts, exemplify extreme environments where microbial life has evolved specialized survival mechanisms. The Central Andean Mountains host extensive salt flats exposed to extreme temperature fluctuations, intense ultraviolet radiation, and high soil salinity. While most studies focus on surface layers, the impact of soil depth on functional diversity remains poorly understood. This study utilized shotgun metagenomics and functional annotation to explore enzymatic diversity across a 8-meter depth gradient in the Uyuni Salt Flat aiming to understand microbial adaptations to depth and abiotic stress. Our findings revealed a complex, stratified microbial ecosystem. Surface layers showed high abundance of amylases, enzymes that degrade accessible carbohydrates, likely derived from photosynthetic communities or surface-imported organic matter. These patterns suggest a dominance of strategies for rapid carbon decomposition. Intermediate depths exhibited elevated lipase and peroxidase activity, reflecting the presence of complex lipids and oxidative stress management, essential for survival in oxygen-limited, high-salinity zones. Lipase support lipid utilization as a carbon source, while peroxidase activity points to redox adaptations for microbial resilience under fluctuating oxidative conditions. Deeper sediment layers showed a shift toward protease and peptidase activity, indicating organic nitrogen recycling in nutrient-deprived environments and suggesting an efficient protein degradation system among halophilic archaea. Peroxidases remained abundant even at these depths, supporting sustained redox regulation and biogeochemical cycling thus enabling microbes to manage redox imbalances in high-salinity, low-oxygen settings. The enzymatic diversity across the depth gradient demonstrates functional stratification and remarkable microbial adaptability to hypersaline conditions. This functional resilience underpins nutrient cycling and organic matter decomposition deep in the salt flats. Notably, the identified halophilic enzymes, stable and active under high-salinity conditions, hold significant potential for biotechnological applications. This study contributes to our understanding of microbial life's complexity in hypersaline environments, enhancing our ability to harness extremophilic enzymes for biotechnological applications while underscoring the ecological value of these unique habitats.},
}

@article {pmid41040656,
year = {2025},
author = {Wilkins, L and Yuen, B and Petersen, J 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 mollusc, Ctena decussata (O.G.Costa, 1829) and its bacterial endosymbiont Candidatus Thiodiazotropha sp. CDECU1 (Chromatiales).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {435},
pmid = {41040656},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Ctena decussata (Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1,658.05 megabases. Most of the assembly (97.83%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 53.28 kilobases in length. The genome of Candidatus Thiodiazotropha sp. CDECU1, a bacterium associated with C. decussata was also assembled.},
}

@article {pmid41040369,
year = {2025},
author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT},
title = {Mining thermophile photosynthesis genes: a synthetic operon expressing Chloroflexota species reaction center genes in Rhodobacter sphaeroides.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.22.677880},
pmid = {41040369},
issn = {2692-8205},
abstract = {Photosynthesis is the foundation of the vast majority of life systems, and therefore the most important bioenergetic process on earth, and the greatest diversity in photosynthetic systems are found in microorganisms. However, understanding of the biophysical and biochemical processes that transduce light to chemical energy has derived from the relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of microbial DNA sequences encoding proteins that catalyze the initial photochemical reactions that has been deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90° C) springs available through the JGI IMG database, to generate a resource of diverse sequences that potentially are adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.},
}

@article {pmid41040146,
year = {2025},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.16.633031},
pmid = {41040146},
issn = {2692-8205},
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collected Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}

@article {pmid41039672,
year = {2025},
author = {Silvester, R and Webster, G and Perry, WB and Farkas, K and Rushton, L and Craine, N and Cross, G and Kille, P and Weightman, AJ and Jones, DL},
title = {Genome-resolved metagenomics uncovers antimicrobial resistance gene carriers in hospital and municipal wastewater environments.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180607},
doi = {10.1016/j.scitotenv.2025.180607},
pmid = {41039672},
issn = {1879-1026},
abstract = {Wastewater-based epidemiology (WBE) is a powerful approach to study antimicrobial resistance (AMR) dynamics at the population level. Using genome-resolved metagenomics, we recovered 3978 metagenome-assembled genomes (MAGs) from archived metagenome sequences generated under the national wastewater surveillance programme across Wales, UK. Taxonomic profiling of MAGs revealed a diverse bacterial community, with significant compositional shifts observed across seasons and sample sources. Approximately 13.6 % of the MAGs carried one or more antimicrobial resistance genes (ARGs), with genes conferring resistance to tetracycline and oxacillin being the most prevalent within the wastewater microbiomes. We also recovered yet-uncultivated microbial genomes- often referred to as "microbial dark matter" harbouring clinically relevant ARGs, offering insights into previously uncharacterised resistance reservoirs in wastewater. ARG-host associations shifted between untreated influent and treated effluent, with effluent profiles also varying significantly between secondary and tertiary treatments, revealing the impact of treatment type on ARG host composition. This study represents the first comprehensive genome-resolved metagenomic characterisation of ARG carriers across both hospital and municipal wastewater in Wales, effectively bridging clinical and environmental compartments. Our findings highlight the need to integrate high-resolution genome-resolved metagenomic surveillance into national AMR monitoring frameworks to track emerging threats, characterise ARG reservoirs and inform targeted public health interventions.},
}

@article {pmid41039256,
year = {2025},
author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y},
title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {607},
pmid = {41039256},
issn = {1471-2180},
support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Metagenomics ; },
abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.},
}

*Soil Microbiology
*Phosphorus/metabolism
China
Soil/chemistry
Grassland
*Carbon/metabolism
Desert Climate
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Microbiota
Metagenomics

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

Animals
Larva/microbiology/growth & development
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Metagenome
*Diptera/microbiology/growth & development
Animal Feed/analysis
RNA, Ribosomal, 16S/genetics
Metagenomics
Diet
Phylogeny
Chickens

@article {pmid41039197,
year = {2025},
author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI},
title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {601},
pmid = {41039197},
issn = {1471-2180},
support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; },
abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.

RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.

CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.},
}

@article {pmid41039183,
year = {2025},
author = {Al-Shaibani, MM and Zin, NM and Remali, J and Sidik, NM and Al-Mekhlafi, NA and Mariappan, V and Sukri, A},
title = {Anticancer compounds from Streptomyces: insights from metagenomics and mechanistic perspective.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41039183},
issn = {1874-9356},
support = {FRGS/1/2016/STG05/UKM/02/5//Ministry of Higher Education/ ; },
abstract = {Cancer continues to be a leading cause of death globally, driving the ongoing search for novel bioactive compounds with therapeutic potential. Metagenomic sequencing has revolutionized this pursuit by enabling the direct detection and genomic assembly of previously uncultured Streptomyces species from environmental DNA, circumventing traditional cultivation limitations. This review explores recent advances in metagenomics-driven discovery of anticancer compounds derived from Streptomyces, with a focus on identifying biosynthetic gene clusters (BGCs) responsible for producing bioactive secondary metabolites. Over the past decade, metagenomic approaches have been adopted to uncover new species of Streptomyces and anticancer compounds. Although metagenomics has been adopted in research and discovery of new Streptomyces, its application in the discovery of Streptomyces-related pathways pertaining to anticancer compounds remains limited. Furthermore, clinical translation remains limited, highlighting the need for further research. By examining metagenomic methodologies and the mechanisms of action of these compounds, this review provides an updated and focused perspective on Streptomyces-derived anticancer agents and their potential for future drug development.},
}

@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}

@article {pmid41038529,
year = {2025},
author = {Liu, J and Dong, Y and Huang, Y and Xie, M and Wang, H and Wang, Q and Wang, S and Wang, N and Jiang, Y and Zhang, W and Wang, M and Chen, J and Huang, L and Cai, H},
title = {Clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections in ICU: A multicenter retrospective study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108094},
doi = {10.1016/j.ijid.2025.108094},
pmid = {41038529},
issn = {1878-3511},
abstract = {BACKGROUND: Central nervous system (CNS) infections impose a substantial global burden of morbidity and mortality, necessitating accurate and timely diagnosis for optimal clinical management. Metagenomic next-generation sequencing (mNGS) has been demonstrated as a valuable tool for pathogen detection in patients with suspected CNS infections.

METHODS: From December 2019 to June 2023, we conducted a comprehensive analysis of 520 cerebrospinal fluid samples collected from patients with suspected intracranial infections across six intensive care units. All pathogen-positive results identified through metagenomic next-generation sequencing were subsequently validated by an independent laboratory.

RESULTS: Metagenomic NGS detected 105 microbial species in 520 clinical samples, comprising 64 bacterial species (61.0%), 16 DNA viruses (15.2%), 13 fungal species (12.4%), and 7 RNA viruses (6.7%). The 30-day mortality rate among all study participants was 18.5%. Metagenomic NGS identified 172 infection cases, whereas conventional culture methods detected only 31 cases. For CNS infections, mNGS demonstrated diagnostic sensitivity, specificity, and accuracy rates of 59%, 90.5%, and 72.5%, respectively.

CONCLUSIONS: Metagenomic NGS testing facilitates accelerated diagnosis of CNS infections and informs evidence-based clinical management decisions.},
}

@article {pmid41038519,
year = {2025},
author = {Surgers, L and Lafont, C and Lamoureux, C and Demontant, V and N'Debi, M and Cheval, J and Boizeau, L and Trawinski, E and Pawlotsky, JM and Woerther, PL and Rodriguez, C and , },
title = {Shotgun metagenomics for the diagnosis of infections: A prospective study.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106619},
doi = {10.1016/j.jinf.2025.106619},
pmid = {41038519},
issn = {1532-2742},
abstract = {BACKGROUND: Shotgun metagenomics (SMg) promises to significantly improve the microbiological diagnosis of infectious diseases. However, the prospective evaluation of its clinical utility in different infectious syndromes remains poorly documented.

METHODS: We conducted a prospective study including all patients who underwent SMg as part of their care at the French Henri Mondor Hospital National Reference Laboratory for accredited SMg between February 2018 and January 2020. Patients were categorized as having either a "high likelihood" or "low likelihood" of infection based on their clinical presentation. The contribution of the SMg to the final diagnosis was assessed by a multidisciplinary team of infectious disease specialists.

FINDINGS: 202 patients were enrolled in the study. Of the 123 patients considered to have a high likelihood of infection, SMg confirmed the cause of infection in 38 cases (30.9%), including 12 cases (9.8%) diagnosed exclusively by this method. In the 79 patients classified as having a "low likelihood" of infection, SMg did not detect any microorganisms compatible with an infectious cause. In particular, patients undergoing immunosuppressive treatment within the latter group showed no deterioration after 6 months.

INTERPRETATION: SMg facilitated microbiological diagnosis in over 30% of complex cases, regardless of sample type or site of infection. Compared with conventional techniques, SMg provided diagnoses in 10% more cases, highlighting its broad utility across different infectious diseases. Our results suggest that SMg is a promising tool for documenting complex infectious diseases alongside traditional microbiology tools. Furthermore, negative SMg results are useful for the management of patients with a low likelihood of infection.

FUNDING: This study was conducted as part of patient care.},
}

@article {pmid41038405,
year = {2025},
author = {Jin, H and Feng, B and Gong, W and Chen, X and Wang, D and Li, Y and Huang, W and Peng, W},
title = {Evaluation of gut microbial diversity and correlation in asymptomatic and symptomatic patients with hand, foot and mouth disease.},
journal = {Genomics},
volume = {},
number = {},
pages = {111126},
doi = {10.1016/j.ygeno.2025.111126},
pmid = {41038405},
issn = {1089-8646},
}

@article {pmid41038354,
year = {2025},
author = {Qing, Z and Haibei, H and Hanxue, Y and Juan, S},
title = {Mitigation of tetracycline resistance genes in silage through targeted lactic acid bacteria inoculation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133416},
doi = {10.1016/j.biortech.2025.133416},
pmid = {41038354},
issn = {1873-2976},
abstract = {The dissemination of antibiotic resistance genes (ARGs) in silage ecosystems poses a critical challenge to ecological stability and public health security. This investigation focuses on tetracycline resistance genes (TRGs), the most prevalent subtype of ARGs in silage, employing a targeted selection strategy for lactic acid bacteria (LAB) inoculants. From 226 isolated LAB strains, four candidates (LP1-3: Lactiplantibacillus plantarum; LC1: Lacticaseibacillus paracasei) demonstrating superior growth kinetics (OD600 > 1.6 within 24 h) and rapid acidification capacity (pH < 3.9 within 24 h) were selected. Strains LP3 and LC1 exhibited minimal intrinsic TRGs content. These four strains reduced (p < 0.001) pH, ammonia-N concentration, and coliform bacterial counts of stylo silage. Metagenomic analysis revealed that strains LP1-3 promoted Lactiplantibacillus dominance (0.709-0.975 vs. 0.379-0.509 in the control), while LC1 enhanced Lacticaseibacillus abundance (0.449-0.612 vs. 0.002-0.013 in the control). Ensiling process downregulated 367 and upregulated 227 ARGs. Inoculation with the four LAB strains further enhanced the suppression of ARGs. Among the top 30 TRGs, 22 were reduced by strains LP1-3 and 20 by LC1. Quantitative PCR results showed that strains LP1-3 decreased (p < 0.05) the contents of tetA and tetG during 30 days fermentation. Among the TRGs increased, tetA(60), tetB(58), tet(T) were positively correlated with Lactiplantibacillus spp., tetA(58), tetB(60), tetA(46), tetB(46), tet(43) were significantly correlated with Lacticaseibacillus spp. (R > 0.4, p < 0.001). In conclusion, the fermentation process induced substantial ARGs profile modifications, LAB-mediated microbiome engineering enables TRGs suppression, providing a scientific foundation for precision silage management strategies targeting antimicrobial resistance mitigation.},
}

@article {pmid41038122,
year = {2025},
author = {Zhao, F and Yang, Z and Xiao, Y and Han, G and Hardie, KR and Bartlam, M and Wang, Y},
title = {Enantioselective interactions of silver nanoparticles and chiral antibiotics in driving resistance evolution in activated sludge.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124656},
doi = {10.1016/j.watres.2025.124656},
pmid = {41038122},
issn = {1879-2448},
abstract = {The stereochemistry of antibiotics significantly affects resistance development. With rising antibiotic resistance, nanotechnology is emerging as a promising solution, potentially increasing the likelihood of nanoparticle coexistence with antibiotics in wastewater treatment plants (WWTPs). However, the influence of nanoparticles on chiral antibiotics induced resistance remains unclear. This study employed chemical characterization, metagenomics, and molecular docking to comprehensively elucidate the resistance mechanisms induced by the combination of silver nanoparticles (AgNPs) and chiral antibiotics (ofloxacin: OFL and levofloxacin: LEV). AgNPs significantly altered the abundance and composition of antibiotic and metal resistance genes, as well as the conjugative transfer of the RP4 plasmid among activated sludge communities, with the OFL_AgNPs combination exhibiting a higher resistance potential than LEV_AgNPs. Mechanistic studies revealed that chiral antibiotics selectively interact with AgNPs, promoting Ag[+] release, enhancing antibiotic uptake, and forming stable complexes. These interactions reshaped microbial functions, including cell membrane permeability, oxidative stress response, quorum sensing, and extracellular secretion, thereby shaping resistance profiles. This study reveals previously overlooked enantiomer-specific risks associated with nanoparticle-antibiotic interactions and provides a foundation for strategies to mitigate ARG dissemination in wastewater treatment and broader environmental systems.},
}

@article {pmid41037216,
year = {2025},
author = {Pan, F and Yu, F and Zhang, H and Chen, P and Weng, W},
title = {Clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected bloodstream infection.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41037216},
issn = {1435-4373},
abstract = {BACKGROUND: Accurate and comprehensive pathogen diagnosis methods are urgently required for the diagnosis of bloodstream infection (BSI).This study retrospectively evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected BSI.

METHODS: Between July 8, 2021 to December 31, 2022, mNGS tests and conventional methods tests (CMTs) were performed simulataneously on samples from children with suspected BSI. The diagnostic performance of mNGS was assessed in comparison CMTs .

RESULTS: A total of 191 patients with suspected BSI were included in the final analysis after excluding 9 patients due to lost to follow-up or duplicated entries. The mNGS yielded positive results in 111 cases, with a positive rate of 58.1% (111/191), significantly higher than that of CMTs (13.1%, 25/191) (P < 0.05). Using CMTs as standard, the sensitivity, specificity, positive predictive value and negative predictive value for mNGS and CMTs were 73.8% vs. 25.0%, 54.2% vs. 96.3%, 55.9% vs. 84.0%, and 72.5% vs. 62.0%, respectively. Among 111 mNGS-positive cases, 46 cases (41.4%) showed ploymicrobial infections, with Torque teno virus, human betaherpesvirus 5, and human gammaherpesvirus 4 being most frequently identified pathogens. Of them, 62 cases (55.9%) were clinically diagnosed as BSI regarded as true positive results, while 49 cases (44.1%) positive for pathogens were diagnosed as non-BSI. The diagnostic time of mNGS was significantly shorter than that of CMTs (30.6 ± 7.7 h vs. 70.5 ± 11.6 h, P < 0.05). It is worth noting that mNGS results guided adjustments to antimicrobial therapy in 50.8% (97/191) patients, including escalation in 74 cases and de-escalation in 23 cases.

CONCLUSIONS: The mNGS significantly improves the detection rate for the pathogens in children with suspected BSI, especially for viruses, which serve as a complement to CMTs.},
}

@article {pmid41037127,
year = {2025},
author = {Arunrat, N and Mhuantong, W and Sereenonchai, S},
title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {102},
pmid = {41037127},
issn = {1432-184X},
support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; },
mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; },
abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.},
}

*Soil Microbiology
Thailand
*Bacteria/classification/genetics/metabolism/isolation & purification
Soil/chemistry
*Microbiota
Nitrogen/metabolism
Nitrification
*Agriculture/methods
Nitrogen Fixation
Nitrogen Cycle

@article {pmid41036867,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Mazza Rodrigues, JL and Peay, KG and Tsai, SM},
title = {A catalog of metagenome-assembled genomes from Amazonian forest and pasture soils.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0064225},
doi = {10.1128/mra.00642-25},
pmid = {41036867},
issn = {2576-098X},
abstract = {The Amazon rainforest is facing multifaceted anthropogenic pressures, and we previously showed that forest-to-pasture conversion has led to soil microbial communities with distinct genomic traits. Here, we present 69 archaeal and bacterial metagenome-assembled genomes and detail their virulence- and antimicrobial resistance-associated genes.},
}

@article {pmid41036845,
year = {2025},
author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M},
title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023425},
doi = {10.1128/msphere.00234-25},
pmid = {41036845},
issn = {2379-5042},
abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.},
}

@article {pmid41036842,
year = {2025},
author = {Zeng, J and Hu, W and Chang, L and Hua, Z and Wu, G and Fang, Y and Wang, G and Xiao, C and Liu, J},
title = {Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117825},
doi = {10.1128/msystems.01178-25},
pmid = {41036842},
issn = {2379-5077},
abstract = {The WOR-3 phylum is widely distributed in various environments, including hot springs, marine ecosystems, and hydrothermal vents, yet its ecological roles and metabolic capabilities remain poorly understood. In this study, we analyzed 181 medium- to high-quality metagenome-assembled genomes, including 59 newly reconstructed from environmental samples and 122 retrieved from public databases. Phylogenetic analyses resolved the WOR-3 lineage into four subgroups (subgroup 1-4). Metabolic reconstruction revealed significant divergence of the carbon, sulfur, nitrogen, and hydrogen metabolism pathways among the different subgroups. Subgroup 1 was characterized by fermentative metabolism involving formate and ethanol and uniquely exhibited potential for carbon fixation via the Calvin cycle, as indicated by the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene. Notably, WOR-3 RuBisCO is phylogenetically affiliated with archaeal form III, although the carbon fixation pathway follows the canonical bacterial Calvin cycle-a feature of potential evolutionary significance. Subgroup 3 exhibits metabolic versatility, including genes for dissimilatory sulfate reduction, sulfur oxidation, partial denitrification, and fatty acid degradation. In addition, all subgroups harbored key components of hydrogen metabolism, including widespread NiFe hydrogenases, supporting H2-dependent electron transfer and energy conservation. Within the WOR-3 lineage, the coexistence of two respiratory enzyme systems-the Rnf complex and the oxidative phosphorylation respiratory chain-indicates distinct anaerobic and aerobic metabolic lifestyles, respectively. Collectively, this study expands the genomic framework for the WOR-3 phylum and provides novel insights into the metabolic versatility and ecological functions of this previously uncharacterized lineage in biogeochemical cycles of carbon, nitrogen, and sulfur.IMPORTANCEThe WOR-3 phylum represents a widespread but poorly understood bacterial lineage inhabiting diverse various environments. By integrating 181 metagenome-assembled genomes, including 59 newly reconstructed, this study provides the most comprehensive genomic framework to date for WOR-3. Phylogenomic and metabolic reconstruction revealed four distinct subgroups with divergent capacities for carbon, sulfur, and nitrogen metabolism. Notably, subgroup 1 encodes a complete Calvin-Benson-Bassham cycle featuring an archaeal-type form III ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting an unusual evolutionary trajectory for carbon fixation in this lineage. Subgroup 3 exhibits versatile metabolic potential, including dissimilatory sulfur metabolism, partial denitrification, and fatty acid degradation, highlighting its possible roles in multiple biogeochemical processes. These findings not only expand the taxonomic and functional landscape of the WOR-3 phylum but also offer key insights into its ecological roles in global element cycling.},
}

@article {pmid41036698,
year = {2025},
author = {Bulteau, S and Braud, M and Petrier, M and Castain, L and Anani, H and Peltier, C and Mobuchon, L and Bouras, M and Flattres, D and Poschmann, J and Josset, L and Roquilly, A and Bressollette-Bodin, C},
title = {Interferon Gamma Injection and Its Effect on the Respiratory Anelloviridae Population in ICU Ventilated Patients.},
journal = {Journal of medical virology},
volume = {97},
number = {10},
pages = {e70612},
doi = {10.1002/jmv.70612},
pmid = {41036698},
issn = {1096-9071},
support = {//This work was supported by the Horizon 2020 Research and Innovation Framework Programme (grant agreement no. 847782, HAP2 project, https://hap2-project.com). S.B. was also supported by a grant from Region Pays de la Loire./ ; },
mesh = {Humans ; Male ; Female ; Intensive Care Units ; Middle Aged ; *Interferon-gamma/administration & dosage/therapeutic use ; Aged ; *Respiration, Artificial/adverse effects ; Viral Load ; DNA, Viral ; Adult ; Metagenomics ; *Healthcare-Associated Pneumonia/prevention & control/virology ; *Immunologic Factors/administration & dosage ; Critical Illness ; },
abstract = {Immune dysfunctions induced by critical illness are associated with an increased risk of hospital-acquired pneumonia (HAP) in intensive care unit (ICU) patients. The use of immunomodulatory molecules in this setting is under evaluation. The presence of persistent viruses, such as anelloviruses (AVs) or herpesviruses, which are frequently detected in respiratory samples, may indicate immune dysfunction. Herpesvirus infections are associated with increased morbidity in ICU patients, and variations in AV DNA loads are associated with rejection events in immunocompromised patients. We investigated the respiratory viral landscape of 94 patients during the first week under invasive mechanical ventilation using quantitative PCR and targeted metagenomics after capture probe enrichment. The patients were included in a placebo-controlled randomized clinical trial testing IFNγ for the prevention of HAP. We measured AV and herpes simplex virus-1 (HSV-1) DNA loads over time in respiratory samples collected at admission (n = 54), and on Days 3 (n = 73) and 7 (n = 57) after admission. There were no significant differences in mortality, HAP, the development of acute respiratory distress syndrome (ARDS), HSV, or AV DNA detection between patients treated with IFNg and those who received a placebo. Patients who developed HAP had a significantly higher AV DNA load in tracheal aspirates over time (p = 0.011) than those who did not. Target enrichment analysis revealed AV presence in all respiratory samples, with no differences observed in AV composition between IFNg-treated and placebo patients, or between HAP and noHAP patients. Trial Registration: CPP Ouest II 17/02/2021 (avis N°2021/03); ClinicalTrial.gov number: NCT04793568.},
}

Humans
Male
Female
Intensive Care Units
Middle Aged
*Interferon-gamma/administration & dosage/therapeutic use
Aged
*Respiration, Artificial/adverse effects
Viral Load
DNA, Viral
Adult
Metagenomics
*Healthcare-Associated Pneumonia/prevention & control/virology
*Immunologic Factors/administration & dosage
Critical Illness

@article {pmid41036626,
year = {2025},
author = {Xia, Y and Liang, L and Wang, X and Chen, Z and Liu, J and Yang, Y and Xie, H and Ding, Z and Huang, X and Long, S and Wang, Z and Xu, X and Ding, C and Chen, Q and Feng, Q},
title = {MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.},
journal = {Nucleic acids research},
volume = {53},
number = {18},
pages = {},
doi = {10.1093/nar/gkaf954},
pmid = {41036626},
issn = {1362-4962},
support = {2022YFA1304100//National Key R&D Program of China/ ; 82 270 980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; 82 202 539//National Natural Science Foundation of China/ ; 2023ZD0501406//National Science and Technology Major Program/ ; 2019//National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; #202412A001//horizontal cooperation project with Shenzhen 01 Life Institute/ ; #202112E401//horizontal cooperation project with Shenzhen 01 Life Institute/ ; },
mesh = {*Metagenomics/methods ; Workflow ; *Software ; *Metagenome/genetics ; *Microbiota/genetics ; Humans ; },
abstract = {Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.},
}

*Metagenomics/methods
Workflow
*Software
*Metagenome/genetics
*Microbiota/genetics
Humans

@article {pmid41036540,
year = {2025},
author = {Pei, Y and Cai, S and Xue, Y and Fu, Y and Zhang, J and Shen, Q and Ji, L and Wu, P and Wang, H and Wang, Y and Zhang, W and Yang, S},
title = {First detection of two cycloviruses in cormorant fecal samples in China by high-throughput sequencing technology.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1677378},
pmid = {41036540},
issn = {2297-1769},
abstract = {INTRODUCTION: The Great Cormorant (Phalacrocorax carbo) is widely distributed across China. As an apex predator in aquatic ecosystems, it plays a tripartite ecological role: acting as a natural host, transmission vector, and indicator species for viruses. Current research confirms that cormorants carry diverse viral pathogens from the families including Flaviviridae, Orthomyxoviridae, Paramyxoviridae, and Polyomaviridae. Significant knowledge gaps persist regarding their virome diversity.

METHODS: In this study,46 cormorant fecal swab samples were collected at Xiamen Garden Expo Park, and viralmetagenomics method was conducted to identify two Cycloviruses.

RESULTS: This study identified two novel cycloviruses, Corcyclo-1 (1,856 bp) and Corcyclo-2 (1,831 bp), from cormorant fecal samples using viral metagenomics. Genomic analyses revealed hallmark features of the genus Cyclovirus, including inversely oriented open reading frames (ORFs) encoding the capsid protein (Cap) and replication-associated protein (Rep), as well as a conserved stem-loop sequence TAATACTAT. The Rep gene of Corcyclo-1 contained a 166-bp intron and shared >96.9% amino acid identity with human-, wild boar-, and chicken-derived cyclovirus strains (HaCV-8) from Vietnam and Madagascar, classifying it as a novel strain of HaCV-8. In contrast, Corcyclo-2 harbored a 98-bp intron in its Rep gene and clustered with unclassified cyclovirus strains from bats and mongooses in China and Saint Kitts and Nevis (>97.4% identity), constituting a putative new species. Phylogenetic and pairwise sequence analyses further supported their taxonomic positions. Epidemiological screening demonstrated a high prevalence of Corcyclo-1 (82.6%, 38/46) and Corcyclo-2 (32.6%, 15/46) in cormorant feces. Cross-species surveillance detected Corcyclo-2 in chickens (25.8%, 16/62) and ducks (11.7%, 9/77), whereas Corcyclo-1 was absent in these hosts.

CONCLUSION: This study represents the first report of cormorant-associated cycloviruses, highlighting their potential for cross-species transmission and providing new insights into the ecological diversity and evolutionary mechanisms of cyclovirus.},
}

@article {pmid41036230,
year = {2025},
author = {Xin, L and Jiao, X and Gong, X and Yu, J and Zhao, J and Lv, J and Feng, Q and Yuan, Y and Pan, W},
title = {Diagnostic value of metagenomic next generation sequencing of bronchoalveolar lavage fluid in immunocompromised patients with pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1602636},
pmid = {41036230},
issn = {2235-2988},
mesh = {Humans ; *Immunocompromised Host ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Middle Aged ; Sensitivity and Specificity ; Aged ; *Pneumonia/diagnosis/microbiology ; Bacteria/genetics/isolation & purification/classification ; Adult ; Fungi/genetics/isolation & purification/classification ; Viruses/genetics/isolation & purification/classification ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables simultaneous sequencing of DNA fragments for comprehensive pathogen identification. Pneumonia in immunocompromised patients-characterized by atypical clinical manifestations and rapid progression-poses diagnostic challenges. Conventional microbiological testing (CMT), which relies on pathogen culture and serological assays, is limited by prolonged turnaround times and suboptimal detection rates. This study was performed to evaluate the clinical utility of mNGS through comparative analysis with CMT in detecting pathogens among immunocompromised patients with pneumonia.

METHODS: We conducted a retrospective cohort study of 146 immunocompromised patients with suspected pneumonia. The mNGS and CMT results were systematically analyzed. Pathogen detection rates and microbial spectrum concordance were visualized using pie and bar charts. Diagnostic performance was compared using McNemar's test and Kappa (κ) statistics for inter-method agreement. The sensitivity, specificity, accuracy, and area under the curve were calculated for pathogen-specific evaluations.

RESULTS: mNGS demonstrated superior detection efficacy, identifying pathogens in 98 cases versus 50 by CMT, with 48 overlapping positives. The microbial spectrum showed substantial differences: mNGS detected 73 bacterial, 46 fungal, and 45 viral pathogens, whereas CMT identified 38 bacterial, 27 fungal, and 21 viral agents. mNGS outperformed CMT across all infection types, including single-pathogen infections (bacterial, fungal, or viral only) and mixed infections (bacterial + fungal, bacterial + viral, fungal + viral, or bacterial + fungal + viral). Bacterial and fungal detections showed low inter-method concordance, while viral detection exhibited moderate agreement (κ = 0.510, p < 0.001). Notably, mNGS achieved significantly higher detection rates for Enterococcus faecalis and Pneumocystis jirovecii in intensive care unit (ICU)-admitted patients with severe pneumonia (p < 0.05). Clinical outcomes improved in 45 patients following mNGS-guided therapeutic adjustments.

CONCLUSIONS: mNGS and CMT demonstrate complementary strengths in bacterial and fungal detection in immunocompromised patients with pneumonia. mNGS provides enhanced diagnostic accuracy for key pathogens such as E. faecalis and P. jirovecii, particularly in severe and ICU-admitted cases. As a high-throughput diagnostic tool, mNGS may improve pathogen detection and clinical management in immunocompromised populations.},
}

Humans
*Immunocompromised Host
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Male
*Bronchoalveolar Lavage Fluid/microbiology/virology
Female
Middle Aged
Sensitivity and Specificity
Aged
*Pneumonia/diagnosis/microbiology
Bacteria/genetics/isolation & purification/classification
Adult
Fungi/genetics/isolation & purification/classification
Viruses/genetics/isolation & purification/classification

@article {pmid41035885,
year = {2025},
author = {Velasco Cardona, DC and Cardona-Acevedo, S and Valencia-Arias, A and Pérez-Delgado, O and Pinella Vega, M},
title = {Bibliometric analysis of the application of artificial intelligence techniques in bacteriology: a PRISMA-guided research agenda.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641967},
pmid = {41035885},
issn = {1664-302X},
abstract = {INTRODUCTION: The integration of artificial intelligence (AI) into bacteriology has marked a pivotal advancement by enabling the analysis of large-scale microbiological datasets. Despite growing adoption, significant research gaps persist, hindering the full exploitation of AI's potential in bacterial research and diagnostics.

OBJECTIVE: To analyze global scientific production on the application of AI techniques in bacteriology and propose a future research agenda based on bibliometric trends.

METHODS: This study conducts a bibliometric analysis of artificial intelligence (AI) applications in bacteriology, explicitly guided by the PRISMA 2020 framework. Unlike traditional reviews, this approach combines PRISMA's methodological rigor with bibliometric techniques to map scientific production. Metadata were retrieved from Scopus and Web of Science using predefined search strategies. Quantitative indicators, co-occurrence networks, and thematic mapping were applied to examine the field's temporal evolution and conceptual structure. The findings provide an evidence-based overview of research trends and gaps, supporting the design of a future research agenda on AI integration in bacteriology.

RESULTS: The findings reveal exponential growth in scientific output, especially between 2022 and 2024. Leading authors include Singh and Waegeman, with high-impact journals such as Frontiers in Microbiology and MSystems. The United States and China are the most productive countries. Thematic evolution shows a shift from early topics like microbial spoilage toward advanced applications including bacterial classification and diagnostic modeling. Key conceptual clusters were identified around microbiomes, classification, and bioinformatics. Emerging terms such as "diagnosis," "metagenomics," and "transfer learning" indicate future research directions.

CONCLUSION: AI applications in bacteriology are expanding rapidly yet still rely heavily on traditional machine learning methods. There is a need to incorporate advanced approaches such as deep learning and transformer-based models. The findings support a strategic agenda for promoting interdisciplinary collaboration and technological innovation in bacteriological research.},
}

@article {pmid41035876,
year = {2025},
author = {Jiang, W and Zhai, J and Li, B and Ma, J and Zhang, S},
title = {Pulmonary Rhizopus arrhizus infection treated with high-dose liposomal amphotericin B in a heart transplant recipient under ECMO: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1631873},
pmid = {41035876},
issn = {2296-858X},
abstract = {Pulmonary mucormycosis caused by Rhizopus arrhizus is an emergent, fulminant threat in immunocompromised hosts, yet therapeutic success remains elusive when extracorporeal membrane oxygenation (ECMO) is required. While liposomal amphotericin B (L-AMB) is endorsed as first-line therapy, its pharmacokinetics are profoundly altered by ECMO-dilution, circuit sequestration, and impaired lung penetration all conspire to sub-therapeutic exposure. We report the first documented case in which these challenges were systematically overcome. A 52-year-old cardiac-transplant recipient, supported on veno-venous ECMO for refractory hypoxaemia, developed rapidly progressive pneumonia. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid returned a definitive Rhizopus arrhizus signature within 24 h, prompting immediate escalation to high-dose L-AMB (10 mg/kg/day). Therapeutic drug monitoring confirmed sustained trough levels above 7 μg/mL despite a 3.5-fold increase in volume of distribution. Serial mNGS quantification demonstrated a logarithmic decline in fungal reads to undetectable levels by day 10, accompanied by radiological resolution and preserved renal function. After 28 days of intravenous therapy, the patient was discharged on oral isavuconazole with no relapse at 6 months. This case establishes that early pathogen identification by mNGS, coupled with aggressive L-AMB dose optimisation under rigorous pharmacokinetic guidance, can achieve cure of pulmonary mucormycosis even in the most pharmacologically hostile environment of ECMO support.},
}

@article {pmid41035666,
year = {2025},
author = {Liu, H and Ding, Z and Xu, L and Guo, T},
title = {Severe Legionella pneumonia mimicking immune-related pneumonitis after chemoimmunotherapy for lung cancer: a case report.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1663978},
pmid = {41035666},
issn = {2234-943X},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have significantly improved survival outcomes and quality of life in patients with various malignancies. Nevertheless, their associated toxicities must not be overlooked. Although not the most common immune-related adverse event (irAE), CIP is recognized as one of the most serious. In particular, grade 3-4 CIP that is not promptly treated may compromise subsequent immunotherapy and can result in respiratory failure or even death. Legionnaires' disease, caused by Legionella pneumophila, is an uncommon but potentially life-threatening form of atypical pneumonia. With the expanding use of ICIs, especially in combination with chemotherapy, early stage CIP and Legionella pneumonia may share similar radiological features, such as ground-glass opacities, which makes early differential diagnosis difficult. However, timely differentiation is critical because the management strategies differ substantially: CIP requires systemic corticosteroids, whereas Legionella pneumonia necessitates quinolone antibiotics. Traditional diagnostic methods for Legionella infection, including culture on specialized media and urine antigen testing, are limited by low sensitivity and the risk of false-negative results. In recent years, targeted next-generation sequencing (tNGS) has emerged as a valuable diagnostic tool. Compared with metagenomic next-generation sequencing (mNGS), tNGS offers a shorter turnaround time, higher sensitivity and specificity, and greater cost-effectiveness. As such, it is becoming increasingly important in the accurate identification of atypical pathogens in pulmonary infections.

CASE SUMMARY: We report the case of a patient with squamous cell lung cancer who developed severe pneumonia following combined chemotherapy and immunotherapy. The initial working diagnosis was immune checkpoint inhibitor-related pneumonia (ICI-P) complicated by bacterial infection. However, sputum-targeted next-generation sequencing (tNGS) subsequently identified Legionella pneumophila infection. Following the administration of quinolone-sensitive antibiotics, the patient's clinical condition improved markedly, and he was discharged in a stable state. A 70-year-old male farmer with a history of lung cancer, type 2 diabetes, and chronic obstructive pulmonary disease (COPD) was admitted on February 4, 2025,with fever, cough, and dyspnea following chemoimmunotherapy. He had received paclitaxel, cisplatin, and tislelizumab on January 24.Initial tests revealed leukopenia, neutropenia, and chemotherapy-induced myelosuppression. On admission, the patient exhibited hypoxemia, hyponatremia, and elevated inflammatory markers, raising suspicion for ICI-P complicated by bacterial infection. Despite empirical broad-spectrum antibiotics and corticosteroids, his condition deteriorated, requiring transfer to the Respiratory Intensive Care Unit (RICU). On February 13, tNGS of sputum identified Legionella pneumophila, Enterococcus faecium, Epstein-Barr virus (EBV),and Herpesvirus-1 (HSV-1). The high relative abundance of Legionella pneumophila indicated it was the primary pathogen; EBV and HSV-1 were presumed latent. Antimicrobial therapy was adjusted to moxifloxacin, cefepime, and ganciclovir, leading to clinical improvement and resolution of hypoxemia. Follow-up chest CT showed partial resolution of pulmonary infiltrates. The patient was discharged with home oxygen and outpatient follow-up.The patient is currently undergoing regular anti-tumor treatment.

CONCLUSIONS: In the era of chemoimmunotherapy, the presence of pulmonary ground-glass interstitial lesions should prompt consideration not only of immune checkpoint inhibitor-related pneumonia (ICI-P) but also of infections caused by uncommon pathogens such as Legionella, particularly when there is no significant improvement after corticosteroid therapy. It is necessary to consider applying advanced molecular diagnostic techniques such as targeted next-generation sequencing (tNGS) as early as possible to make a clear diagnosis of the pathogen and guide individualized treatment.},
}

@article {pmid41035224,
year = {2025},
author = {Farini, A and Strati, F and Molinaro, M and Mostosi, D and Saccone, S and Tripodi, L and Troisi, J and Landolfi, A and Amoroso, C and Cassani, B and Blanco-Míguez, A and Leonetti, E and Bazzani, D and Bolzan, M and Fortunato, F and Caprioli, F and Facciotti, F and Torrente, Y},
title = {Immunoproteasome Inhibition Positively Impacts the Gut-Muscle Axis in Duchenne Muscular Dystrophy.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {16},
number = {5},
pages = {e70054},
doi = {10.1002/jcsm.70054},
pmid = {41035224},
issn = {2190-6009},
support = {M6/C2_CALL 2022//PNRR/ ; FRRB-2022//Unmet Medical Needs, Fondazione Regionale per la Ricerca Biomedica/ ; GJC21084//Cariplo Telethon Alliance GJC2021-2022/ ; //NextGenerationEU/ ; //MUR/ ; PR-0394//Gruppo familiari beta-sarcoglicanopatie/ ; PNC-E3-2022-23683266-CUP: C43C22001630001//Hub Life Science-Diagnostica Avanzata/ ; //Associazione Centro Dino Ferrari/ ; },
mesh = {Animals ; *Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Proteasome Inhibitors/pharmacology/therapeutic use ; *Muscle, Skeletal/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred mdx ; Male ; *Proteasome Endopeptidase Complex/metabolism ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Duchenne Muscular Dystrophy (DMD) features immune-muscle crosstalk, where muscle fibre degeneration enhances pro-inflammatory macrophage infiltration, worsening inflammation and impairing regeneration.

METHODS: We investigated the impact of immunoproteasome (IP) inhibition on the gut-muscle axis in mdx mice, a well-established model of DMD. We employed microbiota perturbation models, including broad-spectrum antibiotic treatment (ABX) and faecal microbiota transplantation (FMT) from IP-inhibited mdx mice. IP inhibition effects were assessed by analysing gut microbiota composition, intestinal inflammation, muscle integrity and associated metabolic and inflammatory pathways.

RESULTS: IP inhibitor ONX-0914 significantly impacted the intestinal inflammatory microenvironment and gut microbiota of mdx mice. ONX-0914 treatment increased gastrointestinal transit (increased wet/dry faecal weights, p = 0.0486 and p = 0.0112, respectively) and partially restored intestinal barrier integrity (reduced FITC-dextran leakage, p = 0.0449). JAM-A was significantly upregulated (p < 0.0001). Colonic CD206+ M2 macrophages increased, while CD68 + M1 cells partially decreased. ONX-0914 downregulated IP isoforms in macrophages (PSMB8: p = 0.0022; PSMB9: p = 0.0186) as well as FOXO-1 (p = 0.0380) and TNF-α (p = 0.0487). Antibiotic-induced microbiota depletion abrogated these effects. Metagenomic analysis revealed significant differences in microbiota composition between C57Bl controls and mdx mice (PERMANOVA p < 0.001), with ONX-0914 inducing enrichment of stachyose degradation pathways. Metabolomic analysis showed enrichment of bacterial metabolites, fatty acid and sugar metabolism pathways, with increased glutathione, galactose, glycerol, glyceraldehyde and TCA cycle intermediates. ONX-0914 improved mitochondrial activity in skeletal muscle, as increased expression of ETC complexes (mdx vs. mdx+ONX: Complex II, p = 0.0338; Complex IV, p = 0.0023) and TCA enzymes (mdx vs. FTMmdx+ONX: IDH p = 0.0258; FH p = 0.0366). This led to a shift towards oxidative muscle fibres and improved muscle morphology (increased fibre size, p < 0.0001 mdx vs. mdx+ONX and mdx vs. FTMmdx+ONX). Muscle performance was enhanced with reduced CPK levels (p = 0.0015 mdx vs. mdx+ONX) and fibrosis (decreased TGFβ: mdx vs. mdx+ONX, p = 0.0248; mdx vs. FTMmdx+ONX, p = 0.0279). ONX-0914 reduced CD68+ (mdx vs. mdx+ONX, p = 0.0024; mdx vs. FTMmdx+ONX, p < 0.0001) and increased CD206+ (mdx vs. FTMmdx+ONX: p = 0.0083) macrophages in muscle, downregulated inflammatory genes (mdx vs. mdx+ONX: ccl2 p = 0.0327, vcam-1p = 0.0378) and reduced pro-inflammatory proteins (MCP1, mdx vs. mdx+ONX, p = 0.0442). Inflammatory cytokines and endothelial vessel density in ONX-0914 treated mdx were restored to wild type mice. These data demonstrate that ONX-0914 enhances muscle function through microbiota-dependent mechanisms.

CONCLUSIONS: Our study advances the understanding of the role of dysbiosis in DMD disease and identifies IP inhibition as a potential therapeutic strategy to modulate the dystrophic gut-muscle axis, offering new perspectives for microbiota-targeted therapies.},
}

Animals
*Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology
Mice
Gastrointestinal Microbiome/drug effects
*Proteasome Inhibitors/pharmacology/therapeutic use
*Muscle, Skeletal/drug effects/metabolism
Disease Models, Animal
Mice, Inbred mdx
Male
*Proteasome Endopeptidase Complex/metabolism
Mice, Inbred C57BL

@article {pmid41035142,
year = {2025},
author = {Wang, B and Fu, Y and Xu, D and Liu, J and Tian, T and Xie, W},
title = {Successful Management of a Rare Keratitis Caused by Mycobacterium Immunogenum After a Series of Misdiagnoses.},
journal = {Eye & contact lens},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICL.0000000000001228},
pmid = {41035142},
issn = {1542-233X},
abstract = {This case report presents the successful diagnosis and management of a rare case of Mycobacterium immunogenum keratitis. A 34-year-old immunocompetent female presented with a 6-month history of recurrent right eye redness and blurred vision. Previous treatment at other hospitals with oral antivirals, topical corticosteroids, and ganciclovir ointment for presumed herpetic keratitis had failed, with progressive vision decline from 20/20 to 20/50. The causative pathogen identification revealed Mycobacterium immunogenum through comprehensive diagnostic workup including microbiological culture, acid-fast staining, and metagenomic next-generation sequencing (mNGS). Initial therapy with topical amikacin proved ineffective and caused significant ocular toxicity, whereas adjunctive oral azithromycin showed no clinical benefit. Subsequent treatment with 0.3% gatifloxacin eye gel resulted in dramatic improvement. During the healing phase, 0.02% fluorometholone was added to control scarring. Complete resolution was achieved within 4 months, with only mild residual scarring and final uncorrected visual acuity of 20/30. The patient remained recurrence-free throughout 4 years of follow-up. This case demonstrates that Mycobacterium immunogenum keratitis does not necessarily occur in immunocompromised individuals or those with a history of trauma or surgery. It is easily misdiagnosed in the early stages, whereas mNGS can aid in pathogen identification. Treatment with 0.3% gatifloxacin eye gel suggests potentially superior efficacy and safety in such condition.},
}

@article {pmid41034963,
year = {2025},
author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL},
title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {199},
pmid = {41034963},
issn = {2049-2618},
support = {Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; DBI 20222070//National Science Foundation/ ; 1K08ES034821-01A1/NH/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.

RESULTS: In relation to urine sample volume, ≥ 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.

CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.},
}

*Metagenomics/methods
Animals
Dogs
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Humans
Metagenome
*Microbiota/genetics
DNA, Bacterial/genetics
*Urinary Tract/microbiology
*Urine/microbiology
Gastrointestinal Microbiome/genetics

@article {pmid41034825,
year = {2025},
author = {Chen, Y and Bai, Y and Li, M and Gan, X and Wang, Y and Zhou, Y and Niu, T},
title = {Machine learning model for differentiating Pneumocystis jirovecii pneumonia from colonization and analyzing mortality risk in non-HIV patients using BALF metagenomic sequencing.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1222},
pmid = {41034825},
issn = {1471-2334},
support = {No. ZYJC21007//1.3.5 Project for Disciplines of Excellence/ ; No. GYYX24003//1.3.5 Project of High Altitude Medicine/ ; No. ZYAI24039//1.3.5 Project for Artificial Intelligence/ ; No. 2023YFS0031//West China Hospital, Sichuan University , Key Research and Development Program of Sichuan Province/ ; No. 82370192, U24A20680//National Natural Science Foundation of China/ ; No. 2022YFC2502600, 2022YFC2502603//West China Hospital, Sichuan University, National Key Research and Development Program of China/ ; },
}

@article {pmid41034705,
year = {2025},
author = {Bruscadin, JJ and Cardoso, TF and Conteville, LC and da Silva, JV and Ibelli, AMG and Pena, GAC and Porto, T and de Oliveira, PSN and Andrade, BGN and Zerlotini, A and Regitano, LCA},
title = {HolomiRA: a reproducible pipeline for miRNA binding site prediction in microbial genomes.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {236},
pmid = {41034705},
issn = {1471-2105},
support = {2022/06281-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/04089-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/04089-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 456191/2014-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*MicroRNAs/metabolism/genetics ; Binding Sites ; *Software ; Humans ; Animals ; *Computational Biology/methods ; Cattle ; *Genome, Microbial ; *Genome, Bacterial ; },
abstract = {BACKGROUND: Small RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. Here, we introduce HolomiRA (Holobiome miRNA Affinity Predictor), a computational pipeline developed to predict target sites for host miRNAs in microbiome genomes. HolomiRA operates within a Snakemake workflow, processes microbial genomic sequences in FASTA format using freely available bioinformatics software and incorporates built-in data processing methods. The pipeline begins by annotating protein-coding sequences from microbial genomes using Prokka. It then identifies candidate regions, evaluates them for potential host miRNA binding sites and the accessibility of these target sites using RNAHybrid and RNAup software. The predicted results that meet the quality filter parameters are further summarized and used to perform a functional analysis of the affected genes using SUPER-FOCUS software.

RESULTS: In this paper, we demonstrate the use of the HolomiRA pipeline by applying it to publicly available metagenome-assembled genomes obtained from human feces, as well as from bovine feces and ruminal content. This approach enables the prediction of bacterial genes and biological pathways within microbiomes that could be influenced by host miRNAs. It also allows for the identification of shared or unique miRNAs, target genes, and taxonomies across phenotypes, environments, or host species.

CONCLUSIONS: HolomiRA is a practical and user-friendly pipeline designed as a hypothesis-generating tool to support the prediction of host miRNA binding sites in prokaryotic genomes, providing insights into host-microbiota communication mediated by miRNA regulation. HolomiRA is publicly available on GitHub: https://github.com/JBruscadin/HolomiRA .},
}

*MicroRNAs/metabolism/genetics
Binding Sites
*Software
Humans
Animals
*Computational Biology/methods
Cattle
*Genome, Microbial
*Genome, Bacterial

@article {pmid41029837,
year = {2025},
author = {Cabrera, C and Carrión, N and Mateo, D and Vicens, P and Pinzón, A and Heredia, L and Forcadell-Ferreres, E and Pino, M and Yerga, B and Zaragoza, J and Vicente-Pascual, M and Moral, A and Arco, T and Arjó, M and Martínez, E and Galvez, S and Lozano, MJ and Torrente, M},
title = {Gut microbiota characterization in ageing, mild cognitive impairment, and Alzheimer's disease in the context of mediterranean lifestyle in a Spanish population.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {211},
pmid = {41029837},
issn = {1758-9193},
support = {PID2019-103888RB-I00//Ministerio de Ciencia e Innovación/ ; PID2019-103888RB-I00//Agencia Estatal de Investigación/ ; },
abstract = {BACKGROUND: Alzheimer’s disease (AD) is a neurodegenerative disorder often preceded by a prodromal stage of Mild Cognitive Impairment (MCI). Previous research suggests that gut microbiota (GMB) dysbiosis may contribute to cognitive decline via the microbiota-gut-brain axis (MGBA). Notably, GMB composition patterns can vary across populations and stages of dementia. This study aimed to characterize the GMB in a cohort of older adults from Tarragona (Spain) diagnosed with AD or MCI, or presenting a healthy cognitive status (HC), all of whom follow a Mediterranean lifestyle (ML).

METHODS: The present cross-sectional, multicenter case–control study analyzed fecal samples from 99 individuals,including 31 with AD, 30 with MCI, and 38 HC,aged 60–85 years, recruited from seven hospitals and specialized cognitive centers in the province of Tarragona, Spain. Shotgun metagenomic sequencing was conducted with taxonomic profiling using Kraken2. APOE genotyping was performed from fecal DNA using TaqMan assays. Richness, alpha and beta diversity, differential abundance, multivariate linear modeling, and Jonckheere–Terpstra trend tests were conducted to identify GMB species signatures associated with MCI and AD.

RESULTS: Richness, alpha and beta diversity did not differ across groups. Differential abundance analysis identified 109 taxa, of which ten microbial species were shared across comparisons. Notably, several species, including Coprococcus comes and Odoribacter splanchnicus, emerged as replicable candidates, showing both discriminatory value and severity-related declines, alongside taxa with context-dependent or adverse associations.

CONCLUSIONS: Overall GMB diversity did not differ across cognitive groups, but specific taxa, particularly short-chain fatty acid producers, showed consistent associations with cognitive decline in this ML cohort. These findings support a role for the GMB in AD pathology and suggest that targeting key microbial species may provide novel avenues for prevention and intervention.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01862-z.},
}

@article {pmid41001489,
year = {2025},
author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Cregeen, SJJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW},
title = {Wastewater Sequencing Reveals Persistent Circulation and Rising Prevalence of Several Oncogenic Viruses Across Texas.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41001489},
abstract = {BACKGROUND: Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exists in the realm of wastewater-based viral epidemiology (WBE) of cancer-causing viruses, with existing studies using targeted approaches (i.e PCR-based approaches) which lack scalability. Our study aims to carry out WBE with hybrid-capture probes to detect and track multiple oncogenic viruses simultaneously in wastewater across Texas, USA, overcoming the drawbacks associated with targeted approaches.

METHODS: Here, we used a hybrid-capture approach to detect, filter and sequence oncogenic virus signals from wastewater samples collected over a duration of three years, from May 2022 to May 2025. Once viral reads were sequenced, we utilized established computational tools to characterize reads into their respective virus of origin. Next, viral abundances of each characterized oncogenic virus were tracked over time and read coverage across their genomes was measured using read mapping techniques.

FINDINGS: We detected six known oncogenic viruses, along with three suspected oncogenic viruses across all sampling locations within Texas. Over three years, viral abundance gradually increased, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as HPV and EBV rose sharply, with increases in abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using a hybrid-capture technique for almost all oncogenic viruses and their types.

INTERPRETATIONS: Our study shows that a hybrid-capture method can efficiently overcome the challenges faced with using targeted approaches for WBE. Using this method, we get broader read coverage, coupled with concurrent and consistent real-time tracking dynamics of multiple oncogenic viruses. Our findings also emphasize the persistent circulation and rising prevalence of high-risk cancer-causing viruses, underscoring the need for sustained public health interventions to protect communities and assess viral prevalence in high-risk populations.

FUNDING: This work was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021), the Baylor College of Medicine and the Alkek Foundation Seed Funds.},
}

@article {pmid41000896,
year = {2025},
author = {Dillard, BA and Sanders, JG and Husain, AP and Yule, KM and Moeller, AH},
title = {Isolation by distance promotes strain diversification in the wild mouse gut microbiota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41000896},
issn = {2692-8205},
abstract = {Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.},
}

@article {pmid41033729,
year = {2025},
author = {Chan, CSY and Georgakopoulos-Soares, I},
title = {From nonexistence to novel applications: Nullomers and related k-mer based concepts in bioinformatics.},
journal = {Advances in clinical chemistry},
volume = {129},
number = {},
pages = {191-206},
doi = {10.1016/bs.acc.2025.06.009},
pmid = {41033729},
issn = {2162-9471},
mesh = {*Computational Biology/methods ; Humans ; Genomics ; Proteomics ; Neoplasms/diagnosis/genetics ; },
abstract = {Underrepresented k-mer sequences, provide insights into evolutionary constraints, molecular mechanisms, and organismal fitness. Analysis of these sequences have broad applications across genomics and proteomics, such as in biomarker development, cancer diagnostics, phylogenetic analysis, synthetic biology and novel drug discovery. Absent sequences (nullomers and neomers) show promise for cancer detection and tissue-of-origin identification using nucleic acids derived from liquid biopsies, while quasi-primes serve as genomic fingerprints that offer potential for evolutionary studies for understanding trait evolution, and in metagenomics, as biomarkers of organismal presence. The chapter also discusses computational challenges associated with analyzing absent sequences and highlights available k-mer based resources and databases. With the continuous expansion of genomic and proteomic data, absent sequences present an innovative framework for addressing fundamental biological questions and advancing applications in basic and translational research.},
}

*Computational Biology/methods
Humans
Genomics
Proteomics
Neoplasms/diagnosis/genetics

@article {pmid41033716,
year = {2025},
author = {Garima, and Dhanawat, M and Wilson, K and Chaubey, P},
title = {High-throughput sequencing technologies for cancer genomics.},
journal = {Methods in cell biology},
volume = {198},
number = {},
pages = {103-133},
doi = {10.1016/bs.mcb.2025.02.018},
pmid = {41033716},
issn = {0091-679X},
mesh = {Humans ; *Neoplasms/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Genome, Human ; Transcriptome ; },
abstract = {In investigations about transcriptomics, epigenomics, and genomics, high-throughput sequencing technologies have become indispensable. Several hundred million of DNA molecules may be sequenced at once thanks to high throughput sequencing (HTS) technologies, which can simultaneously analyze many DNA molecules. Traditionally, sequencing information has been clarified utilizing a low throughput technique known as Sanger sequencing. This added value makes it feasible to employ HTS to generate tremendous amounts of data, which enhances the comprehension of the transcriptome and genetic fingerprints of cells during various stages of evolution and pathology. By identifying somatic changes, morphological deviations, and repetitive changes across the human genome, techniques such as whole exome sequencing (WES) and whole genome sequencing (WGS) provide information about cancer formation as well as prospective therapies. Identifying tumor biology and discovering biomarkers rely on the examination of aberrant networks and variations in gene expression that RNA DNA sequencing, or RNA-Seq, offers. By identifying rare cell kinds and their function in carcinogenesis, the sequencing of one cell offers illumination on the wide range of cells observed across tumors. Metagenomics and chromatin immunoprecipitation sequencing (ChIP-Seq) delivers essential knowledge by discovering alterations that affect the epigenetic configuration and the microenvironment that accompanies tumors. Integrating these recent developments will allow the development of personalized treatments that use unique genetic traits to determine every cancer patient, offering more individualized treatments. The revolutionary implications of high-throughput genome sequencing for cancer research and treatment are addressed in this book chapter, particularly concerning cancer precision as well as effective treatment outcomes.},
}

Humans
*Neoplasms/genetics
*High-Throughput Nucleotide Sequencing/methods
*Genomics/methods
Genome, Human
Transcriptome

@article {pmid41033677,
year = {2025},
author = {Ilbağı, H and Kanakala, S and Masonbrink, R and Lozier, Z and Miller, WA},
title = {Metagenomic Sequencing of Maize Reveals Abundant Genomic RNA of a Comovirus, a Genus Previously Known to Infect Only Dicots.},
journal = {The plant pathology journal},
volume = {41},
number = {5},
pages = {656-670},
doi = {10.5423/PPJ.OA.06.2025.0077},
pmid = {41033677},
issn = {1598-2254},
support = {//The Scientific and Technological Research Council of Turkey/ ; NKUBAP.03.GA.21.289//Tekirdağ Namık Kemal University/ ; 4308//The Iowa Agriculture and Home Economics Experiment Station, Ames, IA/ ; //The Iowa State University Plant Sciences Institute/ ; //DARPA Insect Allies Program/ ; },
abstract = {To better understand the diversity of viral pathogens in Türkiye, a major exporter of cereals in Europe, we performed high-throughput sequencing of total RNA from maize plants collected in the Trakya region. Certain maize plants exhibiting mosaic and mottle symptoms, gathered from Tekirdağ province in Trakya, yielded large numbers of reads corresponding to the genome of a divergent strain of a comovirus, which corresponds to turnip ringspot virus (TuRSV), a recognized species of the genus Comovirus. This finding is unexpected because all known comoviruses infect only dicotyledonous species, and the known host range of TuRSV has been limited to plants in the Brassicaceae family. The nearly complete and partial nucleotide sequences of the bipartite genome of the maize isolate, as named TuRSVTR59, consist of 6,027 nt TuRSV-TR59 RNA1 and 3,920 nt TuRSV-TR59 RNA2, excluding poly (A) tails. RNA1 and RNA2 each encode a single ORF of 1,860 and 1,096 codons, respectively. Phylogenetic analysis demonstrated that TuRSV-TR59 from Türkiye clustered with other TuRSV isolates from diverse hosts and regions, showing highest identity to isolates from Germany, Czech Republic, and Croatia (80.56-77.77% and 92.09-90.50% nucleotide and amino acid sequence identities, respectively). The ability of TuRSV-TR59 isolate to infect maize was confirmed by reverse transcription polymerase chain reaction. Surveys in the Tekirdağ province of Türkiye, done in 2022-2025, revealed that 2 out of 145 maize samples (1.38%) and 8 out of 116 canola samples (6.89%) were found infected with TuRSV. This is the first report of a comovirus in maize from a monocotyledonous plant species.},
}

@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems: (1) iron/manganese oxidation (e.g., feoB) associated with iron-manganese plaque (IP) formation; (2) sulfate reduction (e.g., dsrA) linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}

@article {pmid41033498,
year = {2025},
author = {Saejung, C and Akkahat, S},
title = {Light color-based proliferation of purple phototrophic bacteria in a microbial consortium for sustainable wastewater treatment and bioproduct generation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133411},
doi = {10.1016/j.biortech.2025.133411},
pmid = {41033498},
issn = {1873-2976},
abstract = {Purple phototrophic bacteria (PPB) offer distinct advantages for wastewater treatment. However, the application of pure cultures of PPB in large-scale wastewater treatment is constrained by isolation challenges and microbial competition. Therefore, we investigated light color treatment as a tool to enrich PPB within a natural microbial consortium for integrated wastewater treatment and bioproduct generation. We used metagenomics to assess PPB population dynamics and measured bioproduct yields of pigments, protein, biomass, and polyhydroxybutyrate as well as chemical oxygen demand removal (COD). While an initial enrichment yielded low PPB abundance (12 %), subsequent exposure to specific light color greatly altered the community composition. White light (465 nm) enriched the consortium with 76 % PPB abundance, dominated by Rhodopseudomonas sp., which maximized bacterial biomass, polyhydroxybutyrate accumulation, and COD removal. Conversely, red light (616 nm) suppressed PPB proliferation but enhanced specific yields of photosynthetic pigments and protein, indicating a metabolic trade-off between growth and bioproduction. Thus, light color treatment may be a simple and powerful strategy to boost PPB abundance and performance within a microbial consortium, creating a cost-effective platform for wastewater biorefineries.},
}

@article {pmid41033373,
year = {2025},
author = {Yarim, D and Abay, S},
title = {First Comprehensive Genome Analysis and Antimicrobial Resistance Profile of Clostridium innocuum from a Domestic Cat.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108076},
doi = {10.1016/j.micpath.2025.108076},
pmid = {41033373},
issn = {1096-1208},
abstract = {This study aimed to investigate the molecular and phenotypic properties of a C. innocuum isolate from a healthy cat, which was previously misidentified as C. difficile by molecular testing (tpi-PCR). To resolve the misidentification and obtain more information on the isolate at the genetic level, whole genome sequencing (WGS) on the long-read sequencing platform Oxford Nanopore PromethION was performed. WGS data were analysed to identify virulence factors, antibiotic resistance, and hypothetical prophage genes. The isolate was identified as C. innocuum as a result of WGS. While several virulence genes, including pilM, yabQ, HrcA, and CptIN family toxins, were detected, toxin-coding genes in other Clostridium species were not detected. Four prophage regions were detected; three appeared as intact phage sites, while one was incomplete. The isolate was susceptible to ampicillin, clindamycin, vancomycin, and metronidazole but was resistant to meropenem using the E-test method. The genome also contained resistance genes such as tet(M), aph(2'')-Ia, and VanT, VanW, VanY, VanG, and VanZ. Genetic similarities between our isolate and those obtained from global human-derived metagenome-associated genomes (MAGs) and non-MAG genomes from healthy humans and animals were illustrated through WGS-SNP-based phylogenetic analyses. This study provides insights into the phenotypic and genotypic characteristics of C. innocuum, an emerging pathogen. Taken together, the isolation of this agent-possessing intrinsic resistance mechanisms and emerging after the treatment of C. difficile infections from a domestic cat highlights its potential threat to public health. Nevertheless, many clinical questions remain unanswered, underscoring the need for further research to deepen our understanding of this pathogen and to develop effective control and treatment strategies.},
}

@article {pmid41033148,
year = {2025},
author = {Luo, L and Wong, JWC and Yan, B and Xu, S and Rabaey, K},
title = {Mechanistic insights into fermentative pathway control during solid-state food waste acidogenesis under autogenic pressure.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124679},
doi = {10.1016/j.watres.2025.124679},
pmid = {41033148},
issn = {1879-2448},
abstract = {The efficiency of two-phase anaerobic digestion hinges on the acidogenic phase, where acidogenic off-gas generates autogenic pressure that alters the physicochemical environment and may affect microbial activity, pathways, and intermediates. However, its mechanistic role under solid-state conditions remains unclear. To address this knowledge gaps, we investigated the effects of autogenic pressure on solid-state food waste acidogenesis, focusing on soluble microbial product (SMP) formation and the associated metabolic responses at the molecular level. Autogenic pressure enhanced acidogenic decomposition, increasing SMP yields from 365.3 ± 10.5 g COD/kg VSadded to 407.1 ± 7.3 g COD/kg VSadded. It initially promoted lactate production, followed by enhanced conversion of lactate to butyrate and acetate functioning by Megasphaera. Metagenomic and metabolite analyses revealed that autogenic pressure increased the abundance of functional genes associated with homoacetogenesis and butyrate synthesis. Incubation experiments further confirmed that acetate, stimulated by autogenic pressure, played a key role in driving the reverse β-oxidation pathway while suppressing the acrylate pathway during lactate conversion. As a result, butyrate production increased by 25 %, while propionate decreased by 43 %. These findings provide new insights into how SMP-producing microbial communities respond to autogenic pressure and demonstrate the potential of self-regulation to enhance product yield and process controllability. This strategy advances sustainable solid waste management and promotes the development of circular bioeconomy.},
}

@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}

@article {pmid41032855,
year = {2025},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M},
title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01564},
pmid = {41032855},
issn = {1520-5851},
abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.},
}

@article {pmid41032194,
year = {2025},
author = {Naderian, R and Alibabaei, F and Paraandavaji, E and Dehghan, P and Eslami, M},
title = {Phage-Microbiota Interactions in the Gut: Implications for Health and Therapeutic Strategies.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41032194},
issn = {1867-1314},
abstract = {The diversified ecology of microorganisms, including bacteria, archaea, fungi, protozoa, and viruses known collectively as the gut microbiota, which includes bacteriophages, is crucial to human health because it affects functions like immune system regulation, vitamin production, and pathogen protection. Bacteriophages are viruses that infect bacteria and are increasingly recognized as a viable treatment option for antibiotic-resistant strains, owing to their high host specificity, which enables precise targeting of drug-resistant bacteria while sparing commensal microbiota. The complex relationships between bacteriophages and gut microbiota are examined, with emphasis on their roles in maintaining health and contributing to disease. Gut microbiota homeostasis is influenced by a number of factors, including age, nutrition, and drugs. Bacteriophages, via lytic cycles and lysogenic conversion, influence the gut microbiota composition and microbial community structure. Gaining an understanding of these processes is crucial to appreciating their contribution to the stability and variety of microbes. Recent research highlights the gut phageome's potential for therapeutic interventions by demonstrating its substantial influence on immunological responses and metabolic problems. The study of phage-microbiota interactions has been transformed by cutting-edge technologies, including high-throughput sequencing, CRISPR-Cas systems, and viral metagenomics, which allow for thorough research and the creation of new therapeutics. Even though tailored medicine and pathogen management hold great potential, obstacles such as regulatory difficulties and bacterial resistance call for additional investigation. Phage-based therapeutic strategies are rapidly advancing, ranging from genetically engineered phages and phages with modified capsid proteins designed to enhance efficacy to phage cocktails that target multiple bacterial strains.},
}