@article {pmid41339801,
year = {2025},
author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H},
title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04546-8},
pmid = {41339801},
issn = {1471-2180},
support = {7222026//Natural Science Foundation of Beijing Municipality/ ; },
abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.

METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.

RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score > 5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r = -0.46, P = 0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P < 0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.

CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.},
}

@article {pmid41339548,
year = {2025},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41339548},
issn = {1476-4687},
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}

@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Child
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology
Male
Female
Child, Preschool
RNA, Ribosomal, 16S/genetics
Adolescent
Bacteria/genetics/classification
Case-Control Studies

@article {pmid41339358,
year = {2025},
author = {Li, H and Cao, Y and Liu, X and Ke, Z and Chen, L and Siame, BA and Yaron, S and Leung, KY},
title = {Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1896},
pmid = {41339358},
issn = {2052-4463},
support = {32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; },
mesh = {*Caves/microbiology ; *Metagenome ; *Archaea/genetics/classification ; *Genome, Bacterial ; *Genome, Archaeal ; *Bacteria/genetics/classification ; },
abstract = {Cave microorganisms represent unique extremophiles that have evolved in isolated, nutrient-limited environments and harbor exceptional metabolic capabilities. However, knowledge of cave microbial diversity at genomic level remains limited. Previous studies have focused on individual caves and do not give a global picture. Here, we present the first prokaryotic cave metagenomic catalog from 37 geographical diverse cave environments. We employed an optimized genome reconstruction pipeline to recover 3,837 medium-to-high quality cave metagenome-assembled genomes (MAGs). These MAGs were dereplicated into 1,979 species-level representative clusters that spanned 67 phyla of Bacteria (n = 1,858) and Archaea (n = 121) domains. Classification of representative species showed that 98.7% did not match any existing genome taxonomy classification of named species at ≥ 95% average nucleotide identity (ANI). Most representative genomes harbored putative biosynthetic gene clusters (BGCs) (98.0%) and enzymatic antibiotic resistance genes (ARGs) (95.0%). This comprehensive MAGs catalog provides a foundational resource for exploring cave microbial diversity, secondary metabolism, and the evolutionary origins of antibiotic resistance in subterranean ecosystems.},
}

*Caves/microbiology
*Metagenome
*Archaea/genetics/classification
*Genome, Bacterial
*Genome, Archaeal
*Bacteria/genetics/classification

@article {pmid41339349,
year = {2025},
author = {Coe, A and Mullet, JI and Vo, NN and Berube, PM and Anjur-Dietrich, MI and Salcedo, E and Parker, SM and VonEmster, K and Bliem, C and Arellano, AA and Castro, KG and Becker, JW and Chisholm, SW},
title = {A curated protein dataset for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1895},
pmid = {41339349},
issn = {2052-4463},
support = {OCE-2048470//National Science Foundation (NSF)/ ; OCE-1153588//National Science Foundation (NSF)/ ; DBI-0424599//National Science Foundation (NSF)/ ; 984601//Simons Foundation/ ; 337262//Simons Foundation/ ; 329108//Simons Foundation/ ; GBMF495//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
mesh = {*Synechococcus/classification/genetics ; *Prochlorococcus/classification/genetics ; *Metagenome ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacterial Proteins/genetics ; },
abstract = {Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying classification workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.},
}

*Synechococcus/classification/genetics
*Prochlorococcus/classification/genetics
*Metagenome
Phylogeny
Genome, Bacterial
Metagenomics
*Bacterial Proteins/genetics

@article {pmid41339341,
year = {2025},
author = {Bellankimath, AB and Branders, S and Kegel, I and Ali, J and Asadi, F and Johansen, TEB and Imirzalioglu, C and Hain, T and Wagenlehner, F and Ahmad, R},
title = {Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66865-8},
pmid = {41339341},
issn = {2041-1723},
support = {336420 and 352514//Norges Forskningsråd (Research Council of Norway)/ ; },
abstract = {Urinary tract infections (UTIs) affect 405 million people worldwide. Current diagnostics rely on cultures, which can take 2 to 4 days. This study evaluates eleven culture-independent methods for sample preparation from 78 complicated UTI patients, followed by real-time nanopore sequencing and data analysis. The metagenomic results are highly consistent with culture-based clinical routines (MALDI-TOF/VITEK-2). The optimized method demonstrated an accuracy score of 99% (100/101) for pathogen identification and 90% (589/653) for antimicrobial susceptibility profiling with 95% specificity. The method's robustness is highlighted by its ability to accurately identify pathogens with as few as 32 bacterial cells/µL and a low bacterial-to-host cell ratio limit of 0.5. Additionally, mNGS identified 13 pathogens that routine diagnostics missed, which were subsequently confirmed by Vivalytic or PCR. This method is up to 30% more economical than published studies and commercial kits. DNA yield and flow cytometry can be used for pre-screening to reduce costs, which is crucial for clinical adoption. This research highlights the rapid diagnosis of clinical UTIs using a cost-effective and scalable method that requires around four hours from sample collection to informed decision-making. Furthermore, it aims to improve antimicrobial and diagnostic stewardship by reducing empirical treatment and ensuring more judicious antibiotic use.},
}

@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age }

Humans
*Gastrointestinal Microbiome/genetics
Infant
Australia
Female
Male
Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Infant, Newborn
Indigenous Peoples
Metagenome

@article {pmid41338553,
year = {2025},
author = {, and , },
title = {[The Chinese guidelines for the diagnosis and treatment of invasive fungal disease in patients with hematological disorders and cancers (the seventh revision)].},
journal = {Zhonghua nei ke za zhi},
volume = {64},
number = {12},
pages = {1155-1168},
doi = {10.3760/cma.j.cn112138-20250808-00468},
pmid = {41338553},
issn = {0578-1426},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis/therapy/drug therapy ; *Hematologic Diseases/complications ; Antifungal Agents/therapeutic use ; *Neoplasms/complications ; Hematologic Neoplasms/complications ; *Mycoses/diagnosis/therapy ; China ; },
abstract = {In 2005, the Chinese Invasive Fungal Infection Working Group published the first guidelines for the diagnosis and treatment of invasive fungal disease (IFD) in patients with hematological disorders and cancers, with the sixth revision released in 2020. Numerous advances in the fields of hematological oncology treatment and the diagnosis and management of IFD have significantly influenced the corresponding strategies. Therefore, the Chinese Invasive Fungal Infection Working Group has reviewed key research advances from 2020 to 2024 and released the seventh revision of the Chinese guidelines. Major revisions include: changes in the epidemiology of IFD; evaluation of novel diagnostic methods (especially PCR and metagenomic next-generation sequencing); updated recommendations on therapeutic drug monitoring and in vitro drug sensitivity test; management of breakthrough IFD; targeted therapy of Pneumocystis jiroveci pneumonia and cryptococcosis; and updated recommendation on the duration of antifungal therapy.},
}

Humans
*Invasive Fungal Infections/diagnosis/therapy/drug therapy
*Hematologic Diseases/complications
Antifungal Agents/therapeutic use
*Neoplasms/complications
Hematologic Neoplasms/complications
*Mycoses/diagnosis/therapy
China

@article {pmid41338123,
year = {2025},
author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y},
title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.},
journal = {Journal of psychiatric research},
volume = {193},
number = {},
pages = {223-235},
doi = {10.1016/j.jpsychires.2025.11.029},
pmid = {41338123},
issn = {1879-1379},
abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.},
}

@article {pmid41339745,
year = {2025},
author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G},
title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41339745},
issn = {2058-5276},
support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.},
}

@article {pmid41339710,
year = {2025},
author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL},
title = {Microbial model communities exhibit widespread metabolic interdependencies.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09306-y},
pmid = {41339710},
issn = {2399-3642},
support = {grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; },
abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.},
}

@article {pmid41338426,
year = {2025},
author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y},
title = {Decoding Microbial-Mediated Sulfur Transformation Pathways in Mangrove Wetland: Metagenomic and Hydrogeochemical Insights.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123472},
doi = {10.1016/j.envres.2025.123472},
pmid = {41338426},
issn = {1096-0953},
abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07%) and Salmonella prevailing in mudflat sediments (23.87-60.98%). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.},
}

@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}

@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation & purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}

Humans
*Metagenomics/methods
*Allergens/immunology
*Skin/microbiology/virology
Finland
Adolescent
*Microbiota/genetics
Male
Russia
Female
*Hypersensitivity/microbiology/immunology
Malassezia/genetics/isolation & purification
Immunoglobulin E/immunology
Bacteria/genetics/classification
Child

@article {pmid41335476,
year = {2025},
author = {Docter, J and Mansfeldt, C},
title = {Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00618},
pmid = {41335476},
issn = {2161-5063},
abstract = {Engineered microorganisms in biotechnology present biosafety and environmental management challenges. As the synthetic biology market develops and deploys new technologies, these engineered organisms may escape into unintended environments. Improved predictive computational tools are necessary to assess the potential establishment risk and environmental location of these escaped engineered microorganisms, assisting their design and management. Here, we present EnCen, a risk assessment Python software package that predicts the environmental range of engineered microorganisms through annotated functional one-hot-encoded similarity between the engineered microorganism and resident microorganisms of a given environment. EnCen utilizes publicly available composite metagenomes as representatives of microbial environments that occur along an agriculture-water cycle and can be customized for any additional target environment. This tool was deployed against case studies reported in the literature and to reassess commercially available bacterial biopesticides, highlighting both the successful recapture of previously reported dynamics and the identification of select commercial products that pose a wider establishment risk in multiple environments. When further utilizing EnCen to investigate the receiving environments comprising the central database, key enzyme classes are mapped as characteristics to select environments, prioritizing certain modifications likely leading to a greater risk (or effectiveness) of establishment. The results demonstrate that EnCen meaningfully summarizes publicly available metagenomic data, prioritizes environments to monitor for adverse effects, and analyzes potential impacts on microbial community composition and functioning. Overall, this study demonstrates a computational approach to managing engineered microorganisms, aiding in the safe deployment and benefit of industrial synthetic biology.},
}

@article {pmid41335362,
year = {2025},
author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Wang, H and Huang, Y and Liu, Y and Chen, P and Peng, J},
title = {Astragalin attenuates caerulein-induced acute pancreatitis by targeting the NLRP3 signaling pathway and gut microbiota.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {139},
pmid = {41335362},
issn = {2197-4365},
support = {82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 2025JJ60669//Hunan Provincial Natural Science Foundation of China/ ; 2024M763719//China Postdoctoral Science Foundation/ ; GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) has caused great concern worldwide due to its serious threat to human health. Astragalin is a bioactive natural flavonoid compound with several pharmacological activities, but it remains unclear about its effect on AP. The objective of this experiment was to explore the mitigating efficacy of astragalin on caerulein-induced AP model and examine the underlying mechanisms.

METHODS: Following the assessment of astragalin's direct effects on pancreatic acinar cells using an in vitro AP model, an in vivo mouse model was established to further validate its efficacy and elucidate the underlying mechanisms. Pancreatic histopathology, amylase, and lipase levels of mice were observed to determine the optimal therapeutic dose of astragalin. The network pharmacology and RNA sequencing technology were used to reveal the possible targets and pathways. Subsequent molecular docking and western blot were conducted to validate the association between astragalin and key target molecules, as well as the NLRP3 signaling pathway. Combined with metagenomics and metabolomics analysis, the astragalin effective gut microbiota-metabolite-gene network was constructed. Moreover, fecal microbiota transplantation experiments were performed to clarify the importance of gut microbiota in astragalin-mediated alleviation of AP.

RESULTS: The results showed that astragalin attenuated caerulein-induced injury in AR42J cells in vitro. Consistent with these findings, in vivo experiments revealed that astragalin treatment significantly improved pancreatic pathological injury, cell apoptosis, and systemic inflammatory response in AP mice, particularly at high doses. The integrated analysis of network pharmacology and transcriptomics revealed that the NLRP3 signaling pathway was a key molecular pathway, which was further validated using western blot. Docking analysis showed that 12 target genes had good docking activity with astragalin. More intriguingly, it was found that astragalin could reverse gut microbiota dysbiosis by restoring microbial diversity, altering bacterial community composition, and modulating key metabolic pathways. Specifically, astragalin-effective correlation networks were constructed with Lachnoclostridium sp. YL32, Roseburia intestinalis, Ruminococcus gnavus, Lachnospiraceae bacterium Choco86, Anaerobutyricum hallii, etc. as the core strains, 22 metabolites, including 5-Methoxytryptophan, D-Serine, L-Tryptophan, L-Methionine, etc. as core metabolites, and NLRP3 pathway-related genes as the main regulatory targets. Furthermore, fecal microbiota transplantation experiments confirmed the involvement of gut microbiota in AP remission.

CONCLUSION: Collectively, these findings identify astragalin as a promising therapeutic agent for AP, targeting both the NLRP3 signaling cascade and gut microbial homeostasis.},
}

@article {pmid41334926,
year = {2025},
author = {Shulman, HB and Pyle, JAM and Classen, AT and Inouye, DW and Simberloff, R and Sorensen, PO and Thomas, W and Rudgers, JA and Kivlin, SN},
title = {Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0052325},
doi = {10.1128/msystems.00523-25},
pmid = {41334926},
issn = {2379-5077},
abstract = {In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO4[3-]). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO4[3-] from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO4[3-] and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO4[3][-]. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.},
}

@article {pmid41334911,
year = {2025},
author = {Kandathil, AJ and Clipman, SJ and Anantharam, R and Duchen, D and Cox, AL and Larman, HB and Thomas, DL},
title = {Antibody-mediated control of anellovirus infection: evidence from people who inject drugs.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0161225},
doi = {10.1128/jvi.01612-25},
pmid = {41334911},
issn = {1098-5514},
abstract = {Infections with viruses belonging to the family Anelloviridae are widespread among humans. Although generally considered a commensal, there is evidence to suggest that these infections may be controlled by host immune responses. However, the mechanism of immune control remains unclear. Previous research has also suggested a possible role of anellovirus capsid spikes in immune evasion. To investigate the role of antibodies in controlling infection, we used AnelloScan to profile plasma collected every 6 months over 2 years from 10 persons who inject drugs (PWID). Participants were selected based on viremia patterns: persistent (n = 6) versus intermittent (n = 4). Long-read metagenomic sequencing revealed a higher median number of alphatorquevirus (TTV) species in participants with persistent viremia compared to those with intermittent viremia (P < 0.0001). AnelloScan detected TTV-specific antibodies among all study participants. No significant differences were observed between the two groups when all antibody-reactive peptides located in the capsid were included. However, among participants with intermittent viremia, antibodies were more frequently reactive to peptides located in the amino acid variable region of the capsid spike domain (P = 0.0429). These findings suggest that among PWID, antibodies targeting the sequence variable region of the spike domain appear to be associated with control of anellovirus infection. Additionally, anelloviruses might be susceptible to pre-existing immunity, and the amino acid variable region of the spike protein may play a role in viral infectivity.IMPORTANCEAnelloviruses are highly diverse and are recognized as the major component of the blood virome in healthy humans. Despite this, little is known about their interactions with their hosts. In this study, we found that anelloviruses can elicit antibody responses. Notably, antibodies that targeted a sequence variable region on spikes present on viral capsids were associated with truncation of plasma viremia. These data suggest a possible mechanism of immune control of anellovirus infections while also indicating a role of the capsid spikes in viral infectivity.},
}

@article {pmid41334589,
year = {2025},
author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H},
title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593119},
doi = {10.1080/19490976.2025.2593119},
pmid = {41334589},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; },
abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.},
}

Animals
Humans
*Dipeptidyl Peptidase 4/metabolism/genetics
*Crohn Disease/pathology/drug therapy/microbiology/metabolism
Mice
Fibrosis
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Male
Myofibroblasts/metabolism
Dipeptidyl-Peptidase IV Inhibitors/pharmacology
*Intestines/pathology
Sitagliptin Phosphate/pharmacology
Mice, Inbred C57BL
Female
Dextran Sulfate

@article {pmid41334206,
year = {2025},
author = {Yang, L and Liu, Y and Guo, S and Li, T and Nie, Q and Zhang, Y and Zeng, S and Wang, F and Liu, L},
title = {Mechanism of tobacco-sweet potato intercropping in suppressing Ralstonia solanacearum in flue-cured tobacco.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1688379},
pmid = {41334206},
issn = {1664-462X},
abstract = {Tobacco bacterial wilt (Ralstonia solanacearum) is a fatal pathogen of tobacco, causing severe losses annually. Intercropping has been proposed as a sustainable strategy to mitigate soil-borne pathogens through rhizosphere interactions. However, the mechanisms by which tobacco-sweet potato intercropping specifically affects the microecological environment and suppresses R. solanacearum remain poorly understood. To investigate the effect of the TSP model on the soil-borne pathogen of bacterial wilt (Ralstonia solanacearum) in tobacco-growing soil, this study compared and analyzed the characteristics and differences in bacterial wilt incidence, Ralstonia solanacearum content, phenolic acid components, metabolome, and metagenome between (T) and (TSP) systems. The results showed that compared to the T treatment, the TSP treatment reduced the incidence of bacterial wilt in flue-cured tobacco and significantly decreased the abundance of R. solanacearum in the soil by 21.4%, while increasing the total phenolic acid content by 21.9%. The total phenolic content in the TSP soil was increased by 21.9% compared to T. Differentially abundant metabolites between TSP and T were primarily enriched in carbohydrate metabolic pathways, such as nucleotide sugar biosynthesis, fructose, and mannose metabolism. The content of substances such as rhamnose, D-allose, and mannitol in T-treated soil was 2.14-6.62 times higher than that in TSP-treated soil, with new tobacco alkaloids being up to 91.09 times higher. Compared to the T treatment, the TSP treatment significantly increased the relative abundances of Acidobacteriota, Chloroflexota, Bradyrhizobium, Pseudolabrys, and Sphingomonas by 64.08%, 18.86%, 23.55%, 21.80%, and 12.98%, respectively. The content of Ralstonia solanacearum in the soil was positively correlated with differential metabolites such as mannitol, rhamnose, and D-allose (r = 0.8), while negatively correlated with phenolic acids such as syringic acid, ferulic acid, caffeic acid, and gallic acid, as well as microorganisms such as Chloroflexota, Gemmatimonadota, Acidobacteriota, and Sphingomonas. In summary, TSP can regulate soil metabolites, phenolic acids, and beneficial microorganisms, forming a synergistic network to suppress the content of Ralstonia solanacearum and reduce the risk of tobacco bacterial wilt. This provides a theoretical basis for regulating soil microecology and enhancing crop disease resistance in intercropping systems.},
}

@article {pmid41333806,
year = {2025},
author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M},
title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634631},
pmid = {41333806},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.

RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.

CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Male
Female
Middle Aged
*Adenocarcinoma/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
DNA, Bacterial/genetics/chemistry
Middle East
Feces/microbiology
Phylogeny
DNA, Ribosomal/genetics/chemistry

@article {pmid41333777,
year = {2025},
author = {Zhang, Q and Gong, Q and Sun, X and Zhu, H},
title = {Massive hemoptysis as the sentinel symptom: a case report of pulmonary nocardiosis in an immunocompetent patient.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1677156},
pmid = {41333777},
issn = {2296-858X},
abstract = {Pulmonary nocardiosis is frequently missed or misdiagnosed due to its atypical clinical symptoms and non-specific imaging findings. Moreover, delayed diagnosis and treatment can lead to high mortality rates, underscoring the need to enhance etiological diagnosis. Here, we report a 55-year-old immunocompetent woman who developed pulmonary Nocardia cyriacigeorgica infection with massive hemoptysis as the initial symptom. The patient had no history of chronic respiratory diseases. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid collected via bronchoscopy was performed, which confirmed the diagnosis. After targeted therapy with oral sulfamethoxazole-trimethoprim and linezolid, the patient achieved significant symptomatic and radiological improvement, accompanied by normalization of white blood cell count and neutrophil count. No recurrence was observed during follow-up.},
}

@article {pmid41333773,
year = {2025},
author = {Li, Q and Sun, X and Lei, W and Zhu, Y and Du, W and Jiang, X and Su, N},
title = {Psittacosis chlamydia pneumonia complicated with organizing pneumonia: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1670456},
pmid = {41333773},
issn = {2296-858X},
abstract = {BACKGROUND: Secondary organizing pneumonia (SOP) may develop following infections. Psittacosis, caused by Chlamydia psittaci (C. psittaci), is a zoonotic disease transmitted from birds to humans. It can present with a wide spectrum of symptoms, ranging from mild flu-like illness to life-threatening severe pneumonia. Cases of C. psittaci infection complicated by organizing pneumonia (OP) are rarely reported, and delayed treatment may pose a life-threatening risk.

METHODS: We report a case of C. psittaci pneumonia complicated by OP. To identify additional cases and clarify the clinical features of this condition, a literature search was conducted using the PubMed and Embase databases for the period from January 1995 to May 2025. The search included the following keywords: "psittacosis," "Chlamydia psittaci," "chlamydia," "organizing pneumonia," and "bronchiolitis obliterans with organizing pneumonia."

RESULTS: A 66-year-old male with a history of poultry farming presented with fever, cough, sputum production, and hemoptysis. Empirical antimicrobial therapy with ceftizoxime was ineffective. To identify the etiology of the pulmonary lesions, bronchoscopy was performed, and C. psittaci infection was confirmed by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Although the lesions partially resolved after moxifloxacin therapy, the patient experienced recurrent episodes. Chest CT revealed migratory lesions, which are uncommon in C. psittaci pneumonia. Further pathological examination of the specimen confirmed the diagnosis of OP. The patient's condition improved following corticosteroid therapy. A review of the literature indicated that none of the three previously reported cases were definitively diagnosed at initial admission; all presented primarily with fever and cough. One case progressed to severe pneumonia and resulted in death.

CONCLUSION: OP caused by C. psittaci pneumonia presents with non-specific symptoms and signs, making early diagnosis challenging. During treatment of C. psittaci pneumonia, if empirical anti-infective therapy shows no response after three days, or if imaging reveals features such as consolidation, migratory lesions, or a reverse halo sign, the possibility of concurrent OP should be considered. Pathological examination is recommended in such cases to avoid missed diagnosis and to ensure timely intervention.},
}

@article {pmid41333054,
year = {2025},
author = {Kravchuk, OI and Finoshin, AD and Nikishina, YO and Melnikova, VI and Kublanov, IV and Sutormin, DA and Rusanova, AN and Ri, MT and Isaev, AB and Mikhailov, KV and Ziganshin, RH and Adameyko, KI and Anashkina, AA and Ignatyuk, VM and Gornostaev, NG and Voronezhskaya, EE and Sokolova, AM and Mikhailov, VS and Lyupina, YV},
title = {Evolutionary conservation of dopamine-mediated cellular plasticity in Arctic sponges (Porifera).},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1671771},
pmid = {41333054},
issn = {2296-889X},
abstract = {Dopamine is an evolutionarily ancient signaling molecule implicated in stress responses across the tree of life. The role of dopamine is well-documented in the nervous system of animals, yet in the early-branching animal lineage of sponges its utility is poorly understood. Arctic marine sponges inhabiting the tidal zone of the White Sea, with fluctuating seasonal ice cover and solute concentrations, exhibit remarkable physiological plasticity, making them ideal models for studying conserved stress-response mechanisms. We investigated the dopamine signaling in two sponge species, Sycon ciliatum (class Calcarea) and Halisarca dujardini (class Demospongiae), using metagenomics, transcriptomics, high performance liquid chromatography, mass spectrometry, molecular docking, and immunofluorescence. S. ciliatum expresses an aromatic amino acid decarboxylase-like enzyme and efficiently converts L-DOPA to dopamine, whereas H. dujardini lacks this canonical biosynthetic enzyme, but accumulates dopamine, likely via its symbionts. During morphogenetic transitions in H. dujardini, genes involved in dopamine turnover, including tyrosinase, dopamine β-hydroxylase, and G protein-coupled receptors (GPCRs), showed dynamic expression. Molecular docking revealed that GPCR affinity for dopamine is modulated by cellular redox status. Notably, we report the first evidence of post-translational dopaminylation of cytoskeleton proteins in a non-bilaterian animal. Fluctuations in cellular dopamine levels and actin dopaminylation correlated with structural remodeling of the aquiferous system throughout the sponge life cycle. These findings demonstrate that dopamine regulates cellular plasticity through both transcriptional and post-translational mechanisms. The discovery of dopaminylation in sponges expands the evolutionary scope of catecholamine signaling and underscores the ancient role of dopamine in the regulatory interactions of animal cells.},
}

@article {pmid41332906,
year = {2025},
author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X},
title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.},
journal = {Biochemistry and biophysics reports},
volume = {44},
number = {},
pages = {102361},
pmid = {41332906},
issn = {2405-5808},
abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.

OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.

METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.

RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375 ± 1.302 and 46 ± 9.75 respectively) vs healthy controls (3.425 ± 1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p < 0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P < 0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P < 0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P < 0.05).

CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.},
}

@article {pmid41332561,
year = {2025},
author = {Ahmed, MA and John, J and Campbell, BJ},
title = {Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689735},
pmid = {41332561},
issn = {2692-8205},
abstract = {Actinobacteriota, a bacterial phylum renowned for members that produce bioactive compounds (e.g., antibiotics), has key roles in terrestrial and aquatic ecosystems. Although soil and marine/freshwater Actinobacteriota are well studied, functions and activities of their estuarine counterparts are poorly understood. We characterized 67 metagenome-assembled genomes (MAGs) belonging to 12 Actinobacteriota families from Chesapeake and Delaware Bay water samples across different seasons, salinities, and size fractions. MAGs from four dominant families, Ilumatobacteraceae, Nanopelagicaceae, Microbacteriaceae, and S36-B12, were examined in depth for their abundance, functional potential, estimated growth rates, and gene expression among samples. Actinobacteriota were most abundant in low- to medium-salinity samples during spring and summer. Their abundance patterns were strongly influenced by combinations of salinity, temperature, and phosphate, nitrate and silicate concentrations. Notably, many exhibited high estimated growth rates under low and medium salinities in summer. Members of the four major families showed a range of metabolic capacities from generalist to specialist, and all encoded biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones, that were differentially expressed across conditions. Bay, salinity and size fraction were the primary drivers of gene expression differences. Distinct secondary metabolite genes were expressed between bays, with higher expression generally observed in medium compared to low salinities. These findings underscore the metabolic versatility and environmental responsiveness of Actinobacteriota, highlighting their active role in estuarine microbial communities and their contributions to biogeochemical cycling in dynamic coastal ecosystems.},
}

@article {pmid41332430,
year = {2025},
author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML},
title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593076},
doi = {10.1080/19490976.2025.2593076},
pmid = {41332430},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; },
abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Fatty Acids/metabolism
Carnitine/biosynthesis/metabolism
Oxidation-Reduction
*Mitochondria/metabolism
Zebrafish
Lipid Metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Fecal Microbiota Transplantation
RNA, Ribosomal, 16S/genetics
Male
Humans
Feces/microbiology

@article {pmid41331875,
year = {2025},
author = {Kong, L and Mao, Y and Zheng, R and Feng, Y and Chen, B and Wu, X and Zhu, Q and Feng, J and Liu, S},
title = {Overlooked siderophore producers favor ammonium oxidation in global wastewater treatment plants.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02290-9},
pmid = {41331875},
issn = {2049-2618},
support = {523B2095//National Natural Science Foundation of China/ ; Nos. 52270016//National Natural Science Foundation of China/ ; 2022YFC3203003//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Iron is essential for biological nitrogen removal in wastewater treatment plants (WWTPs), as a significant portion of microbial nitrogen-transforming enzymes require iron. However, iron bioavailability is a global challenge for nitrogen removal microbes in WWTPs, where it often exists in insoluble forms due to its complexation with various wastewater constituents.

RESULTS: Combined laboratory experiment and metagenomic analysis of 52 global WWTPs, we found that siderophore-producing bacteria (SPB) were previously uncharacterized dominant members in activated sludge. SPB enhance the iron uptake of activated sludge microbial communities by facilitating the transport of iron ions from insoluble sources into the cells. Of the 1328 total recovered metagenome-assembled genomes (MAGs) from global WWTPs, 6.2% were identified as SPB, while 79.3% of MAGs could utilize siderophores, indicating widespread sharing of siderophores in WWTPs. Interestingly, nearly all ammonium-oxidizing bacteria (AOB) from WWTPs lacked siderophore-producing capacity, and exogenous siderophore (20 µM pyochelin) addition boosted ammonium oxidation rates by 28.2%. Moreover, strong indications were found for an association between AOB and the SPB in global WWTPs, suggesting their symbiotic interaction is a common and critical process to maintain ammonium oxidation performance. SPB in WWTPs were predominantly aerobic or facultative anaerobic heterotrophic bacteria, exhibiting low taxonomic diversity but high abundance.

CONCLUSIONS: This study reveals SPB as previously overlooked but crucial contributors to biological nitrogen removal in global WWTPs, providing foundational insights into iron-based microbial cooperation within engineered systems. Modulating SPB activity based on their metabolic characteristics is a promising strategy to cope with low iron bioavailability issue for biological processes in WWTPs. Video Abstract.},
}

@article {pmid41331807,
year = {2025},
author = {Rouzban, T and Goudarzi, R and Motamedi, E and Ghollasi, M and Zeinalabedini, M and Ariaeenejad, S},
title = {Metagenomic laccase-catalyzed crosslinking of wheat proteins for enhanced soybean meal nutritional value: applications in poultry feed and food industry.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-025-01081-2},
pmid = {41331807},
issn = {1472-6750},
support = {0//Agricultural Biotechnology Research Institute of Iran (ABRII)/ ; },
}

@article {pmid41331687,
year = {2025},
author = {Abedi, Z and Sheikh Beig Goharrizi, MA and Abbasi, A and Sadat Soleimani Zakeri, N and Jangi, H},
title = {Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis.},
journal = {Genomics & informatics},
volume = {23},
number = {1},
pages = {25},
pmid = {41331687},
issn = {1598-866X},
abstract = {BACKGROUND: Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.

RESULT: We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.

CONCLUSION: We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.},
}

@article {pmid41331561,
year = {2025},
author = {Tian, J and Wang, X and Zhu, Y and Kong, F and Sun, J},
title = {Diagnosis of esophageal pleural fistula via metagenomic next-generation sequencing of pleural effusion: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1689},
pmid = {41331561},
issn = {1471-2334},
}

@article {pmid41331462,
year = {2025},
author = {Xu, W and Wang, W and Liu, Q},
title = {Identification of a novel pegivirus in reindeer (Rangifer tarandus valentinae) in Northeastern China.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05167-z},
pmid = {41331462},
issn = {1746-6148},
support = {2024YFD1800103//This study was financially supported by the National Key Research and Development Program of China ./ ; },
abstract = {BACKGROUND: Pegiviruses (family Flaviviridae), associated with persistent infections in diverse mammalian and avian hosts, are increasingly recognized for their evolutionary significance. Reindeer (Rangifer tarandus valentinae), semi-domesticated in northeastern China's Greater Khingan Mountains, are critical reservoirs for zoonotic pathogens and face growing human contact due to tourism. This study aims to investigate the viral diversity in reindeer, identify potential viruses of public health or veterinary significance, and highlight the need for viral surveillance at the human-animal interface.

RESULTS: The metagenomic sequencing analysis identified a novel pegivirus, Rangifer tarandus pegivirus (RPgV), in reindeer serum from Inner Mongolia. The near-complete genome (10,367 nucleotides; GenBank OQ164633) encodes a polyprotein (3,249 amino acids) processed into four structural (Y, E1, E2, X) and six non-structural (NS2-NS5B) proteins. RPgV shares 57.3% nucleotide and 60.6% amino acid identity with its closest relative, equine pegivirus (EPgV), but exceeds species demarcation thresholds for NS3 (p-distance: 0.340) and NS5B (p-distance: 0.408). Phylogenetic analyses placed RPgV within the equine pegivirus clade, while cophylogenetic models revealed strong host specificity and co-divergence over evolutionary timescales. With a 9.5% prevalence (2/21) in sampled reindeer, RPgV represents the first pegivirus detected in Cervidae, underscoring its potential role in wildlife virome dynamics.

CONCLUSION: This study identified a novel pegivirus, which expands its host range, geographic distribution, and genetic diversity. This discovery highlights the need for enhanced surveillance of understudied viral families in regions where human-wildlife interfaces amplify zoonotic risks.},
}

@article {pmid41331251,
year = {2025},
author = {Zhao, Y and Chen, H and Huang, J and Chistoserdova, L and Yu, Z},
title = {The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66596-w},
pmid = {41331251},
issn = {2041-1723},
support = {32300051//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of methane-consuming bacteria (methanotrophs) within the human gut ecosystem remains a critical, under-explored area. The potential for these bacteria to act as a built-in sink for intestinal methane and thereby mitigate its negative physiological effects is unknown. Here, we isolate an unreported methanotroph from human fecal samples, classified as Methylocystis intestini. Using a mouse model, we observe that methane challenge is associated with gastrointestinal motility and fat metabolism. We then demonstrate that the administration of Methylocystis intestini effectively reverses these dysfunctional processes, restoring motility and metabolic parameters. Additional analysis of methane-oxidation genes abundance in 1207 public metagenomic sequences from individuals with varying health statuses, including obesity and constipation, provides consistent correlative support for our experimental conclusions. Expanding this view to a global scale, we conducted a metagenomic survey of 550 human fecal samples from populations across five continents. This broader analysis reveals that methane-oxidizing genes are not a rarity but a common feature of the human gut microbiome, being detectable in over 91% of samples. This ubiquity underscores their fundamental role in human biology. Collectively, our findings establish gut methanotrophs as key mediators of intestinal methane level. Their presence is widespread across global populations, and their functional capacity can balance the effects of methane on host physiology. This work elucidates a crucial component of gut homeostasis and opens a promising avenue for developing microbiome-based therapeutic strategies aimed at managing methane-related gastrointestinal disorders by harnessing the power of these native methane-consuming bacteria.},
}

@article {pmid41333904,
year = {2024},
author = {Choi, CH and Lee, M and Lee, SE and Shin, H and Choi, MM and Kim, JW and Yi, H and Chung, YS},
title = {[Monkeypox Virus Genomic Analysis in the Republic of Korea: A Comparison of Metagenomic- and Probe Hybridization Capture Sequencing Methods].},
journal = {Jugan geon-gang gwa jilbyeong},
volume = {17},
number = {20},
pages = {859-873},
pmid = {41333904},
issn = {2586-0860},
abstract = {Monkeypox virus (MPXV) whole-genome from specimens of individuals diagnosed with mpox in the Republic of Korea (ROK) between May 2022 and November 2023 was analyzed comprehensively. An infectious disease originating in Africa, mpox gained global significance after the first case was confirmed in the UK in May 2022, subsequently spreading worldwide. In the ROK, 155 infection cases were recorded, predominantly transmitted through close contact with symptomatic individuals. MPXV, consisting of approximately 197,000 base pairs of double-stranded DNA, encompasses approximately 191 genes consisting of inverted terminal repeats at both ends and a central conserved region. The virus is categorized as Clade I (Central African type) and Clade II (West African type), with Clade I and II reporting fatality rates of 1-10% and less than 1%, respectively. Two sequencing methods, metagenomic and hybridization capture sequencing, were used to perform a thorough whole-genome analysis. Compared to metagenomic sequencing, hybridization capture sequencing demonstrated superior efficiency in generating MPXV read sequences. The proportion of virus reads varied based on specimen type, informing the selection of targets for whole-genome analysis. Genomic phylogenetic analysis revealed that the MPXV in the ROK belonged to lineage C.1, indicating sustained domestic transmission and providing crucial insights for national and international responses to MPXV variants. This information will contribute to understanding infection pathways and improving strategies for disease response and prevention.},
}

@article {pmid41330454,
year = {2025},
author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, J and Su, KP and Wang, B},
title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106203},
doi = {10.1016/j.bbi.2025.106203},
pmid = {41330454},
issn = {1090-2139},
abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.},
}

@article {pmid41330298,
year = {2025},
author = {Huang, Y and Li, R and Dai, Y and Ren, Z and Wu, J},
title = {Migration characteristics of ARGs from pig manure in compost - soil - lettuce.},
journal = {Ecotoxicology and environmental safety},
volume = {308},
number = {},
pages = {119447},
doi = {10.1016/j.ecoenv.2025.119447},
pmid = {41330298},
issn = {1090-2414},
abstract = {This study aims to reveal the contamination patterns, persistence characteristics, and fate dynamics of ARGs during aerobic composting of swine manure with different carbon-nitrogen ratios (C/N = 15:1, 25:1, 35:1) and their subsequent dissemination in soil-plant systems following fertilization. The absolute abundances of 101 ARGs of six categories ranged from 10[5] to 10[14] copies/g during the composting process. The tetracyclines, macrolides and β-lactams ARGs were effectively reduced by the maturation phase. Among them, the β-lactam ARGs had the highest abatement efficiency (73-89 %). Quinolones, aminoglycosides and sulfonamides ARGs had relatively high residues during the maturation phase. Composting treatments with higher C/N (25:1 and 35:1) exhibited superior performance in ARGs reduction. Metagenomic analysis revealed the compost microbial community succession from Firmicutes to Proteobacteria and Actinobacteria. Luteimonas may be potential hosts for high-residual ARGs in compost, while Acinetobacter exhibited strong associations with β-lactam and macrolide ARGs that can be easily reduced. The ARGs in the fertilized soil increased significantly. ARGs such as floR, tetG-01, sul1 and sul2 have the highest abundance in the soil where lettuce is grown. The ARGs reduction is better in C/N 25:1 group, and the ARGs abundance of the soil is lower after fertilization with compost products. The sulfonamide sul1 and sul2 genes have always maintained a high abundance in compost, soil and lettuce. This study provides a theoretical basis for controlling the residue and spread of ARGs by regulating the C/N of compost to drive changes in microbial community.},
}

@article {pmid41330199,
year = {2025},
author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ},
title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128411},
doi = {10.1016/j.micres.2025.128411},
pmid = {41330199},
issn = {1618-0623},
abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.},
}

@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}

@article {pmid41329990,
year = {2025},
author = {Choi, HI and Cha, JM},
title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.},
journal = {Clinical endoscopy},
volume = {},
number = {},
pages = {},
doi = {10.5946/ce.2025.246},
pmid = {41329990},
issn = {2234-2400},
abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.},
}

@article {pmid41328758,
year = {2026},
author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA},
title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70086},
doi = {10.1111/1755-0998.70086},
pmid = {41328758},
issn = {1755-0998},
support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; },
abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.},
}

*CRISPR-Cas Systems
*Ecology/methods
*Gene Editing/methods

@article {pmid41328492,
year = {2025},
author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C},
title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592423},
doi = {10.1080/19490976.2025.2592423},
pmid = {41328492},
issn = {1949-0984},
mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation & purification/genetics/growth & development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; },
abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.

METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at < 33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.

RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).

CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.},
}

Humans
*Staphylococcal Infections/epidemiology/microbiology
Infant, Newborn
Feces/microbiology
*Staphylococcus aureus/isolation & purification/genetics/growth & development/classification
Female
Male
Infant, Premature
*Bacteremia/microbiology/epidemiology
Gastrointestinal Microbiome
Germany/epidemiology
Infant
Cohort Studies
Infant, Very Low Birth Weight
Metagenomics
Incidence
Gestational Age

@article {pmid41328416,
year = {2025},
author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR},
title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72546},
pmid = {41328416},
issn = {2045-7758},
abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.},
}

@article {pmid41328415,
year = {2025},
author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X},
title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72565},
pmid = {41328415},
issn = {2045-7758},
abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.},
}

@article {pmid41328248,
year = {2025},
author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN},
title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {3},
pages = {717-727},
pmid = {41328248},
issn = {2311-7710},
abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.

MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.

RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.

CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.},
}

@article {pmid41328030,
year = {2025},
author = {Hickman, B and Korpela, K},
title = {Impact of data compositionality on the detection of microbiota responses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2590841},
doi = {10.1080/19490976.2025.2590841},
pmid = {41328030},
issn = {1949-0984},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; },
abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.},
}

*High-Throughput Nucleotide Sequencing/methods
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Humans
Computer Simulation
*Gastrointestinal Microbiome
Computational Biology/methods
*Metagenomics/methods

@article {pmid41328016,
year = {2025},
author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O},
title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587968},
doi = {10.1080/19490976.2025.2587968},
pmid = {41328016},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; },
abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).},
}

Humans
*Gastrointestinal Microbiome
Internet
*Gastrointestinal Tract/microbiology/metabolism
Models, Biological
Software
Computer Simulation
Computational Biology/methods

@article {pmid41327872,
year = {2025},
author = {Zhang, Y and Zhang, Z and Chen, Z and Yang, B and Cai, S and Chen, J and Guo, J and Zhang, W},
title = {2-line Ferrihydrite Enhance Microbial Synthesis of Plant Biostimulants in Composted Biosolid by Regulating Phyla Pseudomonadota and Actinomycetota.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e06502},
doi = {10.1002/advs.202506502},
pmid = {41327872},
issn = {2198-3844},
support = {U24A20193,52270141//The National Natural Science Foundation of China/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; 122-G1323522145//Fundamental Research Funds for the central Universities, China University of Geosciences/ ; },
abstract = {The discovery of plant biostimulants (PBs) in sewage sludge offers a promising avenue for biosolids valorization. Here, the study investigates how two mineral additives, including 2-line ferrihydrite (a disordered iron oxide) and disordered birnessite (a manganese oxide), modulate microbial activity and molecular pathways to enhance PB production during aerobic sludge composting. Application of 2-line ferrihydrite significantly promotes the synthesis of growth-promoting PBs, including arginine, valine, decanoic acid, and indoleacetic acid (IAA), while disordered birnessite primarily enhances resistance-related PBs, such as decanoic acid, L-pyroglutamate, and trans-aconitic acid. In pot trials, composted biosolids amended with 2-line ferrihydrite significantly improve plant biomass and leaf area compared to mineral-free and birnessite treatments. Metagenomic profiling reveals that PB biosynthesis is dominated by members of the phyla Pseudomonadota and Actinomycetota, with temporal niche partitioning across the thermophilic and maturation stages. 2-line ferrihydrite enhances the abundance of critical biosynthetic genes (e.g., trpA/C/D/E/F), particularly within taxa such as Xanthomonadaceae, Sphingomonadaceae, and Streptosporangiaceae. Additionally, genes involved in IAA and indole biosysnthesis (ALDH, DDC, and tnaA) are enriched, supporting enhanced tryptophan-to-IAA conversion. This study provides a mechanistic link between iron oxide-mediated microbial modulation and PB production in composted biosolids, offering a sustainable approach for upgrading waste into high-value agricultural inputs.},
}

@article {pmid41327491,
year = {2025},
author = {Wu, H and Sun, Z and Chen, B and Hu, X and Li, Y},
title = {Enhanced nitrogen load improved soil phosphorus availability by regulating P-cycling microbial genes in a typical subtropical estuary (Min River), Southeast China.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {151},
pmid = {41327491},
issn = {2524-6372},
support = {No. 42371105//the National Natural Science Foundation of China/ ; No. 2023J02012//the Key Program of Natural Science Foundation of Fujian Province/ ; },
abstract = {BACKGROUND: Enhanced nitrogen (N) load was considered a critical factor influencing phosphorus (P) availability and P-cycling in marsh soils. However, information on the links between soil P availability and microbial genes involved in P-cycling processes under N enrichment conditions remains scarce.

METHODS: A field N load experiment with four treatments (N0, Nlow, Nmedium, and Nhigh) was conducted in Cyperus malaccensis marsh of the Min River estuary, and soil P availability, the relative abundances of P-cycling functional genes and their regulatory roles on P availability were investigated.

RESULTS: The total phosphorus (TP) contents in soils were significantly positively correlated with N load levels (p < 0.05). Compared with the N0 treatment, the TP in the Nlow, Nmedium and Nhigh treatments increased by 8.97%, 17.34% and 15.21%, respectively. With increasing N load levels, the proportions of easily- and moderately-available P in TP contents noticeably increased, suggesting that N additions enhanced soil P availability. Metagenomic sequence analyses showed that N enrichment markedly altered the relative abundances of P-cycling functional genes. Briefly, the abundances of inorganic P solubilization genes (particularly ppa and ppx) increased substantially with increasing N load levels. The total abundances of organic P mineralization genes in the Nlow and Nmedium treatments decreased markedly, while those in the Nhigh treatment increased greatly. The abundances of genes coding for phytase (phy and appA) markedly increased with increasing N load levels, implying that phytase was more sensitive to N enrichment. Furthermore, enhanced N load noticeably reduced the abundances of genes participated in P transportation (particularly ugpABEC) and those involved in P-assimilating process (e.g., phoR, phoB, pstABCS and pit). As affected by enhanced N load, the contents of easily-available P showed strong correlations with the abundances of genes involved in inorganic P solubilization while those of moderately-available P (particularly Sonic-Pi, Sonic-Po and NaOH-Pi) were positively correlated with the abundances of genes involved in P regulation and transportation, indicating strong linkages between P-cycling functional genes and soil P availability.

CONCLUSIONS: This paper found that, under N enrichment conditions, the increased inorganic P solubilization potential and the weakened microbial P immobilization capacity were beneficial to increasing soil P availability.},
}

@article {pmid41327449,
year = {2025},
author = {Zhao, Y and Duanmu, X and Hu, Z and Fan, Y and Mao, R and Zhang, Y and Zhang, X},
title = {Temperature seasonality constrains soil T4-like bacteriophage abundance at large spatial scale.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00824-0},
pmid = {41327449},
issn = {2524-6372},
support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; },
abstract = {BACKGROUND: Viruses play key roles in regulating soil microbial dynamics and biogeochemical cycles. T4-like bacteriophages, one of the best-studied viral groups, are abundant in soils, but their biogeographical patterns and ecological drivers remain poorly understood. In this study, we performed the first large-scale assessment of soil T4-like bacteriophages based on metagenomic data using viral hallmark genes, revealing broad spatial structure, identifying dominant environmental factors, and projecting shifts under future climate scenarios.

RESULTS: We analyzed two viral hallmark genes, gene 20 (g20) and gene 23 (g23), retrieved from global soil metagenomes, and National Center for Biotechnology Information (NCBI) reference sequences, yielding 2,385 and 2,928 full-length sequences clustered into 1,211 and 1,269 operational taxonomic units (OTUs), respectively. Phylogenetic analysis revealed that only a small fraction of soil-derived sequences could be assigned to established viral families, with most remaining unclassified below the class Caudoviricetes. The relative abundances of g20 and g23 were assessed at 116 sites spanning 14 biomes across six continents. Consistent biogeographic patterns were observed for both genes, with higher relative abundance in tropical climates and lower levels in polar and dry regions, indicating strong climatic influence. Temperature seasonality (BIO4) was identified as the primary environmental driver, showing a significant negative correlation with the relative abundance of both genes. Using an extreme gradient boosting (XGBoost) model, we predicted global distribution patterns based on extrapolation, revealing concordant global trends, with lower relative abundances in regions with greater seasonal temperature variation. Future projections of BIO4 and viral gene abundance further supported this significant negative correlation.

CONCLUSIONS: Our findings reveal that temperature seasonality constrains the abundance of soil T4-like bacteriophages, which serve as sensitive indicators of climate-driven environmental shifts and play important ecological roles within soil microbial communities.},
}

@article {pmid41327428,
year = {2025},
author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I},
title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02238-z},
pmid = {41327428},
issn = {2049-2618},
support = {ISF 1947/19//Israel Science Foundation/ ; ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; },
abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.

RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.

CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.},
}

@article {pmid41327409,
year = {2025},
author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L},
title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02287-4},
pmid = {41327409},
issn = {2049-2618},
support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; },
abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.

RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.

CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.},
}

@article {pmid41327304,
year = {2025},
author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S},
title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02275-8},
pmid = {41327304},
issn = {2049-2618},
support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.

RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.

CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.},
}

@article {pmid41327286,
year = {2025},
author = {Xu, W and Top, J and Viveen, MC and Slyzkyi, A and Hermans, N and van Erp, S and Eiloz, D and Anthony, R and Kremer, K and Schürch, AC},
title = {Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.},
journal = {BMC medical genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12920-025-02272-8},
pmid = {41327286},
issn = {1755-8794},
support = {LSHM22031//Health~Holland/ ; },
abstract = {BACKGROUND: Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial ~ 500 bp sequences, selectively increasing target data output. NAS promises up to 5-10 × enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS for profiling clinical sputum metagenomes.

METHODS: We sequenced DNA extracted from clinical sputa and spike-in controls of a mock community of bacterial respiratory pathogens, using the current R10.4.1 MinION flowcell chemistry.

RESULTS: We achieved at best 3.1 × enrichment of bacterial sequence output with NAS due to the shorter read lengths (~ 2.5 kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors.

CONCLUSIONS: We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.},
}

@article {pmid41327021,
year = {2025},
author = {Chen, B and Shu, W and Le, J and Jin, D},
title = {Application of metagenomic next-generation sequencing technology in hematologic malignancy patients with sepsis following antibiotic use.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1678},
pmid = {41327021},
issn = {1471-2334},
}

@article {pmid41327018,
year = {2025},
author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D},
title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07781-3},
pmid = {41327018},
issn = {1471-2229},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; },
}

@article {pmid41326768,
year = {2025},
author = {Polizel, GHG and Cánovas, Á and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, É and de Almeida Santana, MH},
title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {1},
pages = {8},
pmid = {41326768},
issn = {1573-3890},
support = {23/09113-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 17/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; },
abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.

OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.

METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).

RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.

CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.},
}

Animals
Cattle
Female
Pregnancy
*Biomarkers/metabolism/analysis
*Metabolomics/methods
Male
Liver/metabolism
Transcriptome
*Maternal Nutritional Physiological Phenomena
*Prenatal Nutritional Physiological Phenomena
Multiomics

@article {pmid41326588,
year = {2025},
author = {Yadav, MK and Ranjan, R and Verma, P and Sharma, R},
title = {Discovery and characterization of an enantioselective family VIII esterase from effluent treatment plant sludge metagenome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29625-8},
pmid = {41326588},
issn = {2045-2322},
support = {BSC0124//Council of Scientific and Industrial Research (CSIR), India/ ; },
}

@article {pmid41326129,
year = {2026},
author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S},
title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106807},
doi = {10.1016/j.pestbp.2025.106807},
pmid = {41326129},
issn = {1095-9939},
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; },
abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.},
}

Biodegradation, Environmental
*Microbial Consortia
Aniline Compounds/metabolism
Animals
Pseudomonas/metabolism/genetics
*Soil Pollutants/metabolism/toxicity
Zebrafish
*Fungicides, Industrial/metabolism/toxicity
Soil Microbiology

@article {pmid41325946,
year = {2025},
author = {Yin, Z and Ma, J and Bian, R and Wang, Y and Zhang, K and Ma, Y and Zhang, X and Ye, L},
title = {Xenobiotic degradation promotes enrichment but not dissemination of antibiotic resistance genes in activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133748},
doi = {10.1016/j.biortech.2025.133748},
pmid = {41325946},
issn = {1873-2976},
abstract = {Activated sludge in wastewater treatment bioreactors plays a pivotal role in xenobiotic degradation but is also regarded as a hotspot for the dissemination of antibiotic resistance genes (ARGs). Yet, it remains unclear whether pollutant degradation itself also creates conditions that facilitate ARG spread. To address this, we developed a xenobiotic degradation gene (XDG) database covering 22 degradation pathways. Using this database, we analyzed over 30,000 complete bacterial genomes and identified widespread co-occurrence of ARGs and XDGs, particularly within Pseudomonadota and Campylobacterota. Metagenomic profiling of 119 activated sludge samples further revealed strong positive correlations (Pearson's r > 0.8) between XDG and intrinsic ARGs, especially, modules involved in aromatic ring cleavage showed the highest correlations with ARGs. However, only 30.9 % of ARG-HGT events were found in MAGs carrying XDGs, and genome-level proximity analysis indicated that such microorganisms did not exhibit higher horizontal transfer potential. Cultivation-based experiments revealed that Pseudomonas strains with high degradation capacity carried intrinsic but not mobile ARGs. Together, these results demonstrate that xenobiotic degradation promotes ARG enrichment primarily through shifts in community composition rather than by enhancing gene mobility, highlighting that environmental AMR risk assessments based solely on ARG abundance may be misleading, and should avoid misestimation in future research.},
}

@article {pmid41324463,
year = {2025},
author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I},
title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf252},
pmid = {41324463},
issn = {1751-7370},
abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.},
}

@article {pmid41324436,
year = {2025},
author = {Gu, H and Liu, Z and Liu, S and Hu, X and Yu, Z and Li, Y and Li, L and Sui, Y and Jin, J and Liu, X and Jia, Z and Sun, L and Adams, JM and van der Heijden, MGA and Liu, J and Wang, G},
title = {Land conversion to cropland homogenizes variation in soil biota, gene assemblages and ecological strategies on local and regional scales.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf264},
pmid = {41324436},
issn = {1751-7370},
abstract = {It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.},
}

@article {pmid41324077,
year = {2025},
author = {Mah, JK and Hogan, JI and Kothadia, S and Keenan, JE and Berger, J and Carugati, M},
title = {Application of plasma cell-free metagenomic next-generation sequencing for the identification of Aspergillus fumigatus donor-derived infections among solid organ transplant recipients.},
journal = {Medical mycology case reports},
volume = {50},
number = {},
pages = {100751},
pmid = {41324077},
issn = {2211-7539},
abstract = {A cluster of Aspergillus fumigatus donor-derived infections (DDI) was rapidly diagnosed using plasma metagenomic next-generation sequencing (mNGS) among solid organ transplant recipients. The heart recipient, experiencing marginal hemodynamics, underwent an endomyocardial biopsy, which was concerning for a fungal infection on histopathology. Plasma mNGS was performed, identifying A. fumigatus two days prior to conventional diagnostics. This timely diagnosis enabled prompt nephrectomies in the kidney recipients, who survived. This report represents the first published use of mNGS in the diagnosis of Aspergillus fumigatus DDI, highlighting the utility of this novel, underutilized assay for early diagnosis of donor-derived infections.},
}

@article {pmid41323881,
year = {2025},
author = {Aini, N and Wahyuningsih, SPA and Achhlam, DH and Fatimah, and Amin, MHF and Do, HDK},
title = {Modulation of Gut Microbiota, Intestinal Physiology, and Digestive Enzyme Levels by Duo-Strain Probiotics in African Catfish (Clarias gariepinus) Challenged With Aeromonas hydrophila.},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {6624613},
pmid = {41323881},
issn = {1365-2095},
abstract = {This study aimed to determine the effect of dual-strains probiotic (DSP) consisting of Lactobacillus casei and Bacillus subtilis on bacterial metagenomic profile, gut physiology, and digestive enzyme levels of African catfish (Clarias gariepinus) infected by Aeromonas hydrophila. The ratio between L. casei and B. subtilis was 1:1 each with a density of 10[8] CFU/mL. Catfish (n = 8 fish per tank, three replicates per treatment) were fed diets supplemented with 0%, 5%, 10%, or 15% DSP for 42 days. On the 35th day, selected groups were intraperitoneally challenged with A. hydrophila at a dose of 0.1 mL × 10[8] CFU/mL. The observed parameters included bacterial counts and microbial profile in the gastrointestinal tract (analyzed using next-generation sequencing [NGS]), gut physiology, and digestive enzyme levels (amylase, lipase, and protease). The results showed that DSP supplementation increased both the abundance and diversity of gastrointestinal microbes, elevated digestive enzyme levels, and enhanced the number of goblet cells in the intestinal lining. The dominant microbial phyla observed in the control group were Fusobacteria and Pseudomonadota.},
}

@article {pmid41323829,
year = {2025},
author = {Luo, A and Liu, L and Shi, S and Liu, X and Hu, B},
title = {Analysis of Microbial Community Structure and Functional Genes for Volatile Flavor in Stinky Tofu.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71257},
pmid = {41323829},
issn = {2048-7177},
abstract = {The distinctive flavor of stinky tofu arises from intricate microbial metabolic networks during traditional fermentation, yet the genetic mechanisms linking microbial community structure to flavor formation remain incompletely resolved. This study employed metagenomic sequencing (Illumina NovaSeq 6000, Q30 > 92%) to generate 7.32 Gb of high-quality data, integrated with functional annotations from KEGG, eggNOG, and CAZy databases, to systematically dissect core microbial taxa and metabolic genes driving flavor biosynthesis. Dominant genera included Pseudomonas (relative abundance: 74.3%), Acinetobacter (14.4%), and Enterobacter (5%), with Pseudomonas putida (12.5%) and Pseudomonas fluorescens (3.2%) orchestrating carbohydrate metabolism (68.22% KEGG pathways) and amino acid degradation via glycoside hydrolases (GHs, 73% of CAZy-annotated enzymes) and dehydrogenases (e.g., 125 lactate dehydrogenase genes). Key flavor compounds, such as diacetyl (379 α-acetolactate synthase genes) and 3-methylbutanoic acid, were synthesized through synergistic pathways. Additionally, Lactococcus and Kluyvera contributed to ester and short-chain fatty acid production via α-keto acid dehydrogenase complexes (55 genes). A total of 410,231 non-redundant genes were identified, annotated to 4690 microbial species, establishing a multi-layered microbial-gene-metabolite regulatory network. This work elucidates the molecular basis of stinky tofu flavor formation and provides a framework for optimizing traditional fermentation processes through targeted microbial engineering.},
}

@article {pmid41323686,
year = {2025},
author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C},
title = {Multiomics analysis of microbial succession and flavor formation mechanism during the fermentation process of Maotai-flavour Baijiu.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103236},
pmid = {41323686},
issn = {2590-1575},
abstract = {This study employed metagenomics and metabolomics techniques to investigate the complex relationship between microbial succession and the formation of flavor compounds during the fermentation process of Maotai-flavour Baijiu. Results demonstrated that stacking fermentation, characterized by Weissella, Pichia, and Aspergillus, which secreted amylases and proteases to hydrolyze starch and proteins. Pitting fermentation facilitated the enrichment of anaerobic microbes such as Acetilactobacillus and Pichia, significantly promoting the synthesis of key flavor compounds, including esters, alcohols, and acids, through Glycosyltransferase and Esterification activities. Volatile compound analysis revealed distinct stage-specific profiles, with acids, alcohols, and esters accumulating predominantly in pitting fermentation. These findings elucidate the stage-specific microbial metabolic networks and synergistic mechanisms underlying flavor formation, providing a scientific basis for optimizing traditional Baijiu fermentation processes.},
}

@article {pmid41323679,
year = {2025},
author = {He, Y and Qiao, M and Zhang, H and Xiao, D and Guo, X},
title = {Microbial community, metabolic, and flavor differences among high-temperature Daqu with varying Douchi aroma intensities: a comprehensive metagenomic and metabolomic analysis.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103265},
pmid = {41323679},
issn = {2590-1575},
abstract = {The Douchi aroma is widely regarded as a key quality marker of high-quality high-temperature Daqu, but the compounds related to Douchi aroma formation and the key aroma-producing microorganisms remain unclear, which this study seeks to clarify. Therefore, metagenomic and metabolomic approaches were employed to decode the characteristic compounds and core microbial contributors in high-temperature Daqu samples no (NF), light (LF), and strong (SF) Douchi aroma. Esters were the most abundant volatiles across all groups, while acids increased with aroma intensity. Lentibacillus daqui, enriched in SF, showed strong positive correlations with isocetic, phenylacetic, and nonanoic acids. In contrast, Lichtheimia ramosa and Monascus purpureus were dominant in NF and LF, respectively. Furthermore, functional prediction and KEGG analysis further revealed potential biosynthetic pathways for phenylacetic and acetic acid. These findings clarify the molecular and microbial basis of Douchi aroma formation and provide a scientific reference for targeted quality regulation in Daqu production.},
}

@article {pmid41322275,
year = {2025},
author = {Dong, R and Liu, Y and Wang, N and Tan, KKY and Ji, M},
title = {The distribution of antibiotic resistance and virulence factor genes in the sediment of Inexpressible Island, East Antarctica.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {978-988},
pmid = {41322275},
issn = {2662-1746},
abstract = {UNLABELLED: Inexpressible Island is a small rocky island in Terra Nova Bay, Victoria Land, Antarctica, which is an area with limited human activities. Understanding the distribution of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) in this environment can provide key information on their potential risks to humans and their roles for microbial survival. In this study, we investigated the ARGs and VFGs in lake sediments from Inexpressible Island using metagenomic sequencing. We identified 11,502,071 open-reading frames (ORFs), with 1,749 classified as ARGs and 6,838 as VFGs. The dominant ARGs were associated with antibiotic target alteration and efflux pump mechanisms, while the VFGs were related to adherence and immune modulation functions. While associated within microbial genomes, these ARGs and VFGs were mobile genetic elements like viruses and insertion sequences, distinct from ecosystems with strong human influence. We identified 974 metagenome-assembled genomes (MAGs), with 465 being medium-to-high quality. Of these, 325 (69.9%) contained ARGs, primarily affiliated with Actinomycetota and Pseudomonadota. Additionally, 269 MAGs contained VFGs, with 174 MAGs carrying both ARGs and VFGs, highlighting significant microbial antibiotic resistance and pathogenic potential. Our findings highlight the need for ongoing monitoring of ARGs and VFGs in Antarctica, particularly in light of increasing human activity and climate change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00323-8.},
}

@article {pmid41322254,
year = {2025},
author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q},
title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {670-681},
pmid = {41322254},
issn = {2662-1746},
abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.},
}

@article {pmid41322233,
year = {2025},
author = {Chen, X and Yu, X and Deng, J and Yang, J and Chen, P},
title = {Case Report: Blood and cerebrospinal fluid mNGS-assisted diagnosis Toxoplasma gondii infection-associated with hemophagocytic syndrome and systemic lupus erythematosus.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1674391},
pmid = {41322233},
issn = {2296-858X},
abstract = {BACKGROUND: Reactivation of latent Toxoplasma gondii (T. gondii) infection is more prevalent than primary infection in patients with autoimmune diseases. We present a rare case of systemic lupus erythematosus (SLE) and hemophagocytic syndrome (HPS) associated with T. gondii infection.

CASE PRESENTATION: We describe the case of a young girl with SLE and HPS who presented with fever, dyspnea, and pancytopenia. The patient's T. gondii infection was diagnosed through the detection of double-positive IgM and IgG antibodies. Metagenomic next-generation sequencing (mNGS) analysis of both plasma and cerebrospinal fluid (CSF) samples revealed a high concentration of T. gondii DNA. The patient demonstrated a positive response to a combined treatment regimen consisting of anti-Toxoplasma medications and glucocorticoids.

CONCLUSIONS: Co-infection with uncommon pathogens is not uncommon in patients with autoimmune diseases. In individuals with immune disorders and positive T. gondii IgM antibodies, mNGS analysis of peripheral blood samples proves valuable in diagnosing disseminated T. gondii infection.},
}

@article {pmid41322208,
year = {2025},
author = {Duan, J and Li, X and Hu, Y and Pang, F and Cao, Y and You, Z},
title = {Case Report: Next-generation metagenomic sequencing in the diagnosis of Brucella-associated joint infections-a case series analysis and comprehensive literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1688037},
pmid = {41322208},
issn = {2296-858X},
abstract = {BACKGROUND: The application of next-generation metagenomic sequencing (mNGS) in the diagnosis of human brucellosis, particularly in cases of joint brucellosis infection, remains under-explored, with rarely no case reports available in the literature. We present the first case series focusing on the application of mNGS in the diagnosis of Brucella joint infections. The results indicate that mNGS plays a crucial role in diagnosing Brucella joint infections, serving as a valuable complement, particularly for culture-negative patients.

CASE PRESENTATION: This study presents a comprehensive analysis of four cases of human joint brucellosis diagnosed using mNGS on the BGI sequencing platform, involving three male and one female patients aged from 42 to 63 years, all of whom had documented epidemiological exposure histories. mNGS successfully identified Brucella sequences in all cases, with additional diagnostic findings including a positive Brucella agglutination test in Patient 1, positive joint fluid cultures in Patients 3 and 4, and no positive results in Patient 2. Following surgery and targeted antibiotic therapy, all patients exhibited clinical improvement and favorable follow-up outcomes.

CONCLUSION: These findings underscore the utility of mNGS as a critical diagnostic tool for joint brucellosis infections and highlight its potential as a complementary approach in cases of culture-negative joint infections. In cases where clinical suspicion of joint infection persists despite the absence of identifiable etiological evidence, the implementation of mNGS is strongly advised to facilitate timely and accurate clinical decision-making.},
}

@article {pmid41321514,
year = {2025},
author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z},
title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {396-414},
pmid = {41321514},
issn = {2405-6383},
abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.},
}

@article {pmid41321463,
year = {2025},
author = {Wang, W and Jiang, X and Wu, W and Zhang, L},
title = {Case Report: Primary segmental volvulus in an infant.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1707716},
pmid = {41321463},
issn = {2296-2360},
abstract = {Primary segmental volvulus (PSV) is a rare cause of acute abdomen in infants. It is characterized by a form of strangulated intestinal obstruction requiring prompt diagnosis and surgical intervention. This study aimed to report a case of PSV in an infant, which was managed successfully through early recognition, close clinical monitoring, and timely surgical treatment. Although both blood and ascitic fluid cultures were negative postoperatively, metagenomic next-generation sequencing (mNGS) identified the same pathogen in both specimens, enabling targeted antibiotic therapy. This case highlights the importance of including PSV in the differential diagnosis of infants presenting with unexplained abdominal distension and bilious vomiting, particularly when accompanied by anemia. Additionally, the elevated level of the coagulation system biomarker thrombin-antithrombin complex (TAT) may serve as a useful marker for monitoring coagulation status in the perioperative period. The integration of TAT assessment and mNGS-based pathogen identification provides a novel framework for individualized perioperative management in PSV.},
}

@article {pmid41321415,
year = {2025},
author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D},
title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf199},
pmid = {41321415},
issn = {2730-6151},
abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.},
}

@article {pmid41320762,
year = {2025},
author = {Peng, S and Liu, Z and Song, Z and Wang, C and Yu, Z and Zhao, N and Lu, W and Ning, Z and Lyu, A},
title = {Vinegar-processed frankincense extracts alleviate colorectal cancer by butyric acid mediating M1 tumor-associated macrophage pyroptosis.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {208},
pmid = {41320762},
issn = {1749-8546},
support = {CI2021A04201//the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 82003950//the National Natural Science Foundation Committee of China/ ; YZX-202334//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ14-YQ-035//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; },
abstract = {BACKGROUND: Olibanum (RF), a traditional Chinese medicinal resin, shows efficacy in colorectal cancer (CRC) treatment. Its vinegar-processed form (PF) is clinically recognized for enhanced therapeutic effects, with prior mechanistic studies focusing on lipophilic components like boswellic acids. Yet, the regulatory mechanisms of PF's aqueous extracts remain unclear.

METHODS: The aqueous extracts of RF and PF were characterized and compared through transmission electron microscopy (TEM), nanoparticle analysis, and protein profiling. The accumulation of these fractions in feces was confirmed using DiR dye labeling. A mouse CRC model was employed to evaluate and compare the therapeutic effects of RF and PF. The composition of butyric acid-producing microbiota was analyzed using 16S rRNA gene sequencing and metagenomics. Butyric acid levels were quantified using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-TQ-MS). Macrophage phenotypes were assessed via flow cytometry, while mRNA and protein expression levels were determined through RT-qPCR and western blot analysis.

RESULTS: PF aqueous extracts exhibited distinct morphology, particle size, and protein content and had a superior therapeutic effect in alleviating CRC compared to RF. Further analysis confirmed that both RF and PF accumulated in feces and modulated the butyric acid metabolism of gut microbiota. The increased levels of butyric acid contributed to CRC alleviation by promoting the polarization of M1 tumor-associated macrophages (TAMs) and suppressing the pyroptosis of M1 TAMs.

CONCLUSION: The study confirmed that vinegar-processed frankincense enhances its therapeutic effect on CRC by modulating M1 tumor-associated macrophages, which may provide efficient treatment of CRC from the perspective of host-gut metabolic interactions.},
}

@article {pmid41320324,
year = {2025},
author = {Liu, C and Gong, J and Luo, Z and Lai, P and Guo, S and Liang, D and Chen, G and Xing, M and Yu, J and Xie, Y and Liu, D and Zeng, W and He, Z and Lan, P},
title = {Gut microbe alleviates stress-related cancer metastasis by oleic acid degradation.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335627},
pmid = {41320324},
issn = {1468-3288},
abstract = {BACKGROUND: Chronic stress is a known risk factor for cancer metastasis. However, the underlying mechanisms, particularly those involving the gut microbiota and their metabolites, remain unclear.

OBJECTIVE: To investigate whether gut microbiota dysbiosis and metabolic alterations mediate the sustained pro-metastatic effects of chronic stress, even after normalisation of stress hormone levels.

DESIGN: Multiple metastatic models were performed after stress cessation. Shotgun metagenomics and metabolomics were performed to assess changes in microbiota and metabolites. The effects of Bifidobacterium animalis and oleic acid (OA) on metastasis were evaluated in vivo and in vitro. Moreover, we explored how B. animalis degraded OA. Mechanistically, we discovered the interaction between corticosteroids and gut bacteria through guanine metabolism assays. Human samples were collected from patients with colorectal cancer (CRC) with varying perceived stress scores and metastatic status for validation.

RESULTS: Mice that underwent chronic stress exhibited increased metastasis even after hormone levels recovered. The gut microenvironment was altered, with a significant reduction in B. animalis and an increase in OA. B. animalis administration reduced OA levels and suppressed metastasis, while OA supplementation had the opposite effect. B. animalis expresses oleate hydratase, an enzyme that degrades OA. Stress hormones inhibited B. animalis by altering guanine metabolism in the intestinal epithelium. In patients, high stress was associated with more OA, lower B. animalis levels and increased metastasis.

CONCLUSIONS: Chronic stress promotes metastasis by altering microbiota and increasing OA. Targeting B. animalis and OA may help prevent stress-related tumour progression.},
}

@article {pmid41319631,
year = {2025},
author = {Wang, J and Tian, Y and Zhang, G and Li, Y and Chen, L},
title = {Metagenomic insights into nitrogen and phosphorus metabolisms of bacteria in lakes with distinct nutrient conditions.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128121},
doi = {10.1016/j.jenvman.2025.128121},
pmid = {41319631},
issn = {1095-8630},
abstract = {Nitrogen (N) and phosphorus (P) cycling are crucial for preserving ecosystem functioning in lakes, yet our comprehension of the dynamics of N/P cycling genes and microorganisms under diverse nutrient levels is still limited. Herein, we conducted a comprehensive investigation into the profiles of N/P cycling genes and bacteria across three lakes with distinct nutrient levels. We found that N and P cycling genes were most abundant in the high-nutrient lake, particularly those involved in ammonification, assimilatory nitrate reduction, P regulation, and P transportation. Bacteria responsible for mediating most N/P cycling processes (excluding nitrogen fixation and P regulation) were predominant in the high-nutrient lake and mainly affiliated with Cyanobacteria, Proteobacteria, Actinobacteriota, and Bacteroidota. Furthermore, a potential biogeochemical hotspot for the co-metabolism of N and P was identified in the high-nutrient lake, consolidated by the most intricate co-occurrence pattern between N and P cycling genes. More importantly, these versatile bacteria capable of N/P metabolisms, primarily influenced by total nitrogen, total phosphorus, Secchi depth, and total dissolved solids, played important roles in maintaining the stability of bacterial communities in lakes. These findings offer significant insights into microbial-mediated N and P biogeochemical cycling in lakes with varying nutrient conditions, improving our understanding of utilizing N/P co-metabolism microbes to regulate ecosystem function and service amid the challenges of global lake eutrophication.},
}

@article {pmid41319542,
year = {2025},
author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W},
title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147314},
doi = {10.1016/j.foodchem.2025.147314},
pmid = {41319542},
issn = {1873-7072},
abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.},
}

@article {pmid41319383,
year = {2025},
author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L},
title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.},
journal = {Water research},
volume = {290},
number = {},
pages = {125031},
doi = {10.1016/j.watres.2025.125031},
pmid = {41319383},
issn = {1879-2448},
abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.},
}

@article {pmid41318814,
year = {2025},
author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C},
title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41318814},
issn = {1532-1827},
abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.

METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.

RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P < 0.001) and overall survival (OS) (3.9 vs. 9.5 months; P < 0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.

CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.

TRIAL REGISTRATION: NCT03874897.},
}

@article {pmid41318497,
year = {2025},
author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X},
title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07423-0},
pmid = {41318497},
issn = {1479-5876},
support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; },
}

@article {pmid41317994,
year = {2025},
author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM},
title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101129},
doi = {10.1016/j.ajcnut.2025.101129},
pmid = {41317994},
issn = {1938-3207},
abstract = {BACKGROUND: BMD explains fractures incompletely; studies relating lifestyle to bone quality are lacking.

OBJECTIVES: To examine associations of diet quality with bone measures (BMSi, TBS, BMD); evaluate moderation by inflammation; identify gut microbiome features linked to diet quality; and quantify diet-microbiome-bone relationships.

METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored FFQ, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score.. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with MaAsLin regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).

RESULTS: DASH score was not associated with BMSi (β = -0.10; 95% CI: -0.46, 0.27; P = 0.60), TBS (β = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (β = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (β = 0.002; 95% CI: -0.003, 0.006, P = 0.52 but was at total hip (β = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (β = -0.0001, P = 0.89). Lachnospira eligens was one of 4 taxa positively associated with DASH score, and BMD. No microbial pathways were associated with the DASH score.

CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes, and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.},
}

@article {pmid41317922,
year = {2025},
author = {Yang, G and Zhen, Z and Zhang, K and Yin, J and Zhong, X and Li, X and Li, Q and Nie, K and Miao, X and Lin, Z and Zhang, D},
title = {Biochar accelerated soil atrazine degradation by promoting dechlorination pathway: A novel mechanism revealed by DNA stable isotope probing (DNA-SIP).},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133722},
doi = {10.1016/j.biortech.2025.133722},
pmid = {41317922},
issn = {1873-2976},
abstract = {Biochar can accelerate atrazine degradation in soils, with surface modification being a widely accepted method to improve the performance. Nevertheless, the underlying mechanisms remain unclear. This study explored the efficiency of modified biochar in facilitating soil atrazine biodegradation with the aid of DNA stable isotope probing (DNA-SIP) and metabolite profiling. DNA-SIP results confirmed the involvement of ten bacterial genera and six atrazine degradation-related genes in atrazine metabolism in situ. Among them, Candidatus Nitrososphaera, Pedosphaera and Conexibacter were reported to be associated with atrazine degradation for the first time. FeCl3-modified biochar significantly accelerated atrazine degradation (85%) by improving soil physicochemical properties (pH, soil organic matter and humus) and enriching the active atrazine degraders. Notably, atrazine dechlorination pathway was preferentially promoted by modified biochar. The findings suggested that DNA-SIP enabled the discovery of the active atrazine degraders and degradation-related genes in biochar-amended soils, providing novel insights into the mechanisms of biochar-facilitated atrazine removal.},
}

@article {pmid41317625,
year = {2025},
author = {Kharaillah, A and Zhong, M and Soriano, JD and Gambardella, N and Sanz-Sáez, I and Yan, D and Bertilsson, S and Björn, E and Bravo, AG and Capo, E},
title = {Low-oxygen freshwaters as ecological niches for mercury methylators.},
journal = {Water research},
volume = {290},
number = {},
pages = {125014},
doi = {10.1016/j.watres.2025.125014},
pmid = {41317625},
issn = {1879-2448},
abstract = {Methylmercury (MeHg) is a hazardous neurotoxin, predominantly formed by microbial transformation of inorganic mercury in oxygen-depleted aquatic and terrestrial ecosystems. The ongoing deoxygenation of aquatic ecosystems due to global warming is likely to expand microbial niches for MeHg production. Although mercury methylators have also been reported to thrive in oxyge-deficients conditions in a few marine and freshwater ecosystems, there is a lack of comprehensive understanding of how they are distributed in freshwater systems. In this study, we retrieved hgcA genes, genomic marker for mercury methylation potential, from 586 metagenomes from the water column of 186 freshwater systems. Overall, hgcA genes were detected in the water column of 30 lakes, with the highest richness and abundance being detected in anoxic (0 mg O2l[-1]) and hypoxic (>0-2 mg O2l[-1]) compared to oxic conditions (>2 mg O2l[-1]). Although Desulfobacterota had the highest hgcA gene richness across most freshwater systems, certain systems were dominated by hgcA genes from Bacteroidales and Kiritimatiellales, implying metabolic and ecological versatility of mercury methylators as a group. Our findings suggest that projected expanding deoxygenation may lead to new niches for mercury methylators in inland waters.},
}

@article {pmid41317490,
year = {2025},
author = {Qin, Y and Xie, X and Li, D and Wu, Z and Liu, J and Li, W and Tang, D and Chen, S and Zhang, Y and Liu, N and Zhang, Q and Chen, Y},
title = {NADH-driven bioreductive degradation of azo dyes: Mechanisms of high NADH production, electron transfer, and microbial responses.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {140559},
doi = {10.1016/j.jhazmat.2025.140559},
pmid = {41317490},
issn = {1873-3336},
abstract = {Bioreductive co-metabolic degradation of azo dyes represents a promising green technology for addressing the environmental pollution caused by azo dyes. This study investigated the impact of co-metabolized substances on NADH production in microbial systems, focusing on the production of reducing power, electron transfer, and the synergistic effects of microbial communities and associated mechanisms during azo dye degradation. A culture system was developed to maximize NADH production at 3 g/L yeast extract, and it was observed that the system exhibited a significant increase in reducing power, with NADH concentration reaching 909.48 pg/mL (60 h). The electron transfer process in this system primarily depended on factors such as redox mediators, azoreductase, and formic acid. Azo dye reductive degradation and decolorization occurred through an indirect electron transfer pathway. Flavin-based redox mediators (riboflavin and flavin mononucleotide) played a key role in the system, with the application of riboflavin and flavin mononucleotide increasing the system's dye reduction ratio by 14.45 % and 14.40 %, respectively. They were endogenously expressed by the system and facilitated efficient electron transfer by synergizing with specific reductases, particularly when the electron transport chain was inhibited, and alternative pathways ensured the continuation of the reduction reaction. NADH production primarily occurred through glycolysis, the TCA cycle, and fatty acid β-oxidation, with glycolysis contributing the most. Microorganisms such as Enterococcus, Burkholderia, and Escherichia within the microbial community played a crucial role in NADH production while regulating community behavior through a quorum sensing system, thereby enhancing the stability and efficiency of dye degradation. This study investigated the bioreduction of azo dyes in terms of reducing power, offering a theoretical foundation and practical guidance for optimizing the microbial system and enhancing the biodegradation efficiency of azo dyes.},
}

@article {pmid41317467,
year = {2025},
author = {Huang, S and Yu, X and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Unveiling the metabolic mechanism of pesticide in food fermentation through metagenomics and metabolomics: A case study of β-cypermethrin in Pixian broad-bean paste.},
journal = {Food chemistry},
volume = {498},
number = {Pt 2},
pages = {147299},
doi = {10.1016/j.foodchem.2025.147299},
pmid = {41317467},
issn = {1873-7072},
abstract = {Fermented foods contain less chemical pollutants, such as pesticide residues, than raw materials. In this study, using Pixian broad-bean paste as a model system, the pesticide degradation during food fermentation was comprehensively elucidated through metagenomic and metabolomics analyses. As a result, β-cypermethrin (β-CY) at 5 mg/kg was almost completely degraded, with a half-life of 6.1 d. β-CY caused flavor changes in fermented products, reducing esters and increasing ketones. Metagenomic analysis revealed that β-CY promoted bacteria phyla Bacteroidota, Pseudomonadota, and enriched the genes of xenobiotic degradation pathways, which is beneficial to its degradation. Microbial-metabolite correlation analysis identified Cyclobacteriaceae, Sulfurovaceae, FEN-1099 and Rhodocyclaceae as key drivers in the synthesis and metabolism of aromatic compounds following β-CY degradation during PBP fermentation. This dual mechanism offers a crucial theoretical foundation for understanding microbial community adaptability and β-CY detoxification in the process.},
}

@article {pmid41316964,
year = {2025},
author = {Puchol-Royo, R and Pascual, J and Ortega-Legarreta, A and Otto, P and Tideman, J and de Vries, SJ and Abendroth, C and Tanner, K and Porcar, M and Latorre-Perez, A},
title = {Metagenomic Insights Into the Ecology, Taxonomy and Metabolic Capabilities of 'Candidatus Darwinibacteriales' Ord. Nov. (Formerly MBA03), a Potential Key Player in Anaerobic Digestion.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70258},
doi = {10.1111/1751-7915.70258},
pmid = {41316964},
issn = {1751-7915},
support = {101000470//European Union's Horizon 2020/ ; },
mesh = {Anaerobiosis ; Phylogeny ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenome ; Biofuels ; Sequence Analysis, DNA ; },
abstract = {Biogas, a mix of CO2, CH4 and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project (www.micro4biogas.eu) revealed that MBA03, an uncharacterised and uncultured bacterial taxon belonging to phylum Bacillota, was very prevalent and abundant in industrial full-scale AD plants. Despite the efforts, this taxon has not yet been cultivated, which makes the analysis of its taxonomy, ecology and metabolism even more challenging. In the present work, 30 samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome-assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 was classified as a new bacterial order, proposed as 'Candidatus Darwinibacteriales' ord. nov., which includes 'Candidatus Darwinibacter acetoxidans' gen. nov., sp. nov. of 'Candidatus Darwinibacteriaceae' fam. nov., along with 'Candidatus Wallacebacter cryptica' gen. nov., sp. nov. of the 'Candidatus Wallacebacteriaceae' fam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche of 'Candidatus Darwinibacteriales'. Moreover, metabolic predictions identified Darwinibacteraceae members as putative syntrophic acetate-oxidising bacteria (SAOB), as they encode for the reversed Wood-Ljungdahl (W-L) pathway coupled to the glycine cleavage system. This suggests that Darwinibacteraceae members could work in collaboration with hydrogenotrophic methanogenic archaea to produce methane in industrial biogas plants. Overall, our findings present 'Candidatus Darwinibacteriales' as a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxon, which has not yet been cultured.},
}

Anaerobiosis
Phylogeny
Metagenomics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Metagenome
Biofuels
Sequence Analysis, DNA

@article {pmid41316759,
year = {2025},
author = {Li, RX and Qiu, CS and Li, F and Xu, F and Liu, NN and Chen, X and Qi, L and Wang, CC and Wang, D and Wang, SP},
title = {[Effects of Thermal-alkaline and Thermal Hydrolysis Treatments on Antibiotic Resistance Genes in Sludge].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {11},
pages = {6940-6947},
doi = {10.13227/j.hjkx.202410028},
pmid = {41316759},
issn = {0250-3301},
mesh = {*Sewage/microbiology/chemistry ; Hydrolysis ; *Waste Disposal, Fluid/methods ; *Drug Resistance, Microbial/genetics ; Hot Temperature ; Wastewater/microbiology ; Genes, Bacterial ; },
abstract = {Sewage sludge from urban wastewater treatment plants is an important source of antibiotic resistance gene (ARGs) dissemination into various environmental media. In this study, two treatment methods were employed to treat sewage sludge: thermal-alkaline lysis (60-100℃, pH 10-12) and thermal hydrolysis (140-200℃, 60-120 min). Through metagenomic sequencing and quantitative polymerase chain reaction technology (qPCR), the effects of different treatment conditions on the physicochemical properties of sludge and the removal of ARGs were systematically investigated. In addition, the correlation between ARGs, intI1, and the physicochemical properties of sludge was analyzed in detail. The results indicated that both thermal-alkaline lysis and thermal hydrolysis treatments could break sludge cells, with thermal hydrolysis showing a more significant effect. Moreover, both treatment methods could effectively reduce the abundance of ARGs in sludge under certain conditions. Under thermal hydrolysis conditions at 200℃ for 120 mins, the absolute abundance of ARGs in sludge reached its lowest level of 4.08×10[6] copies·g[-1], and the absolute abundance of intI1 also achieved its minimum value of 1.83×10[6] copies·g[-1] under these conditions. Correlation analysis revealed a significant positive correlation (P < 0.05) between soluble polysaccharides and intI1 under thermal-alkaline lysis conditions. However, under thermal hydrolysis conditions, multiple ARGs and intI1 exhibited significant negative correlations (P < 0.05) with physicochemical indicators such as soluble chemical oxygen demand (SCOD), soluble proteins, and soluble polysaccharides. The removal of ARGs by these different treatment methods was mainly influenced by the treatment conditions and the degree of microbial cell disruption in the sludge.},
}

*Sewage/microbiology/chemistry
Hydrolysis
*Waste Disposal, Fluid/methods
*Drug Resistance, Microbial/genetics
Hot Temperature
Wastewater/microbiology
Genes, Bacterial

@article {pmid41316756,
year = {2025},
author = {Huang, W and Zhu, C and Yang, YJ and Zhang, HZ and Hu, SG and Wu, K and Cui, KP and Chen, YH},
title = {[Distribution Characteristics and Driving Mechanism of Antibiotic Resistance Genes in a Water Source in Hefei, China].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {11},
pages = {6906-6916},
doi = {10.13227/j.hjkx.202409265},
pmid = {41316756},
issn = {0250-3301},
mesh = {China ; *Drug Resistance, Microbial/genetics ; *Water Microbiology ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Water Supply ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Drinking Water/microbiology ; },
abstract = {One of the important water sources in Hefei serves as a crucial water supplier, playing a vital role in water provisioning. Its water quality is related to both drinking water safety and ecological water safety. To elucidate the distribution characteristics and influencing factors of antibiotic resistance genes (ARGs) within the water source, water, sediment, and soil samples were collected in July 2021 and December 2021. Metagenomic sequencing was employed to identify and characterize ARGs, mobile genetic elements (MGEs), and bacterial communities in the samples. The correlations between ARGs and physical-chemical properties, antibiotics, MGEs, and bacterial communities were also analyzed. Lastly, the factors were categorized into physical-chemical and biological factors, and their degrees of influence on ARGs were analyzed. The results showed that a total of 544 subtypes of ARGs were detected in the water source, which were classified into 26 major categories. Multidrug, bacitracin, β-lactam, and polymyxin resistance genes were the dominant types of ARGs in all three media, with the subtype bacA exhibiting the highest abundance across all. The numbers of certain classifications of ARGs tended to be higher in soil compared to those in sediment and water, and the abundance of ARGs in the soil was also significantly higher than that in the sediment. PCoA analysis showed significant differences in the structural composition of ARGs among the three media. Correlation analyses showed that TP, pH, LINs, and FQs in the water and SAs in the sediment were significantly correlated with ARGs. Additionally, strong correlations were observed between MGEs and bacterial communities and ARGs in the three media. The VPA results indicated that biological factors played a pivotal role in influencing ARGs in water, whereas physical-chemical factors exerted a stronger influence in soil. However, the synergistic effect of both physical-chemical and biological factors on ARGs in all three media was not negligible.},
}

China
*Drug Resistance, Microbial/genetics
*Water Microbiology
Soil Microbiology
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Water Supply
Bacteria/genetics
*Drug Resistance, Bacterial/genetics
Drinking Water/microbiology

@article {pmid41316726,
year = {2025},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1225},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}

@article {pmid41316344,
year = {2025},
author = {Ren, Y and Liang, J and Xie, J and Hu, W and Lai, M and Li, X and Zhang, J and Zheng, Y and Wu, Q and Zhou, H and Yin, J},
title = {Sodium oligomannate modulates the gut-brain axis to alleviate post-stroke cognitive impairment by restoring butyrate metabolism.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02257-w},
pmid = {41316344},
issn = {2049-2618},
support = {82171317//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Post-stroke cognitive impairment (PSCI) affects up to half of stroke survivors, severely impacting their quality of life. Despite its prevalence, the pathogenesis of PSCI remains poorly understood, and no specific pharmacological treatments are currently available.

RESULTS: In PSCI patients, fecal butyrate levels were significantly reduced and correlated with cognitive scores. A machine learning model incorporating butyrate levels, butyrate-producing bacteria, and clinical factors (education, smoking, body mass index [BMI], hemoglobin) demonstrates strong predictive performance (area under the curve [AUC]: 0.793 internal, 0.795 external validation). In a transient middle cerebral artery occlusion (tMCAO) mouse model, both sexes displayed sustained gut microbiota dysbiosis featuring decreased butyrate-producing bacteria and fecal butyrate concentrations, concomitant with hippocampal neuronal loss and microglial activation. Sodium oligomannate (GV-971) treatment ameliorated cognitive impairment in a sex-independent manner and restored butyrate-producing gut bacteria. Metagenomic analysis revealed that GV-971 enhanced butyrate production by promoting D-glucuronate degradation and upregulating butyrate synthesis pathway abundance. The elevated butyrate promoted acetylation of histone H3 at lysines 9 and 14 (Ac-H3K9/K14) in colonic and hippocampal neurons, stimulating neurogenesis, while concurrently reducing gut-derived lipopolysaccharide (LPS) and microglial inflammation. Antibiotic treatment and fecal microbiota transplantation established the essential role of butyrate-producing microbiota in mediating GV-971's effects. In vitro, butyrate supplementation significantly inhibited HDAC3 enzymatic activity in HT22 cells and alleviated LPS-induced inflammatory responses in BV2 microglia.

CONCLUSIONS: Intestinal butyrate levels are significantly associated with PSCI. GV-971 mitigates post-stroke cognitive decline by modulating the gut microbiota to increase butyrate production, highlighting its potential as a therapeutic agent for PSCI.},
}

@article {pmid41316248,
year = {2025},
author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N},
title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07443-w},
pmid = {41316248},
issn = {1479-5876},
}

@article {pmid41316012,
year = {2025},
author = {Ye, X and Li, JA and Wang, S and Luan, S and Zheng, J and Lv, S and Zheng, G and Jiang, W and Huang, X and Xu, J and Zhu, L and Niu, B},
title = {Submandibular infection in a healthy child caused by Legionella maceachernii.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12203-8},
pmid = {41316012},
issn = {1471-2334},
}

@article {pmid41315949,
year = {2025},
author = {Chen, Y and Hu, Y and Liang, H and Xia, J and Tang, L and Zhang, S},
title = {Embolism of coronary, cerebral, and limb arteries resulting from infective endocarditis of a prosthetic aortic valve: a clinical case report.},
journal = {BMC cardiovascular disorders},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12872-025-05287-2},
pmid = {41315949},
issn = {1471-2261},
abstract = {BACKGROUND: Infective endocarditis (IE) involving prosthetic valves is a critical cardiac condition that can lead to complications such as structural heart damage, heart failure, and arterial embolism, with a high associated mortality rate. This report describes an uncommon instance of infective endocarditis of a prosthetic aortic valve leading to multiorgan embolism.

CASE PRESENTATION: A 52-year-old male with a history of Bentall surgery and prosthetic aortic valve replacement presented with chest pain and dyspnea. Coronary angiography demonstrated blockage of the distal left anterior descending artery, which was addressed with balloon angioplasty. A transesophageal echocardiogram (TEE) detected vegetation on the prosthetic valve, and metagenomic next-generation sequencing of blood confirmed infection with Cardiobacterium hominis. During treatment, he experienced acute ischaemia in the right lower limb necessitating thrombectomy, and MRI disclosed numerous tiny infarct foci in the brain. Following a period of six weeks of antibiotic treatment, the patient was discharged in a better condition. However, the valve dysfunction persisted and regular follow-up was required in order to determine whether to perform a further operation.

CONCLUSION: This case underscores the risk of multi-organ embolic consequences in prosthetic valve infective endocarditis, highlighting the necessity for prompt identification, antimicrobial treatment, and surgical intervention where warranted.},
}

@article {pmid41315849,
year = {2025},
author = {Zhang, R and Wang, M and Liu, X and Yang, F and Xu, X and Zi, L and Liang, Z and Liu, X and Gao, H and Chen, X and Zhou, G},
title = {The bacterial spectrum of spinal infections based on blood culture, tissue culture, and molecular methods: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28576-4},
pmid = {41315849},
issn = {2045-2322},
support = {CB23059C065A//Yunnan Fundamental Research Projects/ ; },
abstract = {Spinal infections (SI) are on the rise due to an aging population and the prevalence of more invasive procedures. This study aims to systematically review the microbiological spectrum of SI to enhance diagnostic accuracy and inform effective antibiotic treatment strategies. The last search was conducted on May 9th, 2024, from databases including EMBASE, PubMed, and Web of Science. The outcome variable is infection rate, and the detection method used should be blood culture, tissue culture, or molecular biology method. Two researchers independently extracted research data and evaluated its quality using the JBI Critical Appraisal Tools. Out of 14,639 identified records, 156 studies (encompassing 13,539 patients) were included. Staphylococcus aureus was identified as the most prevalent pathogen, with pooled infection rates of 17.6% (95%CI: 12.8-22.9%; I[2]=93%) in blood culture, 16.8% (95%CI: 14.0-19.8%; I[2]=96%) in tissue culture, and 12.0% (95%CI: 9.3-15.0%; I[2]=35%) in molecular methods. The bacterial spectrum also featured Staphylococcus epidermidis, Escherichia coli, and Mycobacterium tuberculosis (MTB). Molecular methods, particularly metagenomic next-generation sequencing (mNGS), demonstrated markedly superior sensitivity for MTB detection, with a pooled rate of 9.7% (95%CI: 4.6-16.3%; I[2]=90%) compared to 1.3% (95%CI: 0.6-2.1%; I[2]=86%) by tissue culture. The odds ratio for MTB detection with mNGS versus conventional culture was 4.24 (95%CI: 1.68-10.73). This review confirms that a core group of pathogens, including Staphylococcus aureus, Staphylococcus epidermidis, MTB, and Escherichia coli. Our findings underscore that tissue culture is fundamental for common pyogenic bacteria, while metagenomic next-generation sequencing is indispensable for detecting fastidious organisms like MTB. Trial registration: The protocol was registered with PROSPERO (No. CRD42023427429). Registered on May 28, 2023.},
}

@article {pmid41315738,
year = {2025},
author = {Medvedeva, S and Guyet, U and Pelletier, E and Ruscheweyh, HJ and Sunagawa, S and Ogata, H and Aylward, FO and Gaïa, M and Yutin, N and Koonin, EV and Krupovic, M and Delmont, TO},
title = {Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41315738},
issn = {2058-5276},
support = {ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0022//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Mirusviruses infect unicellular eukaryotes and are related to tailed bacteriophages and herpesviruses. Here we expand the known diversity of mirusviruses by screening diverse metagenomic assemblies and characterizing 1,202 non-redundant environmental genomes. Mirusviricota comprises a highly diversified phylum of large and giant eukaryotic viruses that rivals the evolutionary scope and functional complexity of nucleocytoviruses. Critically, major Mirusviricota lineages lack essential genes encoding components of the replication and transcription machineries and, concomitantly, encompass numerous spliceosomal introns that are enriched in virion morphogenesis genes. These features point to multiple transitions from cytoplasmic to nuclear reproduction during mirusvirus evolution. Many mirusvirus introns encode diverse homing endonucleases, suggestive of a previously undescribed mechanism promoting the horizontal mobility of spliceosomal introns. Available metatranscriptomes reveal long-range trans-splicing in a virion morphogenesis gene. Collectively, our data strongly suggest that nuclei of unicellular eukaryotes across marine and freshwater ecosystems worldwide are a major niche for replication of intron-rich mirusviruses.},
}

@article {pmid41315665,
year = {2025},
author = {Goraj, W and Kagan, K and Kuźniar, A and Banach, A and Jurczyk, S and Podlewski, J and Wolińska, A},
title = {Spatial and functional differentiation of microbial biofilms in a traditional cheese ripening environment.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30318-5},
pmid = {41315665},
issn = {2045-2322},
abstract = {Biofilms in historic buildings represent stable microbial ecosystems shaped by long-term environmental filtering. We investigated bacterial and fungal communities forming biofilms on walls and ceilings in a 19th-century cheese ripening cellar in Poland, characterized by low temperature, high humidity, and minimal light - conditions resembling natural subterranean habitats. Using high-throughput 16 S rRNA and ITS sequencing, we revealed distinct taxonomic and predicted functional profiles associated with surface type (wall vs. ceiling) and material (brick vs. stone). The wall biofilms exhibited greater taxonomic and functional diversity, with enrichment in heterotrophic, fermentative, and polymer-degrading taxa and pathways, whereas ceiling biofilms showed predicted enrichment in aerobic, stress-tolerant, and potentially methanogenic lineages. The co-occurrence network analysis revealed more complex and tightly connected associations in wall biofilms, dominated by Actinobacteriota (21-97%) and Ascomycota (60-97%), suggesting stable ecological organization despite the limited sample size. Environmental factors, such as pH, redox potential, and electrolytical conductivity, explained a substantial proportion of the variance in the microbial diversity and predicted functional traits. Overall, this study highlights traditional ripening cellars as semi-natural built ecosystems that sustain specialized, spatially structured microbiomes. The results provide new insights into microbial adaptation, functional potential, and ecological resilience in heritage food environments.},
}

@article {pmid41315430,
year = {2025},
author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D},
title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42704},
pmid = {41315430},
issn = {2045-2322},
support = {R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; },
mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; },
abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).},
}

Humans
*Celiac Disease/virology/epidemiology/microbiology/immunology/etiology
Female
Male
Longitudinal Studies
Child, Preschool
*Gastrointestinal Microbiome
Autoantibodies/immunology
Risk Factors
Transglutaminases/immunology
Child
Autoimmunity
Cohort Studies
Glutens

@article {pmid41060580,
year = {2025},
author = {Vega-Carranza, AS and Escamilla-Montes, R and Luna-González, A and Diarte-Plata, G and Fierro-Coronado, JA and García-Gutiérrez, C and Ceseña, CE},
title = {Investigating the effects of synbiotics, postbiotics and bacilli in the modulation of gut microbiota and the survival of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {4},
pages = {2845-2854},
pmid = {41060580},
issn = {1678-4405},
abstract = {The effect of feed and water additives was evaluated on the gut microbiota and survival of white shrimp challenged with V. parahaemolyticus. Bacillus licheniformis BCR 4 − 3 and vibrio cultures were spray dried. Inulin, probiotics, and postbiotics of bacilli (SPB) and postbiotics of vibrios (PVp) were added to commercial feed. Viable bacilli cells were added to water. An experiment with four treatments in triplicate was performed to determine the effect of diet on survival and the intestinal microbiota by sequencing the V3 region of the bacterial 16S ribosomal gene. Metagenomic analysis was performed on the Shaman, MicrobiomeAnalyst, and Ivikodak platforms. The growth was not affected by the additives but survival of animals in treatments was significantly higher as compared to control group. The phyla and genera that predominated in the white shrimp intestine were Proteobacteria, Bacteroidetes, Firmicutes, Vibrio, Agarivorans, Tropicibacter, and Roseovarius. The Vibrio genus increased in treatments with bacilli in feed and water and decreased in PVp in feed. The control and treatments shared 219 Operational Taxonomic Units. No changes were observed in the bacterial diversity (richness and relative abundance of species). In the bacterial community of the shrimp intestine (species replacement) changes were observed. Bacterial functional profile (Lipid, amino acid, and energy metabolism and digestive and immune systems) was modulated in treatments. Synbiotics, postbiotics, and bacilli in water enhance survival rates and modulated the gut microbiota of L. vannamei.},
}

@article {pmid41315421,
year = {2025},
author = {Thystrup, C and Gobena, T and Salvador, EM and Fayemi, OE and Kumburu, H and Buys, EM and Gichure, J and Moiane, BT and Belina, D and Hugho, EA and Faife, S and Ogunbiyi, TS and Akanni, G and Ayolabi, CI and Mmbaga, B and Thomas, KM and Pires, SM and Njage, PMK and Hald, T},
title = {Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66400-9},
pmid = {41315421},
issn = {2041-1723},
support = {OPP1195617//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
abstract = {Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.},
}

@article {pmid41315331,
year = {2025},
author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S},
title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {223},
pmid = {41315331},
issn = {2055-5008},
support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; },
mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; },
abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.},
}

Humans
*Microbiota/genetics
Saliva/microbiology
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Mouth Neoplasms/microbiology
Dental Caries/microbiology
*Host Microbial Interactions
*Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
High-Throughput Nucleotide Sequencing/methods
Child
Child, Preschool