@article {pmid41242396,
year = {2025},
author = {Sharma, R and Walia, A and Lakhanpal, D},
title = {Human metapneumovirus: an underdiagnosed public health threat.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105189},
doi = {10.1016/j.idnow.2025.105189},
pmid = {41242396},
issn = {2666-9919},
abstract = {Human metapneumovirus (hMPV), a negative-sense RNA virus in the Pneumoviridae family, has emerged as a major yet under-recognized cause of acute respiratory infections worldwide. Since its identification in 2001, hMPV has shown steady genetic evolution into genotypes A and B, with newer sublineages such as A2.2.1, A2.2.2, and B2 currently detected across continents. A recent global rise in hMPV detections, detailed in reports from China, Europe, and the USA, likely reflects both expanded testing and the re-establishment of seasonal circulation following the COVID-19 pandemic. Co-infections with respiratory viruses, including RSV and influenza, contribute to severe clinical outcomes and hospital burden. Multiplex RT-PCR remains the most sensitive and widely used diagnostic method for detection of hMPV, outperforming conventional PCR approaches, while metagenomic sequencing and CRISPR-based assays are primarily research tools. Diagnostic sensitivity also varies with sample source, and access to advanced technologies remains globally uneven. Despite its growing clinical impact, no approved antiviral is available. Promising candidates, including monoclonal antibodies against the fusion protein, siRNA therapies, and mRNA-based vaccines, are in the early stages of development. This review encompasses recent evidence on hMPV epidemiology, molecular evolution, diagnostic approaches, and therapeutic and vaccine development, underscoring a need for sustained surveillance, equitable diagnostic capacity, and proactive vaccine research more effectively addressing a largely overlooked respiratory pathogen.},
}

@article {pmid41242241,
year = {2025},
author = {Yang, L and Chen, J and Chen, Z and Gao, Y and Su, Y and Zeng, S and He, Q and Qiu, Q},
title = {Integrated metagenomic and metabolomic analyses reveal that nitrogen fertilizer reduction combined with biochar application improves the soil microenvironment of Phoebe bournei seedlings.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127954},
doi = {10.1016/j.jenvman.2025.127954},
pmid = {41242241},
issn = {1095-8630},
abstract = {Biochar has emerged as a globally recognized soil amendment, yet its synergistic effects with nitrogen fertilization on rhizosphere ecosystems remain underexplored. This study employed non-targeted metabolomics and metagenomic analyses to investigate the soil microenvironment of Phoebe bournei seedlings under four treatments: control (CK), optimum nitrogen application (F1), 20 % nitrogen fertilizer reduction with biochar application (F2B1), and 40 % nitrogen fertilizer reduction with biochar application (F3B2). A total of 842 (421 up-/421 down-regulated) and 789 (415 up-/374 down-regulated) differential metabolites were identified in the F2B1 and F3B2 treatments, respectively. Nitrogen fertilizer reduction combined with biochar application significantly reshaped soil metabolomic profiles, with pronounced enrichment in eight key metabolic pathways, including ascorbate and aldarate metabolism pathways and arachidonic acid metabolism pathways. Streptomyces, Pseudomonas, and Afipia exhibited higher relative abundance levels in both F2B1 and F3B2 treatments. Redundancy analysis indicated that soil pH was the dominant influence on the variation of microbial communities. The topological complexity and stability of bacterial co-occurrence networks were significantly improved by F3B2. An upregulation of functional genes involved in soil nitrification (amoAB, hao, and nxrAB) resulted from F3B2. Furthermore, network analysis revealed significant correlations between microbial taxa and differential metabolites, with a preponderance of positive correlations. Our results indicate that nitrogen fertilizer reduction combined with biochar application significantly influences soil microbial metabolism, establishing a theoretical foundation for enhancing soil quality in Phoebe bournei woodlands and for the judicious use of nitrogen fertilizer and biochar in forestry.},
}

@article {pmid41242205,
year = {2025},
author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D},
title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128397},
doi = {10.1016/j.micres.2025.128397},
pmid = {41242205},
issn = {1618-0623},
abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.},
}

@article {pmid41241245,
year = {2025},
author = {Li, L and Yu, X and Wang, M and Sun, H and Zhu, J and Wang, X and Chen, S and Hu, S},
title = {Salicylic acid as a pathway inducer for improved bioremediation of oil-polluted saline-alkali soils by chemotactic S. Stutzeri M3.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133647},
doi = {10.1016/j.biortech.2025.133647},
pmid = {41241245},
issn = {1873-2976},
abstract = {The bioremediation would be inhibited by low-efficiency of mass transfer and persistent high-molecular weight polycyclic aromatic hydrocarbons (PAHs). In this study, chemotactic strain named as Stutzerimonas stutzeri M3 and salicylic acid were employed for enhancing biodegradation of petroleum hydrocarbon. The addition of salicylic acid significantly enhanced the activities of alkane hydroxylase and catechol 1,2-dioxygenase, as well as the biodegradation rate of petroleum hydrocarbons. Moreover, the inputs of salicylic acid reshaped microbial community, and obviously affected their cooperative metabolic process by increasing relative abundance of petroleum-degrading bacteria, such as Stutzerimonas, Pontibacillus, Halobacillus and Virgibacillus. Metagenomic analysis furtherly confirmed that overall metabolic pathways of microbial communities and expression of functional genes associated with petroleum degradation (e.g., fad, cat and nah) were enhanced. Furthermore, chemotactic gene expression in strain M3 was significantly increased, thereby facilitating petroleum hydrocarbons degradation. These findings provide a new regulating strategy for effective bioremediation in oil-contaminated sites.},
}

@article {pmid41241073,
year = {2025},
author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W},
title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120709},
doi = {10.1016/j.jad.2025.120709},
pmid = {41241073},
issn = {1573-2517},
abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.

METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12 ± 15.79 years, 8 males), while 14 were non-responders (40.14 ± 17.28 years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).

RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.

CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.},
}

@article {pmid41240828,
year = {2025},
author = {Liu, J and Xie, S and Ji, Y and Fan, X and Luo, S and Xu, X and Wang, C and Zhu, L},
title = {Dual suppression of methanogenesis by dichloromethane and salinity: Competitive methyltransferase inhibition and energy-coupling disruption.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140408},
doi = {10.1016/j.jhazmat.2025.140408},
pmid = {41240828},
issn = {1873-3336},
abstract = {The pervasive co-occurrence of dichloromethane (DCM), a prevalent chlorinated solvent, with high salinity in industrial wastewater poses a poorly understood combined ecological stress on anaerobic microbial ecosystems. This study deciphered the molecular mechanisms underlying the dual inhibition of methanogenesis under such combined stress. Metagenomic analysis revealed that methanogens (particularly Methanobacterium and Methanothrix) were more sensitive to DCM and salinity stress, while fermentative bacteria and acetogens exhibited better resilience. Under salinity stress, methanogens primarily expelled extra Na[+] was via the Na[+] pump coupled with methyltransferase (Mtr). However, density functional theory (DFT) calculations demonstrated that DCM competitively bound to the cobamide cofactor in Mtr (ΔG = -10.5 kcal/mol for DCM vs. +14.6 kcal/mol for methylated carrier), thereby impairing sodium extrusion (58 % downregulation in mtrH gene abundance) and subsequent ATP synthesis. Concurrently, elevated Na[+] levels forced a metabolic shift towards energy-intensive sodium extrusion pathways, as evidenced by the upregulation of mrpA (Na[+]/H[+] antiporter, +20 %) and natA/natB (ABC sodium transporters, +162 %). These disruptions culminated in a severe bioenergetic crisis, indicated by decreased coenzyme F420 activity (31.11 ± 1.58 vs. 48.66 ± 2.09 U/L in control) and suppression of methane yield (22.31 ± 3.63 CH4/g COD vs. 178.91 ± 1.28 mL CH4/g COD in control). Our findings uncovered a novel dual inhibition mechanism, combining molecular-level competitive enzyme inhibition with cellular-scale energy uncoupling, providing critical insights into the microbial toxicological effects of co-occurring chlorinated solvents and salinity.},
}

@article {pmid41240707,
year = {2025},
author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E},
title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106092},
doi = {10.1016/j.psj.2025.106092},
pmid = {41240707},
issn = {1525-3171},
abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.},
}

@article {pmid39617895,
year = {2024},
author = {Perrin, AJ and Dorrell, RG},
title = {Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {279},
pmid = {39617895},
issn = {1741-7007},
mesh = {*Climate Change ; *Eukaryota/physiology ; *Ecosystem ; Biodiversity ; },
abstract = {Eukaryotic microorganisms, or "protists," while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.},
}

*Climate Change
*Eukaryota/physiology
*Ecosystem
Biodiversity

@article {pmid34286093,
year = {2021},
author = {Cheng, CT and Jeng, ML and Tsai, JF and Li, CL and Wu, LW},
title = {Two mitochondrial genomes of Taiwanese rhinoceros beetles, Oryctes rhinoceros and Eophileurus chinensis (Coleoptera: Scarabaeidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {8},
pages = {2260-2262},
pmid = {34286093},
issn = {2380-2359},
abstract = {Two mitochondrial genomes of the dynastine beetles, Oryctes rhinoceros (Linnaeus, 1758) and Eophileurus chinensis (Faldermann, 1835), were assembled via high-throughput sequencing (HTS). Each of the mitogenomes has 37 genes, showing standard gene order and annotation as the other insects, except for the transfer genes, presenting tQ-tI-tM order. To examine their phylogenetic positions, 118 public mitogenomes of Scarabaeidae were used to infer a ML tree. Overall, our scarabaeid phylogeny reveals clear relationships with high nodal supports, and the two rhinoceros beetles are both grouped with the subfamily Dynastinae. The feeding habit of the two clades seems to represent coprophagous and phytophagous types. However, polyphyletic relationships were observed in the subfamily Melolothinae and in the tribes of Onthophagini and Oniticellini. Further systematic revision is needed.},
}

@article {pmid33898751,
year = {2021},
author = {Jeng, ML and Chen, MY and Wu, LW},
title = {Two complete mitochondrial genomes of Papilio butterflies obtained from historical specimens (Lepidoptera: Papilionidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {4},
pages = {1341-1343},
pmid = {33898751},
issn = {2380-2359},
abstract = {Museum specimens are collected for education, exhibition, and various multiple scientific purposes. However, millions of specimens remain in their collection boxes for years without being analyzed. Historical specimens have been known to contain low-quality DNA; hence, it is difficult to utilize their sequence information in phylogenetic studies. However, recent advances in high-throughput sequencing (HTS) make these collections amenable to phylogenomic studies. In this study, two historical specimens (Papilio xuthus Linnaeus, 1767, and Papilio thoas Linnaeus, 1771) were sampled and DNA extracted for HTS via the Miseq platform. Two complete mitogenomes were assembled, even though the DNA quality of those specimens was highly fragmented, below 250 bp in length. The 37 genes of 60 mitogenomes were aligned and used for inferring the phylogenetic relationships of Papilioninae. These two newly sequenced mitogenomes are correctly grouped in the genus Papilio, and this result indicates that historical specimens show great potential for phylogenetic studies with HTS technology.},
}

@article {pmid32019036,
year = {2020},
author = {Brandon, TA and Stamps, BW and Cummings, A and Zhang, T and Wang, X and Jiang, D},
title = {Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations.},
journal = {The Science of the total environment},
volume = {713},
number = {},
pages = {136698},
doi = {10.1016/j.scitotenv.2020.136698},
pmid = {32019036},
issn = {1879-1026},
mesh = {Biofilms ; Bioreactors ; *Denitrification ; Nitrates ; Thiobacillus ; },
abstract = {Bio-electrochemical denitrification (BED) is a promising organic carbon-free nitrate remediation technology. However, the relationship between engineering conditions, biofilm community composition, and resultant functions in BED remains under-explored. This study used deep sequencing and variation partitioning analysis to investigate the compositional shifts in biofilm communities under varied poised potentials in the batch mode, and correlated these shifts to reactor-level functional differences. Interestingly, the results suggest that the proliferation of a key species, Thiobacillus denitrificans, and community diversity (the Shannon index), were almost equally important in explaining the reactor-to-reactor functional variability (e.g. variability in denitrification rates was 51% and 38% attributable to key species and community diversity respectively, with a 30% overlap), but neither was heavily impacted by the poised potential. The findings suggest that while enriching the key species may be critical in improving the functional efficiency of BED, poised potentials may not be an effective strategy to achieve the desired level of enrichment in substrate-limited real-world conditions.},
}

Biofilms
Bioreactors
*Denitrification
Nitrates
Thiobacillus

@article {pmid31974023,
year = {2020},
author = {Gladding, PA and Legget, M and Fatkin, D and Larsen, P and Doughty, R},
title = {Polygenic Risk Scores in Coronary Artery Disease and Atrial Fibrillation.},
journal = {Heart, lung & circulation},
volume = {29},
number = {4},
pages = {634-640},
doi = {10.1016/j.hlc.2019.12.004},
pmid = {31974023},
issn = {1444-2892},
mesh = {*Atrial Fibrillation/genetics/physiopathology/therapy ; *Coronary Artery Disease/genetics/physiopathology/therapy ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; *Multifactorial Inheritance ; *Polymorphism, Single Nucleotide ; Risk Factors ; },
abstract = {Coronary artery disease (CAD) and atrial fibrillation (AF) are two highly prevalent cardiovascular disorders that are associated with substantial morbidity and mortality. Conventional clinical risk factors for these disorders may not be identified prior to mid-adult life when pathophysiological processes are already established. A better understanding of the genetic underpinnings of disease should facilitate early detection of individuals at risk and preventative intervention. Single rare variants of large effect size that are causative for CAD, AF, or predisposing factors such as hypertension or hyperlipidaemia, may give rise to familial forms of disease. However, in most individuals, CAD and AF are complex traits in which combinations of genetic and acquired factors play a role. Common genetic variants that affect disease susceptibility have been identified by genome-wide association studies, but the predictive value of any single variant is limited. To address this issue, polygenic risk scores (PRS), comprised of suites of disease-associated common variants have been devised. In CAD and AF, incorporation of PRS into risk stratification algorithms has provided incremental prognostic information to clinical factors alone. The long-term health and economic benefits of PRS-guided clinical management remain to be determined however, and further evidence-based data are required.},
}

*Atrial Fibrillation/genetics/physiopathology/therapy
*Coronary Artery Disease/genetics/physiopathology/therapy
*Genetic Predisposition to Disease
Genome-Wide Association Study
Humans
*Multifactorial Inheritance
*Polymorphism, Single Nucleotide
Risk Factors

@article {pmid31942825,
year = {2020},
author = {Ho, J and Yeoh, YK and Barua, N and Chen, Z and Lui, G and Wong, SH and Yang, X and Chan, MC and Chan, PK and Hawkey, PM and Ip, M},
title = {Systematic review of human gut resistome studies revealed variable definitions and approaches.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1700755},
pmid = {31942825},
issn = {1949-0984},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/*genetics ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Humans ; },
abstract = {In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.},
}

Anti-Bacterial Agents/pharmacology
Bacteria/classification/*drug effects/*genetics
Drug Resistance, Bacterial/*genetics
Gastrointestinal Microbiome/*drug effects/*genetics
Gastrointestinal Tract/microbiology
Genes, Bacterial
Humans

@article {pmid31248111,
year = {2019},
author = {Richardson, E and Dacks, JB},
title = {Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.},
journal = {Microorganisms},
volume = {7},
number = {6},
pages = {},
pmid = {31248111},
issn = {2076-2607},
support = {RES0021028, RES0043758, RES0046091//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.},
}

@article {pmid31226241,
year = {2019},
author = {Roth, H and Gallo, S and Badger, P and Hillwig, M},
title = {Changes in microbial communities of a passive coal mine drainage bioremediation system.},
journal = {Canadian journal of microbiology},
volume = {65},
number = {10},
pages = {775-782},
doi = {10.1139/cjm-2018-0612},
pmid = {31226241},
issn = {1480-3275},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; *Coal Mining ; *Microbiota ; *Wetlands ; },
abstract = {Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%-43%), Bacteroidetes (12%-37%), Firmicutes (3%-11%), and Verrucomicrobia (6%-11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.},
}

Bacteria/genetics
Biodegradation, Environmental
*Coal Mining
*Microbiota
*Wetlands

@article {pmid30769763,
year = {2019},
author = {, and Singh, BR and Gupta, VK and Deeba, F and Bajpai, R and Pandey, V and Naqvi, AH and Upreti, DK and Gathergood, N and Jiang, Y and El Enshasy, HA and Sholkamy, EN and Mostafa, AA and Hesham, AE and Singh, BN},
title = {Non-Toxic and Ultra-Small Biosilver Nanoclusters Trigger Apoptotic Cell Death in Fluconazole-Resistant Candida albicans via Ras Signaling.},
journal = {Biomolecules},
volume = {9},
number = {2},
pages = {},
pmid = {30769763},
issn = {2218-273X},
mesh = {Antifungal Agents/chemistry/*pharmacology ; Candida albicans/cytology/*drug effects ; Cell Death ; Cell Survival/drug effects ; Drug Resistance, Fungal/*drug effects ; Fluconazole/chemistry/*pharmacology ; Lichens/chemistry/metabolism ; Metal Nanoparticles/*chemistry ; Particle Size ; Proto-Oncogene Proteins p21(ras)/*antagonists & inhibitors/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; Silver/chemistry/*metabolism ; Surface Properties ; },
abstract = {Silver-based nanostructures are suitable for many biomedical applications, but to be useful therapeutic agents, the high toxicity of these nanomaterials must be eliminated. Here, we biosynthesize nontoxic and ultra-small silver nanoclusters (rsAg@NCs) using metabolites of usnioid lichen (a symbiotic association of algae and fungi) that exhibit excellent antimicrobial activity against fluconazole (FCZ)-resistant Candida albicans that is many times higher than chemically synthesized silver nanoparticles (AgNPs) and FCZ. The rsAg@NCs trigger apoptosis via reactive oxygen species accumulation that leads to the loss of mitochondrial membrane potential, DNA fragmentation, chromosomal condensation, and the activation of metacaspases. The proteomic analysis clearly demonstrates that rsAg@NCs exposure significantly alters protein expression. Most remarkable among the down-regulated proteins are those related to glycolysis, metabolism, free radical scavenging, anti-apoptosis, and mitochondrial function. In contrast, proteins involved in plasma membrane function, oxidative stress, cell death, and apoptosis were upregulated. Eventually, we also established that the apoptosis-inducing potential of rsAg@NCs is due to the activation of Ras signaling, which confirms their application in combating FCZ-resistant C. albicans infections.},
}

Antifungal Agents/chemistry/*pharmacology
Candida albicans/cytology/*drug effects
Cell Death
Cell Survival/drug effects
Drug Resistance, Fungal/*drug effects
Fluconazole/chemistry/*pharmacology
Lichens/chemistry/metabolism
Metal Nanoparticles/*chemistry
Particle Size
Proto-Oncogene Proteins p21(ras)/*antagonists & inhibitors/metabolism
Reactive Oxygen Species/metabolism
Signal Transduction/drug effects
Silver/chemistry/*metabolism
Surface Properties

@article {pmid30278254,
year = {2019},
author = {Wu, LW and Chiba, H and Lees, DC and Ohshima, Y and Jeng, ML},
title = {Unravelling relationships among the shared stripes of sailors: Mitogenomic phylogeny of Limenitidini butterflies (Lepidoptera, Nymphalidae, Limenitidinae), focusing on the genera Athyma and Limenitis.},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {60-66},
doi = {10.1016/j.ympev.2018.09.020},
pmid = {30278254},
issn = {1095-9513},
mesh = {Animals ; Asia ; Butterflies/*classification/*genetics ; Genome, Insect/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; },
abstract = {The phylogenetic relationships of the nymphalid butterfly tribe Limenitidini are best known for the genera Limenitis and Adelpha, model taxa for evolutionary processes such as Batesian mimicry and rapid adaptive radiations. Whereas these American limenitidines have received the most attention, phylogenetic relationships of their Asian relatives are still controversial and largely unexplored. Even one of the largest genera in Asia, Athyma, is polyphyletic. To clarify the phylogenetic relationships of these Asian Limenitidini, a total of 53 representatives were sampled; 37 have their mitogenomes sequenced for the first time. Our phylogenetic results confirm that mitogenomic data provides well-resolved relationships at most major levels of the phylogeny, even using different partition schemes or different inference methods. Interestingly, our results show that some Athyma taxa are embedded within the genus Limenitis, whereas the genus Tacola, previously considered to be a synonym of Athyma, needs to be recognized as a valid clade. Additionally, the other Limenitidini genera in Asia (namely Tarattia, Litinga, Sumalia, Pandita and Patsuia) are now grouped either within Athyma or Limenitis, so these genera need to be sunk. Importantly, we also show that the mainly Old World Limenitis and entirely New World Adelpha are sister groups, confirming the relevance of Asian lineages to global studies of Limenitis evolution.},
}

Animals
Asia
Butterflies/*classification/*genetics
Genome, Insect/*genetics
Genome, Mitochondrial/*genetics
*Phylogeny

@article {pmid28105307,
year = {2016},
author = {Ankenbrand, MJ and Terhoeven, N and Hohlfeld, S and Förster, F and Keller, A},
title = {biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.},
journal = {F1000Research},
volume = {5},
number = {},
pages = {2348},
pmid = {28105307},
issn = {2046-1402},
abstract = {The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.},
}

@article {pmid41240515,
year = {2025},
author = {Wang, S and Xu, R and Xiao, M and Yu, J and Yu, L and Heng, Z and Li, Z and Du, Q and Zhou, Y and Li, Y and Zhu, G},
title = {Comammox ammonia oxidization and N2O production in vadose and saturated zone soils.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124899},
doi = {10.1016/j.watres.2025.124899},
pmid = {41240515},
issn = {1879-2448},
abstract = {Riparian zones are biogeochemical hotspots of N2O emission. The important role of ammonia oxidation in N2O production has been reported in rivers, even higher than heterotrophic denitrification, however, the mechanisms controlling riparian N2O production remain unknown. Here, we found that complete ammonia oxidation (comammox) process significantly contributes to ammonia oxidation and N2O production in subsurface riparian zone. The contribution of comammox to ammonia oxidation in surface soils (38.7 ± 6.5 %) is equivalent to that of bacterial ammonia oxidation (49.4 ± 6.9 %), and both processes are significantly more important than archaeal ammonia oxidation (11.9 ± 4.1 %). Moreover, comammox dominates ammonia oxidation in both vadose and saturated zone soils, especially in summer with the average contributions of over 67.9 %. However, as a biotic N2O production pathway, comammox produces more N2O in vadose (up to 72 %) and saturated zone (up to 100.0 %) soils, significantly higher than that produced by archaeal ammonia oxidation (32.0 ± 4.0 %) and bacterial ammonia oxidation (18.0 ± 5.7 %). We obtained the first metagenome-assembled genomes (MAGs) of comammox bacteria in a riparian profile, and metagenomic binning analysis revealed that the wide niche of comammox may attribute to its diverse metabolic pathways, which not only perform ammonia oxidation but also nitrate reduction to ammonia. This research enhances the understanding of the biogeochemical ammonia cycle in riparian zone systems and provides new insights for the control of nitrogen pollution in riparian zones.},
}

@article {pmid41240423,
year = {2025},
author = {Alzeer, S and Almaghrabi, RS and Magrashi, A and Alzahrani, T and Bakheet, R and Alqasabi, A and Tayeb, H},
title = {Revealing co-infections in pneumonia: A case report on advancing diagnosis with metagenomic sequencing technologies.},
journal = {Journal of infection and public health},
volume = {19},
number = {1},
pages = {103036},
doi = {10.1016/j.jiph.2025.103036},
pmid = {41240423},
issn = {1876-035X},
abstract = {Pneumonia, a frequent and serious complication in kidney transplant recipients, is significantly increased by long-term immunosuppressive medication. This case report details a patient with lung cavitation, in which conventional microbiological methods revealed Escherichia coli as the principal pathogen. Metagenomic long-read sequencing also identified Klebsiella pneumoniae as a co-pathogen, underscoring the shortcomings of traditional diagnostic techniques. In identifying infectious pathogens, this case illustrates the superior diagnostic accuracy of long-read sequencing, offering crucial information that conventional methods might miss. The implementation of sophisticated sequencing technologies may overcome these diagnostic deficiencies, improving infection care in challenging and immunocompromised patients.},
}

@article {pmid41240163,
year = {2025},
author = {Perez-Hernandez, C and Aldaroub, J and Barth, ZK and Aylward, FO},
title = {A novel lineage of large aquatic bacteriophages identified through metagenomics.},
journal = {Archives of virology},
volume = {170},
number = {12},
pages = {253},
pmid = {41240163},
issn = {1432-8798},
support = {#2141862//National Science Foundation/ ; },
mesh = {*Metagenomics ; *Bacteriophages/genetics/classification/isolation & purification ; *Genome, Viral ; Phylogeny ; },
abstract = {"Jumbo phages" are tailed phages with genome sizes >200 kbp and physical dimensions reaching up to 0.45 μm. Although jumbo phages represent only a small fraction of the isolated phages to date, metagenomic surveys have shown that they are broadly distributed in a wide range of environments. In this study, we surveyed metagenomic data from aquatic systems and identified 25 genomes from a heretofore-undescribed lineage of jumbo phages with genomes reaching up to 307 kbp. We refer to these phages as "moraphages", from the Gaelic word 'mór', for large. Moraphages represent a diverse lineage with inter-genome average amino acid identity (AAI) ranging from 39 to 95%, and our pan-genomic analysis identified only 26 viral orthologous groups (VOGs) found in at least 80% of the genomes. Our phylogenomic analysis suggests that moraphages are distant relatives of a recently described lineage of huge phages from marine sediment. Moraphages lack much of the genetic machinery found in other lineages of large phages, but they have a range of genes that may be used to take over host cellular machinery and subvert host defenses, such as glutamine synthetases, antitoxin genes, and chaperones. The predicted hosts of most moraphages are members of the phylum Bacteroidota, and some encode homologs of the chaperones DnaK and DnaJ that bear evidence of recent gene transfer from members of the order Flavobacteriales. Our work sheds light on the emerging diversity of large phages that are found across the biosphere.},
}

*Metagenomics
*Bacteriophages/genetics/classification/isolation & purification
*Genome, Viral
Phylogeny

@article {pmid41240088,
year = {2025},
author = {V, C and Lal, SB and Mishra, DC and Sharma, A and Kumar, S and Chaturvedi, KK and Behera, BK},
title = {In Silico Identification of Enzymes Involved in Bioremediation from Metagenomic Sequence of River Ganga.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {115},
number = {6},
pages = {64},
pmid = {41240088},
issn = {1432-0800},
mesh = {Biodegradation, Environmental ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; Metagenomics ; Computer Simulation ; Environmental Monitoring ; Metagenome ; },
abstract = {Environmental pollution, particularly in aquatic ecosystems, poses a major global threat. The Ganga River, vital to millions, suffers from severe contamination despite multiple remediation efforts. Bioremediation, especially enzyme-mediated approaches, offers an eco-friendly and efficient alternative to conventional methods. This study utilizes metagenomic reads to identify bioremediating enzymes, their host microorganisms, target pollutants, and enzyme abundance at two Ganga sites: Nawabganj, Kanpur (highly polluted), and Below Farakka Bridge, West Bengal (less polluted). In-silico analysis was conducted using RemeDB for enzyme identification and MG-RAST for microbial abundance. Enzyme abundance was determined by integrating microbial profiles with the RemeDB enzyme database. Key enzymes identified include Phenylacetaldehyde dehydrogenase (plastic), Biphenyl dioxygenase (hydrocarbons), and Catechol 1,2-dioxygenase (dyes). Results indicate higher bioremediating enzyme diversity in the more polluted Nawabganj site. The findings highlight the potential of native enzymes for pollutant degradation and support further exploration for environmental cleanup strategies.},
}

Biodegradation, Environmental
*Rivers/chemistry/microbiology
*Water Pollutants, Chemical/metabolism/analysis
Metagenomics
Computer Simulation
Environmental Monitoring
Metagenome

@article {pmid41239457,
year = {2025},
author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K},
title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1287},
pmid = {41239457},
issn = {1479-5876},
mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; },
abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.

METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16 S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).

RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.

CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.},
}

Humans
*Methylamines/blood
*Synbiotics
*Indican/blood
Female
Male
Young Adult
*Students, Medical
*Microbiota
Adult
Gastrointestinal Microbiome
*Healthy Volunteers

@article {pmid41239428,
year = {2025},
author = {Chen, W and Zhang, Y and Gong, H and Cao, Z and Yang, K and Mi, J},
title = {Exploring diversity and distribution patterns of chicken gut bacteriophage community.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {119},
pmid = {41239428},
issn = {2524-4671},
}

@article {pmid41239203,
year = {2025},
author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D},
title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1578},
pmid = {41239203},
issn = {1471-2229},
}

@article {pmid41239201,
year = {2025},
author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A},
title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {86},
pmid = {41239201},
issn = {2730-6844},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration & dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; },
abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.

DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.},
}

Animals
*Rumen/microbiology
*Tannins/pharmacology/administration & dosage
*Acacia/chemistry
Sheep/microbiology
*Metagenomics
Gastrointestinal Microbiome
*Plant Extracts/pharmacology
Animal Feed
Dietary Supplements

@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.},
}