@article {pmid41239026,
year = {2025},
author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H},
title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.},
journal = {Acta parasitologica},
volume = {70},
number = {6},
pages = {211},
pmid = {41239026},
issn = {1896-1851},
support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; },
abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.

METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.

RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3 months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6 months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3 months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6 months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6 months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P < 0.01), and reduced goblet cell counts (P < 0.05), collectively indicating compromised intestinal barrier integrity.

CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.},
}

@article {pmid41238915,
year = {2025},
author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA},
title = {Microbial signals in primary and metastatic brain tumors.},
journal = {Nature medicine},
volume = {31},
number = {11},
pages = {3675-3688},
pmid = {41238915},
issn = {1546-170X},
support = {R21 NS130323/NS/NINDS NIH HHS/United States ; F32 CA260769/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P50 CA221703/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; },
abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.},
}

Humans
*Brain Neoplasms/microbiology/pathology
RNA, Ribosomal, 16S/genetics
Tumor Microenvironment
Female
*Glioma/microbiology/pathology
Male
Prospective Studies
Middle Aged
*Microbiota/genetics
In Situ Hybridization, Fluorescence
Aged
Adult
Bacteria/genetics

@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}

Female
Humans
*Vagina/microbiology
*Premature Birth/microbiology
*Microbiota/genetics
Pregnancy
*Metagenomics/methods
Adult
*Cervix Uteri/microbiology/pathology
Risk Factors

@article {pmid41238615,
year = {2025},
author = {Wang, R and Wang, H and Jiang, J and Xu, S and Dong, M},
title = {Diagnostic value of metagenomic next-generation sequencing in the etiological diagnosis of lower respiratory tract infection.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39987},
pmid = {41238615},
issn = {2045-2322},
support = {GXLIRMMKL-201916//Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has been widely used in infectious diseases. However, reports on mNGS for lower respiratory tract infection (LRTI) diagnosis remain limited, potentially offering significant value for improving pathogen identification. This study evaluates the diagnostic performance and clinical value of mNGS compared to traditional methods in LRTI. We analyzed traditional and mNGS detection results from 165 patients with suspected LRTI using different specimens including bronchoalveolar lavage fluid (BALF), blood, tissue samples, and pleural effusion. We compared diagnostic differences and characteristics between mNGS and traditional methods, and evaluated the effect of mNGS results on antibiotic treatment.Among 165 cases, 146 (88.48%) patients with LRTI had microbial etiology finally identified. Compared with traditional diagnostic methods, mNGS showed significantly higher positive rate (143/165, 86.7% vs 69/165, 41.8%, P < 0.05). The diagnostic performance of mNGS was not affected by sample types. mNGS demonstrated significant advantage in detecting poly-microbial infections and rare pathogens. Twenty-nine kinds of pathogens were detected only by mNGS, including non-tuberculous mycobacteria (NTM), Prevotella, anaerobic bacteria, Legionella gresilensis, Orientia tsugamushi, and viruses. The pathogen spectrum differed between immunocompetent and immunocompromised individuals. mNGS resulted in treatment changes in 119 patients (72.13%), with 54 patients (32.73%) having reduced antibiotics. mNGS has obvious advantages over traditional detection methods with results unaffected by sample types. mNGS demonstrates significant value for pathogen detection and may provide guidance in clinical practice.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Female
Male
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
Middle Aged
*Metagenomics/methods
Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology
Aged, 80 and over

@article {pmid41238538,
year = {2025},
author = {Bilcke, G and Campese, L and Annunziata, R and Amadei Martínez, L and Borgonuovo, C and Rijsdijk, N and Chaerle, P and Van den Berge, K and D'hondt, S and Iudicone, D and Montresor, M and Ferrante, MI and Vandepoele, K and Vyverman, W},
title = {Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10029},
pmid = {41238538},
issn = {2041-1723},
support = {1228423N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 11L2323N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; MARCO-BOLO (101082021)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; AtlantECO (862923)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Diatoms/genetics/physiology ; Reproduction/genetics ; Genetic Markers/genetics ; Oceans and Seas ; Transcriptome ; Phytoplankton/genetics ; Gene Expression Profiling ; Salinity ; Metagenome ; Seawater ; },
abstract = {Sexual reproduction is a nearly universal characteristic of the eukaryotic life cycle, yet it is rarely observed in natural populations of micro-eukaryotes. Sex is particularly relevant for diatoms, a key group of marine and freshwater phytoplankton, where sexual reproduction counters a progressive cell size reduction due to cellular division. Here, we leveraged controlled sex transcriptome experiments of four diatom species to develop a robust method for in situ monitoring of sexual reproduction events. The resulting panel of conserved marker genes was validated for specificity and sensitivity using metatranscriptomic profiling of a natural estuarine community undergoing massive sexual reproduction of multiple species in response to increased salinity. Analysis of metatranscriptomic data linked with Metagenome-Assembled Genomes from the Tara Oceans expedition revealed widespread and coordinated expression of these markers across nine diatom genera, complemented by observations of sexual stages in automated imaging resources. Our results reveal that diatom sexual reproduction is more widespread in the global ocean than previously thought, encompassing both dominant bloom-forming species and rare taxa. Our panel of markers to detect sexual reproduction in natural environments paves the road to better understand the interplay between endogenous and environmental controls of this pivotal process, essential for the diatoms' evolutionary success.},
}

*Diatoms/genetics/physiology
Reproduction/genetics
Genetic Markers/genetics
Oceans and Seas
Transcriptome
Phytoplankton/genetics
Gene Expression Profiling
Salinity
Metagenome
Seawater

@article {pmid41238046,
year = {2025},
author = {Oliveira, RDS and Oliveira Alves Filho, NC and Gomes Netto, WB and Silva, DC and Oliveira, MS and Oliveira, ACFM and Baraúna, RA and Graças, DAD and Silva, A and Oliveira Veras, AA},
title = {ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes.},
journal = {Gene},
volume = {},
number = {},
pages = {149893},
doi = {10.1016/j.gene.2025.149893},
pmid = {41238046},
issn = {1879-0038},
abstract = {To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: https://github.com/allanverasce/contigpolishing.},
}

@article {pmid41237940,
year = {2025},
author = {Borroni, D and Lo Monaco, F and Silvia, F and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C},
title = {Ocular Surface Microbiota in Primary Open Angle Glaucoma.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110734},
doi = {10.1016/j.exer.2025.110734},
pmid = {41237940},
issn = {1096-0007},
abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1×10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.},
}

@article {pmid41237902,
year = {2025},
author = {Pitarch, A and Arribas, V and Gil, C},
title = {Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {101463},
doi = {10.1016/j.mcpro.2025.101463},
pmid = {41237902},
issn = {1535-9484},
abstract = {Invasive candidiasis (IC) is a serious, life-threatening, and costly fungal infection if not diagnosed early and treated appropriately. However, this healthcare-associated mycosis caused by Candida spp. is difficult to diagnose because of its nonspecific clinical signs and symptoms, and the lack of early and accurate detection methods. IC is also difficult to treat due to its late diagnosis, the limited antifungal arsenal, and the rapid emergence and spread of (multi)drug-resistant Candida strains. Therefore, early and accurate innovative methods for species and resistance identification in IC (candidemia and deep-seated candidiasis) are urgently needed to initiate timely and appropriate antifungal therapy, and reduce its high morbidity, mortality, and healthcare costs in hospitalized patients (in particular, severely immunocompromised or critically ill patients). The availability of the complete genome sequences of the most clinically relevant Candida species coupled with recent advances in high-throughput omics technologies have spurred an unprecedented era in the discovery and development of IC diagnostics at different levels of molecular complexity. Here we review the contribution of current and emerging omics technologies, including genomics, transcriptomics, proteomics, peptidomics, metabolomics, lipidomics, glycomics, immunomics (immunoproteomics, immunopeptidomics, and immunoglycomics), imiomics (imaging-omics), and microbiomics (metagenomics, metatranscriptomics, metaproteomics, and metabonomics), to the process of biomarker development for early diagnosis, antifungal susceptibility, prognosis, follow-up, and therapeutic monitoring in IC. We highlight the potential of integrating multiple omic data (through integromics, multiomics or panomics, together with systems biology and artificial intelligence) for the discovery of multidimensional biomarker signatures and computational algorithms for IC diagnosis. Finally, we discuss future challenges and prospects for their clinical implementation. These next-generation IC diagnostics promise to revolutionize medical practice by unraveling the complexity of biological systems at multiple levels. In addition, these could help clinicians make more precise and personalized clinical decisions through multiomics or panomics-based precision medicine approaches, rather than traditional one-size-fits-all approaches.},
}

@article {pmid41237728,
year = {2025},
author = {Meng, Q and Wang, J and Li, K and Zhang, Y and Hu, Z and Wang, F and Pan, F and Fu, J and Dang, C},
title = {Low-dose chlorine disinfection poses a greater potential risk of antibiotic resistance genes and their pathogenic hosts.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124895},
doi = {10.1016/j.watres.2025.124895},
pmid = {41237728},
issn = {1879-2448},
abstract = {Identifying the responses of antibiotic resistance genes (ARGs) and their hosts to chlorine disinfection is necessary because it has been paradoxically reported to both amplify and suppress antibiotic resistance in water treatment processes. In this study, our integrated metagenomic and metatranscriptomic analysis of sequencing batch reactors under different chlorine disinfection conditions (0, 2, 6, and 10 mg/L) in activated sludge reveals that low-dose chlorine obviously increases ARG abundance, diversity, and transcriptional activity, particularly for multidrug, β-lactam, and tetracycline types, while higher doses reduce transcriptional diversity and activity. Acinetobacter johnsonii, a pathogen abundant and active under chlorine-addition conditions, poses a high risk of ARG transmission due to its multiple mobile genetic elements and potential involvement in horizontal gene transfer with non-pathogens. Notably, chlorine disinfection may simultaneously promote the co-transfer of chlorine resistance and antibiotic resistance genes, such as the qacE gene, with the involvement of plasmids and integrons. Overall, this study demonstrates that low-dose chlorine may promote greater ARG enrichment, mobility, and pathogenic potential in activated sludge. The findings highlight overlooked risks of low-concentration residual chlorine, urging reconsideration of disinfection strategies to protect public health.},
}

@article {pmid41237727,
year = {2025},
author = {Zhao, Z and Zhao, Y and Hua, M and Yao, X and Hu, B},
title = {Deep metagenomic insights into the formation characteristics of the resistome in Pristine Saline Lakes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124937},
doi = {10.1016/j.watres.2025.124937},
pmid = {41237727},
issn = {1879-2448},
abstract = {Pristine and isolated ecosystems remain underexplored in resistome research, leaving a major gap in understanding how antibiotic resistance genes (ARGs) persist and spread outside human influence. To address this, we performed the first long-term, systematic, ultra-deep metagenomic survey of four high-altitude pristine saline lakes in the Altun Shan National Nature Reserve-an uninhabited region of the Qinghai-Tibet Plateau-generating 1.8 terabases of sequencing data. We identified a total of 756 ARG subtypes spanning 28 ARG types in all sampled lakes, with the clinically relevant polymyxin resistance gene, ugd, accounting for 30.5 % of the total ARG abundance. Moreover, ugd showed high mobility potential, with 183 horizontal gene transfer (HGT) events identified across 18 genera, and was widely associated with mobile genetic elements (MGEs). Similarity analyses revealed that the ARG profiles of pristine saline lakes were most comparable to those of marine environments, suggesting that salinity is a key ecological driver shaping the prevalence of polymyxin resistance genes. These findings indicate that pristine saline lakes can act as previously underexplored reservoirs and exchange hubs for clinically important resistance genes. Our results reveal the abundance and dissemination potential of ugd in isolated ecosystems and provide new insights into how natural environmental factors independently shape the resistome, with implications for One Health antimicrobial resistance surveillance.},
}

@article {pmid41237724,
year = {2025},
author = {Huang, P and Zhou, Y},
title = {Enhance H2 production by regulating acetyl-CoA supply and reducing equivalent diversion in an enriched purple phototrophic bacteria culture.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124910},
doi = {10.1016/j.watres.2025.124910},
pmid = {41237724},
issn = {1879-2448},
abstract = {Short-chain volatile fatty acids (VFAs) are promising carbon sources for biohydrogen production by purple phototrophic bacteria (PPB), given their high hydrogen conversion potential and low cost. However, most existing studies used a single VFA as the carbon source, providing only partial insights for practical applications, as VFAs in waste streams typically exist in mixtures. Furthermore, the metabolic responses of PPB to VFA mixtures, which determine H2 yield, and the metabolic mechanisms, remain largely unexplored. This study investigated the effects of co-feeding propionate with acetate or butyrate on PPB's hydrogen production and explored the associated metabolic responses through metagenomic and metatranscriptomic analyses. Results show that co-feeding butyrate with propionate (1:1 COD ratio) increased substrate conversion efficiency to 61 %, compared to 54 % from sole propionate. This improvement is linked to increased acetyl-CoA (Ac-CoA) availability, which, on one hand, activates the tricarboxylic acid (TCA) cycle and generates more electrons during carbon assimilation, and on the other hand, reduces the competitiveness of other electron sinks, thereby enhancing electron flow toward hydrogen. In contrast, co-feeding acetate with propionate results in a comparable conversion efficiency (∼50 %), where the increased Ac-CoA availability promotes carbon assimilation through the glyoxylate shunt instead. These findings reveal a synergistic metabolic impact from mixed VFAs and highlight the role of Ac-CoA in regulating carbon assimilation and electron dissipation. Understanding these interactions can guide the selection of waste streams and pretreatment processes to provide PPB with favorable VFA compositions, enabling more efficient and sustainable hydrogen production in practice.},
}

@article {pmid41237630,
year = {2025},
author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L},
title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140469},
doi = {10.1016/j.jhazmat.2025.140469},
pmid = {41237630},
issn = {1873-3336},
abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.},
}

@article {pmid41237622,
year = {2025},
author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J},
title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140425},
doi = {10.1016/j.jhazmat.2025.140425},
pmid = {41237622},
issn = {1873-3336},
abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.},
}

@article {pmid41236809,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY},
title = {Characterization of Gut Microbiota of Honey Bees in Korea.},
journal = {Polish journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.33073/pjm-2025-025},
pmid = {41236809},
issn = {2544-4646},
abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.},
}

@article {pmid41236788,
year = {2025},
author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C},
title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e72950},
doi = {10.2196/72950},
pmid = {41236788},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists & inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; },
abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.

OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.

METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.

RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.

CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.

TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.

DERR1-10.2196/72950.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/drug therapy/pathology
*Diet, Mediterranean
Pilot Projects
Italy
Female
Male
Prospective Studies
ErbB Receptors/antagonists & inhibitors
*Antineoplastic Agents/adverse effects/therapeutic use
Middle Aged
Aged
Randomized Controlled Trials as Topic
Adult

@article {pmid41236769,
year = {2025},
author = {Lima Filho, CM and Santos, AA and Lima, DVN and Silva, LO and Paranhos, RR and Branco, S and Pacheco, ABF and Azevedo, SMFO},
title = {Combining Ludwigia leptocarpa with the dried biomass of Pontederia crassipes for mitigating cyanobacteria: a sustainable way to use macrophyte waste.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/15226514.2025.2579148},
pmid = {41236769},
issn = {1549-7879},
abstract = {Constructed Floating Wetlands (CFWs) with emergent macrophytes offer a low-cost, sustainable strategy to mitigate eutrophication. We evaluated the combined use of Ludwigia leptocarpa, a native macrophyte from the Americas, and dried biomass of Pontederia crassipes (DB Pc) as substrate in small-scale CFWs to suppress a natural cyanobacterial bloom. Ex-situ mesocosm experiments (40 L) were conducted over 16 days with treatments: L. leptocarpa with DB Pc (S+), L. leptocarpa alone (S-), DB Pc alone, and living P. crassipes as positive control. L. leptocarpa (S-) and P. crassipes reduced Soluble Reactive Phosphorus by >85%, but L. leptocarpa produced 10 times less biomass. Treatments with DB Pc increased nutrient and phenol concentrations. All treatments led to reduced chlorophyll-a and phytoplankton density, especially cyanobacteria, along with pH reduction. 16S rRNA sequencing revealed higher bacterial diversity in the L. leptocarpa rhizosphere than in the water, suggesting a role in phytoremediation. The combination of L. leptocarpa and DB Pc in CFWs shows potential for cyanobacterial control through nutrient uptake, allelopathy, and pH modulation. This method supports sustainable water management by utilizing a native, slow-growing macrophyte and repurposing waste biomass that would otherwise harm aquatic ecosystems.},
}

@article {pmid41236031,
year = {2025},
author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ},
title = {Altered oral microbiome diversity in patients with oral candidiasis.},
journal = {Archives of oral biology},
volume = {180},
number = {},
pages = {106430},
doi = {10.1016/j.archoralbio.2025.106430},
pmid = {41236031},
issn = {1879-1506},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.

DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.

RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.

CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.},
}

Humans
*Candidiasis, Oral/microbiology/drug therapy
*Microbiota/drug effects
Male
Saliva/microbiology
Female
*Fluconazole/therapeutic use/pharmacology
Middle Aged
*Antifungal Agents/therapeutic use/pharmacology
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Aged
Adult
Streptococcus salivarius/drug effects
Real-Time Polymerase Chain Reaction

@article {pmid41235937,
year = {2025},
author = {Mills, S and Collins, G and Ijaz, UZ and Lens, PNL},
title = {Metagenome-assembled genomes from microbial communities in lab-scale anaerobic bioreactors treating simulated dairy wastewater.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048725},
doi = {10.1128/mra.00487-25},
pmid = {41235937},
issn = {2576-098X},
abstract = {This dataset describes metagenome-assembled genomes from three lab-scale (4L) expanded granular sludge bed bioreactors treating synthetic dairy wastewater. The resulting MAGs encompass 60 phyla with average genome completeness of 78.68% and average contamination of 2.29%. These genomes represent a valuable resource for studying anaerobic bioreactors used in wastewater treatment.},
}

@article {pmid41235136,
year = {2025},
author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y},
title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {9993-10010},
pmid = {41235136},
issn = {1177-8881},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; },
abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.

METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.

RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.

CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Psoriasis/drug therapy/metabolism/pathology
Mice
Humans
*Cell Differentiation/drug effects
*Sphingolipids/metabolism
*Epidermis/drug effects/pathology/metabolism
Keratinocytes/drug effects/metabolism

@article {pmid41234773,
year = {2025},
author = {Levé, M and Manghi, P and Bredon, M and Lefevre, A and Manara, S and Armanini, F and Emond, P and Planchais, J and Rolhion, N and Segata, N and Sokol, H},
title = {Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113751},
pmid = {41234773},
issn = {2589-0042},
abstract = {Tryptophan metabolism plays a key role in host-microbiota interactions, producing a wide array of bioactive metabolites. However, our understanding of the interactions between tryptophan metabolites and the gut microbiota is still limited. Using targeted quantitative metabolomics and metagenomics in mice across various compartments, we showed that the cecal microbiota massively impacts tryptophan metabolism both in the gut and systemically. Grouping bacterial taxa in co-abundance guilds better reflected the links between gut microbes and tryptophan metabolites than single taxa taken individually and suggested the involvement of complex microbial interactions in tryptophan metabolism regulation. Finally, analyzing functional data, we shed light on the potential links between tryptophan metabolism and bacterial enzymes or metabolic pathways.},
}

@article {pmid41234739,
year = {2025},
author = {Jin, L and Chen, S and Kang, R and Li, C and Yang, S and Yang, Q and Zhao, K and Zou, L},
title = {Variation and spread of resistomes in swine manure, manure slurries, and long-term manure-fertilized soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683394},
pmid = {41234739},
issn = {1664-302X},
abstract = {BACKGROUND: Application of swine manure to soils exacerbates environmental antimicrobial resistance (AMR). However, a comprehensive evaluation of anaerobic digestion's (AD) mitigation potential against AMR and its influencing factors in swine manure-to-soil systems remains lacking.

METHODS: We employed mass spectrometry, metagenomics, and whole-genome sequencing (WGS) to investigate the fate of antibiotics, metals, and antibiotic resistance genes (ARGs) across manures, slurries, and soils from eight pig farms.

RESULTS: Anaerobic digestion reduced antibiotic and metal (except ciprofloxacin) content and risks in manure, but had limited effects on total ARG abundance, while increasing ARG network modularity. High-risk ARG abundance significantly increased from 404.7 in manure to 843.2 in slurries, with health-risk scores rising 1.88-fold during anaerobic digestion. Metagenomic analysis showed metal resistance gene (MRG) diversity and abundance decreased during anaerobic digestion, along with reduced ARG-MRG co-occurrence frequency, whereas mobile genetic element (MGE) diversity and ARG-MGE co-occurrence frequency increased. Escherichia coli was identified as the dominant ARG host. WGS of E. coli strains confirmed horizontal gene transfer (HGT) of nine ARGs (e.g., sul3 and blaTEM-1), and metagenomics suggested HGT of four ARGs (e.g., tet(M)) across different pathogens. Chromium concentrations, bacterial communities and MGEs were significantly associated with ARG profiles. Long-term slurry application resulted in elevated antibiotic, metal, and ARG concentrations in soils, with concomitant increases in high-risk ARGs and health risks.

CONCLUSION: This study demonstrates AD's limited effect on mitigating overall ARG abundance and highlights MGEs as critical drivers of ARG maintenance and dissemination from manure to soil process, guiding manure treatment optimization to reduce agricultural AMR risks.},
}

@article {pmid41234344,
year = {2025},
author = {Yang, L and Zeng, J and Zhang, Y and Li, L},
title = {Purulent Meningitis Due to Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis and Streptococcus constellatus from Oral and Maxillofacial Space Infection: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5843-5851},
pmid = {41234344},
issn = {1178-6973},
abstract = {BACKGROUND: Purulent meningitis caused by polymicrobial oral anaerobes represents a rare but life-threatening clinical challenge, with Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus being pfastidious organisms. Traditional diagnostic methods often fail to identify these fastidious organisms, leading to delayed or inappropriate therapy.

CASE PRESENTATION: We report a rare case of purulent meningitis resulting from a polymicrobial infection involving Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus in a 76-year-old male patient who presented with a 40-day history of left facial pain. This case represents the first documented instance of these four oral anaerobes concurrently causing an infection of the central nervous system.

CONCLUSION: To the best of our knowledge, this case represents the first documented evidence of polymicrobial purulent meningitis caused by oral anaerobes, specifically Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus. Our findings not only provide direct evidence for the oral-central nervous system (CNS) infection pathway but also validate that the valuable approach based on metagenomic next-generation sequencing (mNGS) offers significant clinical insights for diagnostic and therapeutic strategies.},
}

@article {pmid41233937,
year = {2025},
author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M},
title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {231},
pmid = {41233937},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; },
abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.

RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.

CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.},
}

Animals
*Rumen/microbiology/metabolism
*Methane/metabolism/biosynthesis
Cattle
*Seaweed
*Dietary Supplements
*Bacteria/genetics/metabolism/classification/isolation & purification
Animal Feed/analysis
*Gastrointestinal Microbiome
Fermentation
Metagenome
Metagenomics
Hydrogen/metabolism

@article {pmid41233936,
year = {2025},
author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS},
title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {234},
pmid = {41233936},
issn = {2049-2618},
support = {141954/2019-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; },
abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.

RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.

CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.},
}

*Anthozoa/microbiology
Animals
*Symbiosis
*Nitrogen Cycle
Metagenomics/methods
Microbiota
Brazil
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
In Situ Hybridization, Fluorescence

@article {pmid41233919,
year = {2025},
author = {Vohsen, SA and Gruber-Vodicka, HR and Osman, EO and Saxton, MA and Joye, SB and Dubilier, N and Fisher, CR and Baums, IB},
title = {Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {232},
pmid = {41233919},
issn = {2049-2618},
support = {ECOGIG//Gulf of Mexico Research Initiative/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; *Sulfur/metabolism ; Symbiosis ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Chemoautotrophic Growth ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with related bacteria and report here that these associations are widespread.

RESULTS: We screened corals, water, and sediment for Thioglobaceae using 16S metabarcoding and found ASVs associated with corals at high relative abundance (10 - 91%). These ASVs were specific to coral hosts, absent in water samples, and rare or absent in sediment samples. Using metagenomics and transcriptomics, we assembled the genome of one phylotype associated with Paramuricea sp. B3 (ASV 4) which contained the genetic potential to oxidize sulfur and fix carbon, and confirmed that these pathways were transcriptionally active. Furthermore, its relative abundance was negatively correlated with the stable isotopic composition of its host coral's tissue suggesting some contribution of chemoautotrophy to the coral holobiont.

CONCLUSIONS: We propose that some lineages of Thioglobaceae may facultatively supplement the diet of their host corals through chemoautotrophy at seeps or may provide essential amino acids or vitamins. This is the first documented association between chemoautotrophic symbionts and corals at seeps and suggests that the footprint of chemosynthetic environments is wider than currently understood.},
}

Animals
*Anthozoa/microbiology
*Sulfur/metabolism
Symbiosis
Oxidation-Reduction
Phylogeny
RNA, Ribosomal, 16S/genetics
Chemoautotrophic Growth
Metagenomics/methods
Seawater/microbiology

@article {pmid41233799,
year = {2025},
author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA},
title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1276},
pmid = {41233799},
issn = {1479-5876},
abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.

METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.

RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.

CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.},
}

@article {pmid41233543,
year = {2025},
author = {Aroney, STN and Newell, RJP and Tyson, GW and Woodcroft, BJ},
title = {Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41233543},
issn = {1548-7105},
support = {DP230101171//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; },
abstract = {The recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low-abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm that substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritized, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.},
}

@article {pmid41233523,
year = {2025},
author = {Dell, M and Kogawa, M and Streiff, AB and Shiraishi, T and Lotti, A and Meier, CM and Schorn, MA and Field, C and Cahn, JKB and Yokoyama, H and Yamada, Y and Peters, E and Egami, Y and Nakashima, Y and Tan, KC and Rückert, C and Alanjary, M and Kalinowski, J and Kuzuyama, T and Cardenas, P and Pomponi, S and Sipkema, D and Wright, A and Takada, K and Abe, I and Wakimoto, T and Takeyama, H and Piel, J},
title = {Chemical richness and diversity of uncultivated 'Entotheonella' symbionts in marine sponges.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41233523},
issn = {1552-4469},
support = {22H05120//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H02635//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H05128//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been established as the actual producers. Among the known sponge symbionts, 'Candidatus Entotheonella' members stand out because of their abundant and variable biosynthetic gene clusters (BGCs). Here, to obtain broader insights into this producer taxon, we conduct a comparative analysis on eight sponges through metagenomic and single-bacterial sequencing and biochemical studies. The data suggest sets of biosynthetic genes that are largely unique in 14 'Entotheonella' candidate species and a member of a sister lineage named 'Candidatus Proxinella'. Four biosynthetic loci were linked in silico or experimentally to cytotoxins, antibiotics and the terpene cembrene A from corals. The results support widespread and diverse bacterial roles in the chemistry of sponges and aid the development of sustainable production methods for sponge-derived therapeutics.},
}

@article {pmid41233350,
year = {2025},
author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW},
title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1782},
pmid = {41233350},
issn = {2052-4463},
support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; },
mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; },
abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.},
}

Republic of Korea
*Seawater/virology
*DNA Viruses/genetics/classification
DNA, Viral
*Virome
Metagenomics
Bacteriophages/genetics

@article {pmid41233343,
year = {2025},
author = {Lu, JN and Chao, Y and Tian, L and Zhong, X and Chen, Z and He, H and Huang, B and Li, M and Feng, Z and Feng, H and Hu, C and Zhou, S and Zhang, L and Yang, Y and Ruan, Z and Ding, K and Yang, Y and Yuan, K and Liu, W and Qi, H and Cao, Y and Fei, YH and Ling, N and Wang, S and Tang, YT and Luan, T and Xu, Z and Qiu, R},
title = {DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9984},
pmid = {41233343},
issn = {2041-1723},
mesh = {*Carbon Cycle/genetics ; *Soil Microbiology ; Carbon/metabolism ; Soil/chemistry ; China ; *DNA Viruses/genetics/metabolism ; Metagenomics ; *Soil Pollutants/metabolism ; *DNA, Viral/genetics ; Metagenome ; Mining ; },
abstract = {Soil is the largest organic matter repository on land and the virosphere is an essential component of soil carbon cycling. While a few carbon-related auxiliary metabolic genes (AMGs) in viruses are reported to potentially influence the hosts, the effects of virus-host interactions on soil carbon fixation, particularly in carbon-deficient contaminated soils, need further validation. Here, we explore the impact of viruses on carbon fixation in contaminated soils from 58 metal mining areas across eastern China. Eleven different functional categories of carbon fixation AMGs are identified via metagenomic analysis in 323 contaminated soil samples. Enzymatic activities of three key AMGs (i.e., rbcL, ppdK and TKT) are experimentally characterized, indicating the positive role of these genes in carbon fixation. Furthermore, transcriptomic sequencing reveals that after active virus inoculation the carbon fixation genes significantly up-regulate (~73%, p < 0.05). In mesocosms with stable isotope labeling, the accumulation of [13]C-labeled organic carbon significantly increases (~10%, p < 0.01). Our results provide theoretical and experimental evidence for incorporating viral contributions into the assessments of carbon fixation, and improve the understanding of viral roles within the processes of carbon cycling.},
}

*Carbon Cycle/genetics
*Soil Microbiology
Carbon/metabolism
Soil/chemistry
China
*DNA Viruses/genetics/metabolism
Metagenomics
*Soil Pollutants/metabolism
*DNA, Viral/genetics
Metagenome
Mining

@article {pmid41233306,
year = {2025},
author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X},
title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9980},
pmid = {41233306},
issn = {2041-1723},
support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; },
abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.},
}

Animals
*Colitis/chemically induced/microbiology
Mice
Humans
*Indoles/metabolism/pharmacology
Gastrointestinal Microbiome
Receptors, Aryl Hydrocarbon/metabolism/agonists
Mice, Inbred C57BL
*Hypocreales/metabolism/genetics
Inflammatory Bowel Diseases/microbiology
Male
Female
Feces/microbiology
Disease Models, Animal
Colon/microbiology/pathology
Probiotics

@article {pmid41232906,
year = {2025},
author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M},
title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123287},
doi = {10.1016/j.envres.2025.123287},
pmid = {41232906},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13% of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49%), macrolide-lincosamide-streptogramin (15.84%), beta-lactam (7.95%), and tetracycline (6.52%). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.},
}

@article {pmid41232839,
year = {2025},
author = {Fang, L and Jiaqi, L and Zhenwei, Z and Jingang, Z and Xiao, L and Yongdong, C},
title = {Remediation of soil contaminated by waste drilling slurry in oilfield with mixed bacteria immobilized by fly ash modified biochar.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133644},
doi = {10.1016/j.biortech.2025.133644},
pmid = {41232839},
issn = {1873-2976},
abstract = {Organic and heavy metal combined pollution from large-scale landfill of waste drilling slurry in oilfields poses a significant remediation challenge. This study innovatively combined fly ash doping with physicochemical modification to regulate the morphology and functionalize the surface of reed straw biochar, developing a low-cost modified biochar-based carrier material. This material, validated through leachate adsorption experiments and characterization (SEM, FT-IR, BET, XRD, TEM-EDS), exhibited both high-efficiency organic pollutant adsorption capacity and strong microbial immobilization performance. To simulate practical conditions, pot experiments were conducted, with ICP-OES and metagenomic analyses used to investigate pollutant transformation and fate. Key findings showed that unmodified biochar and fly ash formed a "glass phase-carbon matrix" structure, and under optimal conditions (biochar-fly ash mass ratio 5:1, NaOH-H2O2-assisted ultrasonic modification, 700℃ calcination), the specific surface area of modified material increased by 158.60 % compared to unmodified biochar, with an organic pollutant adsorption capacity of 32.56 mg·g[-1]. When immobilized with specific degrading bacteria, this material achieved 80.54 % COD removal in contaminated soil over 63 days, a rate significantly higher than that of free bacterial or biochar-based material groups, thereby demonstrating stable degradation advantages. Mechanistically, the synergistic integration of high-efficiency adsorption and biodegradation leveraging local oilfield wastes highlights this as an engineerable, efficient, and low-cost strategy for remediating waste drilling slurry-contaminated sites, with broad implications for addressing legacy composite pollution in energy industries.},
}

@article {pmid41232286,
year = {2025},
author = {Romero-Arguelles, R and Gómez-Govea, MA and Adame-Martinez, AE and Guzman-Velazco, A and Gonzalez-Rojas, JI and Ham-Dueñas, JG and Amezquita-Garcia, HJ and Rios-Del Toro, EE},
title = {Sulfammox in sediments of a natural wetland in northeastern Mexico: a sustainable approach to nitrogen and sulfur removal.},
journal = {The Science of the total environment},
volume = {1006},
number = {},
pages = {180920},
doi = {10.1016/j.scitotenv.2025.180920},
pmid = {41232286},
issn = {1879-1026},
abstract = {The simultaneous removal of nitrogenous and sulfate compounds in natural environments represents a major environmental challenge. The sulfammox process, a microbial pathway that couples anaerobic ammonium oxidation with sulfate reduction, has recently been proposed as a sustainable alternative for the removal of these pollutants. In this study, we evaluated for the first time the presence and activity of sulfammox microbial communities in sediments from a natural wetland in northeastern Mexico under controlled microcosm conditions. Physicochemical parameters, sediment composition, and ammonium dynamics were analyzed in two natural wetlands: Cachorritos pond (CHP) and Azul turqueza pond (AZP), during a four-week incubation period under controlled conditions. A decrease in ammonium concentration (up to 41.38 mM) was observed only in the CHP, with a stoichiometric NH4[+]/SO4[2-] ratio of 2.45 (92 %), confirming the activity of the sulfammox process. Metagenomic analysis revealed an enrichment of bacterial phylum associated with the sulfammox process, such as Chloroflexi, Chlorobi and Proteobacteria, which increased markedly in sulfate and ammonium treatments. This study represents the first report of sulfammox activity in a natural wetland in Mexico, highlighting the ecological potential of these ecosystems as natural treatment systems and supporting their consideration in sustainable bioremediation strategies.},
}

@article {pmid41232227,
year = {2025},
author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M},
title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110783},
doi = {10.1016/j.vetmic.2025.110783},
pmid = {41232227},
issn = {1873-2542},
abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.},
}

@article {pmid41231980,
year = {2025},
author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH},
title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {eadx7604},
doi = {10.1126/science.adx7604},
pmid = {41231980},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth & development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Gene Editing/methods
*Bacteroides/genetics/growth & development
Humans
Metagenomics/methods
*CRISPR-Cas Systems
Symbiosis
Mice, Inbred C57BL
Metagenome
Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41231970,
year = {2025},
author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO},
title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148025},
doi = {10.1128/aem.01480-25},
pmid = {41231970},
issn = {1098-5336},
abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.

IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.},
}

@article {pmid41231285,
year = {2025},
author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN},
title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {191},
pmid = {41231285},
issn = {1572-9699},
support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; },
abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.},
}

Animals
*Elephants/microbiology
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
*Animals, Wild/microbiology
*Bacteria/classification/genetics/isolation & purification
Endangered Species
Biodiversity
Phylogeny
Animals, Zoo/microbiology
Male
DNA, Bacterial/genetics/chemistry
Feces/microbiology
Female

@article {pmid41231233,
year = {2025},
author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE},
title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001510},
pmid = {41231233},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; },
abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.},
}

*Metagenomics/methods
*Microbiota/genetics
*Stramenopiles/genetics/metabolism/classification
Bacteria/genetics/metabolism/classification
Phylogeny

@article {pmid41231016,
year = {2025},
author = {Wang, YL and Aghdam, SA and Brown, AMV and Deonarine, A},
title = {Global Survey of Mercury Methylation and Demethylation Microbial Communities in Wastewater and Activated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11448},
pmid = {41231016},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are an understudied source of mercury methylating and demethylating microbes to downstream aquatic and terrestrial environments, where methylmercury production and subsequent bioaccumulation in the food web occur. To identify methylators and demethylators and evaluate their occurrence in WWTPs, metagenomic and metatranscriptomic analyses of raw sewage, activated sludge, and effluent samples from WWTPs across the globe were conducted. Results indicated that hgcA- and merB-carriers were widespread in WWTPs, with higher abundance in raw sewage and sludge compared to treated effluent. Bdellovibrionota were identified as merB-carriers, linking them to demethylation for the first time. Novel conserved motifs of hgcB and fused hgcAB were also identified. 30% of hgcA genes were colocalized with arsenic-resistance operons on the same contig, while all merB-carriers contained arsenic resistance genes (ars), though merB and arsR were not colocated. Antibiotic resistance genes were also present in the genomes of multiple hgcA- amd merB-carriers, including one sample where hgcA and the antiseptic/antibiotic resistant gene (qacG) were colocated on the same contig, suggesting possible coselection in environments containing antibiotics. Mobile genetic element-mediated horizontal gene transfer was identified as a mechanism facilitating the genetic transfer of hgcA. Overall, these findings highlight WWTPs as reservoirs of genes involved in mercury methylation and demethylation, with potential implications for mercury cycling in downstream environments.},
}

@article {pmid41230645,
year = {2025},
author = {El-Mayet, FS and Moharam, I and El-Nahas, EM and El-Habbaa, AS and Najar, FZ and Stayton, E and El Nagar, EMS and Radi, M and Khalil, NW and Abaza, MA},
title = {First identification of concurrent infections with novel emerging duck astrovirus and duck hepatitis A virus type 3 (DHAV-3) in ducklings in Egypt using metagenomic next-generation sequencing (m-NGS).},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/03079457.2025.2581279},
pmid = {41230645},
issn = {1465-3338},
abstract = {First complete genome sequencing of a DHAV-3 strain from Egypt using m-NGS.Discovery of a novel duck astrovirus co-infecting with DHAV-3.Phylogenetic analysis reveals cross-border transmission links with Asian strains of both DHAV-3 and DAstV-5.},
}

@article {pmid41230492,
year = {2025},
author = {Rodriguez-Fernandez, IA and Santiago-Rodriguez, TM and Figueroa-Pratts, PG and Cintrón-Berríos, K and Rodriguez-Cornier, ND and Toranzos, GA},
title = {Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1676003},
pmid = {41230492},
issn = {2673-8600},
abstract = {Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns motivate microbiome-informed alternatives. However, limited information exists on the gut anatomy, physicochemical environment, and microbial composition of D. abbreviatus. In this study, we provide the first comprehensive characterization of the gut morphology, pH, and microbiota of adult D. abbreviatus in both females and males collected in Puerto Rico. Using dye-based gut tracing, we identified foregut, midgut, and hindgut or posterior gut compartments, and confirmed the presence of a muscular, sclerotized gizzard. Colorimetric analysis revealed a mildly acidic gut environment (approximately pH 4-5, based on qualitative ranges), consistent across sexes and regions. Shotgun metagenomic sequencing of dissected guts from males and females revealed microbial communities distinct from the leaf samples microbiota. While alpha and beta diversity did not differ significantly between sexes, co-occurrence analyses identified sex-specific correlation patterns among bacterial taxa. Notably, Enterobacter cloacae, Pantoea vagans, Lactococcus lactis, and Pseudomonas monteilii were repeatedly detected across individuals and generated metagenomic datasets, and some were localized to the hindgut, suggesting possible niche specialization. The presence of taxa, such as Enterobacter cloacae, previously reported as symbionts in other phytophagous insects further supports the hypothesis that certain bacteria may contribute to host digestion or adaptation. These findings establish a framework for understanding the gut environment and microbial community of D. abbreviatus, and highlight candidate taxa for future functional studies. More broadly, this work supports further research into the potential roles of gut microbiota in the ecology and management of this pest.},
}

@article {pmid41230491,
year = {2025},
author = {Juhász, J and Ligeti-Nagy, N and Bodnár, B and Juhász, J and Pongor, S and Ligeti, B},
title = {ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf188},
pmid = {41230491},
issn = {2635-0041},
abstract = {MOTIVATION: Phage lifestyle prediction, i.e. classifying phage sequences as virulent or temperate, is crucial in biomedical and ecological applications. Phage sequences from metagenome or virome assemblies are often fragmented, and the diversity of environmental phages is not well known. Current computational approaches often rely on database comparisons that require significant effort and expertise to update. We propose using genomic language models (LMs) for phage lifestyle classification, allowing efficient direct analysis from nucleotide sequences without the need for sophisticated preprocessing pipelines or manually curated databases. We trained three genomic LMs (DNABERT-2, Nucleotide Transformer, and ProkBERT) on datasets of short, fragmented sequences. These models were then compared with dedicated phage lifestyle prediction methods in terms of accuracy, prediction speed, and generalization capability.

RESULTS: ProkBERT PhaStyle achieves accuracy comparable to, and in many cases higher than, state-of-the-art models across various scenarios. It demonstrates the ability to generalize to unseen data in our benchmarks, accurately classifies phages from extreme environments, and also demonstrates high inference speed.

Genomic LMs offer a simple and computationally efficient alternative for solving complex classification tasks, such as phage lifestyle prediction. ProkBERT PhaStyle's simplicity, speed, and performance suggest its utility in various ecological and clinical applications.},
}

@article {pmid41230489,
year = {2025},
author = {Scherz, V and Nassirnia, S and Chaabane, F and Castelo-Szekely, V and Greub, G and Pillonel, T and Bertelli, C},
title = {zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf255},
pmid = {41230489},
issn = {2635-0041},
abstract = {SUMMARY: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules: one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs in microbiota profiling.

Comprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.},
}

@article {pmid41230409,
year = {2025},
author = {Tian, Y and Xu, N and Chen, Y and Xu, Z and Zhou, JX and Zhang, L},
title = {Cost-effectiveness analysis of metagenomic next-generation sequencing versus traditional bacterial cultures for postoperative central nervous system infections in critical care settings: a prospective pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1710412},
pmid = {41230409},
issn = {2235-2988},
mesh = {Humans ; *Cost-Benefit Analysis ; Pilot Projects ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/economics/methods ; Female ; Male ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology/economics ; *Metagenomics/economics/methods ; *Critical Care/economics ; Aged ; *Bacteria/genetics/isolation & purification/classification ; Adult ; *Postoperative Complications/microbiology/diagnosis ; Intensive Care Units ; China ; *Bacteriological Techniques/economics/methods ; Cost-Effectiveness Analysis ; },
abstract = {BACKGROUND: Early and accurate pathogen identification is crucial for managing central nervous system infections (CNSIs). While Metagenomic Next-Generation Sequencing (mNGS) offers rapid and sensitive pathogen detection, its cost-effectiveness in postoperative neurosurgical patients in critical care settings remains underexplored. Our study aims to investigate the clinical health economic value of mNGS in detecting pathogens of CNSIs after neurosurgery.

METHODS: In this prospective pilot study, 60 patients with CNSIs at Beijing Tiantan Hospital ICU (March 2023-January 2024) were randomized 1:1 to mNGS or conventional pathogen culture groups. A decision-tree model compared cost-effectiveness using incremental cost-effectiveness ratios (ICERs). A decision-tree model was used to compare the cost-effectiveness between mNGS and traditional pathogen culture methods using incremental cost-effectiveness ratios (ICERs).

RESULTS: From March 2023 to January 2024, 60 patients were included. mNGS demonstrated superior diagnostic efficiency with shorter turnaround time (1 vs 5 days; _P_<0.001) and lower anti-infective costs (¥18,000 vs ¥23,000; _P_=0.02). Despite higher detection costs (¥4,000 vs ¥2,000; _P_<0.001), the ICER of ¥36,700 per additional timely diagnosis suggested cost-effectiveness at China's GDP-based WTP threshold. No significant differences in hospitalization duration or total costs were observed (_P_>0.05).

CONCLUSION: mNGS improves diagnostic efficiency and reduces antimicrobial expenditure for postoperative CNSIs in critical care, demonstrating favorable cost-effectiveness when considering clinical outcome gains.},
}

Humans
*Cost-Benefit Analysis
Pilot Projects
Prospective Studies
*High-Throughput Nucleotide Sequencing/economics/methods
Female
Male
Middle Aged
*Central Nervous System Infections/diagnosis/microbiology/economics
*Metagenomics/economics/methods
*Critical Care/economics
Aged
*Bacteria/genetics/isolation & purification/classification
Adult
*Postoperative Complications/microbiology/diagnosis
Intensive Care Units
China
*Bacteriological Techniques/economics/methods
Cost-Effectiveness Analysis

@article {pmid41230408,
year = {2025},
author = {Lin, L and Li, X and Li, J and Wu, B and Lin, Y and Li, W and Li, H and Guo, Y and Huang, C and Huang, Z and Zhang, W and Fang, X},
title = {Microbial culture vs. mNGS: diagnostic variations in periprosthetic joint infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1611332},
pmid = {41230408},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/isolation & purification/genetics/classification ; Aged, 80 and over ; *Metagenomics/methods ; *Microbiological Techniques/methods ; Retrospective Studies ; },
abstract = {OBJECTIVE: This study aimed to compare the diagnostic performance of conventional microbial culture and metagenomic next-generation sequencing (mNGS) in detecting pathogens in periprosthetic joint infection (PJI) and to identify factors contributing to discrepancies between these two methods.

METHODS: A total of 167 patients with suspected PJI (including PJI patients and aseptic failure patients) who underwent revision joint replacement at our center from September 2017 to April 2024 were enrolled. Demographic data, prior antibiotic use, and results of microbial culture and mNGS were documented. Joint fluid, periprosthetic tissue, or prosthetic ultrasonic fluid samples were collected, and at least one sample from each patient underwent both microbial culture and mNGS testing. In the light of the concordance between culture and mNGS results, patients were divided into the detection consistent and detection inconsistent groups. The differences in pathogen detection between the two models were compared, and factors contributing to discordant results were analyzed.

RESULTS: The prior antibiotic use (OR = 2.137, 95% CI = 1.069-4.272, P = 0.032), polymicrobial infections (OR = 3.245, 95% CI = 1.278-8.243, P = 0.013), infection caused by rare pathogens (OR = 2.735, 95% CI = 1.129-6.627, P = 0.026), and intraoperative tissue specimens (OR = 2.837, 95% CI = 1.007-7.994, P = 0.049) were identified as risk factors for discordance between microbial culture and mNGS results, particularly in cases with negative microbial culture but positive mNGS findings. Conversely, consistency in specimen type (OR = 0.471, 95%CI=0.254-0.875, P = 0.017) was identified as a protective factor against discordance.

CONCLUSION: Clinicians should optimize diagnostic strategies by tailoring microbial culture methods to the patient's clinical condition and integrating mNGS testing where appropriate. It is recommended to use tissue specimens from the same anatomical site across multiple tests while sampling from different regions when necessary. Although this approach may increase costs, it significantly enhances the accuracy of pathogen identification and facilitates more effective treatment.},
}

Humans
*Prosthesis-Related Infections/diagnosis/microbiology
Male
Female
Aged
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/isolation & purification/genetics/classification
Aged, 80 and over
*Metagenomics/methods
*Microbiological Techniques/methods
Retrospective Studies

@article {pmid41229791,
year = {2025},
author = {Wang, W and Mo, Q and Yu, Q and Ding, X},
title = {Clinical characteristics of Pneumocystis jirovecii pneumonia in 20 non-HIV-infected patients.},
journal = {Journal of thoracic disease},
volume = {17},
number = {10},
pages = {8904-8914},
pmid = {41229791},
issn = {2072-1439},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PCP) is a life-threatening disease in clinics, commonly associated with human immunodeficiency virus (HIV) infected patients. Nowadays, with the increasing use of immunosuppressants, the incidence of PCP in non-HIV-infected patients is also on the rise. This study aimed to investigate the clinical diagnosis and treatment of PCP in non-HIV-infected patients.

METHODS: We collected and retrospectively analyzed 20 cases of PCP diagnosed in HIV-negative patients at Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University.

RESULTS: All cases were diagnosed using metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL). Of all 20 patients, 11 were men and nine were women. The median age was 66.5 (range, 18-83) years old. Three out of 20 patients had no immunosuppressive background, while 17 were exposed to immunosuppressants due to different diseases. Among them, four had solid malignancies, four had kidney disease, three had hematological malignancies, two had skin diseases, one had thrombocytopenia, one had rheumatoid arthritis, one had anaphylactoid purpura and one had knee arthritis. All patients had not received prophylactic drugs for PCP. All patients underwent antimicrobial treatment, 16 cases received glucocorticoid treatment, and seven underwent mechanical ventilation. A total of six out of 20 patients died. Bivariate Pearson's test revealed a negative correlation between patients' oxygenation index and age (r=-0.493, P=0.03). Serum lactate dehydrogenase (LDH) levels were positively correlated with serum creatinine levels (r=0.557, P=0.01). LDH levels were positively correlated with the time between symptom onset and oral administration of compound sulfamethoxazole (SMZ-TMP) (r=0.477, P=0.03). There was also a positive correlation between creatinine levels and the time to oral SMZ-TMP administration (r=0.607, P=0.005).

CONCLUSIONS: HIV-negative patients with PCP have atypical clinical symptoms and a high mortality rate. mNGS technology may facilitate early diagnosis based on its rapid turnaround time. To reduce mortality, SMZ-TMP drug treatment should be initiated promptly once PCP is considered clinically.},
}

@article {pmid41229688,
year = {2025},
author = {Zhao, J and Zeng, R and Zhang, C and He, B and Zhang, Q and Zhou, Q and Gong, Z and Liu, H and Liu, S},
title = {Comparative analysis of soil properties before and after Morchella sextelata cultivation across various soil types.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1700246},
pmid = {41229688},
issn = {1664-302X},
abstract = {Morchella, a highly nutritious edible fungus, has been successfully cultivated through artificial means. However, as cultivation areas have expanded, declining yield have emerged more prominently. Soil physicochemical characteristics and microbial communities were critical to production on cultivating morels. In this study, our results reveals that cultivation significantly alters soil properties and microbial communities in a soil type-dependent manner. In sandy soil, pH and key nutrients (total nitrogen, total phosphorus, available phosphorus) increased, while potassium and calcium levels decreased. Microbial diversity decreased in sandy soil but increased in paddy soil, with the overall community structure in sandy soil being more drastically reshaped. Metagenomic profiling identified distinct differential taxa and functional shifts, showing that sandy soil exhibited greater enrichment of microbial genes, including soil-borne diseases. These findings demonstrate that M. sextelata cultivation induces considerable and contrasting changes in soil nutrient profiles and microbiome composition, with sandy soil being more susceptible to microbial restructuring and potential pathogen enrichment.},
}

@article {pmid41229344,
year = {2025},
author = {Sures, K and Esser, SP and Bornemann, TLV and Moore, CJ and Soares, AR and Plewka, J and Figueroa-Gonzalez, PA and Ruff, SE and Moraru, C and Probst, AJ},
title = {Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf201},
pmid = {41229344},
issn = {1759-6653},
mesh = {*CRISPR-Cas Systems ; *Genome, Archaeal ; *Archaea/genetics ; Genome, Bacterial ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Bacteria/genetics ; Metagenome ; Evolution, Molecular ; *DNA, Intergenic/genetics ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer analyses revealed a very specific acquisition of CRISPR spacers derived from genomes of related species or from closely interacting episymbiont genomes as recently shown for subsurface archaea. However, the origin of most of the spacers that can be found in CRISPR-Cas systems from natural environments has not been deciphered. Here, by analyzing CRISPR-Cas systems of metagenome-assembled genomes (MAGs) from two subsurface environments spanning more than 1 Tb of sequencing data, we show that a substantial proportion of CRISPR spacers are acquired from DNA of other prokaryotes inhabiting the same environment. As such, we found that the number of respective spacers can be up to three times higher than the number of self-targeting spacers. Statistical analyses demonstrated that the acquisition of CRISPR spacers from other prokaryotic genomes is partly explained by the relative abundance of the MAG containing the protospacer, as well as by other factors, such as the total number of CRISPR arrays present in a MAG with the respective spacers. Further, we found that spacer acquisition from foreign prokaryotic DNA occurs in almost all types of CRISPR-Cas systems, but shows preferences for subtypes of CRISPR-Cas systems that differ across the investigated ecosystems. Taken together, our results shed new light on the diversity of CRISPR spacers in natural microbial communities and provide an explanation for some of the many unmatched spacers in public databases.},
}

*CRISPR-Cas Systems
*Genome, Archaeal
*Archaea/genetics
Genome, Bacterial
*Clustered Regularly Interspaced Short Palindromic Repeats
*Bacteria/genetics
Metagenome
Evolution, Molecular
*DNA, Intergenic/genetics

@article {pmid41229166,
year = {2025},
author = {Houttu, N and Mokkala, K and Lindgren, H and Lotankar, M and Benchraka, C and Pärnänen, K and Saros, L and Muhli, E and Vahlberg, T and Lahti, L and Laitinen, K},
title = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70128},
doi = {10.1002/mbo3.70128},
pmid = {41229166},
issn = {2045-8827},
support = {//This clinical trial was supported by the State Research Funding for university-level health research in the Turku University Hospital Expert Responsibility Area, Research Council of Finland (#258606), the Diabetes Research Foundation, the Juho Vainio Foundation, the Finnish Cultural Foundation, Päivikki and Sakari Sohlberg Foundation, Sigrid Juselius Foundation, and the Finnish Foundation for Cardiovascular Research. Funding to the University of Turku for the metagenomics analyses was provided by Janssen Research and Development, LLC. Himmi Lindgren was partially supported by the Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC)./ ; },
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Adiposity ; *Postpartum Period ; Adult ; Body Mass Index ; *Obesity/microbiology ; Metagenomics ; Young Adult ; Bacteria/classification/genetics/isolation & purification ; Overweight/microbiology ; Waist-Hip Ratio ; },
abstract = {Gut microbiota is linked with health, including obesity, in the general population. It is unknown whether adiposity at postpartum is influenced by gut microbiota already during pregnancy. We investigated the association between the gut microbiota's composition and predicted function by metagenomics during pregnancy and the women's adiposity (body mass index [BMI], waist-to-hip ratio [WHR], body fat%) assessed at 1-, 2-, and 5-6-years' postpartum in 257 women with overweight or obesity based on prepregnancy BMI values. Body fat% at 1-year, but not at 2- or 5-6-years' postpartum, was associated inversely with α-diversity during pregnancy. Bacterial species GGB3034 SGB4030 (family Erysipelotrichaceae) was higher in women with normal weight than those in women with obesity at 1-year postpartum (q = 0.02), other species being borderline statistically significant (q < 0.25). High WHR and body fat% at 1-year postpartum were associated with two species (q < 0.25). Considering predicted functions of bacteria, an association was detected for BMI, WHR, and body fat%, e.g., body fat% and glycogen biosynthesis I (q < 0.25). Gut microbiota during pregnancy predicted the BMI and body fat% at 1-year postpartum (ROC > 0.50, p < 0.02). Postpartum adiposity was associated with several species and α-diversity. Gut microbiota during pregnancy may be involved in the persistence of obesity and its comorbidities after pregnancy.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
*Adiposity
*Postpartum Period
Adult
Body Mass Index
*Obesity/microbiology
Metagenomics
Young Adult
Bacteria/classification/genetics/isolation & purification
Overweight/microbiology
Waist-Hip Ratio

@article {pmid41228422,
year = {2025},
author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S},
title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213350},
pmid = {41228422},
issn = {2072-6643},
support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; },
abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Affect/physiology
*Decision Making/physiology
Animals
Cognition
Probiotics
Dysbiosis/microbiology
Fecal Microbiota Transplantation
Prebiotics/administration & dosage

@article {pmid41228409,
year = {2025},
author = {Xu, C and Cui, H and Fang, Q and Tu, P and Cui, X},
title = {Steamed Panax notoginseng Saponins Ameliorate Cyclophosphamide-Induced Anemia by Attenuating Gut-Liver Injury and Activating the cAMP/PI3K/AKT Signaling Pathway.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213335},
pmid = {41228409},
issn = {2072-6643},
support = {202202AG050021//the Yunnan Major Scientific and Technological Projects/ ; },
mesh = {Animals ; *Saponins/pharmacology ; *Panax notoginseng/chemistry ; *Cyclophosphamide/adverse effects ; Signal Transduction/drug effects ; *Anemia/chemically induced/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Cyclic AMP/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism ; Colon/metabolism/drug effects ; },
abstract = {Background: Steamed Panax notoginseng saponins (SPNSs) can alleviate cyclophosphamide-induced anemia. However, the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia remain unexplored. Objective: To elucidate the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia. Methods: Blood samples were collected and analyzed on days 7 and 14. Liver tissues and small intestinal villi structures were observed via HE staining. Liver and colon content metabolites were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Liver proteins were analyzed by using an Orbitrap Astral mass spectrometer. Colon content microbiota composition was assessed via metagenomics. Signaling pathway protein expression was analyzed via Western blotting (WB). Results: SPNSs significantly increased the red blood cell (RBC) count and hemoglobin (HGB) level by day 14 and alleviated hepatointestinal damage. Hepatic metabolomics revealed: the most abundant metabolites were fatty acids and stachyose on day 7 and amino acid and arachidonic acid derivatives on day 14. KEGG analysis implicated cAMP signaling. Proteomics revealed upregulated immune-related proteins and enhanced PI3K pathway activity (WB-validated). Colon content metabolomics showed increased daidzein, 3-(2,5-dimethoxyphenyl) propanoic acid, γ-CEHC, and adenosine in SPNS groups on day 14. Metagenomics indicated differential abundances of Heminiphilus faecis, Phocaeicola sartorii, and s-bacterium_J10.2018 on day 14. Multiomics integration demonstrated significant correlations between hepatic metabolites, hematopoietic proteins, colon content metabolites, and probiotic bacteria. Conclusions: SPNS alleviates cyclophosphamide-induced hepato-intestinal injury in anemic mice by modulating the gut microbiota and enhancing hepato-intestinal immune defense. Additionally, SPNSs ameliorate anemia in cyclophosphamide-treated mice by activating the cAMP/PI3K/AKT pathway, promoting hepatocyte proliferation, and increasing hematopoietic protein expression.},
}

Animals
*Saponins/pharmacology
*Panax notoginseng/chemistry
*Cyclophosphamide/adverse effects
Signal Transduction/drug effects
*Anemia/chemically induced/drug therapy
Proto-Oncogene Proteins c-akt/metabolism
Mice
Cyclic AMP/metabolism
Phosphatidylinositol 3-Kinases/metabolism
Gastrointestinal Microbiome/drug effects
Male
Liver/drug effects/metabolism
Colon/metabolism/drug effects

@article {pmid41227654,
year = {2025},
author = {Liscano, Y and Caicedo, N and Oñate-Garzón, J},
title = {Unlocking New Bioactive Peptides from Coffee Pulp: A Metagenomics and AI-Driven Discovery Paradigm.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227654},
issn = {2304-8158},
support = {call No. DGI-01-2025//Universidad Santiago de Cali/ ; },
abstract = {This perspective reframes Colombian coffee pulp from an environmental liability into a strategic asset by proposing a new discovery paradigm. We argue that the pulp's challenging chemical environment is not a barrier but its key advantage, having acted as a natural evolutionary filter that has sculpted a unique, highly resilient microbiome. Our vision is a technology pipeline that harnesses this natural pre-selection. By converging deep metagenomic data from the pulp's microbiome with generative artificial intelligence, we can create and validate novel, high-performance bioactive peptides and enzymes that are already pre-optimized for industrial robustness. This approach transcends traditional waste valorization, establishing a new framework for "biointelligence" in action. It offers a strategic roadmap for Colombia to generate knowledge-intensive value chains from its most iconic agricultural product, turning a national challenge into a global opportunity in the bioeconomy.},
}

@article {pmid41227630,
year = {2025},
author = {Luo, Q and Li, X and Li, J and Lu, Y and Chen, J and Su, J and Zhao, D and Hu, J and Zhang, X and Zhao, P and Zhang, Z and Zhang, Q and Lei, X and Bai, J and Zheng, J and Zhao, X},
title = {Multi-Metaomics Unveils the Development Process of Microbial Communities During the Fermentation of Baobaoqu.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227630},
issn = {2304-8158},
support = {JUSRP202504012//Fundamental Research Funds for the Central Universities/ ; BK20233003//Jiangsu Basic Research Center for Synthetic Biology/ ; 32021005//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
abstract = {In order to understand the dynamic interaction process among species, enzymes, and metabolites during the fermentation process of Baobaoqu, which is a representative Daqu starter for Chinese baijiu, the intimate connection between the progression of microbial communities and the diversities and activities of enzymes was examined by metagenomics, metatranscriptomics and metaproteomics. It was found that while 5211 species of microorganisms were detected by metagenomics, only 1774 active species were detected by metatranscriptomics, which indicated that only a small proportion (34.04%) were active. The metabolic routes associated with the breakdown of substrates and synthesis of metabolites were redesigned, and the special functional microorganisms for lactate, pyrazines and phenylethyl alcohol production were isolated. It was found that the progression of the microbial community was highly coupled with the components of enzymes and flavor substrates, precisely corresponding to the three stages of the Baobaoqu fermentation process, and were regulated by multiple physical factors. During the Baobaoqu-making process of the fermentation, microorganisms with different functions work together to complete metabolism in different stages. These findings will aid us in gaining a deeper and clearer understanding of the "species-enzyme-metabolite" system within the Daqu starter culture, thus offering valuable perspectives for developing artificial synthetic communities and the production of high-quality Baobaoqu.},
}

@article {pmid41227601,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Li, B and Zhu, J},
title = {The Presence of Stone Moroko (Pseudorasbora parva) Drives Divergent Sediment Resistome Profiles in Chinese Mitten Crab (Eriocheir sinensis) Polyculture Pond.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227601},
issn = {2304-8158},
support = {CARS-45//China Agriculture Research System of MOF and MARA/ ; 31802302//National Natural Science Foundation of China/ ; 2023TD64//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; BK20231140//Jiangsu Provincial Natural Science Foundation of China/ ; 2019YFD0900305//National Key R&D Program of China/ ; },
abstract = {The propagation of antibiotic resistance genes (ARGs) in aquatic environments poses a significant threat to global health. This study compared sediment resistome profiles in river crab (Eriocheir sinensis) polyculture systems with and without stone moroko (Pseudorasbora parva). The results showed that, compared to the control group (MC group), the sediment from the polyculture system containing stone moroko (PC group) exhibited significant reductions in the total abundances of ARGs, metal resistance genes (MRGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Crucially, the total abundance and composition of MGEs in pond sediment were substantially correlated with ARGs, MRGs, and BRGs, respectively. Co-occurrence network analysis revealed that there was only one edge between ARGs and MGEs in the PC group, whereas the MC group had eight edges. Additionally, the proportion of mobile ARGs in the PC group was significantly lower than that in the MC group. Alterations in resistome profiles were markedly associated with decreased levels of total carbon (TC) and phosphate in the sediment. All of the findings demonstrated that the introduction of stone moroko in the river crab polyculture system effectively mitigated the sediment resistome primarily by altering environmental factors and suppressing MGEs, thereby disrupting the horizontal transfer network of resistance genes. This study highlights the potential of leveraging aquatic biota as a novel biological strategy for the in situ management of environmental antimicrobial resistance.},
}

@article {pmid41227457,
year = {2025},
author = {Soto-López, JD and Fernández-Soto, P and Muro, A},
title = {Bacterial Composition Across Bat Species: A Human Health Perspective.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227457},
issn = {2076-2615},
abstract = {Bats are widely recognized as reservoirs of diverse bacterial pathogens with important implications for human health. Recent zoonotic disease outbreaks have intensified interest in bat microbiomes, with high-throughput sequencing increasingly used to assess microbial diversity. In this article, we review literature from the past five years on bacterial species associated with bats and their potential clinical relevance. Using automated searches and manual filtering, we extracted data from 47 peer-reviewed studies. Most research has focused on guano samples, though interest in skin microbiomes is rising, particularly in relation to Pseudogymnoascus destructans, the agent of white-nose syndrome. China leads in the number of publications, followed by the United States, and amplicon sequencing remains the predominant metagenomic method. Across studies, 4700 bacterial species were reported, including several known human pathogens capable of aerosol transmission or opportunistic infections in immunocompromised individuals. Many of these taxa are classified as global priority targets for antimicrobial drug development by the World Health Organization and the U.S. Centers for Disease Control and Prevention. Given the clinical severity of diseases linked to some species, bats should be integrated into epidemiological surveillance systems. However, the lack of standardized reporting practices significantly limits the comparability and utility of bat microbiome data for robust ecological and epidemiological analyses.},
}

@article {pmid41227433,
year = {2025},
author = {Yang, B and Shen, P and Xu, Z and Yang, J and Song, B and Jiang, H and Chai, J and Zhao, J and Deng, F and Li, Y},
title = {Functional and Compositional Changes in Ileal Microbiota in Piglets During the Nursing Period Revealed by 16s rRNA Gene and Metagenomics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227433},
issn = {2076-2615},
support = {2023YFE0124400//the National Key Research and Development Program of China/ ; 2023B10564001//the Specific University Discipline Construction Project/ ; 2022A1515110819//Youth Project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; No. 32202715//the National Natural Science Foundation of China/ ; },
abstract = {In piglets, the gut microbiota matures in a segment-specific manner during the nursing period, while fecal-based studies provide limited functional resolution across intestinal sites. We profiled the ileum using 16s rRNA gene sequencing and assessed segmental functions by shotgun metagenomics at selected ages. Ileal species richness and diversity were relatively stable across days. Lactobacillus were prominent from day 7, with stage-associated taxa including Lactobacillus johnsonii, Lactobacillus delbrueckii, Ligilactobacillus salivarius, and Limosilactobacillus pontis. Through metagenomic functional analysis, at 21 days, genes were enriched in butanoate metabolism, and Limosilactobacillus pontis as a potential probiotic played an important role in it. At day 28, metagenomic analysis indicated higher relative abundance in the ileum of pathways linked to cysteine and methionine metabolism and lysine biosynthesis, largely carried by Limosilactobacillus mucosae, Limosilactobacillus oris, and Limosilactobacillus pontis. These data describe the composition and function of the ileum in the intestines of piglets and indicate a differentiation period around day 21 to day 28.},
}

@article {pmid41227430,
year = {2025},
author = {Deng, L and Yao, Y and Li, H and Lu, Q and Wu, R},
title = {Effects of Antimicrobial Peptides on the Growth Performance of Squabs Were Investigated Based on Microbiomics and Non-Targeted Metabolomics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227430},
issn = {2076-2615},
support = {2023B02036//Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; XJARS-12-01//Xinjiang Uygur Autonomous Region Modern Agricultural Industrial Technology System/ ; 2025XJJQ-z-01//Xinjiang Uygur Autonomous Region Modern Livestock and Poultry Breeding Industry Promotion Project/ ; },
abstract = {This study aims to investigate the effects of dietary supplementation with AMPs on the growth performance, antioxidant capacity, and intestinal health of squabs. Furthermore, metagenomic and metabolomic approaches were employed to identify key differential bacterial species and metabolites associated with growth performance, and thereby the potential mechanisms underlying the enhancement of squab growth and development by AMPs being elucidated. One hundred and twenty pairs of healthy adult White Carneau pigeons (2 years old) were randomly divided into two groups, the control group (CK, fed with basal diet) and antimicrobial peptide group (AP, fed with basal diet +200 mg/kg antimicrobial peptide), with 10 replicates per group and 6 pairs of breeding pigeons per replicate. The experiment lasted for 53 days, including 7 days of prefeeding, 18 days of incubation and 28 days of feeding. In this study, squabs were weighed at 0 and 28 days of age to evaluate growth performance. At 28 days of age, duodenal contents were collected to assess digestive enzyme activities, while jejunal and liver tissues were harvested to determine antioxidant capacity. Intestinal morphology was examined using tissue samples from the duodenum, jejunum, and ileum. Finally, ileal contents were collected for a comprehensive analysis of microbial composition and metabolite profiles in the two experimental groups, employing high-throughput sequencing and LC-MS/MS techniques. The results showed that body weight, liver total antioxidant capacity (T-AOC), jejunal malondialdehyde (MDA) content, jejunum and ileum villus height-to-crypt depth ratio (VH/CD) were significantly increased, and jejunal crypt depth (CD) was significantly decreased in the AP group at 28 days of age (p < 0.05). In addition, the microbiome data showed that Lactobacillus in the AP group was a biomarker with significant differences (p < 0.05). Metabolomics analysis showed that the steroid hormone biosynthesis pathway was significantly different between the two groups (p < 0.01). In addition, the content of potentially beneficial metabolites (Biotin, beta-Tocotrienol, 7-Chloro-L-tryptophan and Dihydrozeatin) was significantly increased in the AP group (p < 0.05). These results indicate that dietary AMPs can significantly improve the body weights, liver antioxidant capacity and jejunum and ileum VH/CD of squabs.},
}

@article {pmid41227427,
year = {2025},
author = {Lu, H and Wang, H and Li, B and Lv, Z and Li, S and Xia, Y and Wang, L},
title = {Effects of Soybean Meal Replacement on Growth Performance, Rumen Fermentation, Rumen Microorganisms, and Metabolites in Dumont Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227427},
issn = {2076-2615},
support = {BR231520//Basic Research Operating Funds of Universities under the Direct Administration of the Inner Mongolia Autonomous Region/ ; project No. BR22-13-13//Basic Research Fund for Universities in Inner Mongolia Autonomous Region/ ; YLXKZX-NND-007//Inner Mongolia Education Department Special Research Project For First Class Disciplines/ ; },
abstract = {This study investigated the effects of replacing part of the soybean meal in the diet of Dumont lambs with urea, rapeseed meal, and cottonseed meal on their growth performance and rumen fermentation and combined rumen microbial metagenomics and metabolomics to explain the reasons for the changes in phenotypic data. Twenty-four healthy male Dumont lambs were divided into four groups: soybean meal group (T1, control group), group with 1.5% urea replacing 6.4% soybean meal (T2), group with 1% urea replacing 4.3% soybean meal (T3), and group with 1% urea + 6.6% cottonseed meal +5% rapeseed meal replacing all soybean meal (19%) (T4), following the principle of equal energy and nitrogen. Urea, rapeseed meal, and cottonseed meal have different degradation rates in the rumen, primarily stimulating arginine biosynthesis, sulphur metabolism, and carbon fixation in photosynthetic organisms through Prevotella genus mediation, thereby influencing the accumulation of metabolites such as 9,10-DiHOME, DG (PGJ2/a-15:0/0:0), isonicotinate and taxifolin, affecting rumen fermentation. Compared with the T1 group, the T2 group showed significantly increased ammonia nitrogen (NH3-N) and microbial protein (MCP) content (p < 0.01) and improved fructose and mannose metabolic capacity (p < 0.05). The T3 group showed a significant increase in total volatile fatty acids (TVFA) and MCP content (p < 0.01), which facilitated the absorption of subsequent nutrients. In the T4 group, different degradation rates of nitrogen resources and rapeseed meal + cottonseed meal contained abundant and complementary amino acids, which improved rumen fermentation, enhanced rumen microbial and metabolite diversity, and optimized the synergistic metabolic efficiency of carbon, nitrogen and sulphur. However, the specific mechanisms of post-rumen metabolism and absorption require further investigation.},
}

@article {pmid41227163,
year = {2025},
author = {Armbruster, J and Thomas, B and Stengel, D and Spranger, N and Gruetzner, PA and Hackl, S},
title = {Managing Nonunions and Fracture-Related Infections-A Quarter Century of Knowledge, and Still Curious: A Narrative Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {21},
pages = {},
pmid = {41227163},
issn = {2077-0383},
abstract = {Nonunions and fracture-related infections represent a significant complication in orthopedic and trauma care, with their incidence rising due to an aging, more comorbid global population and the escalating threat of multi-resistant pathogens. This narrative review highlights pivotal advancements in diagnostics and therapeutic approaches, while also providing an outlook on future directions. Diagnostic methodologies have significantly evolved from traditional cultures to sophisticated molecular techniques like metagenomic next-generation sequencing and advanced imaging. Simultaneously, therapeutic strategies have undergone substantial refinement, encompassing orthoplastic management for infected open fractures and the innovative application of antibiotic-loaded bone substitutes for local drug delivery. The effective integration of these possibilities into daily patient care critically depends on specialized centers. These institutions play an indispensable role in managing complex cases and fostering innovation. Despite considerable progress over the past 25 years, ongoing research, interdisciplinary collaboration, and a steadfast commitment to evidence-based practice remain crucial to transforming management for the future.},
}

@article {pmid41226831,
year = {2025},
author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E},
title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110796},
pmid = {41226831},
issn = {1422-0067},
support = {КП-06-Н83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; },
mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; },
abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.},
}

Humans
Female
*Endometrium/microbiology
*Microbiota
*Embryo Implantation
Dysbiosis/microbiology
*Reproduction

@article {pmid41226812,
year = {2025},
author = {Kondo, T and Kondo, S and Nakayama-Imaohji, H and Tada, A and Tabassum, N and Munyeshyaka, E and Koyano, K and Nakamura, S and Kusaka, T and Kuwahara, T},
title = {Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110775},
pmid = {41226812},
issn = {1422-0067},
support = {24K14726//JSPS KAKENHI/ ; 23K28020//JSPS KAKENHI/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; *Intestinal Mucosa/microbiology/pathology ; Adolescent ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Dysbiosis/microbiology ; },
abstract = {Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease, are chronic disorders relating to gut microbiota dysbiosis. Despite severe pancolitis being more prevalent in pediatric UC than in adults, alterations in the colon mucosa-associated microbiota (MAM) and their association with disease severity remain to be elucidated. The present study aimed to compare the gut microbiota in colon lavage fluids (CLFs) and fecal samples from 19 pediatric UC and 19 non-IBD patients. The community structure of MAM inferred by 16S metagenomic analysis was similar throughout the colon regardless of disease type. Bacterial compositions between MAM and feces were significantly different in non-IBD, while no difference was observed in pediatric UC, indicating a compromised mucous layer that could not sufficiently separate the MAM and luminal microbiota in UC. In pediatric UC, homogenous distribution of MAM was gradually disordered with increases in disease activity or mucosal inflammation, and bacterial groups of upper digestive tract or environmental origin were more abundant in MAM. Monitoring key bacterial markers in MAM, which include Lactobacillus and Enterococcus or Faecalibacterium and Blautia as increased or reduced members in pediatric UC, respectively, might be useful for evaluation of patient prognosis.},
}

Humans
*Colitis, Ulcerative/microbiology/pathology
*Gastrointestinal Microbiome/genetics
Child
Male
Female
*Intestinal Mucosa/microbiology/pathology
Adolescent
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Child, Preschool
Dysbiosis/microbiology

@article {pmid41226502,
year = {2025},
author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT},
title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110463},
pmid = {41226502},
issn = {1422-0067},
support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; },
abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.},
}

Humans
*Gastrointestinal Microbiome
*Tryptophan/metabolism
*Serotonin/metabolism
Male
Female
Middle Aged
*Renal Dialysis
Aged
Melatonin/metabolism
Metagenomics/methods
Adult

@article {pmid41225603,
year = {2025},
author = {Rong, H and Wu, Z and Zhao, K and Ding, Y and Ning, S and Tian, Y and Wang, X and Qiao, Q and Zhu, X and Wu, T and Ge, Y and Chu, H and Cui, L},
title = {Identification and characterization of Jingmen tick virus in Jiangsu, China.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {372},
pmid = {41225603},
issn = {1743-422X},
support = {BK20231374//Natural Science Foundation of Jiangsu Province/ ; 2023YFC2605100, 2023YFC2605104//National Key Research and Development Program of China/ ; },
mesh = {China ; Phylogeny ; Animals ; Genome, Viral ; *Flaviviridae/isolation & purification/genetics/classification ; Genetic Variation ; Sequence Analysis, DNA ; *Ticks/virology ; *Ixodidae/virology ; },
abstract = {Jingmen virus (JMV) is a group of viruses that belong to the Flaviviridae family. These viruses have been shown to cause widespread infections in various hosts and can lead to febrile illnesses in humans. Jingmen tick virus (JMTV) as an important member of the JMV group, has been detected in multiple countries worldwide and poses a significant threat to public health. This study utilized metagenomic sequencing technology to detect JMV in tick samples collected in Jiangsu Province. The results demonstrated the presence of JMTV in Jiangsu and identified two complete genomes (ZJ-7-4-2 and ZJ-7-9) from Haemaphysalis campanulate ticks. These gene sequences exhibited the highest sequence similarity to the known Japanese isolate of JMTV. Phylogenetic analysis showed that the JMTV identified in this study clustered within the same clade as the Japanese JMTV. In summary, this study reported for the first time that JMTV is prevalent in Jiangsu Province, China. These findings expand the known geographic distribution and genetic diversity of JMTV, providing new insights into its epidemiology and viral evolution.},
}

China
Phylogeny
Animals
Genome, Viral
*Flaviviridae/isolation & purification/genetics/classification
Genetic Variation
Sequence Analysis, DNA
*Ticks/virology
*Ixodidae/virology

@article {pmid41225454,
year = {2025},
author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T},
title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.},
journal = {BMC pregnancy and childbirth},
volume = {25},
number = {1},
pages = {1198},
pmid = {41225454},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; },
abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).

METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n = 31) and those with normal thyroid function (Control group, n = 30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16 S rRNA metagenomic sequencing.

RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p = 0.034; Shannon index, p = 0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p = 0.002, p = 0.049, and p = 0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.

CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.},
}

Humans
Female
Pregnancy
*Hypothyroidism/microbiology
*Microbiota
*Mouth/microbiology
Adult
Prospective Studies
Infant
Infant, Newborn
*Pregnancy Complications/microbiology
Case-Control Studies
Postpartum Period

@article {pmid41225248,
year = {2025},
author = {Bignami, G and Monzón-Atienza, L and Leuzzi, D and Scicchitano, D and Candela, M and Gómez-Mercader, A and Jlidi, M and Gustinelli, A and Tedesco, P and Fioravanti, ML and Castro, PL and Acosta, F},
title = {"Effects of Bacillus Velezensis D-18 on Health Status of European Seabass (Dicentrarchus labrax) Experimentally Challenged with Vibrio harveyi".},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41225248},
issn = {1867-1314},
support = {28740//Horizon 2020/ ; },
abstract = {In recent years, the use of probiotics as a possible alternative to antibiotics has generated a growing interest in the global aquaculture field. In this study, the probiotic Bacillus velezensis D-18 was evaluated for its potential protective effect against the marine pathogen Vibrio harveyi. The probiotic was administered through the diet of European seabass (Dicentrarchus labrax) for 30 days, followed by an in vivo challenge with V. harveyi to assess whether the D-18 strain could enhance host resistance to infection. Biofilm formation in tanks was also investigated to analyze its composition and if there are antagonistic interactions between the two bacterial species. From a histological perspective, significant changes were observed in intestinal morphological parameters after infection, the area and base of the villi appeared to increase in the probiotic-fed groups as did the number of goblet cells and in the serum antibacterial activity which was increased in the infected group that received the probiotic compared to baseline levels. The intestinal microbiome was also analyzed to monitor the composition and determine whether different diets before and after infection induced any changes. Although no significant differences were found in the metagenomics of the tank biofilm and the gut microbiome, mortality rates showed that the probiotic provided effective protection against the pathogen. These findings support the potential of B. velezensis D-18 as a viable alternative to antibiotics, particularly when included in the diet prior to disease onset.},
}

@article {pmid41225104,
year = {2026},
author = {Kars, G and Alkebsi, BLA and Keleş, S and Altan, H and Özer, H and Holyavkin, C and Karaselek, MA},
title = {Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {291-313},
pmid = {41225104},
issn = {0065-2598},
mesh = {Humans ; *Dental Caries/microbiology/immunology ; *Microbiota/immunology ; Child ; Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; },
abstract = {Inborn errors of immunity (IEIs) are genetic disorders that impair immune defense and regulation, increasing susceptibility to infections, including those in the oral cavity. The oral microbiota plays a vital role in maintaining oral health, and in pediatric patients with IEIs, disruptions in this balance can lead to dental caries and other oral diseases. This chapter provides a comprehensive analysis of the relationship between immune deficiencies and oral microbiota dysbiosis, focusing on dental caries in children with IEIs. Omics technologies, particularly metagenomics, have enhanced understanding of the microbial diversity and metabolic activities within the oral microbiota of the patients. Key findings reveal that compromised immune responses in children with IEIs disrupt the balance of oral bacteria, making them more prone to dental caries. The chapter highlights the importance of an interdisciplinary approach, integrating microbiology, immunology, dentistry, and bioinformatics, to uncover the complex interactions between the oral microbiome and the immune system. The insights gained from this research will contribute to the development of personalized therapeutic strategies, improving the dental and overall health of pediatric patients with IEIs.},
}

Humans
*Dental Caries/microbiology/immunology
*Microbiota/immunology
Child
Dysbiosis/immunology/microbiology
*Mouth/microbiology/immunology

@article {pmid41225090,
year = {2026},
author = {Ziaei, H and Rezaei, N},
title = {Introduction to Oral Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {3-21},
pmid = {41225090},
issn = {0065-2598},
abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.},
}

@article {pmid41224996,
year = {2025},
author = {Nadel, O and Hanna, R and Rozenberg, A and Shitrit, D and Tahan, R and Pekarsky, I and Béjà, O and Kleifeld, O and Lindell, D},
title = {Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41224996},
issn = {1476-4687},
abstract = {Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages-viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phage's benefit[1-5]. One such gene is nblA, which is present in multiple cyanophage families[2,6-8]. Under nutrient deprivation cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome[9-11], the large cyanobacterial photosynthetic light-harvesting complex. This increases the pool of amino acids available for essential tasks[11], serving as a survival mechanism[12]. Ectopic expression of different cyanophage nblA genes results in host pigment protein degradation[6,8,13]. However, the benefit of the virus-encoded NblA for cyanophages and the broader impact on the host are unclear. Here, using a recently developed genetic manipulation system for marine cyanophages[14], we reveal that viral NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins, and reduces host photosynthetic light-harvesting efficiency. Metagenomic analysis revealed that cyanophages carrying nblA are widespread in the oceans and comprise 35% and 65% of oceanic T7-like cyanophages in surface and deep photic zones, respectively. Our results show a large benefit of NblA to the cyanophage, while it exerts a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest that cyanophage NblA has an adverse global impact on light harvesting by oceanic picocyanobacteria.},
}

@article {pmid41224779,
year = {2025},
author = {Secaira-Morocho, H and Jiang, X and Zhu, Q},
title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9943},
pmid = {41224779},
issn = {2041-1723},
support = {RFGA2023-008-15//ADHS | Arizona Biomedical Research Commission (ABRC)/ ; },
abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes representing major microbial phyla, covering only a small fraction of gene families. However, most microbial diversity resides in metagenome-assembled genomes, which exhibit taxonomic imbalance and harbor gene families that do not fit the criteria for universal orthologs. To address these limitations, we introduce TMarSel, a software tool for automated, free-from-expert opinion, and tailored marker selection for deep microbial phylogenomics. TMarSel allows users to select a variable number of markers and copies based on KEGG and EggNOG gene family annotations, enabling a systematic evaluation of the phylogenetic signal from the entire gene family pool. We show that an expanded marker selection tailored to the input genomes improves the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes compared to previous markers, even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. TMarSel provides flexibility in the number of markers, copies, and annotation databases while remaining robust against taxonomic imbalance and incomplete genomic data.},
}

@article {pmid41224755,
year = {2025},
author = {Gupta, S and Almeida, A},
title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9959},
pmid = {41224755},
issn = {2041-1723},
support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; },
abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.},
}

@article {pmid41224035,
year = {2025},
author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F},
title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133630},
doi = {10.1016/j.biortech.2025.133630},
pmid = {41224035},
issn = {1873-2976},
abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane (CH4) yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.},
}

@article {pmid41223797,
year = {2025},
author = {Xu, YY and Tan, X and Dang, CC and Liu, LY and Wang, X and Zhao, ZC and Ren, NQ and Wu, YN and Xie, GJ},
title = {Thermophilic Sulfide-Driven autotrophic Denitrification: High-Rate nitrogen removal and metagenomic insights into microbial cooperation.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109918},
doi = {10.1016/j.envint.2025.109918},
pmid = {41223797},
issn = {1873-6750},
abstract = {Sulfide-driven autotrophic denitrification (SDAD) plays a pivotal role in linking nitrogen and sulfur cycles, particularly in thermophilic environments. However, the performance and metabolic mechanisms of thermophilic SDAD systems remain underexplored. This study successfully enriched thermophilic sulfide-oxidizing denitrifiers from hot spring sediments (60 °C) in an expanded granular sludge bed (EGSB) reactor, achieving a stable nitrate removal rate of 250 mg N L[-][1] d[-][1]. This thermal system demonstrated a higher tolerance threshold for sulfides (250 mg TDS L[-1]) than mesophilic processes. The influent sulfide-to-nitrate (S/N) molar ratio critically influenced nitrogen removal efficiency with nitrite accumulation at low S/N ratios (1:1), whereas higher ratios (2:1) restored complete nitrate reduction. Microbial community analysis demonstrated Thermus (52.89 %) as the predominant genus in the SDAD system, marking the first report of its dominance in thermophilic nitrogen-sulfur coupling, alongside uc_Aquificales (21.78 %). Metagenomic insights further revealed two high-quality genomes: Thermus scotoductus exclusively executed complete sulfide-to-sulfate oxidation via the Sox system and partially catalyzed denitrification (narGHI); while Aquificaeae_UBA11096 adopted Sox-independent enzyme system and complete denitrification. Strikingly, Thermus scotoductus encoded nrfH, and it might be the overlooked " nitrogen retainer" in geothermal ecosystems. This work elucidates the cooperative and competitive interactions between thermophilic denitrifiers, and establishes a multi-level thermal adaptability analysis. These findings advance understanding of their biogeochemical roles in geothermal ecosystems, and provide a sustainable strategy for nitrogen removal in high-temperature wastewater treatment.},
}

@article {pmid41223750,
year = {2025},
author = {Yao, S and Luo, Y and Zhou, Y and Wang, Y and Yang, L and Kong, Q and Zhang, H},
title = {Microbial functional shifts in a paradigmatic petrochemical brownfield: Mechanisms of adaptation in soil and groundwater.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119380},
doi = {10.1016/j.ecoenv.2025.119380},
pmid = {41223750},
issn = {1090-2414},
abstract = {The long-term presence of pollutants from the petrochemical industry, including benzene, nitro compounds, and amine-based aromatics, poses a significant threat to soil and groundwater, resulting in shifts in microbial community structures. In this study, 48 soil and groundwater samples from contaminated environments were analyzed using metagenomic technology and gas chromatography-mass spectrometry to examine the metabolic strategies employed by microorganisms in response to these pollutants. The results revealed that microbial community composition was significantly influenced by varying contamination levels, primarily determined by the distance from contamination sources and the diffusion characteristics of the environmental media. In highly contaminated areas, specific bacterial genera, including Pseudomonas and Stutzerimonas, became dominant, suggesting an adaptation toward pollutant degradation. Soil and groundwater microorganisms exhibited distinct adaptive mechanisms: in soils, enhanced motility, metabolism, and toxicant transport were associated with the expression of genes such as mcp, tktA, and pleD, while in groundwater, pollutant degradation and the maintenance of cellular function were driven by genes including xylA, dmpB, nfnB, and glnA. These findings emphasise the capacity of microbes to adapt to pollutants from petrochemical industry environments, thus providing valuable insights into microbial remediation strategies for environmental pollution management.},
}

@article {pmid41223625,
year = {2025},
author = {Yang, B and Wang, H and Yan, Y and Bao, P and Feng, Q and Chen, B and Jia, Y and Shu, WS and Lu, H},
title = {Coupling Microalgae-based Biochar with MBGS Enhances Microbial Synergy and Multi-Pollutant Removal from Saline Aquaculture Wastewater.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124881},
doi = {10.1016/j.watres.2025.124881},
pmid = {41223625},
issn = {1879-2448},
abstract = {The microalgal-bacterial granular sludge (MBGS) system has gained attention as an energy-efficient, multifunctional approach for wastewater treatment, yet its stability and pollutant removal under combined salinity and antibiotic stress remain unclear. In this study, we developed an MBGS system integrated with nitrogen-rich microalgae-derived biochar to enhance removal of organic matter, nutrients, and enrofloxacin (ENR) from saline aquaculture wastewater. The biochar-coupled MBGS achieved high removal efficiencies: 94.2±4.8% COD, 87.1±3.6% NH4[+]-N, 60.3±4.6% PO4[3-]-P, and 60.1±3.5% ENR. Microbial community analysis revealed enrichment of ammonia-oxidizing bacteria (Nitrosomonas, 3.3-9.7%), nitrite-oxidizing bacteria (Nitrospira, 2.3-6.4%), denitrifiers (Thauera, 14.9-27.6%), phosphate-accumulating organisms (Acinetobacter, 0.8-7.7%), and photosynthetic microalgae (Chlorophyceae, 1.4-23.6%). Fluorescence in situ hybridization (FISH) confirmed that biochar enhanced the spatial organization of these functional microbes within MBGS. Metagenomics revealed increased abundance of genes associated with carbon (porCD, CS, korD), nitrogen (amoAB, narGHI, norBC), phosphorus (ppk, phaA, acs), and photosynthesis-related (petABCD, psaA) genes, indicating improved metabolic capacity and synergy. Genome-resolved metagenomics further identified Nitrosomonas europaea, Acinetobacter sp002296655, Thauera aminoaromatica, and Chlorobium sp013334435 as core taxa driving carbon, nitrogen, and phosphorus cycling and energy flow, promoting synergistic interactions and enhancing pollutant removal under stress. Coupling MBGS with microalgae-based biochar improves resilience and multi-pollutant removal, offering a robust, sustainable strategy for advanced aquaculture wastewater treatment.},
}

@article {pmid41223471,
year = {2025},
author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X},
title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140406},
doi = {10.1016/j.jhazmat.2025.140406},
pmid = {41223471},
issn = {1873-3336},
abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.},
}

@article {pmid41222958,
year = {2025},
author = {Yang, Y and Li, Q and Xiao, Y and Shen, Y and Zhang, Y and Zhang, W and Lei, N and Pei, X and Xie, Y},
title = {Elucidating the Mechanism of PFOA Regulation of Biofilms in Aquatic Systems at Gene and Metabolic Levels.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06467},
pmid = {41222958},
issn = {1520-5851},
abstract = {Perfluorooctanoic acid (PFOA) is prevalent in aquatic ecosystems and exhibits significant toxicity to aquatic organisms. Microorganisms can adhere to the surfaces of submerged plants, forming complex extracellular structures referred to as attached biofilms. However, the mechanisms underlying the regulation of biofilm formation by PFOA remain unclear. This study cultured plant-attached biofilms under PFOA stress to investigate the mechanisms by which PFOA regulates biofilm formation, utilizing metagenomics and metabolomics. Results show that the biofilm structure was significantly altered under PFOA exposure, characterized by an increase in polysaccharide and protein content. Furthermore, PFOA bound to proteins within extracellular polymeric substances contributes to a reduction in PFOA toxicity. PFOA regulates biofilm formation by modifying the content of signaling molecules and the abundance of genes (bapA and ABC.PE.S) associated with quorum sensing, establishing a natural barrier against the toxic effects of PFOA. In addition, PFOA was found to inhibit the metabolism of linoleic and linolenic acids, thus indirectly promoting the formation of biofilms, which allowed microbial aggregation and coresistance to the toxic effects of exogenous pollutants. This study provides a comprehensive understanding on the mechanisms by which PFOA regulates biofilm formation, which is crucial for enhancing our understanding of microbial processes in aquatic ecosystems.},
}

@article {pmid41222645,
year = {2025},
author = {Rana, S and Das, KK and Singh, SK and Bhattacharyya, D},
title = {Deciphering Fungal Communities in Three Species of Phlogacanthus Nees (Acanthaceae) Using Amplicon-Metagenomic Analysis.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {16},
pmid = {41222645},
issn = {1432-0991},
abstract = {Fungal communities play vital roles in plant health, nutrient cycling, and ecological balance. Species of Phlogacanthus Nees, valued for their medicinal and ecological importance, harbor diverse fungal microbiomes that may influence growth, resilience, and metabolite production. This study investigated fungal communities associated with three Phlogacanthus species-P. tubiflorus Nees (SKS-1), P. thyrsiformis (Roxb. ex Hardw.) Mabb. (SKS-2), and P. curviflorus (Wall.) Nees (SKS-3)-using high-throughput amplicon-metagenomic sequencing of the ITS2 region on the Illumina MiSeq platform. A total of 153 operational taxonomic units (OTUs) were identified, with SKS-2 showing the highest richness (129 OTUs), followed by SKS-1 (112) and SKS-3 (95). Seventy OTUs were shared across all species, while 10, 22, and 8 were unique to SKS-1, SKS-2, and SKS-3, respectively. Alpha diversity indices (Chao1, ACE, Shannon, Simpson, Inverse Simpson, Fisher's alpha) confirmed SKS-2 as the most species-rich fungal habitat. A high proportion of unclassified taxa in SKS-2, along with dominance of Pleosporales, suggests the presence of novel fungi with ecological and biotechnological significance. Beta diversity analysis using Bray-Curtis dissimilarity and Principal Coordinate Analysis revealed significant differences among the fungal communities of the three species. Overall, SKS-2 emerged as the most diverse habitat, while SKS-3 supported a unique but less diverse assemblage. This is the first report profiling fungal microbiomes of Phlogacanthus species. The results highlight their potential as reservoirs of endophytes with applications in plant growth promotion, stress tolerance, biocontrol, enzyme production, and bioactive metabolite discovery, offering leads for sustainable agriculture and biotechnology.},
}

@article {pmid41222234,
year = {2025},
author = {Sinno, A and Baghdadi, R and Narch, R and El Rayes, S and Tokajian, S and Al Khoury, C},
title = {Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0155425},
doi = {10.1128/jvi.01554-25},
pmid = {41222234},
issn = {1098-5514},
abstract = {The advancement of metagenomic sequencing has revealed a vast viral diversity while simultaneously exposing limitations of homology-based tools such as BLAST and HMMER, which often fail to detect highly divergent viral genomes. The integration of artificial intelligence (AI) into viromics has transformed this landscape, introducing machine learning and deep learning models-including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and transformers-that extend viral discovery beyond sequence similarity constraints. Structure-based frameworks such as AlphaFold, ESMFold, and Foldseek further enable annotation of divergent viral proteins through conserved 3D folds, while graph neural networks (GNNs) model host-virus interaction and explainable AI enhances interpretability of prediction. Despite their high sensitivity and scalability, AI-driven approaches face notable challenges: computational burden, data set bias, limited explainability, and elevated false discovery rates. This review traces the evolution of computational virology from traditional methods to AI-based and hybrid frameworks. We examine landmark AI tools while underscoring the continuing importance of phylogenetics and functional annotation in contextualizing AI predictions. We propose an integrated workflow that combines AI pattern recognition with classical bioinformatics to enhance both scalability and interpretability. By addressing the limitations of solely AI-driven or traditional approaches, this review presents a unified computational strategy to accelerate viral discovery, enhance evolutionary insights, and strengthen global preparedness for emerging infectious diseases.},
}

@article {pmid41222171,
year = {2025},
author = {Lazov, CM and Larsen, LE and Johnston, CM and Rasmussen, TB and Hjulsager, CK},
title = {Announcement of two complete coding genomes of mink coronavirus and one partial coding genome of mink enteric calicivirus from mink in Denmark.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0045925},
doi = {10.1128/mra.00459-25},
pmid = {41222171},
issn = {2576-098X},
abstract = {Two complete coding genomes of mink coronavirus and one partial coding genome of the sapovirus mink enteric calicivirus were assembled from metagenomic sequencing data from mink on different farms with diarrhea outbreaks in 2015 in Denmark.},
}

@article {pmid41222160,
year = {2025},
author = {Liu, W and Nagasaka, K and Wu, J and Ban, H and Mimick, E and Meng, L and Neches, RY and Moniruzzaman, M and Yoshida, T and Nishimura, Y and Endo, H and Okazaki, Y and Ogata, H},
title = {Giant viruses specific to deep oceans show persistent presence and activity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093225},
doi = {10.1128/msystems.00932-25},
pmid = {41222160},
issn = {2379-5077},
abstract = {Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate mesopelagic GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To further investigate the distribution and phylogenomic features of GVs at a global scale across broader depths, we compiled 4,473 species-level GV genomes from the OceanDNA MAG project and other resources and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included a GV genome identified in our Muroto data, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat.IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the mesopelagic water. Using a global marine data set, we further uncovered geographically widespread and vertically extensive groups of deep-sea-specific giant viruses and characterized their distinctive gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.},
}

@article {pmid41222147,
year = {2025},
author = {Vogel, H and Weiss, B and Rama, F and Rinklef, A and Engl, T and Kaltenpoth, M and Vilcinskas, A},
title = {A multi-partner symbiotic community inhabits the emerging insect pest Pentastiridius leporinus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0310325},
doi = {10.1128/mbio.03103-25},
pmid = {41222147},
issn = {2150-7511},
abstract = {The planthopper Pentastiridius leporinus has emerged as a severe crop pest, rapidly expanding both its host plant range and the affected areas in central Europe. Originating as a monophagous herbivore of reed grass, P. leporinus recently adopted polyphagous feeding and is now a pest of sugar beet, potato, carrot, and onion, suggesting rapid ecological niche expansion. P. leporinus vectors two bacterial pathogens: the γ-proteobacterium Candidatus Arsenophonus phytopathogenicus (CAP) and the stolbur phytoplasma Candidatus Phytoplasma solani (CPS), which are responsible for a range of disease syndromes, including syndrome basses richesses in sugar beet. We used long-read metagenomic sequencing to characterize the genomes of microbes associated with P. leporinus, resulting in the complete sequences of CAP and CPS, as well as obligate symbionts of the genera Purcelliella, Karelsulcia, and Vidania, and facultative symbionts Rickettsia and Wolbachia. The obligate symbionts are inferred to provide or contribute to the biosynthesis of 10 essential amino acids and to B vitamin. The genomes of CPS and CAP encode numerous pathogenicity factors, enabling the colonization of different hosts. Bacterial fluorescence in situ hybridization revealed the tissue distribution, cellular localization, relative abundance, and transmission patterns of these bacteria. The intracellular presence of all obligate symbionts in bacteriomes, the intracellular presence of Wolbachia, and the intranuclear localization of Rickettsia suggest vertical transmission. CPS was restricted to salivary glands, suggesting strict horizontal, plant-mediated transmission, whereas CAP colonized all tissue types, allowing for horizontal and vertical transmission. Our data suggest that P. leporinus hosts an exceptionally broad range of symbionts, encompassing mutualistic, commensal, and pathogenic interactions.IMPORTANCEThe planthopper Pentastiridius leporinus has recently expanded its host plant range and emerged as a severe pest of sugar beet and potato crops in central Europe, which is exacerbated by its capacity to vector bacterial pathogens to its host plants. Because microbial symbionts may play an important role for both the host plant shifts and the transmission of pathogens, we used metagenomic sequencing and fluorescence in situ hybridization to characterize the microbial community associated with P. leporinus. We detected three bacteriome-localized obligate symbionts that together provision all essential amino acids and several B-vitamins to the host, as well as two intracellular bacteria with a broader tissue distribution. In addition, we infer localization, transmission, and putative pathogenicity factors for the two major phytopathogens that are vectored by P. leporinus. Our results reveal a complex community of symbiotic bacteria that likely shapes the interaction of this emerging pest with its host plants.},
}

@article {pmid41222145,
year = {2025},
author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE},
title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234125},
doi = {10.1128/mbio.02341-25},
pmid = {41222145},
issn = {2150-7511},
abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.

IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.},
}

@article {pmid41222144,
year = {2025},
author = {Ericsson, AC and McAdams, ZL and Dorfmeyer, RA and Hart, ML and O'Neill-Blair, A and Amos-Landgraf, J and Franklin, CL},
title = {Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0111225},
doi = {10.1128/msystems.01112-25},
pmid = {41222144},
issn = {2379-5077},
abstract = {Studies using genetically engineered mouse (GEM) models are often performed over extended periods. The microbiomes of GEM colonies are expected to retain some of the microbial features present in the founder mice used to generate each GEM model and to acquire new features through dietary and environmental sources. The rate at which these processes occur over time likely varies between institutions. To assess the relative effect size of environment on the microbiome of GEMs used in biomedical research, we performed 16S rRNA metabarcoding of fecal samples from 275 distinct GEM lines (n = 351) maintained by 139 different laboratories at 84 different research institutions in 34 U.S. states or districts and seven other countries, and compared intra-strain, inter-strain, inter-lab, and inter-institution similarities. Reference data from mice harboring supplier-origin (SO) microbiomes (n = 1,171) were used to determine the relative contribution and nature of microbes from known and unknown sources. Paradoxically, the data indicate that the immediate laboratory-level environment is the dominant factor shaping the microbiome of GEM models, but that the microbiome of GEMs develops similarities in beta-diversity, regardless of other factors. Related to this, we detected an unexpectedly high prevalence and abundance of Helicobacter spp. in GEM microbiomes, the abundance of which correlated significantly with the abundance of multiple resident taxa colonizing the mucosa. These findings suggest a higher prevalence of Helicobacter spp. in laboratory mice than previously appreciated, and the possibility of positive and negative interactions with other taxa is found to affect GEM model phenotypes.IMPORTANCEThere are concerns regarding the reproducibility and predictive value of mouse models of human disease. Notwithstanding those legitimate concerns, genetically engineered mouse (GEM) models provide an invaluable platform to investigate gene function or effects of environmental factors in a biological system. The microbiome of GEM models significantly influences model phenotypes and thus represents a possible source of poor reproducibility. While the microbiome is often incorporated in research investigating disease mechanisms using GEMs, limited information is available regarding the similarity of the microbiome of GEM models within and between research labs at the same institution, or across institutions. Moreover, while the microbiome of founder mice from different suppliers is known to differ, the degree to which features present in supplier-origin microbiomes are retained in GEM colonies throughout experimentation is unclear. These data demonstrate the robust effect of lab-level environment and the need for sample collection concurrent with phenotyping.},
}

@article {pmid41222143,
year = {2025},
author = {Liu, P and Zhang, R and Meng, F and Zhang, C and Roberts, AP and Wang, Y and Zhu, K and Cao, Z and Pan, Y and Li, J},
title = {Deep-branching magnetotactic bacteria form intracellular carbonates enriched in trace metals.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113125},
doi = {10.1128/msystems.01131-25},
pmid = {41222143},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial biomineralization is a fundamental driver of global biogeochemical cycles, yet the ability of prokaryotes to form intracellular carbonates remains rarely documented. Here, we report three ecotypes of magnetotactic bacteria (MTB) affiliated with the Pseudomonadota and the deep-branching Nitrospirota phyla that concurrently synthesize magnetite magnetosomes and intracellular calcium carbonate inclusions enriched in Ba, Mg, and Ni. These carbonate granules are typically spherical and contrast with the highly ordered morphology of magnetite crystals. Comparative genomic analyses reveal that these MTB encode multiple metal-permease systems (e.g., GDT1, CorA, ZnuA2), which suggests both a capacity for selective uptake of divalent cations from their environment and a process likely linked to intracellular carbonate precipitation. By uncovering new examples of bacterial intracellular calcification, our findings expand the known diversity and genetic basis of prokaryotic biomineralization. Moreover, they highlight a potential role of MTB in mediating heavy-metal cycling and provide a refined framework for understanding microbially driven carbonate formation.

IMPORTANCE: Intracellular biomineralization is a hallmark of animals and algae, yet among prokaryotes, it has traditionally been associated with a limited range of lineages and minerals. This study reveals that magnetotactic bacteria (MTB) from both the Pseudomonadota and the deep-branching Nitrospirota phyla are capable of intracellularly forming carbonate granules enriched in diverse divalent cations, including environmentally scarce trace metals Ba²⁺ and Ni²⁺, and biologically essential Mg²⁺. These findings significantly expand the known taxonomic and functional diversity of prokaryotic intracellular calcifiers. By integrating electron microscopy, metagenomics, and structural protein modeling, we propose a potential metal-selective transport system that facilitates trace element accumulation and carbonate precipitation. This work establishes a previously underappreciated role for MTB in trace metal biogeochemical cycling (i.e., Ba²⁺ and Ni²⁺) and suggests that intracellular calcification may be a more widespread bacterial trait than previously assumed.},
}

@article {pmid41221535,
year = {2025},
author = {Xie, K and Zhang, Y and Tan, S and Luo, J and Ou, X and Tan, S},
title = {Gut microbiota involvement in the alteration of inflammatory cell infiltration and gut barrier integrity in liver cirrhosis.},
journal = {Biomedical reports},
volume = {23},
number = {6},
pages = {193},
pmid = {41221535},
issn = {2049-9442},
abstract = {The gut microbiota is essential for the development and regulation of the immune and intestinal homeostasis of the host. The present study aimed to investigate the composition, diversity and functional features of the microbiota in patients with liver cirrhosis. and healthy volunteers using high-throughput sequencing of the 16S rRNA gene, and evaluated inflammatory cell infiltration and the gut barrier in both the colonic mucosa and liver sections using histological analysis. Diversity and metagenome function of the gut microbiota significantly differed between healthy volunteers and patients with liver cirrhosis. Patients with cirrhosis showed decreased microbial richness, evenness, and diversity, with functional prediction indicating enrichment of phosphotransferase and membrane transport pathways, while amino acid and energy metabolism pathways were predominant in healthy controls. Furthermore, gut microbial dysbiosis associated with liver cirrhosis augmented inflammatory cell infiltration in the colonic mucosa and liver sections, impaired gut barrier function and enhanced intestinal permeability and bacterial translocation. The gut microbiota contributes to the pathophysiology of liver cirrhosis, which may impact prevention and treatment strategies for patients with liver cirrhosis.},
}

@article {pmid41221508,
year = {2025},
author = {Siljanen, HMP and Manoharan, L and Hilts, AS and Bagnoud, A and Alves, RJE and Jones, CM and Kerou, M and Sousa, FL and Hallin, S and Biasi, C and Schleper, C},
title = {Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf183},
pmid = {41221508},
issn = {2730-6151},
abstract = {Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.},
}

@article {pmid41221507,
year = {2025},
author = {Clinton, CK and Jackson, FLC},
title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf181},
pmid = {41221507},
issn = {2730-6151},
abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.},
}

@article {pmid41221399,
year = {2025},
author = {Huang, Y and Zhou, Q and Gui, M and Guo, D and Cheng, J and Ma, W and Shu, P and Liu, X},
title = {Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host-microbiome metabolic interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668712},
pmid = {41221399},
issn = {1664-302X},
abstract = {BACKGROUND: Retinol remains an essential component in anti-aging skincare; however, a subset of users develop intolerance, characterized by compromised barrier integrity and inflammation. The temporal dynamics of how skin microbiota and host metabolism co-evolve during retinol tolerance establishment remain poorly understood.

METHODS: We conducted a prospective 28-day longitudinal study with 18 Chinese women (aged 25-40): 9 retinol-intolerant subjects monitored at baseline, adverse reaction phase, and tolerance establishment, while baseline data from 9 retinol-tolerant individuals served as controls. We integrated cutaneous phenotypic measurements, metagenomic sequencing, and untargeted metabolomics.

RESULTS: In the intolerant group, skin phenotype assessment revealed a distinct biphasic response-an acute phase marked by increased stratum corneum hydration, reduced sebum secretion, lower skin pH, and improved wrinkle metrics, followed by a re-equilibration phase characterized by sustained barrier restoration. Metagenomic profiling of 969 microbial species demonstrated that, although overall microbial α-diversity remained stable across time points in both groups, key taxa in the intolerant group exhibited transient "rise-and-fall" dynamics. At baseline, the intolerant group exhibited overrepresentation of Cutibacterium acnes, whereas the tolerant group was enriched in potentially protective species, including Sphingomonas hankookensis and Acinetobacter johnsonii. Untargeted metabolomics showed marked temporal fluctuations with an initial phase of metabolic turbulence, followed by partial recovery. During the early adverse reaction phase in intolerant subjects, lipid and fatty acid metabolic pathways-specifically, glycerophospholipid, linoleic acid, α-linolenic acid, and ether lipid metabolism-were significantly upregulated, concomitant with the suppression of TCA cycle and sphingolipid activity. Conversely, as tolerance was established, enhanced activity in the TCA cycle, sphingolipid, ascorbate, and pentose metabolism pathways-coupled with a reduction in pro-inflammatory arachidonic acid derivatives-indicated metabolic reconstitution and restoration of barrier integrity.

DISCUSSION: Integrated multi-omics correlation analyses further underscored the tightly interconnected regulation of host-microbe energy metabolism, antioxidant defenses, and membrane repair in response to retinol-induced stress. These findings elucidate the temporal interplay between host and microbial processes underpinning retinol tolerance and highlight baseline biomarkers that may facilitate personalized skincare interventions.},
}

@article {pmid41221168,
year = {2025},
author = {Yu, X and Cheng, J and He, J and Wu, X and Wang, W and Chen, M and Zhuo, B and Ge, Y},
title = {First Documented Case of Pneumonia with Nocardia africana and SARS-CoV-2 Co-Detection in Mainland China.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5721-5730},
pmid = {41221168},
issn = {1178-6973},
abstract = {Nocardia spp. are zoonotic pathogens that can cause infections ranging from localized lesions to systemic dissemination, primarily via pulmonary inhalation or percutaneous inoculation. We report the first confirmed case of Nocardia africana pneumonia with SARS-CoV-2 co-detection in mainland China, diagnosed through bronchoalveolar lavage fluid (BALF) analysis using metagenomic next-generation sequencing (mNGS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A 76-year-old male presented with persistent cough and fever, accompanied by radiographic evidence of progressive pneumonia. Targeted antimicrobial therapy with trimethoprim-sulfamethoxazole and amoxicillin-clavulanate resulted in clinical resolution within 12 days. This case underscores three critical implications for post-COVID-19 pandemic medicine: the requirement for heightened vigilance for opportunistic pathogens (eg, Nocardia species) in pneumonia patients with recurrent fever, the essential role of advanced diagnostics (eg, mNGS and MALDI-TOF MS) in identifying fastidious organisms like actinomycetes, and the potential for antimicrobial resistance in N. africana, which necessitates susceptibility-guided therapy.},
}

@article {pmid41220843,
year = {2025},
author = {Kwon, K and Kim, M and Jung, Y and Yoon, MY and Lee, JY and Yoon, SS and Rho, M and Chung, YW and Ryu, JH},
title = {Intestinal Dysbiosis Caused by Epithelial Fabp6 Gene Disruption Exacerbates Gut Inflammatory Disease.},
journal = {Immune network},
volume = {25},
number = {5},
pages = {e35},
pmid = {41220843},
issn = {1598-2629},
abstract = {Ileal lipid binding protein (Ilbp), encoded by Fabp6 gene, plays a critical role in intracellular transport of bile acids (BAs) from apical to basolateral side of ileal enterocytes, maintaining BA homeostasis within enterohepatic circulation. However, pathophysiological consequences of Ilbp deficiency remain largely unexplored. Here, we demonstrate that disruption of BA balance, caused by intestinal epithelial cell (IEC)-specific Fabp6 gene knockout (Fabp6 [ΔIEC]), exacerbates dextran sulfate sodium (DSS)-induced gut inflammation. Fecal microbiota transplantation from Fabp6 [ΔIEC] mice to germ free recipient mice replicated the adverse effects observed in Fabp6 [ΔIEC] mice, which were mitigated when these mice were co-housed with control (Fabp6 [f/f]) mice. Metagenomic analysis identified Ligilactobacillus murinus as a primarily diminished strain in Fabp6 [ΔIEC] mice. Oral administration of L. murinus isolated from feces of Fabp6 [f/f] mice ameliorated DSS-induced colitis in Fabp6 [ΔIEC] mice by restoring epithelial barrier integrity and lowering pro-inflammatory cytokines IL-1β, IL-6 and TNF-α. Furthermore, daily administration of taurodeoxycholic acid-one of the BAs reduced in Fabp6 [ΔIEC] mice and that promotes the growth of L. murinus in an in vitro growth assay-also exhibited a protective effect against DSS-induced colitis through a similar mechanism. These findings suggest that deficiency of specific BAs due to epithelial Fabp6 deletion leads to gut dysbiosis, predisposing the host to inflammatory disease.},
}

@article {pmid41220286,
year = {2025},
author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK},
title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl250360},
pmid = {41220286},
issn = {2005-1212},
abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.},
}

@article {pmid41219964,
year = {2025},
author = {George, NA and Zhou, Z and Anantharaman, K and Hug, LA},
title = {Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {370},
pmid = {41219964},
issn = {1743-422X},
support = {R35GM143024/GM/NIGMS NIH HHS/United States ; 2016-03686//Natural Sciences and Engineering Research Council of Canada/ ; Tier II chair//Canada Research Chairs/ ; },
abstract = {BACKGROUND: Viruses are the most abundant microbial entities on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering bacteria and archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of bacteria and archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America.

RESULTS: We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~ 678 kbp), and noted a large diversity of viruses in landfills that has limited overlap across landfills and is distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect hosts across multiple phyla. Auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in the literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector-like proteins appear distinct relative to previously reported Cas effectors and are interesting targets for potential genome editing tools.

CONCLUSIONS: Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.},
}

@article {pmid41219190,
year = {2025},
author = {Chung, D and Brask, N and Matar, S and Gallot-Lavallée, L and Pringle, ES and Duguay, BA and Blais, C and Latimer, J and Haro, R and Slamovits, CH and Leyland, B and Rest, JS and Collier, JL and McCormick, C and Archibald, JM},
title = {Persistent mirusvirus infection in the marine protist Aurantiochytrium.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9922},
pmid = {41219190},
issn = {2041-1723},
support = {GBMF5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {Mirusviruses are abundant and broadly distributed double-stranded (ds) DNA viruses recently discovered in marine metagenomic data. Their host range and ecological impact are unclear. The protist Aurantiochytrium limacinum possesses two mirusvirus-like genomic elements, one a circular episome (AurliV-1) and the other (AurliV-2) a chromosomal integrant. Here we show that genes in both genomes are expressed and viral particles containing mainly AurliV-1 DNA are produced under starvation conditions and when cells are cultured in standard growth medium. We detected viral particles of ~140 nm in the nucleus, in cytoplasmic vesicles, between the plasma membrane and cell wall, and in the extracellular environment. Of 67 AurliV-1-encoded proteins detected using proteomics, 45 are enriched under starvation conditions, including the structurally important major capsid and triplex proteins. Our results establish Aurantiochytrium as a model system for elucidating mirusvirus-host interactions and demonstrate persistent viral infection in a microbial eukaryote.},
}

@article {pmid41218604,
year = {2025},
author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O},
title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102426},
doi = {10.1016/j.xcrm.2025.102426},
pmid = {41218604},
issn = {2666-3791},
abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).},
}

@article {pmid41214576,
year = {2025},
author = {Feng, Y and Zhang, R and Wen, G and Xie, L and Chen, T and Liu, W},
title = {The role of gut microbiota tyrosine decarboxylases in levodopa pharmacokinetics: insights from a levodopa challenge test.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {460},
pmid = {41214576},
issn = {1471-2377},
support = {822QN459//Youth Project of Hainan Natural Science Foundation/ ; 82371268//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gut microbiota is known to influence levodopa metabolism in the intestinal tract, primarily through the action of tyrosine decarboxylase, an enzyme encoded by the tyrosine decarboxylase gene (tyrDC). However, the effect of the abundance of the tyrDC gene on levodopa pharmacokinetics remains unclear.

METHODS: The aim of this study was to investigate this relationship in Parkinson’s disease (PD) patients undergoing a levodopa challenge test. Our study enrolled 12 PD patients with a good response to levodopa. Plasma levodopa pharmacokinetics were determined via liquid chromatography‒tandem mass spectrometry, while tyrDC gene abundance in faecal samples was assessed via metagenomic shotgun sequencing.

RESULTS: A total of 12 PD patients (age: 58.00 ± 8.80 years) with an Hoehn and Yahr stage of 2.25 (2.0–3.0) and a disease duration of 8.46 ± 4.94 years were enrolled. After levodopa administration, the MDS-UPDRS-III score decreased 71.28%±17.09%. We found no significant association between tyrDC gene abundance and levodopa pharmacokinetics.

CONCLUSION: These findings indicate that the influence of the intestinal microbiota on PD patients with a good response to levodopa during the levodopa challenge test may be minimal, which may provide new insight into levodopa therapy.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12883-025-04428-6.},
}

@article {pmid41206538,
year = {2025},
author = {Hall, MB and Zhou, C and Coin, LJM},
title = {Genome size estimation from long read overlaps.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
doi = {10.1093/bioinformatics/btaf593},
pmid = {41206538},
issn = {1367-4811},
support = {FSPGN000045//Australian Government Medical Research Future Fund (MRFF) Genomics Health Futures Mission (GHFM) Flagships-Pathogen Genomics/ ; //META-GP/ ; //DELIVERING A CLINICAL METAGENOMICS PLATFORM FOR AUSTRALIA/ ; },
abstract = {MOTIVATION: Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existing tools are primarily optimized for short-read data.

RESULTS: We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. We validate LRGE on a large, diverse bacterial dataset and confirm it generalizes to eukaryotic datasets. On bacterial genomes, LRGE outperforms k-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources.

Our method, LRGE (Long Read-based Genome size Estimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available at https://github.com/mbhall88/lrge and an archive at https://doi.org/10.5281/zenodo.17183812 under an MIT license.},
}

@article {pmid41218490,
year = {2025},
author = {Qingrui, L and Hongyang, L and Guijun, W and Yiqiao, Z and Yue, C and Changqun, D and Chang'e, L},
title = {Synergistic ecotoxicity of nanoscale zero-valent iron and cadmium in soil: Insights from Eisenia fetida.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119381},
doi = {10.1016/j.ecoenv.2025.119381},
pmid = {41218490},
issn = {1090-2414},
abstract = {Nano-zero-valent iron (nZVI) has been extensively applied as a soil conditioner in remediation practices. However, studies have suggested that excessive doses of nZVI can adversely affect soil organisms and even exacerbate the toxicity of contaminants such as cadmium (Cd) in earthworms. This study investigated whether nZVI induces stress and exacerbates Cd toxicity in Eisenia fetida under controlled laboratory conditions. Four treatments were established: control (no nZVI or Cd), nZVI (10 g∙kg[-1]), Cd (30 mg∙kg[-1]), and Cd-nZVI (30 mg∙kg[-1] Cd + 10 g∙kg[-1] nZVI). Survival rate, biomass, Cd bioaccumulation, enzyme activity, and other indicators were measured. On day 7 of exposure, reactive oxygen species (ROS) levels in the nZVI, Cd, and Cd-nZVI groups were 1.4-, 1.5-, and 1.6-fold higher than those in the control group, respectively (P < 0.05). Over time, both survival rate and biomass declined, with the lowest survival rate and greatest biomass loss observed in the Cd-nZVI group on day 28. Histological staining revealed that under Cd or nZVI stress, the circular muscle layer of the earthworms was loosened, intestinal tissue was partially detached, and the number of villi decreased. Metagenomic sequencing indicated significant alterations in the community structure of the earthworm intestinal microbiota under different treatments. Both 30 mg∙kg[-1] Cd and 10 g∙kg[-1] nZVI disrupted gut microbial balance, which was further exacerbated by combined exposure.},
}

@article {pmid41218435,
year = {2025},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}

@article {pmid41218045,
year = {2025},
author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N},
title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336700},
doi = {10.1371/journal.pone.0336700},
pmid = {41218045},
issn = {1932-6203},
abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.},
}