@article {pmid41188680,
year = {2025},
author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA},
title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).},
journal = {Environmental geochemistry and health},
volume = {47},
number = {12},
pages = {547},
pmid = {41188680},
issn = {1573-2983},
support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; },
abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.},
}

@article {pmid41188618,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1295},
pmid = {41188618},
issn = {1573-2959},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; },
mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; },
abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.},
}

*Ibuprofen/metabolism/analysis
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism/analysis
*Microbial Consortia
*Bacteria/metabolism
*Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis
RNA, Ribosomal, 16S

@article {pmid41188566,
year = {2025},
author = {Kondratov, IG and Ogarkov, OB and Sinkov, VV and Suzdalnitsky, AE and Koshcheyev, ME and Orlova, EA and Belkova, NL and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI},
title = {Prediction of Metabolic Profile and Virulence Factors of Facultative-Anaerobic Bacteria from Tuberculous Necrosis Foci Based on Whole-Genome Sequencing Data.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {41188566},
issn = {1573-8221},
abstract = {Metagenomics of bacterial communities in tuberculosis caseous necrotic mass indicates the predominance of facultative anaerobes. Nine strains isolated from the tuberculosis necrosis were identified to species and whole-genome sequencing was performed: Staphylococcus hominis (3 strains), S. epidermidis (3 strains), Corynebacterium ureicelerivorans (2 strains), and C. kefirresidentii (1 strain). Prediction of metabolic pathways and virulence factors showed that Corynebacterium and Staphylococcus possess gene sets that are absent in Mycobacterium tuberculosis: lipases and proteases for the degradation of caseous necrosis, glutamate and polysaccharide capsules, ureases capable of increasing pH of the caseum; and Fe(III) uptake systems. The isolated species can form a bacterial consortium with M. tuberculosis at the early (Corynebacterium) and later (Staphylococcus) stages of necrotization of the tuberculosis focus in the lungs.},
}

@article {pmid41188334,
year = {2025},
author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T},
title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38587},
pmid = {41188334},
issn = {2045-2322},
mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; },
abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.},
}

*Rumen/microbiology
Animals
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Species Specificity
Metagenomics/methods
*Bacteria/classification/genetics

@article {pmid41188324,
year = {2025},
author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI},
title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38611},
pmid = {41188324},
issn = {2045-2322},
support = {NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; R37CA249007/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; },
abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.},
}

Humans
*Colorectal Neoplasms/genetics/pathology/microbiology
*Lymphatic Metastasis/genetics
DNA Methylation
Male
Female
*Biomarkers, Tumor/genetics
Middle Aged
*Gastrointestinal Microbiome
Aged
Transcriptome
Gene Expression Regulation, Neoplastic
Gene Expression Profiling
Multiomics

@article {pmid41188219,
year = {2025},
author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P},
title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9738},
pmid = {41188219},
issn = {2041-1723},
mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.},
}

Animals
*Bacteriophages/genetics/classification/physiology
*Gastrointestinal Microbiome/genetics
Bees/microbiology/virology
*Bacteria/genetics/classification/virology
Biodiversity
Metagenomics
Metagenome

@article {pmid41187758,
year = {2025},
author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and , and König, B and Sauer, U and Stelling, J and Macpherson, AJ},
title = {A global survey of taxa-metabolic associations across mouse microbiome communities.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.010},
pmid = {41187758},
issn = {1934-6069},
abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.},
}

@article {pmid41187361,
year = {2025},
author = {Zhang, T and Xia, Q and Wang, Y and Sun, Y and Pan, D and Cao, J and Zhou, C},
title = {The molecular mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development of dry-cured ham: the insights of metagenomics and metabolomics.},
journal = {International journal of food microbiology},
volume = {445},
number = {},
pages = {111511},
doi = {10.1016/j.ijfoodmicro.2025.111511},
pmid = {41187361},
issn = {1879-3460},
abstract = {To explore the mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development in Jinhua ham, the influences of R. mucilaginosa on fungal community structure, functional enzyme gene expression, key enzyme activities, γ-glutamyl peptides accumulation and taste attributes were investigated during the dry-ripening. In comparison with Pichia kudriavzevii XS-5 (PK), Rhodotorula mucilaginosa XZY63-3 (RX) and no inoculation (CK), the inoculation with Rhodotorula mucilaginosa EIODSF019 (RE) showed the highest overall acceptance and richness. Metagenomics revealed that RE inoculation inhibited Aspergillus abundance, and the profile of Rhodotorula reached 45.94 % at genus level. The treatment of RE increased the gene abundance of amino acid metabolism pathways; the expression levels of γ-glutamyl transpeptidase gene in RE were increased by 83.27 % compared with CK, and the activities of γ-glutamyl transpeptidase increased from 214 U/g proteins of CK to 567 U/g proteins of RE. LC-MS/MS analysis revealed the total contents of γ-glutamyl peptides increased from 136.40 μg/g of CK to 518.18 μg/g of RE. Partial least squares regression and correlation analysis indicated that γ-Glu-Cys and γ-Glu-Gln were mainly responsible for the improvement of overall acceptance and richness of Jinhua ham with RE inoculation.},
}

@article {pmid41187181,
year = {2025},
author = {Xu, P and Huang, Z},
title = {Omadacycline treatment of severe Chlamydia psittaci pneumonia with septic shock diagnosed via metagenomic next-generation sequencing.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {10},
pages = {1570-1576},
doi = {10.3855/jidc.21299},
pmid = {41187181},
issn = {1972-2680},
mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation & purification/drug effects ; High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; *Psittacosis/drug therapy/diagnosis/microbiology ; *Shock, Septic/drug therapy/diagnosis/microbiology ; *Tetracyclines/therapeutic use ; Metagenomics ; Male ; Treatment Outcome ; Doxycycline/therapeutic use ; },
abstract = {INTRODUCTION: Parrot fever, caused by Chlamydia psittaci, is a zoonotic disease typically treated with tetracyclines. Omadacycline, a novel aminomethyl tetracycline, has limited reports on its efficacy in severe Chlamydia psittaci pneumonia in the literature.

CASE PRESENTATION: We present a case of a patient with severe Chlamydia psittaci pneumonia showing symptoms of chills, high fever, shock, hepatic and renal insufficiency, and acute respiratory failure with copious yellow watery sputum. Chlamydia psittaci was confirmed by metagenomic next-generation sequencing (mNGS). Despite initial treatment with moxifloxacin and doxycycline, the patient did not improve and was subsequently discharged after receiving omadacycline.

CONCLUSIONS: Our findings highlight the potential of mNGS for rapid diagnosis of Chlamydia psittaci pneumonia and suggest omadacycline as a potential therapeutic option for severe cases that do not respond to conventional treatment.},
}

Humans
*Chlamydophila psittaci/genetics/isolation & purification/drug effects
High-Throughput Nucleotide Sequencing
*Anti-Bacterial Agents/therapeutic use
*Psittacosis/drug therapy/diagnosis/microbiology
*Shock, Septic/drug therapy/diagnosis/microbiology
*Tetracyclines/therapeutic use
Metagenomics
Male
Treatment Outcome
Doxycycline/therapeutic use

@article {pmid41187070,
year = {2025},
author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S},
title = {An Ocean of Opsins.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf189},
pmid = {41187070},
issn = {1759-6653},
support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; },
mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; },
abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.},
}

*Opsins/genetics
Animals
Phylogeny
*Evolution, Molecular
Oceans and Seas
Vertebrates/genetics

@article {pmid41186403,
year = {2025},
author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M},
title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154725},
doi = {10.1128/aem.01547-25},
pmid = {41186403},
issn = {1098-5336},
abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.

IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.},
}

@article {pmid41186329,
year = {2025},
author = {Liu, Y and Liu, X and Hu, Y and Gao, F and Yu, W and Cheng, F},
title = {Evaluating untargeted metabolomics pipelines for sports nutrition research: a review.},
journal = {Analytical methods : advancing methods and applications},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5ay01484k},
pmid = {41186329},
issn = {1759-9679},
abstract = {Untargeted metabolomics has emerged as a transformative approach in sports nutrition research, offering an unbiased means to characterize the complex biochemical responses to exercise, training, and dietary interventions. Unlike targeted assays restricted to predefined metabolites, untargeted strategies capture broad metabolic perturbations across lipid, carbohydrate, amino acid, and nucleotide pathways, enabling the discovery of novel biomarkers and unanticipated physiological mechanisms. This review critically evaluates the design and application of untargeted metabolomic pipelines in the context of exercise and nutrition science, from pre-analytical sample handling and analytical platforms such as NMR, LC-MS, and GC-MS, to data processing using tools like XCMS, MZmine, and MS-DIAL, and subsequent statistical and bioinformatic interpretation. Key applications include delineating acute metabolic shocks induced by endurance exercise, identifying athlete-specific metabolic phenotypes shaped by chronic training, and assessing the impact of nutritional interventions such as fruit intake, amino acid supplementation, or polyphenol-rich foods on exercise recovery and oxidative stress. The integration of metabolomics with other omics, particularly microbiome metagenomics and lipidomics, highlights the potential for systems-level insights into host-microbe-diet interactions. Nonetheless, significant challenges remain, including the reproducibility of findings, difficulties in metabolite identification, and the translational gap between large datasets and actionable nutritional strategies. By synthesizing current strengths, limitations, and controversies, this review emphasizes that the future of sports metabolomics lies in methodological standardization, multi-omics integration, and validation of candidate biomarkers in independent cohorts. Collectively, these efforts position untargeted metabolomics as a cornerstone for advancing precision nutrition and personalized performance monitoring in athletes.},
}

@article {pmid41186225,
year = {2025},
author = {Chuang, H-Y and Chen, W-Y and Chen, S-H and Shao, Y-H and Wu, J-H},
title = {Metagenome-assembled genome sequence of Candidatus Loosdrechtia sp. KJ reconstructed from an alkaline anammox reactor.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0102425},
doi = {10.1128/mra.01024-25},
pmid = {41186225},
issn = {2576-098X},
abstract = {Candidatus Loosdrechtia sp. KJ is an anaerobic ammonium-oxidizing bacterium enriched from a bioreactor operated under alkaline conditions (pH 9.2 ± 0.4). We report its 3.39 Mb draft genome, containing 3,065 predicted coding sequences, 47 tRNA genes, and a single rrn operon.},
}

@article {pmid41186205,
year = {2025},
author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W},
title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {94},
number = {5},
pages = {e70178},
doi = {10.1111/aji.70178},
pmid = {41186205},
issn = {1600-0897},
support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; },
abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.

OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.

RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.

CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.},
}

Animals
Female
Cattle
*Staphylococcus aureus/physiology
*Staphylococcal Infections/microbiology/immunology/veterinary
*Microbiota
*Uterus/microbiology/immunology
*Endometritis/microbiology/immunology/veterinary
*Cattle Diseases/microbiology/immunology

@article {pmid41186087,
year = {2025},
author = {Bortoletto, E and Rosani, U},
title = {Domoic Acid Risk and the Potential of Meta-Omics for Environmental Surveillance.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70593},
doi = {10.1111/gcb.70593},
pmid = {41186087},
issn = {1365-2486},
support = {101186013//HORIZON EUROPE European Innovation Council/ ; },
}

@article {pmid41185941,
year = {2025},
author = {Al-Husseini, A and Komijani, M and Sabah, R},
title = {Impact of Dust Storms on Airborne Bacteria, Heavy Metals, and Inflammatory Markers in Asthmatic Patients.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70109},
doi = {10.1002/mbo3.70109},
pmid = {41185941},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Asthma/blood/microbiology ; *Metals, Heavy/analysis ; *Bacteria/classification/isolation & purification/genetics ; Iraq ; *Dust/analysis ; Female ; Male ; Biomarkers/blood ; Adult ; *Air Microbiology ; Cytokines/blood ; Metagenomics ; Middle Aged ; Young Adult ; Adolescent ; Child ; },
abstract = {Asthma, a chronic bronchial disorder prevalent in children/adolescents, is exacerbated under environmental conditions like dust storms. The current study investigated heavy metal levels, airborne bacteria, and serum IL-4/IL-8 in asthmatics during before/after dust storms in Iraq's Al-Anbar, Baghdad, and Kirkuk provinces. Airborne heavy metals were quantified by ICP-MS, serum cytokines by ELISA, and bacterial communities via metagenomics. Statistical analysis was performed using GraphPad Prism (p < 0.05 significant). ICP-MS revealed considerably elevated post-storm concentrations of As, Ag, B, Ba, Co, Hg, Mg, Mn, Ni, Sn, S, Ti, and V. Asthmatic subjects presented with considerably elevated IL-4 and IL-8 post-storm (p < 0.05) compared to controls (p > 0.05). Metagenomics revealed storm-induced bacterial alterations: Al-Anbar contained elevated Burkholderiaceae, Methylophilaceae, and Rhodobacteraceae; Kirkuk contained elevated Ilumatobacteraceae, Microbacteriaceae, Burkholderiaceae, and Rhodobacteraceae. Baghdad's most prevalent species included Rhodocyclaceae (50%), Burkholderiaceae (17%), and Arcobacteraceae (4.5%). Al-Anbar was significantly richer in microbes (Chao1) and more diverse (Shannon) than other regions following the dust storm (p < 0.0001). These findings indicate that dust storms raise heavy metals, alter airborne bacteria, and increase inflammatory cytokines in asthma sufferers, and these emphasize their role in exacerbating asthma in Iraq.},
}

Humans
*Asthma/blood/microbiology
*Metals, Heavy/analysis
*Bacteria/classification/isolation & purification/genetics
Iraq
*Dust/analysis
Female
Male
Biomarkers/blood
Adult
*Air Microbiology
Cytokines/blood
Metagenomics
Middle Aged
Young Adult
Adolescent
Child

@article {pmid41185633,
year = {2025},
author = {Villarreal, CX and Chan, DD},
title = {Multiomic Integration Reveals Taxonomic Shifts Correlate to Serum Cytokines in an Antibiotics Model of Gut Microbiome Disruption.},
journal = {Cellular and molecular bioengineering},
volume = {18},
number = {5},
pages = {369-385},
pmid = {41185633},
issn = {1865-5025},
abstract = {PURPOSE: The gut microbiome interacts with many systems throughout the human body. Microbiome disruption reduces bone tissue mechanics but paradoxically slows osteoarthritis progression. The microbiome also mediates inflammatory and immune responses, including serum cytokines. Towards our long-term goal of studying how the gut microbiome interacts with synovial joint health and disease, we examined how antibiotics-induced changes to microbial taxa abundance associated to serum cytokine levels.

METHODS: Mice (n = 5 + ) were provided ad libitum access to water containing antibiotics (1 g/L neomycin, 1 g/L ampicillin, or 1 g/L ampicillin with 0.5 g/L neomycin) or control water from 5- to 16-weeks old, corresponding in skeletal development to ~ 10 to ~ 25 years in humans. At humane euthanasia, we collected cecum contents for 16S metagenomics and blood for serum cytokine quantification for comparison to control and among antibiotic groups. We used dimensional reduction techniques, multiomic integration, and correlation to discriminate antibiotic groups and identify specific relationships between high-abundance taxa and serum cytokines.

RESULTS: Antibiotic treatment significantly lowered diversity, altered phylum relative abundance, and resulted in significant association with specific taxa. Dimensional reduction techniques and multiomic integration revealed distinct antibiotic-associated clusters based on genera relative abundance and cytokine serum concentration. Cytokines IL-6, MIP-1B, and IL-10 significantly contributed to antibiotic discrimination, significantly different among antibiotic treatments, and had significant correlations with specific taxa.

CONCLUSIONS: Antibiotic treatment resulted in heterogenous response in gut microbiome and serum cytokines, allowing significant microbe-cytokine links to emerge. The relationships identified here will enable further investigation of the gut microbiome's role in modifying joint health and disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-025-00861-2.},
}

@article {pmid41185359,
year = {2025},
author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y},
title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117622},
doi = {10.1016/j.foodres.2025.117622},
pmid = {41185359},
issn = {1873-7145},
mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; },
abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.},
}

*Fermentation
Machine Learning
Metagenomics
*Temperature
Microbiota
Hot Temperature
Quality Control
*Food Microbiology

@article {pmid41185305,
year = {2025},
author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T},
title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117551},
doi = {10.1016/j.foodres.2025.117551},
pmid = {41185305},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; },
abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}

*Metagenomics/methods
*Taste
Fermentation
*Microbiota
Fungi/classification/genetics/metabolism
*Alcoholic Beverages/microbiology/analysis
China
Bacteria/classification/genetics/metabolism
*Food Microbiology
Gas Chromatography-Mass Spectrometry
Flavoring Agents

@article {pmid41185132,
year = {2025},
author = {Lonsing, A and Martens, GA and Resteu, A and Kizina, J and Wilkie, I and Bahr, A and Harder, J},
title = {Anaerobic Limonene Metabolism in a Methanogenic Enrichment Involves a Glycine Radical Enzyme.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70192},
doi = {10.1111/1462-2920.70192},
pmid = {41185132},
issn = {1462-2920},
support = {//Max Planck Society/ ; },
mesh = {*Limonene/metabolism ; *Methane/metabolism ; Anaerobiosis ; *Bacteria/genetics/metabolism/enzymology/classification ; *Archaea/genetics/metabolism/enzymology/classification ; *Terpenes/metabolism ; Metagenome ; *Glycine/metabolism ; *Cyclohexenes/metabolism ; Phylogeny ; Metagenomics ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Limonene is a natural monoterpene omnipresent in human environments. It enters wastewater and is also metabolised in methanogenic digesters. A stable limonene-degrading methanogenic enrichment culture was investigated by metagenomic, metatranscriptomic and metaproteomic data sets to characterise the microbial community and identify the limonene degradation pathway. Thirty-two metagenome-assembled genomes revealed a complex community of bacteria and methanogenic archaea dominated by Candidatus Velamenicoccus archaeovorus as the top predator, contributing two-thirds of the reads in the metagenome. The presence of several fermenting bacteria (Anaerolineaceae, Aminidesulfovibrio, Smithellaceae, Lentimicrobium) indicated the recycling of necromass in a microbial loop. Only one hydrocarbon-activating enzyme system was expressed, a member of the alkyl- and arylsuccinate synthase family which is a glycine radical enzyme that adds fumarate to hydrocarbons. The limonenylsuccinate synthase gene encodes a modified substrate binding pocket with two smaller amino acids, suggesting an adaptation for the larger structure of limonene. The limonenylsuccinate synthase operon and a ring cleavage operon, as well as genes for the final syntrophic fermentation to acetate, hydrogen and formate were encoded in a Syntrophobacteraceae genome. Almost all genes for this degradation pathway were highly transcribed and expressed, demonstrating a catalytic role for glycine radical enzymes in methanogenic systems degrading limonene.},
}

*Limonene/metabolism
*Methane/metabolism
Anaerobiosis
*Bacteria/genetics/metabolism/enzymology/classification
*Archaea/genetics/metabolism/enzymology/classification
*Terpenes/metabolism
Metagenome
*Glycine/metabolism
*Cyclohexenes/metabolism
Phylogeny
Metagenomics
Bacterial Proteins/metabolism/genetics

@article {pmid41185061,
year = {2025},
author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , },
title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {225},
pmid = {41185061},
issn = {2049-2618},
support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation & purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; },
abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.

METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.

RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.

CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.},
}

Animals
Humans
*Campylobacter/classification/genetics/isolation & purification
Infant
*Campylobacter Infections/microbiology/epidemiology/veterinary
Ethiopia/epidemiology
*Livestock/microbiology
Rural Population
Longitudinal Studies
Female
Male
Chickens/microbiology
Feces/microbiology
Metagenomics/methods
Gastrointestinal Microbiome
Adult
Cluster Analysis
Family
Child, Preschool

@article {pmid41183495,
year = {2025},
author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC},
title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish Sauce.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf128},
pmid = {41183495},
issn = {1472-765X},
abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/L) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.},
}

@article {pmid41183487,
year = {2025},
author = {Xu, Q and He, N and Tian, Y and Wu, Z and Wang, H and Liu, B and Yang, Z and Zhang, H and Luo, Q and Zhong, Y and Xiao, L and Li, S and Zou, Y},
title = {Lactobacillus gasseri TF08-1 ameliorate high-fat diet induced Nonalcoholic fatty liver disease and regulates gut microbiota in mice.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf271},
pmid = {41183487},
issn = {1365-2672},
abstract = {AIMS: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.

METHODS AND RESULTS: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing Lactobacillus gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-α level decreased by 42.91%. Meanwhile the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered pro-inflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.

CONCLUSIONS: L. gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.},
}

@article {pmid41183417,
year = {2025},
author = {Liu, S and Xiang, Y and Liu, P and Deng, J and He, J and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z},
title = {Application of metagenomic next-generation sequencing in the precise and rapid diagnosis of spinal infections.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117165},
doi = {10.1016/j.diagmicrobio.2025.117165},
pmid = {41183417},
issn = {1879-0070},
abstract = {OBJECTIVE: To evaluate the comparative diagnostic efficacy of metagenomic next-generation sequencing (mNGS) versus conventional microbiological culture in spinal infections.

METHODS: A retrospective analysis was conducted in a cohort of 80 patients with suspected spinal infections who underwent concurrent testing via metagenomic next-generation sequencing (mNGS), microbial culture, and histopathological examination. Diagnostic performance of mNGS and microbial culture was compared using a composite clinical reference standard (definitive diagnosis integrating histopathology, clinical history, and laboratory findings) as the diagnostic gold standard.

RESULTS: Pathogens were detected in 64 cases (80 %) by mNGS, compared to 34 cases (42.5 %) via conventional microbial culture, demonstrating a statistically significant difference in detection rates (P < 0.001). Using clinical diagnosis (histopathology combined with medical history and laboratory findings) as the gold standard, mNGS exhibited superior sensitivity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) in tissue specimens. Conversely, microbial culture showed higher specificity. In pus specimens, mNGS maintained advantages in sensitivity, accuracy, and PPV, while culture demonstrated higher specificity and NPV.

CONCLUSION: Compared to conventional microbial culture, mNGS demonstrates superior diagnostic performance in spinal infections, with significantly higher pathogen detection rates and enhanced sensitivity, accuracy PPV and NPV. mNGS exhibits significant advantages over culture in identifying both common pathogens and fastidious organisms, while also demonstrating robust fungal detection capabilities. Additionally, in tissue specimens, mNGS demonstrates relatively pronounced advantages compared to conventional microbial culture. For purulent specimen testing, comprehensive sensitivity and specificity in diagnosis can be achieved through a combined strategy of mNGS and microbial culture.},
}

@article {pmid41183305,
year = {2025},
author = {Yang, R and Ma, J and Abebe, H and Tu, Y},
title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08498},
pmid = {41183305},
issn = {1520-5118},
abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.},
}

@article {pmid41183096,
year = {2025},
author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ},
title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013667},
doi = {10.1371/journal.ppat.1013667},
pmid = {41183096},
issn = {1553-7374},
abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.},
}

@article {pmid41182689,
year = {2025},
author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ},
title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {21},
pages = {e71207},
doi = {10.1096/fj.202502006RR},
pmid = {41182689},
issn = {1530-6860},
mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; },
abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.},
}

Humans
*Feces/microbiology
Infant, Newborn
RNA, Ribosomal, 16S/genetics
*Infant, Premature
*Gastrointestinal Microbiome/genetics
Female
Male
Intensive Care Units, Neonatal
*Bacteria/genetics/classification

@article {pmid41182549,
year = {2025},
author = {Dandare, SU and Dabai, IA and Kumaresan, D and Allen, CCR},
title = {A Novel Salicylaldehyde Dehydrogenase from Alpine Soil Metagenome Reveals a Unique Catalytic Mechanism.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41182549},
issn = {1559-0291},
support = {NGCA-2014-78//Commonwealth Scholarship Commission/ ; },
abstract = {Metagenomic approaches have revolutionised the discovery of novel enzymes with ecological and biotechnological significance from different environments. Here, we report the comprehensive characterisation of a novel salicylaldehyde dehydrogenase (SALDAP) obtained from an alpine soil metagenome. Phylogenetic analysis revealed that SALDAP is the first experimentally characterised Alphaproteobacterial SALD, forming a distinct evolutionary clade among known bacterial enzymes. The recombinant enzyme exhibited strict specificity for NAD[+] and exceptional catalytic efficiency toward aromatic aldehydes, with benzaldehyde as the preferred substrate. Kinetic analyses showed catalytic efficiencies exceeding 10[6] M[-1] s[-1] for aromatics, whereas aliphatics were oxidised with much lower efficiency, consistent with ecological specialisation for aromatic catabolism in alpine soils enriched in lignin-derived compounds. SALDAP was most active under mildly alkaline conditions (optimum pH 8.0) and tolerated a range of chemical environments, though high concentrations of certain metals and solvents were inhibitory. Differential scanning fluorimetry demonstrated that the enzyme was stabilised by ligand binding, with maximal thermal stability observed when both substrate and cofactor were present. Structural alignment with Pseudomonas NahF and docking analyses revealed that SALDAP employs a distinctive catalytic configuration involving ASN-137, ARG-145, GLU-238, and CYS-272, highlighting a non-canonical role for ASN-137 in substrate binding and stabilisation. Based on these findings, we propose a mechanistic model for SALDAP that expands the catalytic diversity of the aldehyde dehydrogenase superfamily. This study establishes a new paradigm for aromatic aldehyde oxidation, underscores the ecological significance of SALDAP in alpine soil microbiomes, and provides a foundation for engineering novel biocatalysts for bioremediation and synthetic biology applications.},
}

@article {pmid41182235,
year = {2025},
author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E},
title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf247},
pmid = {41182235},
issn = {1751-7370},
abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or non-toxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed non-toxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on non-toxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.},
}

@article {pmid41181472,
year = {2025},
author = {Iftikhar, F and Iftikhar, A and Khalid, M and Talha, M and Waafira, A},
title = {Gut microbial signatures in autoimmune hepatitis: unlocking diagnostic and therapeutic potential.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {10},
pages = {6868-6869},
pmid = {41181472},
issn = {2049-0801},
abstract = {Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease with unclear etiology but likely results from a complex interplay of genetic susceptibility and environmental triggers. Emerging evidence highlights the role of gut microbiota in AIH pathogenesis, with specific genera such as Veillonella, Lactobacillus, and Oscillospira demonstrating diagnostic value. Dysbiosis-associated biomarkers like lipopolysaccharide and aspartate aminotransferase further support a microbial role in disease onset and progression. Despite these promising developments, rare AIH variants remain poorly characterized due to methodological and population-level limitations. Moving forward, large-scale, longitudinal studies integrating metagenomics, metabolomics, and host genomic data are needed to establish subtype-specific microbial markers and assess the efficacy of targeted interventions such as probiotics and bacteriophage therapy.},
}

@article {pmid41181328,
year = {2025},
author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS},
title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660939},
pmid = {41181328},
issn = {2235-2988},
mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation & purification ; Haemophilus influenzae/isolation & purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Infant ; },
abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.

METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.

RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.

DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.},
}

Humans
*Otitis Media with Effusion/microbiology
Child
*Adenoids/microbiology
Male
Female
Child, Preschool
Age Factors
Chronic Disease
*Microbiota
Feces/microbiology
Streptococcus pneumoniae/isolation & purification
Haemophilus influenzae/isolation & purification
Gastrointestinal Microbiome
Metagenomics
Bacteria/classification/genetics/isolation & purification
Infant

@article {pmid41181319,
year = {2025},
author = {Wang, Z and Song, L and Li, D and Jin, Y},
title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1693796},
pmid = {41181319},
issn = {2235-2988},
mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; },
abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.},
}

Humans
*Virome
*Microbiota
*Symbiosis
*Respiratory System/virology/microbiology
Bacteriophages
*Viruses/classification/genetics
Animals
Metagenomics
Host-Pathogen Interactions
Respiratory Tract Infections/virology

@article {pmid41181040,
year = {2025},
author = {Jeyaraman, M and Balasubramanian, E and Jeyaraman, N and Nallakumarasamy, A and Muthu, S},
title = {Metagenomic analysis of gut microbiome and spondyloarthropathy: A systematic review.},
journal = {World journal of orthopedics},
volume = {16},
number = {10},
pages = {108374},
pmid = {41181040},
issn = {2218-5836},
abstract = {BACKGROUND: Spondyloarthritis (SpA), a prevalent chronic inflammatory disorder, predominantly impacts the axial skeleton, including the spine and sacroiliac joints. Emerging evidence implicates gut dysbiosis in the pathogenesis of SpA.

AIM: To evaluate the association between gut microbiome alterations and SpA through metagenomic sequencing analyses.

METHODS: A systematic review was conducted by querying English-language databases, including PubMed, EMBASE, and Google Scholar, spanning 2000 to 2023. From an initial pool of 150 studies, four articles meeting stringent inclusion and exclusion criteria were selected for analysis.

RESULTS: The reviewed studies identified an enrichment of opportunistic pathogenic bacterial species, such as Clostridium spp., Prevotella spp., and Bacteroides spp., alongside viral families including Gratiaviridae and Quimbyviridae, in individuals with ankylosing spondylitis compared to healthy controls. Dysregulated metabolic pathways were highlighted as potential mediators of chronic inflammation and arthritic manifestations. Notably, treatment with tumor necrosis factor inhibitors demonstrated efficacy in mitigating SpA symptoms and restoring gut microbial balance.

CONCLUSION: The findings underscore a significant presence of pathogenic gut microbiota in SpA patients, suggesting a pivotal role in disease progression. Future investigations should focus on species-specific microbial targets to develop innovative therapies for preventing and managing SpA and associated gut dysbiosis.},
}

@article {pmid41180884,
year = {2025},
author = {Sharma, P and Kapoor, N and Langer, S},
title = {Comparative Analysis of Gut Bacterial Communities in Fish and Shellfish of Great Himalayan River System.},
journal = {Indian journal of microbiology},
volume = {65},
number = {3},
pages = {1734-1747},
pmid = {41180884},
issn = {0046-8991},
abstract = {The gut microbiota comprises a unique micro-ecosystem and plays important role in various metabolic functions of the host. Cirrhinus mrigala and Maydelliathelphusa masoniana are two important species of fish and shellfish found in Chenab and Ravi rivers of Himalayan river system. This is the first report on the core gut microbiota of M. masoniana and C. mrigala using Illumina Miseq Sequencing. Gut bacterial diversity of crabs and fishes are studied from the rivers as well as farms. The core microbiome of crab gut samples consists of genera: Bacteroides, Dysgonomonas, Lactobacillus, Leptotrichia, Acinetobacter, Prevotella, Prevotella 1, Pseudomonas, Fusobacterium and Streptococcus. The core microbiome of fish gut samples consists of genera: Acinetobacter, Lactobacillus, Methanosaeta, Prevotella and Pseudomonas. The result shows higher relative abundance of Bacteroides and Lactobacillus in river Ravi than Chenab. Gut bacterial diversity of fishes and crabs of river Chenab is comparatively lower than the river Ravi. Three genera (Bacteroides, Oceanobacillus and Lactococcus) show significant variation (p value < 0.05) in fishes and crabs. Our study generated sequencing data on the gut microbiota of M. masoniana and C. mrigala can establish a base for the development of therapeutic approaches in dealing with the health conditions of diseased fishes and crabs. Gut microbial characterization will not only help in growth and development of the host but also helps in minimizing the disease susceptibility.},
}

@article {pmid41180871,
year = {2025},
author = {Kumari, A and Rao, KVB},
title = {Exploring the Bacterial Diversity of Rajgir Hot Spring in India and its Antibacterial Potential.},
journal = {Indian journal of microbiology},
volume = {65},
number = {3},
pages = {1490-1497},
pmid = {41180871},
issn = {0046-8991},
abstract = {UNLABELLED: Hot springs naturally produce geothermally heated water and are renowned for their diverse microbial communities. Metagenomics studies unveil this microbial diversity. In this study, the bacterial community, along with thermophilic actinobacteria from the Rajgir hot spring, located in Bihar, India, was analyzed using 16S rRNA gene metagenomics sequencing. The sediment temperature was recorded at 45 °C. Investigation of the hot spring ecology revealed the presence of 16 bacterial phyla, with actinobacteria being abundant. Streptomyces, Sphingomonas, Gemmatimonas, Paracoccus, Aeromicrobium, and Actinomyces were among the most common genera found in the sediment samples. These six genera exhibited the highest abundance, with Streptomyces being the most prevalent at 19%, followed by other genera at 13%, 11%, 11%, 10%, and 9%, respectively. Actinobacteria isolated from the hot spring samples were further examined for their antibacterial activities against pathogenic bacteria. Isolates from the Rajgir hot spring demonstrated potential antibacterial activity based on their inhibition zones on agar plates. The results of the antimicrobial screening revealed that AIBRSS1 exhibited the most significant inhibition zone, measuring 26 mm, against Listeria monocytogenes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01482-z.},
}

@article {pmid41180687,
year = {2025},
author = {Muhammad Abdur Rehman, A and Rizwan, MH and Khalid, M and Talha, M and Waafira, A},
title = {Revolutionizing endocarditis diagnosis: AI meets metagenomics for rare Bartonella detection.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {11},
pages = {7772-7773},
pmid = {41180687},
issn = {2049-0801},
abstract = {Bartonella endocarditis is notoriously challenging to diagnose due to its insidious onset, nonspecific symptoms, and the limitations of conventional culture-based techniques. Artificial intelligence (AI)-driven metagenomic next-generation sequencing (mNGS) represents a transformative diagnostic approach by integrating machine learning algorithms with culture-independent sequencing data to improve accuracy and sensitivity. This technique overcomes barriers such as culture bottlenecks and post-surgical sample limitations, achieving high diagnostic specificity while enabling the detection of rare or novel pathogens. Despite challenges including limited reference databases, contamination risks, and cost-related barriers in low-resource settings, AI-enhanced metagenomics offers a promising path toward faster and more precise diagnosis of Bartonella endocarditis. Its integration into clinical workflows, supported by continuous algorithm development, cost optimization, and standardized protocols, has the potential to improve patient outcomes in rare infectious diseases.},
}

@article {pmid41180610,
year = {2025},
author = {Deng, Q and Yang, Y and Gao, S and Lu, M and Zhao, Y and Wang, Z},
title = {Integrated Molecular Diagnostics Unmask Legionella Pneumophila and Fungal Coinfection in an Immunocompromised Host: A Case Study of Precision Antimicrobial Stewardship.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5549-5556},
pmid = {41180610},
issn = {1178-6973},
abstract = {BACKGROUND: Legionella pneumophila poses significant diagnostic challenges in immunocompromised hosts due to its fastidious growth requirements and nonspecific clinical presentation. Conventional culture methods have limited sensitivity (30-80%), while molecular diagnostics require multi-platform validation to ensure reliability.

CASE DESCRIPTION: A 57-year-old woman with rheumatic heart disease, chronic renal failure, and immunosuppression presented with acute respiratory failure. Initial investigations revealed leukocytosis (19.03×10[9]/L), hyponatremia (127 mmol/L), elevated procalcitonin (42.55 ng/mL), and bilateral pulmonary infiltrates. Bronchoalveolar lavage fluid (BALF) analysis employed three molecular methods: isothermal amplification for screening (positive for L. pneumophila on ICU admission), digital PCR (dPCR, 4,455 copies/mL after 10-fold dilution) reconfirmed L. pneumophila infection, and metagenomic next-generation sequencing (mNGS; 384,661 Legionella reads alongside 3,474 Candida glabrata reads). Subsequent fungal β-D-glucan testing (674.8 pg/mL) and culture validated Candida glabrata coinfection. Antimicrobial therapy from targeted moxifloxacin/azithromycin to co-infection therapy with carbapenem escalated from Imipenem-cilastatin to sulbactam/cefoperazone for suspected gram-negative coinfection and fluconazole escalated to amphotericin B for resistant candidiasis guided by CRP/PCT trends.

CONCLUSION: Integrated molecular diagnostics enable rapid pathogen identification in critically ill immunocompromised hosts. Multi-platform verification (isothermal amplification/dPCR/mNGS) overcomes technical limitations of single methods, while serial biomarker monitoring optimizes antimicrobial stewardship for mixed infections.},
}

@article {pmid41180402,
year = {2025},
author = {Chen, C and Xu, D and Jiang, B and Lu, X and Yu, C and Wang, Y and Wang, H and Li, J and Zhu, J},
title = {Precipitation-driven restructuring of rhizosphere microbiota enhances alpine plant adaptation.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1641511},
pmid = {41180402},
issn = {1664-462X},
abstract = {INTRODUCTION: Climate-driven precipitation changes are increasingly threatening alpine ecosystems, yet the adaptive responses of soil microbiomes to rainfall variability remain poorly characterized. This knowledge gaphinders our ability to predict ecosystem resilience under future climate scenarios.

METHODS: We combined metagenomic sequencing with detailed physicochemical analyses to examine how natural precipitation events reshape the microbial communities in both rhizosphere and bulk soils associated with Poa alpigena in the alpine sandy ecosystems of Qinghai Lake.

RESULTS: Rainfall significantly reduced bacterial alpha diversity, particularly in bulk soils, and triggered a compositional shift from drought-resistant taxa (e.g., Geobacter, Pseudomonas) to moisture-adapted genera (e.g., Azospirillum, Methylobacterium). Actinobacteria remained consistently dominant (31.56-34.62%), while Proteobacteria abundance decreased markedly in the rhizosphere post-rainfall. Metabolic reconstruction revealed a transition from pre-rainfall carbohydrate catabolism to post-rainfall anaerobic energy production and carbon fixation pathways. The rhizosphere microbiome uniquely displayed drought-induced biofilm formation and rainfall-enhanced branched-chain amino acid metabolism. Soil moisture and total carbon were identified as primary drivers of microbial restructuring in bulk soils, whereas root exudates conferred stability to rhizosphere communities against hydrological fluctuations.

DISCUSSION: These results elucidate microbiome-mediated adaptive strategies to precipitation changes in alpine sandy ecosystems, highlighting the critical buffering role of plant-microbe interactions. The study provides a mechanistic basis for predicting and restoring climatevulnerable wetlands under increasingly variable hydrological regimes.},
}

@article {pmid41180097,
year = {2025},
author = {Jin, S and Meng, S and Huang, Q and Xie, H and Zheng, J and Wang, R},
title = {Joint application of multiplex drop-off digital PCR, droplet digital PCR, and metagenomic next-generation sequencing for the diagnosis of suspected infectious diseases: A retrospective cohort study.},
journal = {Journal of intensive medicine},
volume = {5},
number = {4},
pages = {407-418},
pmid = {41180097},
issn = {2667-100X},
abstract = {BACKGROUND: Critically ill patients in ICUs are highly vulnerable to infectious diseases. Early and accurate identification of pathogens is vital for initiating appropriate antimicrobial therapy. To evaluate the diagnostic effectiveness in patients with suspected infectious diseases; three different molecular technologies and conventional microbiological tests were used.

METHODS: A total of 97 individuals suspected of having infectious diseases were retrospectively enrolled from July 2023 to January 2024 at Shanghai General Hospital. Samples were collected for metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction (ddPCR), multiplex drop-off digital polymerase chain reaction (MDO-dPCR), and conventional microbiological tests (CMTs) for suspected pathogen detection. The diagnostic efficacies of the three molecular technologies and CMTs were compared, and the effects of their joint application on clinical outcomes were evaluated. Intergroup comparisons were performed using the Kruskal-Wallis test, with a P-value <0.05 considered statistically significant.

RESULTS: Joint detection exhibited a high negative predictive value. The sensitivity of MDO-dPCR, ddPCR, and mNGS was 52.6%, 48.5%, and 96.6%, respectively; and the corresponding specificity was 72.5%, 73.3%, and 50.0%. A positive correlation was observed between pathogen copies detected using MDO-dPCR and procalcitonin (Pearson's ρ=0.21, P=0.039), acute physiology and chronic health evaluation II (Pearson's ρ=0.24, P =0.018), and sequential organ failure assessment (Pearson's ρ=0.25, P=0.012). Therapeutic regimens were adjusted in 51.5% of the patients (50/97) based on the results of the combination tests.

CONCLUSIONS: In the present study, we highlighted the significance of molecular technologies for the early diagnosis of patients with suspected infections. These technologies can serve as a complement to CMTs and should be implemented promptly to guide clinicians in providing timely and effective anti-infective treatments. Future studies should aim to confirm these findings in large-scale clinical trials to refine diagnostic protocols, while also incorporating cost-utility analyses.},
}

@article {pmid41179961,
year = {2025},
author = {Schnabel, E and Xavier, CAD and Whitfield, AE and Dubrow, Z and Pham, G and Cieniewicz, E},
title = {Exploring the Virome of Blackberry and Wild Rubus spp. in South Carolina.},
journal = {Phytobiomes journal},
volume = {9},
number = {1},
pages = {80-94},
pmid = {41179961},
issn = {2471-2906},
abstract = {Numerous viruses infect blackberry, and they are associated with virus disease complexes with complicated etiologies. Blackberry virus diseases limit the lifespan of blackberry production in the Southeastern United States. Although some previous research has been conducted to understand which viruses are prevalent in South Carolina, a comprehensive study on the virome of blackberry has not been done in this region. Additionally, the role of wild Rubus as a virus inoculum source is likely underappreciated and represents a potential opportunity for disease management. We took a comprehensive approach to characterize viral genome sequences from known and novel viruses using metatranscriptomic sequencing of blackberry and wild Rubus spp. leaf samples collected in 2021 from eight sites across South Carolina. We detected 17 known and 6 novel plant viruses and describe relevant genome sequence information. Although the etiologies of these novel viruses are yet to be elucidated, they should be considered part of the blackberry/wild Rubus virome and further studied. We describe instances of potential connectivity of virus populations between cultivated blackberry and wild Rubus for several viruses at several sites. In addition to plant viruses, we describe numerous viruses likely associated with foliar fungi, referred to as Rubus leaf-associated viruses. This study revealed a diverse landscape of both known and novel viruses in blackberry and wild Rubus in South Carolina and has stimulated topics for future research, such as temporal analyses of virus spread at the landscape scale and investigating potential vectors and the biological relevance of novel viruses.},
}

@article {pmid41179353,
year = {2025},
author = {Carboni, S and Poirier, AC and Peralta-Aguilar, AP and Watsa, M and Erkenswick, G and Melin, AD},
title = {The Scent Gland Microbiomes of Wild Tamarins Provide New Insight Into Microbial Contributions to Olfactory Communication.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72335},
pmid = {41179353},
issn = {2045-7758},
abstract = {The microbiome of mammalian scent glands is thought to contribute to the production of odorant compounds involved in sensory communication. Yet, the extent to which glandular microbiomes contain bacteria relevant to odor production and vary by host species, scent marking behavior, or gland morphology remains poorly understood, particularly in wild animals. We sampled microbes collected from skin swabs of suprapubic and sternal scent glands in wild Peruvian saddleback tamarins (Leontocebus weddelli; n = 19) and emperor tamarins (Tamarinus imperator; n = 20) to better understand glandular microbial communities. We aimed to: (1) profile glandular microbiomes of both species, focusing on odor-related taxa and metabolic pathways, and (2) determine whether suprapubic glands, more often in contact with the external environment, had higher diversity and distinct composition of odor-related taxa and pathways compared to sternal glands. We generated metagenomic reads using short-read DNA shotgun sequencing from glandular swabs. We identified 18 odor-associated microbial taxa in both tamarin species, mainly Staphylococcus and Corynebacterium, and 26 pathways, including pyruvate fermentation and amino acid metabolism. Suprapubic glands had lower Shannon alpha diversity relative to sternal glands, especially in L. weddelli. The glands of L. weddelli also differed in taxonomic composition, with odor-related taxa more abundant in suprapubic glands. Our results provide evidence for the involvement of scent gland microbiomes in host communication biology. Glandular specializations differed not only between closely related tamarin species but also between gland types within the same individuals, suggesting a nuanced pattern of host-microbe coevolution that may shape interactions important for olfactory communication.},
}

@article {pmid41179309,
year = {2025},
author = {Yan, L and He, B and Deng, Q and Qiu, Y and Lin, L and Shi, B and Wang, J and Chen, F},
title = {Is systemic inflammation a missing link between oral microbiome and oral squamous cell carcinoma? Results from multi-omics integration analyses.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2574326},
pmid = {41179309},
issn = {2000-2297},
abstract = {OBJECTIVES: To investigate whether systemic inflammation mediates the relationship between oral microbiome alterations and oral squamous cell carcinoma (OSCC) through multi-omics integration analyses.

METHODS: Metagenomic sequencing of unstimulated saliva samples from 65 OSCC patients and 65 matched controls was performed. Plasma levels of 34 inflammatory cytokines were profiled using Luminex assay. Six machine learning models identified potential diagnostic microbial markers. Mediation analysis assessed whether inflammation serves as a mechanistic link between oral microbiota and OSCC.

RESULTS: OSCC patients exhibited reduced species richness and significant beta diversity alterations. Among 155 differential species identified, 25 were enriched in OSCC, including Capnocytophaga sputigena, Gemella haemolysans, Staphylococcus aureus, and several Streptococcus species, with higher abundance in poor oral hygiene conditions. The Boruta-CatBoost model achieved exceptional diagnostic performance (bootstrap AUC = 0.991; 5-fold cross-validation AUC = 0.947). Functional profiling revealed 22 metabolic pathways over-represented in OSCC, notably lipopolysaccharide biosynthesis. Nine circulating cytokines (IL-22, IL-6, IL-2, CCL5, GM-CSF, IL-1β, TNF-α, IL-18, IFN-α) were significantly elevated in OSCC patients. Mediation analysis revealed that IL-22 partially mediated the effect of Staphylococcus aureus on OSCC risk, while CCL5 mediated associations of Gemella haemolysans and Streptococcus species with OSCC (mediation proportions: 29.9-50.1%).

CONCLUSION: Our multi-omics integration suggests that systemic inflammation, particularly through IL-22 and CCL5 upregulation, serves as a mechanistic link between specific oral bacteria and OSCC risk, which could provide new strategies for OSCC prevention and early intervention.},
}

@article {pmid41178975,
year = {2025},
author = {Li, B and Xu, W and Wang, W and Mao, M and Huang, X and Zhang, E},
title = {Discrepancies in gut microbial communities and serum metabolites of Hu sheep with different backfat thickness.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667088},
pmid = {41178975},
issn = {1664-302X},
abstract = {Although market demand for lean meat continues to rise, the regulatory mechanisms governing backfat thickness (BFT) metabolism remain poorly understood. This study employed a multi-omics approach to investigate BFT-associated differences in Hu sheep with distinct fat deposition phenotypes. From 160 genetically similar Hu sheep, we selected 12 individuals with non-significant weight differences (P > 0.05) but extreme divergence in BFT [6 high-BFT (HBF) and 6 low-BFT (LBF) individuals]. Using integrated metagenomics and metabolomics, we systematically compared ileal microbial community structure and serum metabolic profiles between the two groups. HBF sheep showed significantly increased adiposity and altered ileal microbiota composition, characterized by elevated abundances of Carnobacterium, Parabacteroides distasonis, Lactiplantibacillus, and Bifidobacterium. Serum metabolomics identified key differential glycerophospholipids-1-(9Z-octadecenoyl)-2-(11Z-eicosenoyl)-glycero-3-phosphate, PE-NMe(15:0/20:3(5Z,8Z,11Z)), PE-NMe2(18:1(9Z)/20:0), and PE-NMe2(18:1(9Z)/22:1(13Z))-all enriched in glycerophospholipid metabolism pathways. Integrated correlation analysis revealed strong associations between P. distasonis abundance and these phospholipids. These results demonstrate BFT-related adaptive remodeling of the serum metabolome and gut microbiota, identifying P. distasonis as a potential modulator of the host-microbe metabolic axis in ovine adiposity regulation.},
}

@article {pmid41178973,
year = {2025},
author = {Teixeira, MJ and Barbosa, DJ and Dinis-Oliveira, RJ and Freitas, AR},
title = {Redefining postmortem interval estimation: the need for evidence-based research to bridge science and justice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1646907},
pmid = {41178973},
issn = {1664-302X},
abstract = {Classical methods for postmortem interval (PMI) estimation have been applied for nearly a century. Contrary to the notion of being simple or easily accessible, these approaches require highly specialized training, including a medical degree, postgraduate specialization in forensic pathology, and extensive practical experience. Classical PMI estimation relies on observable physical and chemical changes in the human cadaver, such as rigor mortis, livor mortis, algor mortis, and transformative processes during decomposition. These methods are fundamental in medicolegal practice but remain largely influenced by environmental and individual variability. Recent advances in forensic research, particularly in microbiology and biochemistry, have introduced innovative approaches that complement traditional methods, offering greater accuracy and reliability, though resource-intensive. Emerging approaches leverage the predictable postmortem succession of microbial communities (thanatomicrobiome) and biochemical alterations in cadaver fluids and tissues. Techniques such as metagenomics, metatranscriptomics, and metabolomics enable detailed analysis of these changes, while computational models and machine learning further refine PMI estimates. Despite advancements, challenges persist, including variability due to environmental factors and limited access to human decomposition data. Integrating multi-omics approaches and artificial intelligence offers a path forward, addressing these limitations and enhancing the accuracy of PMI estimation. This review provides a comprehensive overview of PMI estimation, critically examining classical approaches and highlighting cutting-edge methodologies rooted in thanatomicrobiology and thanatochemistry. We emphasize the transformative potential of multi-omics integration and artificial intelligence in improving PMI accuracy. Importantly, we propose a paradigm shift: redefining PMI estimation through evidence-based, interdisciplinary research that bridges scientific rigor and judicial application. Transdisciplinary collaboration and standardized methodologies will be essential to translate emerging knowledge into robust forensic tools that serve both science and justice.},
}

@article {pmid41178971,
year = {2025},
author = {Du, H and Hao, X and Lin, B and Zhu, Y and Yang, Y and Tang, M and Wu, W and Wang, D and Lin, B and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X},
title = {Exploring the role of intestinal microbiota in mitigating acute radiation-induced intestinal injury through high-energy X-ray FLASH radiotherapy via metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1601244},
pmid = {41178971},
issn = {1664-302X},
abstract = {OBJECTIVES: This study preliminarily examines the potential correlation between the gut microbiome and the protective effects of FLASH radiotherapy (FLASH-RT) on intestinal tissue using metagenomic analysis.

METHODS: Compact single high-energy X-ray source (CHEXs) FLASH-RT was employed for FLASH irradiation, while EBT3 radiochromic film and a fast current transformer were used to measure the absolute dose and the pulsed beam characteristics. Sham radiotherapy (control), FLASH-RT (333 Gy/s), and Conventional dose rate radiotherapy (CONV-RT, 0.07 Gy/s) were performed on whole abdomen of normal C57BL/6J female mice (10 Gy, 12 Gy, 14 Gy). At 72 h post-irradiation, intestinal contents from normal C57BL/6J female mice were collected for metagenomic analysis. The survival status, body weight, and damage to normal tissues were observed.

RESULTS: At 28 days post-whole abdomen irradiation with doses of 12 Gy, the survival rate of the FLASH group was higher than that of the CONV group (p < 0.05). Histological analysis of intestinal tissues by H&E staining revealed significantly less acute intestinal damage and inflammation in the FLASH group compared to the CONV group. Further macrobiome analysis using LEfSe indicated that the abundance of beneficial bacteria, including Weissella, Lactobacillus ruminis and Lactobacillus taiwanensis was significantly higher in the FLASH group than in the CONV group. Moreover, compared to the CONV group, the FLASH group exhibited significant upregulation of several signaling pathways, including the glycosaminoglycan degradation, PI3K/Akt and arabinogalactan biosynthesis Mycobacterium signaling pathway.

CONCLUSION: Compared to CONV-RT, high-energy X-ray FLASH irradiation exerts radioprotective effects on normal intestinal tissue. Alterations in the gut microbiota and associated signaling pathways may be linked to the protective effects of FLASH.},
}

@article {pmid41178960,
year = {2025},
author = {Abildinova, GZ and Benberin, VV and Vochshenkova, TA and Mussin, NM and Afshar, A and Tamadon, A},
title = {Distinct gut microbial species, but not phylum-to-genus composition, associate with insulin resistance: a unique perspective from the Kazakh population.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683885},
pmid = {41178960},
issn = {1664-302X},
abstract = {OBJECTIVES: Links between gut microbiota and insulin resistance (IR) vary across populations. We profiled the fecal microbiota of Kazakh adults to test whether community composition associates with IR at broad (phylum → genus) and species levels.

METHODS: In a cross-sectional case control study (N = 200; IR = 183, controls = 17), TyG indexed IR status. 16S rRNA sequencing (two primer pools; nine hypervariable regions) characterized taxa. After CSS normalization, we compared presence/absence across groups (χ[2]) and modeled species with univariate and multivariable logistic regressions, using absence of each species as the predictor.

RESULTS: High-level composition did not differ between IR and controls (phylum, class, family, genus; all p > 0.05). In contrast, several species differed. In univariate models, absence of Actinomyces odontolyticus (OR = 25.55, p = 0.010), Bifidobacterium kashiwanohense (OR = 12.69, p = 0.015), Lactobacillus sp. (OR = 5.71, p = 0.020), and Streptococcus lactarius (OR = 6.27, p = 0.044) associated with higher IR odds, suggesting protection when present; whereas absence of Alistipes onderdonkii (OR = 0.30, p = 0.044) and Prevotella copri (OR = 0.19, p = 0.003) associated with lower IR odds, suggesting risk when present. In multivariable models, these signals persisted: absence of P. copri (OR = 0.146, p = 0.003) and Roseburia inulinivorans (OR = 0.143, p = 0.011) predicted lower IR odds (risk alignment), while absence of Lactobacillus sp. (OR = 8.29, p = 0.016) and Coprococcus catus (OR = 7.04, p = 0.004) predicted higher IR odds (protective alignment).

CONCLUSION: In this Kazakh cohort, no broad compositional signal emerged, but species-specific associations were strong and bidirectional. Findings highlight population-specificity and identify candidate species associated with IR that may serve as hypothesis-generating targets for future validation. Any attempt to modulate these taxa for insulin resistance is unproven and requires function-resolved, diet-measured longitudinal studies and randomized trials before clinical application. The IR:control imbalance (183:17) increases uncertainty for low-prevalence taxa; species-level findings are hypothesis-generating and require validation in a more balanced design. Because 16S rRNA profiling does not measure gene functions or metabolites, these species-IR associations are hypothesis-generating and warrant validation using shotgun metagenomics and metabolomics.},
}

@article {pmid41177622,
year = {2026},
author = {Sun, C and Zhao, W and Yue, W and Cheng, H and Long, A and Yin, J and Sun, F and Wang, Y},
title = {Degradation of polymeric carbohydrates coupled with cellular motility driving microbial niche separation in the Pearl River Estuary surface sediment.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {414-423},
doi = {10.1016/j.jes.2025.04.032},
pmid = {41177622},
issn = {1001-0742},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Estuaries ; Rivers/microbiology ; Carbohydrates ; Metagenome ; *Carbohydrate Metabolism ; },
abstract = {Estuaries are key areas for organic carbon cycling, where polymeric carbohydrates are abundant and chemically diverse. The recycling of these polymers by microbes depends on a variety of carbohydrate-active enzymes (CAZymes). However, it remains unclear whether other gene traits, particularly those related to cell motility toward polymeric carbohydrates, are intertwined with carbohydrate depolymerization and niche specialization in estuarine sediment soils. In this study, estuarine sediments were incubated with four prevalent polymeric carbohydrates (laminarin, fucan, cellulose, and chitin) under anaerobic conditions. Based on metagenomic analysis, we identified potential responses to the degradation and utilization of polymeric carbohydrate substrates from the perspectives of CAZymes and sugar transporters. The analysis of metagenomic gene data also revealed a positive correlation between chemotaxis and the abundance of CAZymes genes. Furthermore, metagenomes-assembled genomes (MAGs) that exhibited higher abundance in polysaccharide-treated samples compared to controls also featured elevated copies of genes involved in polysaccharide utilization loci (PULs), chemotaxis, as well as those associated with flagellar or gliding movement. SprB and CTDs associated with gliding proteins genes are essential for type IX secretion system-mediated secretion of CAZymes and gliding motility in Bacteroidota. The enhanced potential for mobility, coupled with the ability to degrade polymeric carbohydrates, may enable these bacteria to exploit nutrients beyond carbon sources, thereby potentially broadening their ecological niches.},
}

*Geologic Sediments/microbiology/chemistry
*Estuaries
Rivers/microbiology
Carbohydrates
Metagenome
*Carbohydrate Metabolism

@article {pmid41177619,
year = {2026},
author = {Yang, R and Wei, Y and Jiang, J and Kong, X and Wu, S and Tang, Q and Liu, Y and Luo, L and Ali, EAE and Chen, H},
title = {Adaptation of microbial gene polymorphisms of the partial nitritation-anammox process for maintaining denitrification performance and robustness under salinity stress.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {39-50},
doi = {10.1016/j.jes.2025.04.028},
pmid = {41177619},
issn = {1001-0742},
mesh = {*Denitrification ; *Salt Stress ; Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; Wastewater ; Salinity ; Ammonium Compounds/metabolism ; Nitrification ; Bacteria/genetics ; },
abstract = {To explore the adaptive mechanisms of the partial nitritation-anammox (PNA) process under high salinity stress during kitchen wastewater treatment, focusing on their physiological and molecular responses through metagenomic analysis. An airlift inner-circulation partition bioreactor (AIPBR) was developed, featuring an inner cylinder and a flow guide tube to create distinct oxygen gradients, facilitating the study of microbial adaptation under varying salt conditions. The AIPBR was operated with synthetic wastewater containing ammonium concentrations of 1800 ± 100 mg/L and salinity gradients ranging from 1 to 10 g/L, followed by a fixed salinity period at 6 g/L, with ammonium concentrations approximately 850 mg/L. High-throughput metagenomic analysis revealed shifts in functional genes and metabolic pathways in response to salinity stress. Anammox bacteria adapted by enriching genes involved in the synthesis of osmoprotective compounds and activating energy-producing pathways like the tricarboxylic acid cycle (TCA). These adaptations, along with modifications in membrane composition, were essential for sustaining system stability under elevated salinity. Under prolonged high salinity stress, anaerobic ammonium oxidizing (AnAOB) exhibited improved salt tolerance, maintaining a total nitrogen removal efficiency above 85 % and stabilizing after an adaptation phase. The metagenomic data revealed a marked enrichment of genes associated with ion transport, stress response mechanisms, and DNA repair pathways. Changes in microbial community composition favored salt-tolerant species, supporting system stability. These findings highlight the applicability of the developed bioreactor for scaling up the PNA process to handle high-salinity wastewater, providing a promising avenue for sustainable nitrogen removal in challenging environments.},
}

*Denitrification
*Salt Stress
Bioreactors/microbiology
*Waste Disposal, Fluid/methods
Wastewater
Salinity
Ammonium Compounds/metabolism
Nitrification
Bacteria/genetics

@article {pmid41177609,
year = {2026},
author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W},
title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {300-307},
doi = {10.1016/j.jes.2025.04.024},
pmid = {41177609},
issn = {1001-0742},
mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; },
abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.},
}

*Fluorocarbons/analysis/toxicity
*Water Pollutants, Chemical/analysis/toxicity
*Geologic Sediments/microbiology/chemistry
Rivers/microbiology/chemistry
*Drug Resistance, Microbial/genetics
China
*Environmental Monitoring
Metagenomics
*Microbiota/drug effects
Caprylates/toxicity

@article {pmid41177409,
year = {2025},
author = {Lin, S and Pan, M and Ma, Y and Chen, Z and Lyu, T and Dong, R and Ruan, R and Liu, S},
title = {Microalgae-mediated shaping of bacterial communities enhances antibiotic removal and antibiotic resistance control.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133577},
doi = {10.1016/j.biortech.2025.133577},
pmid = {41177409},
issn = {1873-2976},
abstract = {The microalgae-bacteria symbiosis sludge (MBSS) system offers a promising strategy for efficient wastewater treatment and nutrients upcycling. However, maintaining stable and effective performance facing antibiotic stress remains a significant challenge. This study explored the regulation strategy of microbial succession towards sulfadiazine (SDZ)-containing wastewater remediation while controlling antibiotic resistance genes (ARGs) spread in MBSS system. The MBSS achieved efficient SDZ removal of up to 99.8%, with an optimal microalgae-to-activated sludge inoculation ratio of 1:3. However, the highest nutrient upcycling efficiencies (33.7% for nitrogen and 98.6% for phosphorus) were observed at an inoculation ratio of 1:1. Metagenomics analysis revealed that genera Chlorella and Micractinium of Chlorophyta were strongly positively correlated with SDZ removal. Moreover, microalgae inoculation significantly modulated the microbial community structure, promoting the dominance of genera Rhodanobacter and Dokdonella in MBSS. This microbial succession could potentially facilitate bacterial co-degradation of SDZ and contribute to a substantially reduced level of ARGs (with the relative abundance of sul1 and sul2 decreasing to 22.9% post-treatment). Overall, the strategy of regulating microalgae inoculation in the MBSS significantly enhanced antibiotic removal and nutrient recovery while controlling the proliferation and spread of ARGs by directing microbial community succession.},
}

@article {pmid41177051,
year = {2025},
author = {Guo, Y and Lin, X and Song, B and Zhao, C and Riaz, M and Ishfaq, M},
title = {Biochar remodeled rhizosphere microbial community structure and function to alleviate sugar beet under fomesafen phytotoxicity.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127821},
doi = {10.1016/j.jenvman.2025.127821},
pmid = {41177051},
issn = {1095-8630},
abstract = {Residual fomesafen in soybean field soil can adversely affect subsequent sugar beet crops. Biochar has been shown to alleviate this damage, the regulatory mechanisms by which it influences the rhizosphere microbial community and its functions in the presence of fomesafen residues remain unclear. This study employed plant physiological assessments, amplicon sequencing, and metagenomic analysis to investigate root physiology, the rhizosphere soil microbial community, and their functional responses to fomesafen toxicity with biochar addition. By comparing sterilized soil with normal soil, that all measured indices in the sterilized soil were reduced, confirming that biochar mitigates fomesafen phytotoxicity through soil microorganisms. Biochar increased root biomass by 37.50 % under fomesafen residue stress, reduced malondialdehyde content in sugar beet roots, enhanced antioxidant enzyme activity, and improved soil multifunctionality by 13.95 %. Furthermore, biochar significantly restored the richness and diversity of rhizosphere fungi and bacteria under fomesafen residue stress. The relative abundance of Dehalococcoidia, a potential herbicide-degrading bacterium, increased significantly under fomesafen stress (90.32 %) and peaked under biochar mitigation treatment (94.02 %), suggesting its potential as a biomarker for fomesafen residues. Biochar alleviated fomesafen's impact on the microbial network, restoring it to a molecular ecological network similar to the control. Metagenomic analysis revealed that biochar increased the Calvin-Benson-Bassham cycle (29.87 %), the nitrogen fixation pathway (21.42 %), and the phosphate transport pathway (10.60 %). By enhancing soil multifunctionality and reshaping rhizosphere microbial communities, biochar improves the stress resistance of sugar beet roots and mitigates damage caused by fomesafen. This finding is significant for maintaining the microecological balance of the rhizosphere.},
}

@article {pmid41177050,
year = {2025},
author = {Su, F and Li, Y and Zhu, C and Gurmesa, GA and Fang, Y},
title = {Impact of freeze-thaw cycle on metagenomics in subsurface wastewater infiltration systems: Ecological implications for greenhouse gas emissions.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127839},
doi = {10.1016/j.jenvman.2025.127839},
pmid = {41177050},
issn = {1095-8630},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, with a global warming potential 273 times that of carbon dioxide (CO2) and is a significant byproduct of wastewater treatment. Subsurface wastewater infiltration systems (SWIS) effectively treat nitrate-rich wastewater but can also contribute to N2O emissions, particularly during freeze-thaw cycles. This study used metagenomics and [15]N isotope tracing to investigate the impacts of freeze-thaw on microbial ecology and nitrogen transformation in SWIS. Results show that freeze-thaw significantly increased abundances of denitrifying bacteria (Bradyrhizobium, Streptomyces and Nocardioides), on average, by 16-63 %. Denitrification genes (nirK and norB) were also increased by 40 ± 16 % and 22 ± 5 %, while the N2O reductase gene (nosZ) decreased by 19 ± 0.46 %. These impacts collectively increased N2O emissions by more than 20 %. During freezing, about one-third of the added [15]NO3[-]-N was recovered as gas (25 % as N2O and 13 % as N2), increasing to 43 % during thawing (29 % N2O and 15 % N2). This study underscores the need for targeted strategies N2O emission in SWIS, particularly under freeze-thaw conditions, to maximize their sustainability in wastewater treatment.},
}

@article {pmid41177031,
year = {2025},
author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Bernstein, A and Cupples, AM},
title = {Identification of the dominant methanotrophs in trichloroethene degrading enrichment cultures from multiple sources.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140268},
doi = {10.1016/j.jhazmat.2025.140268},
pmid = {41177031},
issn = {1873-3336},
abstract = {The current study examined the potential of bioremediation to clean up trichloroethene (TCE) contaminated sites using co-metabolic TCE biodegradation in methanotrophic enrichment cultures. Methanotrophic cultures were developed from both uncontaminated soils (agricultural soils) and impacted sediment from two sites. Following the enrichment of methanotrophs, the cultures were tested for their ability to degrade TCE. Whole genome sequencing data indicated the dominance of the genus Methylocystis and, to a lesser extent, the genera Methylobacter and Methylomicrobium. Fourteen Methylocystis, Methylobacter and Methylomicrobium metagenome assembled genomes (MAGs) were obtained. Twelve particulate methane monooxygenase operons (pmoCAB) were also obtained. The collected operons contained sequences similar to those classifying within the genera Methylocystis, Methylobacter and Methylomicrobium phylotypes. Three operons (mmoXYBZDC) were obtained for soluble methane monooxygenase, with mmoX classifying most closely to other Methylocystis mmoX genes. The newly obtained sequences were compared to commonly used primers for the biomarkers pmoA (A189f and mb661r) and mmoX (536 f and 898r). In summary, TCE degrading methanotrophic cultures were easily developed from both uncontaminated soils and impacted sediments and whole genome sequencing data indicated the importance of the genus Methylocystis across many of the methanotrophic enrichments.},
}

@article {pmid41177025,
year = {2025},
author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S},
title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140254},
doi = {10.1016/j.jhazmat.2025.140254},
pmid = {41177025},
issn = {1873-3336},
abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.},
}

@article {pmid41176044,
year = {2025},
author = {Sodré, IC and Prist, PR and Mancini, MCS and Bettoni-Rodríguez, G and de Andreazzi, CS and Tambosi, LR and Dos Santos, AFA and da Costa, MDF and Bueno, MG},
title = {Forest cover influences the fecal virome of Oligoryzomys nigripes in Atlantic Forest remnants, Brazil.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107894},
doi = {10.1016/j.actatropica.2025.107894},
pmid = {41176044},
issn = {1873-6254},
abstract = {Landscape changes driven by human activities can alter host-pathogen interactions, favoring generalist mammal species that act as reservoirs for zoonotic pathogens, potentially leading to spillover events and outbreaks. Here, we investigated how forest cover influences viral diversity in Oligoryzomys nigripes, a generalist rodent known to harbor zoonotic viruses in the Brazilian Atlantic Forest. We employed high-throughput sequencing to explore the fecal virome of 20 specimens collected across three landscapes with varying forest cover (20%, 40%, and 60%) within Atlantic Forest fragments in São Paulo state. We identified 48 viral families, predominantly bacteriophages and vertebrate-associated viruses. Some, found for the first time in this host, exhibited zoonotic potential, including Papillomaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, Alloherpesviridae, Arenaviridae, Paramyxoviridae, Peribunyaviridae, and Picornaviridae. Alpha and beta diversity indices were used to assess the viral community structure. Although alpha diversity indices did not show a statistically significant difference among landscapes, a significant compositional difference in viral community was detected through beta diversity index (Jaccard dissimilarity), indicating that forest cover may shape the composition of viral families present. The presence of a core virome shared across all landscapes, including families with pathogenic potential, reinforces O. nigripes role as a natural reservoir. While forest cover influences viral community structure, it doesn't necessarily reflect greater ecological complexity within fragments, indicating that other landscape-related factors must also be considered. This pioneering study characterizes the fecal virome of O. nigripes, revealing how forest cover may shape viral communities in wild rodents and underscoring their potential for zoonotic virus surveillance.},
}

@article {pmid41175772,
year = {2025},
author = {Eshghdoostkhatami, Z and Li, Z and Faghihinezhad, M and Cupples, AM},
title = {Characterization of propanotrophic enrichments from agricultural soils capable of 1,4-dioxane biodegradation to sub-μg/L levels.},
journal = {The Science of the total environment},
volume = {1005},
number = {},
pages = {180824},
doi = {10.1016/j.scitotenv.2025.180824},
pmid = {41175772},
issn = {1879-1026},
abstract = {Major challenges to 1,4-dioxane bioremediation concern chemical characteristics that result in migration and persistence, often resulting in large and dilute plumes. In this study, the objectives were to 1) develop propanotrophic enrichment cultures from agricultural soils and determine if they could degrade high and low concentrations of 1,4-dioxane, 2) investigate the feasibility of bioaugmentation for 1,4-dioxane biodegradation in laboratory microcosms and 3) identify dominant propanotrophs and propane monooxygenase genes in the propanotrophic enrichments. Agricultural soils were selected as inocula as they commonly contain microorganisms capable of the biodegradation of a wide range of agricultural chemicals. Propanotrophic enrichment cultures were established from three soils by repeatedly amending propane. Following this, the biodegradation trends for high (3 mg/L) and low (∼200 μg/L) concentrations of 1,4-dioxane were investigated. The experiments also involved bioaugmentation to impacted site sediment microcosms. Prior to their use in bioaugmentation, DNA was extracted from the propanotrophic cultures for shotgun sequencing and analyses with KBase. The easy development of propanotrophic enrichments from agricultural soils suggests a natural abundance of propanotrophs in the soils. Rapid (often <2 weeks) 1,4-dioxane biodegradation was observed in the enrichment cultures at high or low 1,4-dioxane concentrations. 1,4-Dioxane was degraded close to or below the limit of detection (0.46 μg/L) following bioaugmentation. Eighteen propanotrophic metagenome assembled genomes, classifying as Methylibium, Mycobacterium, Rhodococcus opacus, Rhodococcus wratislaviensis and Mesorhizobium, contained full propane monooxygenase operons. Sequences for twenty-two propane monooxygenase operons were retrieved. Sequences for one subunit (prmA) were compared to the closest matches in GenBank. Overall, the developed cultures have potential for use in bioaugmentation to address in situ 1,4-dioxane contamination.},
}

@article {pmid41147335,
year = {2025},
author = {Gurnani, B and Kaur, K},
title = {Advancing diagnostics in Pythium insidiosum keratitis: the emerging role of point-of-care imaging and biosensor-based detection devices.},
journal = {Expert review of medical devices},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/17434440.2025.2582616},
pmid = {41147335},
issn = {1745-2422},
abstract = {INTRODUCTION: Pythium insidiosum keratitis (PIK) is a rapidly progressive, aggressive corneal infection that closely mimics fungal keratitis but fails to respond to conventional antifungal therapy. Misdiagnosis and delayed intervention frequently result in poor outcomes, including high rates of therapeutic keratoplasty and irreversible vision loss. Timely and accurate identification is therefore vital, yet conventional microbiological methods are slow, and histopathology is invasive and often inconclusive. Recent advances in imaging, molecular diagnostics, and biosensor technology are revolutionizing diagnostic possibilities.

AREAS COVERED: Modern tools such as anterior segment optical coherence tomography (AS-OCT) and in vivo confocal microscopy(IVCM) permit rapid, noninvasive visualization of characteristic stromal patterns. Molecular platforms, including PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and multiplex panels, provide precise results within hours. Innovative lateral flow immunoassays (LFIA), aptamer-based electrochemical biosensors, and artificial intelligence (AI)-assisted image interpretation expand point-of-care capabilities, while metagenomic sequencing aids in culture-negative cases.

EXPERT OPINION: The integration of imaging, molecular, and biosensor modalities marks a paradigm shift in PIK diagnostics. PortableAS-OCT, handheld IVCM, and rapid multiplex panels promise to reduce diagnostic delay, minimize unnecessary antifungal use, lower keratoplasty rates, and improve visual prognosis. Collaborative validation and affordable access remain essential for global impact.},
}

@article {pmid41175763,
year = {2025},
author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X},
title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140321},
doi = {10.1016/j.jhazmat.2025.140321},
pmid = {41175763},
issn = {1873-3336},
abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.},
}

@article {pmid41175752,
year = {2025},
author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H},
title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140318},
doi = {10.1016/j.jhazmat.2025.140318},
pmid = {41175752},
issn = {1873-3336},
abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.},
}

@article {pmid41175696,
year = {2025},
author = {Li, N and Zhang, Y and Qu, Z and Xu, J and Ming, A and Sun, H and Huang, L},
title = {Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128381},
doi = {10.1016/j.micres.2025.128381},
pmid = {41175696},
issn = {1618-0623},
abstract = {The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)-which plays a key role in soil phosphorus cycle-was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (rbcL and ppc) and phosphorus cycle (phoP and ppk2). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.},
}

@article {pmid41175632,
year = {2025},
author = {Patel, AB and Jain, KR and Gupta, V and Lal, R and Madamwar, D},
title = {Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107665},
doi = {10.1016/j.marenvres.2025.107665},
pmid = {41175632},
issn = {1879-0291},
abstract = {Coastal ecosystems, like many others on the planet, face chronic threats from anthropogenic activities. The Alang-Sosiya Ship Breaking Yard (ASSBY) located near Bhavnagar in Gujarat, India, represents one such ecosystem impacted by decades of ship-breaking activities. This study aimed to assess the differences in microbial community composition between polluted coastal samples and pristine samples through high-throughput sequencing. Additionally, microbial co-occurrence networks and genes related to antibiotic and heavy metal resistance were predicted using metagenome mining. The analysis confirmed elevated heavy metal concentrations, particularly iron, in polluted samples. In non-polluted sites, alpha diversity indices showed a high microbial diversity compared to polluted sites. The bacterial communities from Deltaproteobacteria at non-polluted sites noticeably shifted to Gammaproteobacteria at polluted sites. Unclassified reads constituted a significant portion of the bacterial diversity. LEfSe (Linear discriminant analysis Effect Size) analysis identified potential bacterial biomarkers, including Pseudomonas, Halomonas and Rhodovulum, which were differentially abundant at polluted sites and may play roles in the biodegradation of xenobiotic compounds. Moreover, Co-occurrence network analysis validated these bacterial biomarkers from polluted sites and revealed their habitat-specific nature. Polluted metagenomes were enriched with genes related to aromatic compound degradation and stress responses, particularly genes for heavy metal and antibiotic resistance. These findings suggest that chronic pollution from ship-breaking activities has led to a shift in microbial communities, leading to an increased presence of resistance mechanisms in the polluted coastal environment to adapt to prolonged heavy pollution.},
}

@article {pmid41175494,
year = {2025},
author = {Ramirez Pavon, JA and Aparecido da Silva Neves, N and de Oliveira Martins, A and Pinho, JB and Juscineide de Souza, V and Patroca da Silva, S and Ribeiro Cruz, AC and Barbosa de Almeida Medeiros, D and Teixeira Nunes, MR and Slhessarenko, RD},
title = {Viral diversity in vertebrates from Alto Pantanal, Mato Grosso, 2019.},
journal = {Virology},
volume = {614},
number = {},
pages = {110729},
doi = {10.1016/j.virol.2025.110729},
pmid = {41175494},
issn = {1096-0341},
abstract = {The Alto Pantanal is a key yet unexplored Brazilian wetland for studying vertebrate viral profiles. This study presents viral taxonomic profiles from vertebrate sera sampled in May, June and October of 2019 in Porto São Luiz and Pirizal, Alto Pantanal. A total of 13 frogs, 19 bats, 23 caimans, 36 equids, 20 domestic hens, 140 birds and 16 humans were sampled. After nucleic acid extraction, individual samples were pooled by species and subjected to a metagenomic approach. Viral reads accounted for less than 0.2 % in each pool, except in domestic hens (35.8 %), yielding an overall viral abundance variation among pools of 48.83 %. In total, twenty-nine viral genomic sequences were retrieved from five pools. In equids, two coding-complete genomes were identified belonging to species Copiparvovirus ungulate8 and Mutorquevirus equid2. In domestic hens, four coding-complete genomes of species Alpharetrovirus avileu were detected, along with partial genomes of three gyroviroviruses of species Gyrovirus homsa1, Gyrovirus galga1 and a putative novel unclassified gyrovirus. In humans, 15 genomes of known human anelloviruses were identified, as well as partial sequences of Orthoflavivirus ilheusense and Erythroparvovirus primate species. In caimans, a partial genome belonging to genus Betadintovirus was detected. In frogs, one partial sequence of a putative novel pegivirus, and a coding-complete sequence of an unclassified retrovirus (Rhinella marina endogenous retrovirus) were found. These findings provide valuable insights into viral circulation within the diverse Pantanal biome, and support viral genomic surveillance efforts in the region.},
}

@article {pmid41175489,
year = {2025},
author = {Fan, Z and Wu, H and Feng, Y and Sun, L and Yuan, L and Muhammad, T},
title = {Biochar mitigates biodegradable microplastic-induced greenhouse gas emissions in lake sediments: Unraveling microbial mechanisms and particle-size effects.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127799},
doi = {10.1016/j.jenvman.2025.127799},
pmid = {41175489},
issn = {1095-8630},
abstract = {Accumulation of biodegradable microplastics (MPs) in freshwater sediments exacerbates greenhouse gas (GHG) emissions, though effective mitigation strategies are still poorly understood. This study investigated the potential of biochar (BC) for carbon sequestration and its role in suppressing MP-induced GHG emissions. Herein, we elucidated the effects of biodegradable MPs Poly (butylene-adipate-co-terephthalate) (PBAT) and different-sized (bulk- and nano-) BC on carbon dioxide (CO2) and methane (CH4) emissions. Results revealed that PBAT significantly reduced sediment pH and oxidation-reduction potential while increasing carbon content, leading to a 50.5 % rise in CO2 and 487.9 % in CH4 emissions. Nano-BC alone reduced CO2 emissions by 46.8 %, whereas no inhibitory effect was observed under MPs pollution. Critically, bulk- and nano-BC strongly inhibited cumulative CH4 emissions in MP-polluted sediment by 14.7 % and 50.6 %, respectively. BC countered PBAT-induced increases in sedimentary amino acids and humic substances by limiting key bacterial phyla involved in organic matter decomposition. Furthermore, BC reduced the abundance of MP-enriched microbes such as p_Firmicutes, f_Methanoregulaceae, and f_Methanotrichaceae, suppressed microbial metabolic functions and carbohydrate-active enzymes, and promoted CH4 oxidation and carbon fixation via genes including cutL, coxL, and coxA. Simultaneously, BC diminished methanogenic gene expression (mcrB, mcrA2). This work demonstrates the pronounced stimulatory effect of biodegradable MPs on sediment carbon mineralization and establishes the multi-level mechanism through which BC (particularly nano-BC) mitigates climate change effectively.},
}

@article {pmid41175312,
year = {2025},
author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S},
title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41175312},
issn = {2509-2723},
support = {22A17//Florida Department of Health/ ; },
abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.},
}

@article {pmid41175161,
year = {2025},
author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV},
title = {Gellan gum-based media recover more diverse microbial communities from soil material.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {338},
pmid = {41175161},
issn = {1432-072X},
support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation & purification/classification/genetics/growth & development ; *Microbiota ; },
abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.},
}

*Polysaccharides, Bacterial/chemistry
*Soil Microbiology
*Culture Media/chemistry
*Bacteria/isolation & purification/classification/genetics/growth & development
*Microbiota

@article {pmid41174950,
year = {2025},
author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, MÀ and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G},
title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {12},
pages = {e70418},
doi = {10.1111/liv.70418},
pmid = {41174950},
issn = {1478-3231},
support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; },
mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; },
abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.},
}

Humans
*Liver Cirrhosis/complications/therapy/microbiology
*Frailty/therapy/microbiology
Male
Metagenomics
*Gastrointestinal Microbiome
Female
*Probiotics/therapeutic use
Middle Aged
Aged
Feces/microbiology
Amino Acids, Branched-Chain/therapeutic use

@article {pmid41174628,
year = {2025},
author = {Wei, M and Ai, X and Gu, D and Zhang, S and Xu, K and Li, S and Mao, S and Li, M},
title = {Ultra-broad hybrid capture-based targeted next-generation sequencing for sensitive plasma pathogen cfDNA detection in bloodstream infections.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1203},
pmid = {41174628},
issn = {1479-5876},
support = {2025YFC3409100//National Key Research and Development Program/ ; 24SF1903500//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 23YF1431300//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Female ; Male ; Middle Aged ; Aged ; *Sepsis/microbiology/blood ; Adult ; Retrospective Studies ; },
abstract = {BACKGROUND: The limited genomic targeting range of current targeted next-generation sequencing (tNGS) workflows results in limited detection of pathogen-derived cell-free DNA (cfDNA), making it challenging to apply this approach to bloodstream infections (BSIs). Here, we developed an ultra-broad hybrid capture-based tNGS method to detect plasma pathogen-derived cfDNA and evaluate its suitability for the diagnosis of BSI.

METHODS: This study introduced an ultra-broad hybrid capture-based tNGS method featuring an ultra-broad pathogen panel (1872 pathogens) and high-density probe coverage. To adequately evaluate its performance, we conducted retrospective tests in 208 suspected BSI patients (139 immunocompromised), comparing tNGS results with mNGS, conventional microbiological testing (CMT), and comprehensive clinical diagnoses.

RESULTS: In pathogen detection, the concordance between ultra-broad hybrid capture-based tNGS and mNGS results was 93.75%. The diagnostic accuracy of tNGS in BSI was comparable to mNGS (76.44% vs. 75.00%) and significantly higher than CMT (45.67%, p < 0.0001). In immunocompromised populations, the diagnostic accuracy of tNGS was similar to mNGS (77.70% vs. 76.98%). tNGS detected 92.09% (163/177) of pathogens identified by mNGS. Two of the missed pathogens were not included in the 1872 pathogens panel, and both were from the immunocompromised group.

CONCLUSIONS: Ultra-broad hybrid capture-based tNGS exhibits sensitivity and accuracy comparable to mNGS, effectively covering a relatively wide range of pathogens, and may serve as an economic screening tool for BSI in the future.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Cell-Free Nucleic Acids/blood/genetics
Female
Male
Middle Aged
Aged
*Sepsis/microbiology/blood
Adult
Retrospective Studies

@article {pmid41174528,
year = {2025},
author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S},
title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {703},
pmid = {41174528},
issn = {1471-2180},
}

@article {pmid41174518,
year = {2025},
author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B},
title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {704},
pmid = {41174518},
issn = {1471-2180},
mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; },
abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.

RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.

CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.},
}

*Lakes/microbiology/chemistry
*Metagenomics/methods
India
*Bacteria/genetics/metabolism/classification/isolation & purification
*Xenobiotics/metabolism
Microbiota
Metagenome
Inactivation, Metabolic

@article {pmid41174459,
year = {2025},
author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C},
title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117386},
doi = {10.1016/j.foodres.2025.117386},
pmid = {41174459},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.},
}

*Metabolomics/methods
*Citrullus/microbiology
*Metagenomics/methods
*Glycine max/microbiology
*Taste
Fermentation
*Microbiota
Food Microbiology
Flavoring Agents/metabolism
Bacteria/metabolism/classification/genetics

@article {pmid41174397,
year = {2025},
author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C},
title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117319},
doi = {10.1016/j.foodres.2025.117319},
pmid = {41174397},
issn = {1873-7145},
mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; },
abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.},
}

*Citrullus/microbiology/chemistry
*Fermentation
*Taste
*Fermented Foods/microbiology/analysis
Volatile Organic Compounds/analysis
*Microbiota
Acetic Acid/analysis
Odorants/analysis
Cresols/analysis
*Food Microbiology
Flavoring Agents/analysis
Bacteria/classification/metabolism/genetics
Gas Chromatography-Mass Spectrometry
China

@article {pmid41174177,
year = {2025},
author = {Simmonds, P and Butković, A and Grove, J and Mayne, R and Mifsud, JCO and Beer, M and Bukh, J and Drexler, JF and Kapoor, A and Lohmann, V and Smith, DB and Stapleton, JT and Vasilakis, N and Kuhn, JH},
title = {Taxonomic expansion and reorganization of Flaviviridae.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {3026-3037},
pmid = {41174177},
issn = {2058-5276},
support = {MC_UU_00034/1//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 107653/Z/15/Z//Wellcome Trust (Wellcome)/ ; NIHR203338)//DH | National Institute for Health Research (NIHR)/ ; },
mesh = {Phylogeny ; *Flaviviridae/classification/genetics/enzymology ; RNA-Dependent RNA Polymerase/genetics ; Evolution, Molecular ; Genome, Viral ; Host Specificity ; Viral Proteins/genetics ; RNA Helicases/genetics ; },
abstract = {Flaviviridae is a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and 'flavi-like' viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae, Pestiviridae and Hepaciviridae) and 12 genera in the established order Amarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family.},
}

Phylogeny
*Flaviviridae/classification/genetics/enzymology
RNA-Dependent RNA Polymerase/genetics
Evolution, Molecular
Genome, Viral
Host Specificity
Viral Proteins/genetics
RNA Helicases/genetics

@article {pmid41174125,
year = {2025},
author = {Dobrzyński, J and Jakubowska, Z},
title = {Pseudomonas protegens as a biocontrol agent against phytopathogenic fungi - mini review.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {11},
pages = {428},
pmid = {41174125},
issn = {1573-0972},
mesh = {*Plant Diseases/microbiology/prevention & control ; *Pseudomonas/metabolism/physiology/genetics ; *Biological Control Agents/metabolism ; *Fungi/pathogenicity ; Antifungal Agents/metabolism/pharmacology ; Phloroglucinol/analogs & derivatives/metabolism ; Secondary Metabolism ; Chitinases/metabolism ; Phenols ; Pyrroles ; },
abstract = {Pseudomonas protegens, a member of the P. fluorescens complex, is an important biocontrol agent with high potential in sustainable agriculture. It produces diverse secondary metabolites, including 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT), orfamides, and protegenins, as well as hydrolytic enzymes such as chitinases, which contribute to antifungal activity, fungal cell wall degradation, and induction of systemic resistance (ISR) in plants. Despite these insights, gaps remain in understanding the regulation of metabolite biosynthesis, variability of ISR across crops, and the field efficacy of P. protegens. Future research should employ omics approaches (metagenomics, transcriptomics) to optimize biocontrol strategies, explore natural inducers of metabolite production, and evaluate colonization efficiency under field conditions. This review synthesizes current knowledge on P. protegens, highlighting its importance, mechanisms of action, existing knowledge gaps, and directions for future research.},
}

*Plant Diseases/microbiology/prevention & control
*Pseudomonas/metabolism/physiology/genetics
*Biological Control Agents/metabolism
*Fungi/pathogenicity
Antifungal Agents/metabolism/pharmacology
Phloroglucinol/analogs & derivatives/metabolism
Secondary Metabolism
Chitinases/metabolism
Phenols
Pyrroles

@article {pmid41173910,
year = {2025},
author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW},
title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9658},
pmid = {41173910},
issn = {2041-1723},
support = {R01NS055349//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32GM148382//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Dysbiosis/microbiology/mortality/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; *Malaria/mortality/microbiology/complications ; Female ; Male ; Infant ; Feces/microbiology ; Child ; Escherichia coli/isolation & purification/genetics ; Metagenome ; Enterobacteriaceae/isolation & purification/genetics ; Patient Discharge ; },
abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.},
}

*Dysbiosis/microbiology/mortality/complications
Humans
*Gastrointestinal Microbiome/genetics
Child, Preschool
*Malaria/mortality/microbiology/complications
Female
Male
Infant
Feces/microbiology
Child
Escherichia coli/isolation & purification/genetics
Metagenome
Enterobacteriaceae/isolation & purification/genetics
Patient Discharge

@article {pmid41173905,
year = {2025},
author = {Adhikary, R and Alkhatib, AEA and Hazra, S},
title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38127},
pmid = {41173905},
issn = {2045-2322},
mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; },
abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.},
}

India
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification
RNA, Ribosomal, 16S/genetics
*Ecosystem
*Drug Resistance, Bacterial/genetics
beta-Lactamases/genetics/metabolism
Gastrointestinal Microbiome
Metagenomics/methods
Humans
Microbiota
Metagenome

@article {pmid41173568,
year = {2025},
author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I},
title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {9},
pages = {501624},
doi = {10.1016/j.endien.2025.501624},
pmid = {41173568},
issn = {2530-0180},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; },
abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/metabolism
Bacteria/classification

@article {pmid41173365,
year = {2025},
author = {Liu, H and Qu, Y and Yue, Y and Cui, X and Wang, X and Wang, C and Geng, Z and Zhang, L and Sun, M and Huo, M},
title = {Low-dose chlorite drives stable nitrite accumulation for partial denitrification.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123234},
doi = {10.1016/j.envres.2025.123234},
pmid = {41173365},
issn = {1096-0953},
abstract = {Achieving stable and efficient nitrite accumulation in partial denitrification (PD) requires precise control techniques, which poses a challenge to its practical application. This study introduces a new strategy using chlorite (ClO2[-]) as a regulatory factor to halt denitrification at the nitrite stage, ensuring stable and efficient PD. The effectiveness of this approach was assessed in a continuously operated PD biofilter. At different ClO2[-] concentrations, the nitrite accumulation rate (NTR) reached its peak at 97.6% at 1.00 mg/L ClO2[-], with effluent nitrate-nitrogen (NO3[-]-N) as low as 0.61 mg/L. The chlorite-regulated PD filter exhibited a rapid start-up period, reaching optimal performance within 7 days and maintaining stable operation for over 30 days. Moreover, this PD biofilter sustained a nitrite accumulation rate above 67.5% across a wide range of carbon/nitrogen ratios (C/N) (2-4) and remained efficient at an extremely short hydraulic retention time of 30 min. Additionally, ClO2[-] easily degrade into non-toxic chloride ion (Cl[-]) and oxygen (O2) in the environment, thereby preventing secondary pollution. Metagenomic analysis identified Thauera (16.4%), Simplicispira (14.7%), and Flavobacterium (14.0%) as key contributors to nitrite accumulation. Furthermore, according to the real-time quantitative polymerase chain reaction (qPCR) results, chlorite exposure upregulated the nitrate reductase gene (nar) and downregulated the nitrite reductase gene (nir). Finally, the final effluent Total Inorganic Nitrogen (TIN) concentration of 10.26 mg/L was achieved through the Partial denitrification/Anammox (PD/A) coupling process. This study provides new insights into nitrite accumulation in PD/A and presents valuable guidance for optimizing the PD/A process in engineering applications.},
}

@article {pmid41173342,
year = {2025},
author = {Vanbiervliet, Y and Aerts, R and Maessen, L and Wauters, J and Maertens, J and Lagrou, K},
title = {Laboratory innovations to diagnose invasive mould infections - what is relevant, what is not?.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.10.017},
pmid = {41173342},
issn = {1469-0691},
abstract = {BACKGROUND: Invasive mould infections (IMI) carry high morbidity and mortality. Conventional diagnostics - histopathology, culture and microscopy - rely on invasive sampling and lack sensitivity, particularly during early phases of infection. Rare and mixed mould infections are frequently diagnosed too late or missed.

OBJECTIVES: To provide a narrative review of recent innovations in diagnosing IMIs, highlighting advances, identifying areas where progress remains limited, and assessing gaps in current diagnostic algorithms to guide future directions.

SOURCES: We performed a literature search regarding diagnostic methods for IMIs without date restrictions, including experimental and clinical studies, systematic reviews and meta-analyses.

CONTENT: Rapid lateral-flow assays and single-sample chemiluminescent immunoassays for detecting Aspergillus antigens in blood and BALF now complement enzyme immunoassays (EIA). Novel targets, such as urinary glycans and siderophores in various biological matrices, show potential to diagnose IMI. Targeted PCRs for Aspergillus and Mucorales enable earlier detection than conventional methods and rapid detection of resistance in case of A. fumigatus, though isolated Aspergillus PCR positivity is challenging to interpret. Metagenomic next-generation sequencing (mNGS) expands pathogen detection but is limited by costs and technical and interpretative challenges. A shift towards assays based on the host immune response (functional immune assays and biochemical markers) shows promise but remains investigational.

IMPLICATIONS: Due to different commercially available test formats, Aspergillus antigen detection assays can now be implemented in many hospitals. Implementation of Mucorales PCR tests improves the diagnosis of mucormycosis also in the setting of coinfections. Multimodal pathogen-based strategies that integrate antigen assays, targeted PCRs, and, in select cases, mNGS enable earlier, more accurate, and comprehensive diagnosis of IMIs ultimately improving clinical outcomes; but the need for rapid, accurate, non-invasive diagnostic tests for IMIs remains. Host-response based assays are not yet clinic-ready. Prospective multicentre studies are needed to standardize diagnostic thresholds, validate novel diagnostic markers and to evaluate impact on patient outcomes and cost-effectiveness.},
}

@article {pmid41173130,
year = {2025},
author = {Gonzalez, G and Carr, MJ and Byrne, H and Colgan, A and Hare, D and Sawa, H and De Gascun, CF and Matthijnssens, J and Yandle, Z},
title = {Complex evolutionary dynamics including reassortment drive genome diversity in human rotavirus species a circulating in Ireland.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105848},
doi = {10.1016/j.meegid.2025.105848},
pmid = {41173130},
issn = {1567-7257},
abstract = {Rotavirus A (RVA), belonging to the species Rotavirus alphagastroenteritidis, is among the most frequently diagnosed viral causes of gastroenteritis. The inclusion of RVA vaccines in the primary childhood immunisation schedules of multiple countries has led to significant reductions in yearly-reported cases. Nevertheless, such interventions may exert selective pressures that could result in the emergence of novel vaccine escape variants. RVA classification has traditionally focused on two of eleven gene segments encoding the capsid proteins, VP4 and VP7, which limits evolutionary assessments of genomic diversity and reassortments involving the other segments. A viral metagenomics approach (NetoVIR) was employed to investigate the genomic diversity of RVA in Ireland. The analysis focused on clinical samples (n = 140) collected from patients between 2015 and 2021. Besides the Wa-like or DS-1-like genotype constellations, 4/140 genomes (3 %) were identified as reassortant, with an NSP2 genotype 1 in a DS-1-like constellation. Also, we confirmed the circulation of OP354-like P[8] strains in six G9P[8] samples. Notably, these strains show dissimilarity in the antigenic epitopes of the VP4 protein compared to the Rotarix vaccine. Furthermore, we detected strains with an equine-like G3 (EQL-G3) VP7 gene within a DS-1-like constellation (n = 5/140, 4 %) and the unusual combination of G1P[8] with a DS-1-like constellation in 6/22 (27 %) of the G1P[8] samsples. Our study supports using a viral metagenomic approach for RVA genetic characterisation to determine pathogen diversity and reassortments. The public health implications of the identified reassortant RVA strains, requires investigations for any potential impacts on vaccine efficacies.},
}

@article {pmid41172871,
year = {2025},
author = {Lalucat, J and Busquets, A and Mulet, M and Riesco, R and García-Valdés, E and Gomila, M},
title = {Genome insights into Hydrogenophaga taeniospiralis and its R-body genetic determinants.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {6},
pages = {126664},
doi = {10.1016/j.syapm.2025.126664},
pmid = {41172871},
issn = {1618-0984},
abstract = {The genome of Hydrogenophaga taeniospiralis 2K1[T], the type and only strain of the species, was analysed. The genes encoding elements involved in autotrophic and chemolithotrophic growth that oxidize H2 in addition to other metabolic traits, such as potential nitrogen fixation capability, are described. A phylogenomic analysis of the taxonomy of members of the genus reveals a high number of species not yet described in the genus, especially if the numerous metagenomes obtained from environmental samples are included. The differences from the closest related genera, Malikia and Serpentinimonas, are highlighted and the delineation of the genus Hydrogenophaga is discussed based on phylogenomic analysis. Furthermore, a survey of metagenomes available in public databases demonstrates the wide environmental and geographic distribution of Hydrogenophaga strains. H. taeniospiralis 2K1[T] is the first free-living bacterium described for its ability to synthesize R- bodies, which are intracytoplasmic extendable protein ribbons associated mainly with toxic effects. The genetic determinants of R-body synthesis are analysed and compared with those found in other Hydrogenophaga genomes and strains from other genera.},
}

@article {pmid41172852,
year = {2025},
author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140283},
doi = {10.1016/j.jhazmat.2025.140283},
pmid = {41172852},
issn = {1873-3336},
abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.},
}

@article {pmid41172529,
year = {2025},
author = {Lima, JD and Rivadavea, WR and Calgaro, LC and Alberton, O and Costa, MSSM and Lima, JC and Monteiro, PHR and Kuhn, EV and Silva, GJ},
title = {Biological dynamics of no-tillage soils in the western region of Paraná.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e298630},
doi = {10.1590/1519-6984.298630},
pmid = {41172529},
issn = {1678-4375},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Brazil ; Nitrogen/analysis ; *Agriculture/methods ; Biomass ; Biodiversity ; Fungi/classification ; Carbon/analysis ; },
abstract = {This study investigates soil dynamics on farms in the western region of Paraná, Brazil, highlighting the importance of biological parameters in agriculture. In particular, focusing on the interaction of management practices with soil biodiversity and biological functions, the aim is to understand and promote sustainable and efficient agricultural practices. To do this, we collected soil samples from 15 farms close to Toledo, Paraná, Brazil. These samples were then analyzed to determine biological and physicochemical parameters using techniques such as carbon and nitrogen microbial biomass, metabolic coefficient, basal respiration, bacterial and fungal biomass, and length of the hyphae. The most contrasting soils were evaluated for physicochemical composition and metagenomic analyses. The results showed significant differences in biological parameters between 2020 and 2021, including fungal biomass, hyphae length, and soil basal respiration. Statistical analyzes revealed strong relationships between biological variables, notably the correlation between fungal hyphae and total nitrogen. Climate changes and management practices appear to influence the microbial composition and biological functions of the soil over the years. Soil P9 stood out with superior biological activity and richer microbial diversity, contrasting with soil P13. These differences reflect the influence of management and climatic conditions on soil composition and biological functions. The microbial comparison of the soils emphasized the need for continuous and careful agricultural management, highlighting the importance of biodiversity and ecological functionality of the soil for agricultural sustainability. So, the study underscores the relevance of considering soil biological parameters, in addition to physicochemical aspects, to optimize soil health and productivity.},
}

*Soil Microbiology
*Soil/chemistry
Brazil
Nitrogen/analysis
*Agriculture/methods
Biomass
Biodiversity
Fungi/classification
Carbon/analysis

@article {pmid41172139,
year = {2025},
author = {Yang, S and Zhang, J and Ou, Y and Liu, W and Tian, X and Hou, LJ and Dong, HP},
title = {Ammonia oxidation by aerobic methanotrophs as a source of marine nitrous oxide.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf242},
pmid = {41172139},
issn = {1751-7370},
abstract = {Aerobic methanotrophs encode a hydroxylamine oxidoreductase, which facilitates the oxidation of ammonia to nitrite or nitric oxide, potentially leading to nitrous oxide production. Aerobic methane oxidation has been documented in shallow marine waters or the water column of the open ocean. However, little is known about the distribution pattern of marine aerobic methanotrophs containing hydroxylamine oxidoreductase and their contribution to marine nitrous oxide emissions. Here, by analyzing global marine metagenomes, we show that hydroxylamine oxidoreductase-containing aerobic methanotrophs were widely distributed across diverse marine habitats, with higher abundances in methane seep systems and estuary regions than in other environments. Among these, aerobic methanotrophs belonging to Gammaproteobacteria were the most widely distributed and abundant functional group. We also identified a second order within Gammaproteobacteria (Ga0077536) potentially capable of aerobic methanotrophy, and a complete repertoire of denitrification genes in a gammaproteobacterial methanotroph, expanding the phylogenetic and functional diversity of marine aerobic methanotrophs. By using enrichments of estuarine methanotrophs in combination with 15N stable isotope tracing and metatranscriptomic analysis, we indicate that marine aerobic methanotrophs take part in ammonia oxidation and nitrous oxide production. The ammonia oxidation can persist for approximately 6 days, and the nitrous oxide produced is at least partially derived from the hydroxylamine oxidation. Given the prevalence of denitrification genes in aerobic methanotrophs, methane oxidation may also be coupled to NOx- reduction under anoxic marine conditions, potentially contributing to nitrous oxide production. The intrinsic nature of aerobic methanotrophs could partially offset the mitigation of global warming achieved through the methane consumption.},
}

@article {pmid41171744,
year = {2025},
author = {Jia, X and Peng, J and Lv, J and Li, Y and Luo, Z and Xiang, J and Hou, Y and Zheng, Q and Han, B},
title = {Metagenomic analysis reveals the abundance changes of bacterial communities and antibiotic resistance genes in the influent and effluent of hospital wastewater.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0335723},
pmid = {41171744},
issn = {1932-6203},
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification ; Hospitals ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Sewage/microbiology ; },
abstract = {The presence of substantial quantities of antibiotics and their metabolites in hospital wastewater can lead to the accumulation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Research on the influent and effluent sewage of hospitals is crucial for understanding the effectiveness of wastewater treatment systems in inactivating ARB and ARGs. Key features of microbial communities and ARGs in influent and effluent wastewater - including taxonomic diversity and relative abundance - were assessed via metagenomic sequencing. The treatment process resulted in a reduction of the overall bacterial count in hospital wastewater. However, a notable increase in relative abundance was observed for three phyla, 16 genera, and 21 species post-treatment. Bacteria harboring ARGs were predominantly identified as belonging to Pseudomonadota and Bacillota. A total of 354 ARGs were detected in the influent, while 331 were identified in the effluent samples, with a general decrease in absolute abundance. Nevertheless, the relative abundance of certain ARGs, such as mphG, fosA8, and soxR, was found to increase in the effluent across all samples. Seasonal fluctuations also played a role in the distribution of microbial communities and ARGs. These findings underscore the role of hospital wastewater treatment systems in reducing the discharge of ARB and ARGs into the environment, while also revealing potential shortcomings in the wastewater treatment process that necessitate further improvement for more effective removal of these ARGs.},
}

*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/drug effects/classification
Hospitals
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
*Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Metagenome
Sewage/microbiology

@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
Biodiversity
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid41171444,
year = {2025},
author = {U, A and Chacko, A and Priyadarshini, M and P P, R},
title = {Utilization of Chlorella vulgaris biomass in microbial fuel cell as a feed and the study on its degradation pathway.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {8},
pages = {1104-1117},
pmid = {41171444},
issn = {0273-1223},
support = {//Cochin University of Science and Technology/ ; },
mesh = {*Chlorella vulgaris/metabolism ; *Bioelectric Energy Sources/microbiology ; *Biomass ; Waste Disposal, Fluid/methods ; },
abstract = {Microbial fuel cells (MFCs) represent an advanced and environmentally friendly bioenergy technology with significant potential for simultaneous power generation and wastewater treatment. This study specifically compared the anodic performance of MFCs with Chlorella vulgaris versus those fed with acetate. Dual-chamber MFCs were constructed for simultaneous electricity generation and wastewater treatment. In addition, microbial communities of both the MFCs and the gene function of MFC-Ch were analyzed through metagenomic sequencing. When comparing all the electrochemical parameters produced from MFCs, MFC-Ch is slightly more efficient than MFC-A. Metagenomic analysis showed that Proteobacteria was the predominant phylum in MFC-A, whereas Bacteroidota was predominant in MFC-Ch. COG (Clusters of Orthologous Groups) analysis of the primary metabolic pathways in the anolyte of MFC-Ch revealed a relatively high abundance of genes associated with several metabolic pathways during MFC operation, including amino acid transport and metabolism, carbohydrate transport and metabolism, and coenzyme transport and metabolism. The study on carbohydrate and protein degradation indicated that protein metabolism occurred to a greater extent than carbohydrate metabolism. This aligns with the known ability of some bacteria present in the sludge to promote amino acid metabolism in MFCs, a finding further supported by the positive correlation observed in the COG analysis.},
}

*Chlorella vulgaris/metabolism
*Bioelectric Energy Sources/microbiology
*Biomass
Waste Disposal, Fluid/methods

@article {pmid41171134,
year = {2025},
author = {Sun, Y and Chen, Q and Fan, G and Sun, Q and Zhou, Q and Zhang, J and Nie, J and Ma, J and Wu, L},
title = {gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1115},
pmid = {41171134},
issn = {1362-4962},
support = {2021YFA0717001//National Key R&D Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 153211KYSB201900211//Chinese Academy of Science/ ; //Chinese Academy of Sciences/ ; },
abstract = {The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.},
}

@article {pmid41171126,
year = {2025},
author = {She, J and Qian, PY and Wu, L},
title = {DOO: integrated multi-omics resources for deep ocean organisms.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1096},
pmid = {41171126},
issn = {1362-4962},
support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; },
abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.},
}

@article {pmid41171125,
year = {2025},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1118},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; ERC-AdG-669830/ERC_/European Research Council/International ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}

@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

@article {pmid41170985,
year = {2025},
author = {Gamage, C and Graves, A and Li, G and Thieulent, CJ and Balasuriya, UBR and Morrow, J and Vissani, A and Parreño, V and Matthijnssens, J and Carossino, M},
title = {Coding-complete genome sequences of group B equine rotavirus from central Kentucky, USA, reveal circulation of a single genome constellation.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0074425},
doi = {10.1128/mra.00744-25},
pmid = {41170985},
issn = {2576-098X},
abstract = {Equine rotavirus B (ERVB) has caused foal diarrhea in central Kentucky since 2021. Coding-complete genome sequences from 14 strains circulating in 2024 revealed >99% nucleotide identity to the 2021 prototype ERVB strain RVB/Horse-wt/USA/KY1518/2021, with a conserved genomic constellation (G3-P[3]-I3-R3-C3-M3-A4-N3-T3-E3-H3).},
}

@article {pmid41170455,
year = {2025},
author = {Ruan, L and Chen, S and Zhang, J and Peng, G},
title = {Infected left atrial myxoma with Streptococcus gordonii: case report and literature review.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1635642},
pmid = {41170455},
issn = {2234-943X},
abstract = {Cardiac myxoma is a relatively common type of benign heart tumor, but infectious myxoma is rare. The symptoms of non-infected cardiac myxoma and infected cardiac myxoma are similar and mostly nonspecific, which can easily lead to delayed diagnosis, missed diagnosis, and delayed treatment. A 57-year-old male patient presented with nonspecific systemic symptoms such as anorexia, fever, and cough, and was initially considered to have gastrointestinal disease or pulmonary infection. Preoperative bacterial culture was negative, and imaging features were consistent with cardiac myxoma. A small amount of vegetation was found attached to the surface of the tumor. Postoperative blood culture, surgical specimen culture, and postoperative blood metagenomic next-generation sequencing (mNGS) examination all showed positive results for Streptococcus gordonii, confirming the diagnosis of infectious left atrial myxoma. For patients with febrile cardiac myxoma, it is crucial to be vigilant against concurrent infections. Blood cultures should be performed before administering antibiotics. In cases where blood cultures are negative, a combination of mNGS, PCR, and transesophageal echocardiography (TEE) should be utilized for differential diagnosis, with particular attention paid to the characteristics of vegetations on the tumor surface.},
}

@article {pmid41170433,
year = {2025},
author = {Zhang, S and Chu, M and Sun, X},
title = {The arms race in bacteria-phage interaction: deciphering bacteria defense and phage anti-defense mechanisms through metagenomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687307},
pmid = {41170433},
issn = {1664-302X},
abstract = {Bacteriophages are viruses that specifically infect bacteria and co-evolve with their hosts through mutual interactions. They represent one of the most significant drivers of microbial diversity, influencing its evolution, generation, and maintenance. To counter bacteriophage infection, bacteria have developed sophisticated immune systems, including both passive adaptations, such as inhibiting phage adsorption and preventing DNA entry, and active defense systems such as restriction-modification systems and CRISPR-Cas systems. The ongoing arms race between bacteriophages and bacteria has left distinct evolutionary signatures in their genomic sequences. Advances in large-scale genomic and metagenomic sequencing technologies, coupled with bioinformatics approaches, have greatly enhanced our understanding of bacteria-phage interaction mechanisms, driving progress in bacteriophage biology. This review systematically analyses the diverse immune strategies bacteria employ against phage infection, elucidates the coordination and interrelationships among different anti-phage mechanisms, and highlights potential directions for future research.},
}

@article {pmid41170420,
year = {2025},
author = {Guo, Y and Zhang, N and Pei, D},
title = {Gut microbiota heterogeneity in non-alcoholic fatty liver disease: a narrative review of drivers, mechanisms, and clinical relevance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1645298},
pmid = {41170420},
issn = {1664-302X},
abstract = {Non-alcoholic fatty liver disease (NAFLD), a prevalent metabolic disorder, is increasingly recognized as a complex condition influenced by gut microbiota dysbiosis. However, the heterogeneity in findings across studies has hindered the clinical translation of microbiota-based interventions. In this narrative review, we synthesize current evidence on gut microbial alterations in patients with NAFLD, with a focus on the sources of variability that contribute to inconsistent results. We included human studies (2000-2024) that compared gut microbiota profiles between NAFLD patients and healthy controls using 16S rRNA or metagenomic sequencing; key drivers of microbial changes include clinical factors (metabolic comorbidities, disease progression), biological variables (diet, genetics), and methodological biases (sequencing platform differences, diagnostic criteria variability). Emerging evidence highlights the role of non-bacterial components (fungi, viruses) in modulating bacterial communities and disrupting host metabolic pathways, exacerbating hepatic inflammation and lipid accumulation. To overcome current limitations, we propose integrating multi-omics approaches (metagenomics, metabolomics, and proteomics) with a longitudinal study design to capture dynamic microbiota-host interactions. Precision microbiota therapies, including strain-specific probiotics, engineered microbial consortia, and fecal microbiota transplantation tailored to individual dysbiosis profiles, are emerging as promising strategies for targeted interventions. Addressing these challenges is essential to identifying reliable microbial biomarkers and developing personalized strategies for NAFLD prevention and treatment. Future research should harmonize methodologies, validate causal mechanisms, and optimize microbiota-based therapies to bridge experimental findings and clinical application.},
}

@article {pmid41170165,
year = {2025},
author = {Shi, Y and Lin, Z and Chen, Z and Ye, C and Yu, J and Xi, J and Geng, Y and Zou, M and Ren, H and Wang, L and Wang, B and Xu, F and Zheng, X and Xiang, G},
title = {High-throughput and Efficient Assay for Central Nervous System Infection with Targeted Nanopore Sequencing Technology.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5461-5471},
pmid = {41170165},
issn = {1178-6973},
abstract = {INTRODUCTION: Central nervous system (CNS) infections represent a significant global public health concern and are characterized by high morbidity and mortality rates. In this study, we developed an integrated diagnostic approach for CNS infections by combining high-throughput nanopore sequencing with multiplex PCR amplification, designated targeted nanopore sequencing (tNPS).

METHODS: The tNPS assay employed a dual detection strategy incorporating pathogen-specific primers targeting 17 prevalent CNS pathogens (seven bacteria, one fungus and nine DNA viruses), with universal primers for the comprehensive amplification of full-length 16S ribosomal RNA (16S rRNA) and internal transcribed spacer (ITS) regions.

RESULTS: Analytical validation of tNPS was successfully carried out using the 12 positive reference strains (seven bacteria, one fungus, and four DNA viruses) individually, the ZymoBIOMICS microbial community (eight bacteria and two fungi), the laboratory synthetic community of bacteria and fungi (seven bacteria and one fungus), and the laboratory synthetic community of viruses (five DNA viruses). With accelerated turnaround time within 8 h, the tNPS also assayed 11 clinical cerebrospinal fluid (CSF) samples, which further confirmed the feasibility of precise identification of CNS pathogens compared to CSF culture and metagenomic next-generation sequencing.

DISCUSSION: Our tNPS as a culture-independent diagnostic assay offered enhanced efficiency, high-throughput capability, and an expanded pathogen detection spectrum, facilitating potential implementation in molecular diagnosis of CNS infection.},
}

@article {pmid41169729,
year = {2025},
author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P},
title = {Unveiling Common Bean (Phaseolus vulgaris L) RNA- and DNA-Based Virome in Western Kenya: Insights From Metatranscriptomic and Metagenomic Signatures.},
journal = {Advances in virology},
volume = {2025},
number = {},
pages = {6690945},
pmid = {41169729},
issn = {1687-8639},
abstract = {Common bean (Phaseolus vulgaris L) is Kenya's second most important agricultural product after maize, serving as a vital source of protein for many rural families in Western Kenya. However, viral diseases caused by RNA and DNA viruses greatly impair bean productivity, often leading to yield losses of up to 100%, thus contributing to food insecurity. Global research has isolated 168 viruses of plants that have detrimental effects on common beans; however, no extensive profiling of these viruses has been done in Western Kenya. The scope of this study was to delineate the whole virome that infects common beans through a comprehensive disease diagnostic survey. Sixty-one diseased samples were collected, and nucleic acids were extracted using standard extraction protocols (DNA &RNA Qiagen) and sequenced on the Illumina platform. Metagenomic analysis revealed several DNA-based viruses, such as Badnavirus spp, Caulimovirus maculatractylodei, Pandanus badnavirus, Okra enation leaf curl virus, and Paper mulberry vein-banding virus, while metatranscriptomic analysis uncovered viruses like Tomato leaf curl Cameroon alphasatellite, Physalis Rugose Mosaic Virus, Citrus endogenous paretrovirus, Natevirus nate, and Bracoviriform facetosae. To the best of our knowledge, this study provides a comprehensive inventory of viral entities associated with common beans not documented in Africa. This information is essential for defining plant defense mechanisms, guiding crop protection strategies, lowering agriculture-related risks, strengthening resistance, and advancing resilience.},
}

@article {pmid41168883,
year = {2025},
author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M},
title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {224},
pmid = {41168883},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; },
mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth & development/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.

RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (> 23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2 days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15 days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.

CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.},
}

*Groundwater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/growth & development/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Phylogeny
DNA, Bacterial/genetics
Adaptation, Physiological
Sequence Analysis, DNA

@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Tracheophyta/microbiology
Metagenome
Phylogeny
*Plant Leaves/microbiology
Pinus/microbiology

@article {pmid41168776,
year = {2025},
author = {Heng Wu, and Dong, T and Li, A and Chen, J and Zhang, H and Lv, H and Yang, C and Guo, X and Yang, X and Qiu, L and Miao, C and Yao, Y},
title = {An innovative strategy for overcoming ultra-high ammonia nitrogen inhibition on anaerobic methanogenesis via stepwise domestication.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {223},
pmid = {41168776},
issn = {2049-2618},
mesh = {*Methane/biosynthesis/metabolism ; Anaerobiosis ; *Ammonia/metabolism ; Animals ; Cattle ; Methanosarcina/metabolism/genetics ; *Nitrogen/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/classification/genetics ; Manure/microbiology ; Domestication ; Metagenomics/methods ; },
abstract = {BACKGROUND: The world is facing both an increasingly severe energy crisis and a growing problem of agricultural pollution. The utilization of agricultural waste by anaerobic digestion (AD), has received increasing attention. AD using representative waste cow dung results in total ammonia nitrogen (TAN) accumulation and inhibition of methanogens resulting in reduced CH4 production. However, there is a lack of highly efficient in-situ biological domestication strategies to enhance the TAN tolerance of methanogens in AD systems.

RESULTS: In this study, an incremental approach to gradually increasing the TAN concentration has been used for overcoming the problem. The results showed that at an ultra-high concentration of 6124.09 mg/L TAN, a 48-day domesticated AD system functioned stably and the cumulative CH4 production reached 72.81 mL/g volatile solids, whereas the undomesticated AD system failed to produce CH4. After domestication, the lactate dehydrogenase concentration decreased to 96.44 ng/L and the adenosine triphosphate concentration increased to 48.77 nmol/L, confirming that microbial activity improved. Hydrolytic and acidogenic bacteria were enriched, with Methanosarcina (79.73%) dominating the domesticated AD system, primarily Methanosarcina mazei. Metagenomic analysis showed that with two-component system enrichment, the key inhibited steps from glycerate-1,3P2 to pyruvate (2.498‰), and from acetyl-CoA and acetyl phosphate to acetic acid (1.141‰ and 0.798‰), as well as vital methanogenic genes mcrA (0.128‰), mcrB (0.127‰), and mcrG (0.065‰), were both enriched, which favored a stable methanogenic system. More importantly, this ultra-high resistance AD system also showed the potential to increase the CH4 production per unit substrate at the Minhe biogas plant with 24,000 m[3] operation scale in Shandong Province, China.

CONCLUSIONS: Stepwise increase the TAN concentration is a novel method that was demonstrated to be a practical and sustainable way to overcome ultra-high TAN inhibition (6124.09 mg/L). During domestication, the two-component system may regulate the microbial collaborative network to ensure microbial activity and high abundance enrichment, thus potentially constructing a methanogenic system dominated by hydrogenotrophic and acetoclastic methanogenesis, holding a promising application prospect. This study helped recognize the potential of methanogens in tolerating ultra-high inhibition and developed an achievable AD technology for robustly treating fecal residue and wastewater in practice.},
}

*Methane/biosynthesis/metabolism
Anaerobiosis
*Ammonia/metabolism
Animals
Cattle
Methanosarcina/metabolism/genetics
*Nitrogen/metabolism
Bioreactors/microbiology
Bacteria/metabolism/classification/genetics
Manure/microbiology
Domestication
Metagenomics/methods

@article {pmid41168702,
year = {2025},
author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML},
title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {64},
pmid = {41168702},
issn = {1297-9686},
support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.

RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.

CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.},
}

Animals
Cattle/genetics/physiology
*Rumen/microbiology
*Metagenome
*Weight Gain/genetics
*Eating/genetics
Metagenomics/methods
Animal Feed
Phenotype
Genomics/methods
Diet/veterinary
Gastrointestinal Microbiome