@article {pmid41397341,
year = {2025},
author = {Sun, Z and Dong, D and Song, X and Wei, Y and Li, Y and Dai, H and Liu, C and Zhang, M and Li, M},
title = {Halophytes regulate microbial synergy to enhance N removal and mitigate greenhouse gas in low C/N mariculture wastewater: Revealed by isotopic & metagenomics.},
journal = {Water research},
volume = {290},
number = {},
pages = {125154},
doi = {10.1016/j.watres.2025.125154},
pmid = {41397341},
issn = {1879-2448},
abstract = {Constructed wetlands (CWs) are promising for nitrogen removal from mariculture wastewater, but their efficiency under low C/N ratios remains limited by halophytes selection and unclear microbial mechanisms. Here, we investigated three halophytes (Sesuvium, Suaeda and Mangrove) in seawater CWs under C/N ratios of 5, 2.5 and 1, with unplanted controls, using metagenomics and [15]N-isotope tracing. Plants significantly enhanced total nitrogen (TN) removal under low C/N, with Sesuvium performing best (85.5% and 63.3% at C/N = 2.5 and 1), significantly surpassing Suaeda, Mangrove and controls. It also minimized greenhouse gas (GHG) emissions and reduced NH4[+]-N/NO2[-]-N accumulation. Microbial processes dominated TN removal (71.7-78.9%), whereas direct plant uptake contributed only 5.2-7.6%. Novelly, stable isotope tracing with [15]N-labeled CH4N2O confirmed that urea-N and NO3[-]-N are simultaneously removed via anammox. Under low C/N (2.5 and 1), Sesuvium selectively enriched anammox and sulfur autotrophic denitrification (SAD) taxa. Shifts in NO3[-]-N reduction pathways-from heterotrophic denitrification/dissimilatory nitrate reduction to ammonium (DNRA) under high C/N to anammox/SAD under low C/N-explained the superior performance of Sesuvium. This study highlights Sesuvium as an optimal halophyte for efficient nitrogen removal and lowest GHG emissions in low-C/N seawater CWs, providing mechanistic insights into plant-microbe interactions for mariculture wastewater treatment.},
}

@article {pmid41396836,
year = {2025},
author = {Xie, D and Tian, Y and Zheng, F and Wu, L and Xu, G and Liu, Q and Lu, G},
title = {Multi-Omics and Integrative Analytics in Natural Products Discovery.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {225},
pages = {},
doi = {10.3791/69458},
pmid = {41396836},
issn = {1940-087X},
mesh = {*Biological Products/chemistry/metabolism/analysis ; *Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Drug Discovery/methods ; Computational Biology/methods ; Multiomics ; },
abstract = {Natural products (NPs) have long been an essential source of new bioactive compounds for drug discovery; however, traditional methods for screening and isolating these compounds can be slow and often yield diminishing returns. Fortunately, advanced multi-omics and computational approaches present powerful solutions to these challenges. This review highlights innovative methodologies that integrate metabolomics, genomics, transcriptomics, and proteomics with bioinformatics and analytical chemistry to accelerate NP discovery. For instance, untargeted metabolomics platforms like high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Global Natural Products Social (GNPS) molecular networking allow for comprehensive profiling of new compounds, while targeted isotope-labeling strategies enhance this process. Additionally, genome and metagenome mining tools such as antibiotics and secondary metabolite analysis shell (antiSMASH), Deep Biosynthetic Gene Cluster (DeepBGC), and Pipeline for Reconstructing Integrated Syntheses of Metabolites (PRISM) quickly identify biosynthetic gene clusters (BGCs) in both cultured and uncultured organisms, often using heterologous expression to validate products. Transcriptomic analyses, including RNA sequencing (RNA-seq), co-expression networks, and fluxomics, help clarify how pathways are regulated, while quantitative proteomics techniques like tandem mass tags/isobaric tags for relative and absolute quantitation (TMT/iTRAQ) and label-free methods, along with chemoproteomics approaches such as cellular thermal shift assay and thermal proteome profiling (TPP), uncover molecular targets and their mechanisms of action. This review also places significant emphasis on the role of artificial intelligence (AI) and machine learning (ML) in integrating multi-omics data, spanning activities from constructing gene-metabolite correlation networks to leveraging knowledge graphs and graph neural networks for data fusion and functional prediction. Finally, this review concludes by discussing the synergistic benefits of multi-omics for natural-product discovery, addressing current technical challenges, and exploring future directions toward high-throughput, intelligent data integration for next-generation NP research.},
}

*Biological Products/chemistry/metabolism/analysis
*Genomics/methods
*Metabolomics/methods
*Proteomics/methods
*Drug Discovery/methods
Computational Biology/methods
Multiomics

@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Animal Feed/analysis
Plant Leaves/chemistry
Aquaculture
Diet/veterinary
*Perciformes/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Bacteria/classification/genetics
Diet, Plant-Based

@article {pmid41396065,
year = {2025},
author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E},
title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0180625},
doi = {10.1128/spectrum.01806-25},
pmid = {41396065},
issn = {2165-0497},
abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.

IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.},
}

@article {pmid41396034,
year = {2025},
author = {Xu, F and Yang, B and Cui, S and Yang, Z and Dai, N and Stanton, C and Ross, RP and Zhao, J and Lai, J and Chen, W and Wang, Y},
title = {Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04527d},
pmid = {41396034},
issn = {2042-650X},
abstract = {While the interplay between gestational diabetes mellitus (GDM) and the maternal-infant microbial axis is increasingly recognized, the specific pathways of influence remain unclear. This study comprehensively investigated the impact of GDM on the breast milk microbiota, human milk oligosaccharides (HMOs), and the subsequent development of the infant gut microbiota. We analyzed breast milk and paired infant fecal samples collected from healthy and GDM-affected mothers at two time points (0-7 and 42 days postpartum). The microbiota of both sample types was profiled by metagenomic sequencing, and HMOs in breast milk were quantified via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed that GDM had a strong influence on the infant gut microbiota via reducing HMO concentrations than via direct alterations to the breast milk microbiota. These GDM-associated HMO alterations induced stage-specific shifts in the offspring's gut microbiota. Notably, the correlation between specific HMOs and gut bacteria reversed from the colostrum stage to the mature milk stage. This suggests that HMOs influence microbial colonization not only through direct utilization but also, and perhaps more importantly, via indirect ecological mechanisms such as cross-feeding. Collectively, our results identify maternal HMOs as a critical link between maternal metabolism and infant gut health, highlighting their potential as a promising nutritional target to improve long-term metabolic outcomes in GDM-exposed infants.},
}

@article {pmid41395987,
year = {2025},
author = {Sun, Z and Zhang, P and Li, Y and Zhang, C and Liu, Y and Ma, B and Lan, Q and Qi, H},
title = {Microsporidia keratoconjunctivitis identified as an emerging zoonotic threat from pet parrots: Clinical and metagenomic next-generation sequencing evidence.},
journal = {Virulence},
volume = {},
number = {},
pages = {2605385},
doi = {10.1080/21505594.2025.2605385},
pmid = {41395987},
issn = {2150-5608},
abstract = {Microsporidia are opportunistic, obligate intracellular fungi capable of causing keratoconjunctivitis. Because the clinical manifestations of microsporidia keratoconjunctivitis are indistinguishable from those of other etiologies, and the organism is difficult to culture, its diagnosis is challenging. The transmission routes of microsporidia keratoconjunctivitis remain poorly defined, and zoonotic sources have long been suspected but rarely confirmed. Between September 2024 and October 2025, a total of 15 confirmed cases of microsporidia keratoconjunctivitis were identified at Peking University Third Hospital. The diagnosis was established based on Giemsa-stained corneal scrapings and/or metagenomic next-generation sequencing (mNGS) of conjunctival lavage samples. Among these 15 patients, microsporidia spores were observed in corneal scrapings from nine individuals, while 13 tested positive for Encephalitozoon hellem (E. hellem) by mNGS. Notably, all affected patients reported a history of parrot exposure. Self-reported parrot exposures included direct ocular contact (n = 3) and indirect contact (n = 12). Six patients reported that their parrots had exhibited ocular abnormalities and diarrhea before the onset of the patients' symptoms, and two patients stated that their parrots had died prior to their clinical presentation. Ocular and fecal samples from three parrots associated with four patients were collected, and all the parrots tested positive for E. hellem by mNGS. These findings provide both clinical and molecular evidence supporting pet parrots as a zoonotic source of microsporidia keratoconjunctivitis. This emerging zoonotic threat calls for greater clinical awareness and attention to animal exposure history during diagnosis.},
}

@article {pmid41395968,
year = {2025},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198525},
doi = {10.1128/aem.01985-25},
pmid = {41395968},
issn = {1098-5336},
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}

@article {pmid41395946,
year = {2025},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}

@article {pmid41395940,
year = {2025},
author = {Karamycheva, S and Wolf, YI and Koonin, EV and Makarova, KS},
title = {Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0312725},
doi = {10.1128/mbio.03127-25},
pmid = {41395940},
issn = {2150-7511},
abstract = {Evolution of prokaryotic genomes is highly dynamic, including extensive gene gain via horizontal gene transfer and gene loss, as well as different types of genome rearrangements. Most quantitative analyses of prokaryotic genome evolution are based on single-gene events, although the distribution of genes is known to be non-random at the scales of operons and various genomic islands. Here, we present a spatial-temporal phylogenomic approach for detecting arrays of genes that are likely to have been acquired as a single block. It is shown that the acquisition of multi-gene blocks makes a major contribution to prokaryotic genome evolution and that these blocks consist primarily of co-directed, functionally coherent genes. A detailed analysis of the spatial-temporal data for the genomes of multiple groups of bacteria and archaea shows that the larger blocks of co-acquired genes represent primarily mobile genetic elements (MGEs), in many cases not identified previously. For example, this includes a new group of pleolipoviruses in Haloarchaea and a group of MGEs specific for Bacteroidota with hypervariable gene content and carrying a unique RNA polymerase enzyme. We also show that some ancestral phage-related large islands correspond to previously unnoticed R-type pyocins in Proteus and Morganella genomes. Many of the smaller gene blocks prone to high genome flux are expected to comprise antivirus defense systems and toxins-antitoxins. In a pilot analysis, eight novel toxin-antitoxin and seven novel defense systems were predicted in archaea of the phylum Thermococcaceae.IMPORTANCEWith many thousands of diverse bacterial and archaeal genomes made available by the fast advancing genomic and metagenomic sequencing, methods for in-depth analysis of genome organization and evolution are essential for extracting the maximum amount of information from this wealth of genomic data. We present a spatial-temporal approach for genome analysis that detects blocks of genes that were simultaneously acquired during genome evolution and shows that genes in such blocks are mostly transcribed in the same direction and have related functions, allowing for the prediction of previously unknown functional systems. The predictive power of the approach is demonstrated by detecting multiple novel mobile genetic elements and antivirus defense systems. Unlike most other functional prediction methods, the spatial-temporal approach does not require prior knowledge of the functions of any genes and has the potential to predict hundreds of novel functional systems amenable to further in-depth study, especially for poorly characterized groups of bacteria and archaea.},
}

@article {pmid41395693,
year = {2025},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70364},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestlé Health Science/ ; //Pierre Mercier Foundation/ ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).

METHODS: In a randomised trial, patients with BMI >35 kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.

RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.

CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}

@article {pmid41395487,
year = {2025},
author = {Bai, Z and Wang, Y and Li, Y and Xu, J and Lai, Z},
title = {The gut microbiota in liver transplantation recipients during the perioperative and postoperative recovery period.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684303},
pmid = {41395487},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic Liver Disease (CLD) is one of the frequent causes of death, especially in the developing world. Liver transplantation (LT) is an effective modality to treat end-stage liver disease. Perioperative management of liver transplantation patients and prevention of postoperative complications are the key to improving patient prognosis and quality of life, and the intestinal flora of these patients can affect postoperative complications and overall prognosis.

METHOD: We collected a total of 151 fecal samples from 59 liver transplantation patients at different stages from the First Hospital of Shanxi Medical University. Using 16S rRNA sequencing technology, we compared the characteristics and changes of their microbiota. We selected 42 samples for metagenomic sequencing using the microPITA method to further analyze the composition and functional differences of the microbiota during the perioperative period of liver transplantation across various time points.

RESULTS: After liver transplantation (LT), the diversity of gut microbiota initially decreased and then increased. Firmicutes, Proteobacteria, and Bacteroidota were the main bacterial groups during the perioperative period. Firmicutes and Proteobacteria initially decreased and then increased, while Bacteroidota exhibited the opposite process. Alpha diversity and beta diversity analyses indicated that 1 month post-transplantation was a turning point for microbiota recovery (P < 0.01). Metagenomic sequencing, analyzed using the LEfSe method, identified a total of 50 genera that played significant roles in this process. The changes in microbiota exhibited the same trend as the 16S rRNA results. KEGG pathway analysis also indicated that 1 month was a critical time point, with Ko02010 potentially being a key pathway for recovery in LT patients, and it showed a negative correlation with Bacteroidota (P < 0.05).

CONCLUSION: The diversity of intestinal flora in the perioperative period of LT patients decreased first and then increased, and the turning point of intestinal flora recovery was 1 month after LT surgery.},
}

@article {pmid41395483,
year = {2025},
author = {Lawal, OU and Parreira, VR and Rizvi, F and Precious, M and Anderson, REV and Overton, AK and Knapp, JJ and Maxwell, B and Thomas, S and Zambrano, M and Landgraff, C and Fleury, MD and Knox, NC and Charles, TC and Goodridge, L},
title = {Evaluation of sampling methods for genomic surveillance of SARS-CoV-2 variants in aircraft wastewater: advancing global early-warning systems for future pandemics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717424},
pmid = {41395483},
issn = {1664-302X},
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven to be an important tool for tracking the dissemination of SARS-CoV-2 variants of concern (VOCs) in the community. In Canada, metagenomic analysis of aircraft wastewater was adopted at an early stage of the pandemic to track importation of emerging variants into the country. However, the acute need to determine the presence of emerging SARS-CoV-2 sublineages meant that the sampling methods utilized were not adequately validated. Here, we compared two different sampling methods for genomic surveillance of SARS-CoV-2 VOCs in aircraft sewage samples.

METHODS: Eighty-eight composite wastewater samples were collected over 9 weeks using both autosampler and passive torpedo samplers at the same location. SARS-CoV-2 nucleic acid in the samples was quantified using RT-qPCR. RNA samples were extracted and sequenced with the MiniSeq system using the tiled-amplicon sequencing approach with ARTIC V4.1 primer sets. Raw reads were preprocessed and SARS-CoV-2 mutations, variants lineages, and other sequence metrics from the two sampling methods were compared.

RESULTS: The two sampling methods yielded comparable viral load by RT-qPCR, but the autosampler produced higher genome coverage relative to the passive samplers. The Omicron lineages identified differed by sampling method. BQ.1* and BA.5.2*, which were the predominant lineages in wastewater and clinical samples at the time, were identified as dominant in the autosampler and passive sampler, respectively. Additionally, the autosampler captured higher diversity and relative abundance of VOCs, including emerging variants (XBB* and CH.1* lineages), as well as more clinically relevant mutations (S:K444T, T22942A, S:R346T) relative to passive sampler. Overall, the passive samplers produced concordant results with the autosampler for measuring SARS-CoV-2 load with RT-qPCR in aircraft wastewater.

CONCLUSION: Taken together, our results suggest underestimation of the diversity and abundance of SARS-CoV-2 VOCs and mutations in aircraft sewage using passive torpedo samplers. These data can be used to optimize genomic surveillance approaches for SARS-CoV-2 VOCs in aircraft wastewater samples.},
}

@article {pmid41395471,
year = {2025},
author = {Cheng, YN and Chen, GT and Huang, WC and Chiu, YP and Tang, Y and Fu, PK and Lee, TY},
title = {Lung microbiome signatures and explainable predictive modeling of glucocorticoid response in severe community acquired pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706432},
pmid = {41395471},
issn = {1664-302X},
abstract = {INTRODUCTION: Systemic glucocorticoids (SG) are administered to quell hyper-inflammation in severe community acquired pneumonia (SCAP), yet trials report inconsistent efficacy and no mechanistic explanation.

METHODS: We enrolled 200 ventilated SCAP patients, whom received hydrocortisone within 48 h of ICU admission, and generated longitudinal lower-airway microbiome profiles by 16S rRNA amplicon and metagenomic sequencing on ICU Days 1, 3 and 7. Compositional data were integrated with clinical variables through a fully reproducible bioinformatics analysis workflow.

RESULTS: Baseline community structures did not differ between SG and control cohorts, but by Day 7 survivors exhibited enrichment of Actinobacteria and Gammaproteobacteria whereas non-survivors accumulated Alphaproteobacteria and Campylobacteria. A random-forest model restricted to Bacilli and Alphaproteobacteria achieved AUROC = 0.89 (sensitivity 0.83, specificity 0.81) on a patient-held-out test set, significantly outperforming conventional severity indices like APACHE II, SOFA and mNUTRIC scores.

DISCUSSION: Collectively, our results demonstrate that SG therapy imposes reproducible ecological pressures on the lung microbiome and that a two-feature microbial fingerprint can forecast treatment success with single-sample resolution. These findings show that SG therapy actively reshapes the respiratory ecosystem and that lightweight microbiome-aware machine learning can stratify treatment response, offering a tractable path toward precision corticosteroid stewardship.},
}

@article {pmid41395467,
year = {2025},
author = {Hagarová, L and Kupka, D},
title = {Insights into the microbiome of mine drainage from the Mária mine in Rožňava, Slovakia: a metagenomic approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675058},
pmid = {41395467},
issn = {1664-302X},
abstract = {The Mária mine, particularly the Strieborná vein, in Rožňava, is one of the most important mines in Slovakia, containing Ag-bearing tetrahedrite (40-46 wt% Cu, 26 wt% Sb, ~1 wt% Ag), making it an important source of strategic and critical raw materials. This mine discharges a unique neutral-pH (6.9), metal-rich mine water drainage (402 mg L[-1] SO4 [2-], 4.65 mg L[-1] Fe) that has remained microbiologically uncharacterized. This study presents the first comprehensive shotgun metagenomic survey of this mine effluent, generating ~227 million high-quality reads that assembled into 157,676 contigs and 378,023 non-redundant genes. Taxonomic analysis revealed a community dominated by Betaproteobacteria (> 66%), with abundant lithotrophic genera Sulfuritalea (6.93%), Ferrigenium (5.45%), Gallionella (3.79%), and Sideroxydans (3.65%), alongside the heterotrophic genus Pseudomonas (5.2%). Among the most prevalent neutrophilic iron-oxidizing bacterial strains were Sulfuritalea hydrogenivorans (6.93%), Ferrigenium kumadai (5.45%) and Gallionella capsiferriformas (3.79%). Acidophilic genera (e.g., Thiobacillus sp. at 0.43%, Ferrovum myxofaciens, Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans) collectively accounted for <1% of the community. Functional annotation against KEGG, CAZy, COG, eggNOG, Swiss-Prot, CARD and BacMet databases demonstrated pronounced enrichment of iron cycling (e.g., the iron complex outer-membrane receptor protein TC.FEV.OM), sulfur oxidation (e.g., SoxA, SoxX, SoxB), carbon turnover (glycosyltransferase and glycoside hydrolase families) and nitrogen cycling (e.g., NifH, NifD, NirK, glnA). The antibiotic-resistance profile was dominated (> 95%) by tetracycline and fluoroquinolone determinants, while metal-resistance systems for Ni, Ag, As, Cu and Zn (including CzcD, CzcA, CznA, ArsD and AioX/AoxX) were likewise pervasive. This integrated taxonomic-functional portrait highlights a microbiome finely adapted to this unique geochemistry, combining lithotrophic metabolisms with multi-metal resistance. Our findings establish a critical baseline for long-term monitoring and highlight a high abundance of neutrophilic Fe(II)-oxidizers, suggesting they may represent promising candidates for targeted cultivation and subsequent evaluation in biotechnology applications.},
}

@article {pmid41394950,
year = {2026},
author = {Krishnan, LRA and Nair, S and Girija, D and Vishnu, BR},
title = {Unravelling the complex bacterial diversity in the rice rhizosphere of Kole lands of Thrissur through the metagenomics approach.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {27},
pmid = {41394950},
issn = {2190-572X},
abstract = {UNLABELLED: The Kole wetlands of Kerala are highly productive rice ecosystems that lie below mean sea level and alternate between flooded and dry phases, shaping their ecological structure. This study focused on assessing bacterial diversity in the rice rhizosphere of Thrissur Kole lands. Rhizosphere soil was sampled from three Kole wetland locations, Puzhakkal (Pzk), Mullassery (Mls), and Cherpu (Chr). Bacterial communities were profiled by constructing metagenomic libraries and sequencing the 16S rRNA V3-V4 regions using the Illumina MiSeq platform. The sequences of the samples Pzk, Mls, and Chr were submitted in the SRA portal under the bioaccession numbers SAMN17776076, SAMN17776077, and SAMN17776078, respectively. High-quality, chimera-free sequences were clustered into OTUs using the QIIME pipeline. Taxonomic assignment was performed in MEGAN by matching reads to sequence databases and allocating NCBI-based taxon IDs. Phylum-level bacterial and archaeal diversity was further analyzed using the MG-RAST pipeline. The predominant bacterial phyla identified were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae, with bacterial relative abundance being highest in the Pzk sample and comparatively lower in the Chr sample. The major archaeal phyla included Euryarchaeota, Crenarchaeota, and Thaumarchaeota. Many members of these bacterial and archaeal groups are known to thrive in waterlogged, oxygen-limited, or anoxic conditions, characteristic of Kole lands. Plant Growth Promoting Rhizobacteria (PGPR) such as Azospirillum, Paenibacillus, and Cellulosimicrobium were detected and could potentially be exploited as acid-tolerant biofertilizers. Biocontrol agents belonging to the genera Bacillus and Pseudomonas were also present. Further investigation is required for the characterization of the 'Unclassified' genera at taxonomic and functional levels to elucidate their ecological functions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04630-w.},
}

@article {pmid41394910,
year = {2025},
author = {Barton, KA and Finnerty, PB and Rupasinghe, R and González-Crespo, C and Mahar, JE and Eden, JS and Meisuria, NY and Martínez-López, B and Newsome, TM and Peel, AJ and Smith, JA and Brookes, VJ},
title = {The final frontier: using carcasses for one health surveillance at the ecosystem interface.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1683110},
pmid = {41394910},
issn = {2297-1769},
abstract = {Anthropogenic activities such as agricultural intensification, urbanisation, globalisation, and climate change are accelerating disease emergence globally, yet surveillance systems have largely overlooked the critical role of vertebrate carcasses in pathogen transmission. This omission is concerning because animal mass mortality events (MMEs) are increasing in frequency and magnitude, while populations of key vertebrate scavengers, especially obligate scavengers like vultures, are declining, resulting in longer carcass persistence and altered disease risks. Carcasses serve as essential resources in food webs but also act as complex microbe transmission hubs through direct consumption, environmental contamination, vector-mediated dispersal, and increased host aggregation, facilitating cross-species and trophic spillover events. Scavengers can amplify or mitigate microbe transmission: their consumption of carcasses can remove infectious material, but their mobility and sociality may also disperse potential pathogens across large areas. Technological advances, including remote sensing, camera traps, GPS telemetry, and machine learning, now enable detailed tracking of scavenger-carcass interactions and identification of transmission hotspots. Simultaneously, metagenomic sequencing allows untargeted detection of known and novel pathogens in carcass-associated microbial communities ("necrobiome"), with portable platforms supporting field-based surveillance. Integrating carcass-based surveillance into One Health frameworks through interdisciplinary collaboration among ecologists, epidemiologists, and data scientists offers a proactive approach to early outbreak detection, improved pandemic preparedness, and ecosystem health monitoring. Given the projected increase in climate-driven mortality events, incorporating carcass-scavenger networks into disease surveillance strategies is a valuable and under-utilised complement to existing approaches, enhancing our ability to monitor and mitigate emerging infectious diseases.},
}

@article {pmid41394788,
year = {2025},
author = {Zhang, B and Wang, J and Li, Q and Ge, J and Zhang, C and Zhou, T and Guo, H and Yang, B and Jiang, H},
title = {Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing (mNGS) in Hospital-Acquired Pneumonia: A Stratified Retrospective Study of Responders and Non-Responders.},
journal = {Risk management and healthcare policy},
volume = {18},
number = {},
pages = {3803-3818},
pmid = {41394788},
issn = {1179-1594},
abstract = {INTRODUCTION: Hospital-acquired pneumonia (HAP) remains a major challenge in clinical practice, particularly due to polymicrobial infections and antimicrobial resistance. Traditional diagnostic methods, such as culture and PCR, are limited by low sensitivity, slow turnaround time, and inability to detect fastidious or novel pathogens. Metagenomic next-generation sequencing (mNGS) offers an unbiased approach to pathogen detection and may improve diagnostic accuracy and clinical decision-making.

METHODS: We conducted a retrospective study of 300 adult HAP patients admitted to Beijing Rehabilitation Hospital, China. Bronchoalveolar lavage fluid samples were analyzed using the Illumina sequencing platform for mNGS. Detection rates, pathogen spectrum, resistance gene identification, and treatment modifications were compared with conventional culture methods.

RESULTS: mNGS achieved a pathogen detection rate of 92%, significantly higher than the 72% achieved by culture. It identified a broader spectrum of bacteria, fungi, and viruses, including Pseudomonas, Klebsiella, and Aspergillus, which were often missed by culture. Polymicrobial infections were detected in 28% of cases, and antibiotic resistance genes were identified in 30% of samples. The median turnaround time for mNGS results was 48 hours after BAL sampling. Based on mNGS findings, treatment regimens were adjusted in 26% of patients.

CONCLUSION: mNGS demonstrated superior diagnostic performance compared with culture by increasing pathogen detection rates, identifying resistance genes, and guiding treatment adjustments in HAP patients. Despite its promise for precision medicine, further studies are needed to assess cost-effectiveness and generalizability, given the retrospective and single-center design of this study.},
}

@article {pmid41394752,
year = {2025},
author = {Hillary, LS and Knotts, TA and Adams, SH and Ali, MR and Olm, MR and Emerson, JB},
title = {DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.25.690293},
pmid = {41394752},
issn = {2692-8205},
abstract = {Accurately characterising the human gut virome is critical to understanding virus-microbiome-host interactions. However, widely used methods introduce biases that complicate data interpretation and limit cross-study comparability. For instance, multiple-displacement amplification (MDA) preferentially amplifies single-stranded DNA viruses, while total metagenomes are dominated by non-viral sequences, reducing viral signal. These traditional methods have not been systematically compared to viral size-fraction metagenomes (viromes) prepared without MDA. To address this, we applied four common methods for characterising human gut viral community composition (total metagenomes, viromes with/ without DNase treatment (to remove free DNA), and MDA viromes) to a human stool sample, with technical triplicates for each approach. MDA biased viral community composition to a shocking degree: Microviridae formed ∼90% of MDA viromes compared to just 2% of non-MDA viromes. Removing ssDNA viruses from data analyses substantially reduced, but did not eliminate, MDA bias. Metagenomes were enriched for putative temperate phages and predicted Bacillota-phages , whereas predicted Bacteroidetes -phages dominated all viromes, suggesting that metagenomes and viromes select for different populations within the total viral community. DNase treatment had little-to-no effect on virome richness or community composition. This proof-of-principle experiment demonstrates that preparatory methods for viral community analysis can lead to substantially different conclusions from the same faecal sample, and we provide a comprehensive omic data analysis framework for comparing laboratory methodologies for viral ecology. With sufficient DNA yields now easily achievable from human gut viromes without the use of MDA, our results suggest that this biased amplification method should be avoided in human gut virome studies.},
}

@article {pmid41394329,
year = {2025},
author = {Yao, X and Sang, H and Gao, S and Hu, X and Yan, J and Liu, T and Chang, H and Pang, G and Dong, H and Meng, X and Jiang, L and Kong, M},
title = {Diagnostic Utility of Bronchoalveolar Lavage Metagenomic Next-Generation Sequencing for Pulmonary Mucormycosis: A Single-Center Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6469-6480},
pmid = {41394329},
issn = {1178-6973},
abstract = {BACKGROUND: Although pulmonary mucormycosis is rare, it is highly invasive and carries a significant mortality rate. Due to its nonspecific clinical manifestations, it is often misdiagnosed as other invasive fungal diseases. Bronchoalveolar lavage fluid metagenomic next-generation sequencing is a rapid, precise, and comprehensive method for pathogen detection, showing great potential in the early diagnosis of pulmonary mucormycosis in a single-center retrospective series. It provides clinicians with faster and more accurate etiological information, thereby improving patient outcomes and reducing mortality rates.

METHODS: This study conducted a retrospective analysis of the clinical data from 14 patients diagnosed with pulmonary mucormycosis between 1/6/2021 and 30/6/2024. Peripheral blood samples were collected to perform a complete blood count, measure C-reactive protein levels, and conduct 1,3-β-D-glucan and Galactomannan tests. Lung tissue samples were sent to the pathology laboratory for histological examination. Bronchoalveolar lavage fluid was subjected to fungal culture and metagenomic next-generation sequencing. Additionally, a three-month follow-up on the patients' survival status was carried out via telephone.

RESULTS: Males accounted for 57.14% of the cases. Diabetes mellitus was present in 12 patients (85.71%, 12/14), and fever was observed in 12 patients (85.71%, 12/14). The 14 patients were categorized as proven cases (4 cases), probable cases (4 cases), and possible cases (6 cases). Two patients (14.29%, 2/14) were diagnosed with disseminated mucormycosis. Chest Computed Tomography scans revealed cavities in half of the patients (50.00%, 7/14). Fungal hyphae were identified in all the histopathological examinations (100%, 4/4). Metagenomic next-generation sequencing detected Mucorales pathogens in all the (100%, 14/14) cases, which is higher positivity than the positive rates of the 1,3-β-D-glucan test (35.71%, 5/14), Galactomannan test (42.86%, 6/14) and fungal culture (7.14%, 1/14). The turnaround time for metagenomic next-generation sequencing reports is 1-3 days, which is much shorter than the time required to obtain results from fungal culture (2-5 days). Additionally, metagenomic next-generation sequencing identified bacterial and viral co-infections, with 11 patients diagnosed as having mixed infections. All patients were treated with antifungal agents targeting Aspergillus species, such as voriconazole, posaconazole, isavuconazole, or amphotericin B, resulting in 9 patients improving, 2 patients being transferred to higher-level hospitals, and 3 patients discontinuing treatment. The 90-day follow-up revealed a mortality rate of 28.57%.

CONCLUSION: Metagenomic next-generation sequencing can serve as an important complement to traditional diagnostic methods, enabling rapid and accurate differentiation of Mucorales from other fungi. This allows patients to receive timely and targeted antifungal therapy, playing a critical role in early intervention and improving prognosis.},
}

@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.

AIM: This study aimed to investigate the effects of the JWC on gastric mucosal inflammation and the expression of drug-resistance genes in H. pylori-infected mice.

METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.

RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1β, and tumor necrosis factor-α (TNF-α) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.

CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}

Animals
*Helicobacter Infections/drug therapy/microbiology/pathology
*Helicobacter pylori/drug effects
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Disease Models, Animal
*Gastric Mucosa/pathology/drug effects/microbiology
*MAP Kinase Signaling System/drug effects
*Drug Resistance, Bacterial/drug effects
Anti-Bacterial Agents/pharmacology
Male
Inflammation/drug therapy
*Gastritis/drug therapy/microbiology
Capsules

@article {pmid41394104,
year = {2025},
author = {Xuan, F and Li, C and Zhao, H and Liu, N and Zhao, X and Zhang, B and Wu, X},
title = {Diagnosis, treatment, and monitoring of cytomegalovirus pneumonia in a hematopoietic stem cell transplantation child.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1665477},
pmid = {41394104},
issn = {2235-2988},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Child ; Female ; *Cytomegalovirus Infections/diagnosis/drug therapy ; Antiviral Agents/therapeutic use ; *Cytomegalovirus/isolation & purification/genetics ; *Pneumonia, Viral/diagnosis/drug therapy/virology ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy/complications ; Bronchoalveolar Lavage Fluid/virology ; Acetates/therapeutic use ; Quinazolines/therapeutic use ; },
abstract = {BACKGROUND: Cytomegalovirus (CMV), an opportunistic pathogen, can cause severe pneumonia in Chronic myeloid leukemia (CML) children undergoing hematopoietic stem cell transplantation (HSCT), resulting in a high mortality rate.

CASE PRESENTATION: An 11-year-old girl was hospitalized with a 3-day history of fever and vomiting, presenting with anemia and massive splenomegaly. A series of diagnostic tests, including blood cell count, bone marrow analysis, flow cytometry, chromosomal examination, and genetic testing, confirmed a diagnosis of CML at blast-phase. Following a one-year course of tyrosine kinase inhibitor-based chemotherapy, the patient entered the chronic phase and underwent a 6/12 human leukocyte antigen (HLA)-matched HSCT from her father. Two weeks after HSCT, the patient developed grade III skin graft-versus-host disease and hemorrhagic cystitis, which were effectively treated and symptoms were alleviated. One month after transplantation, the patient presented with serious pneumonia and pancytopenia. Although five blood cultures and two sputum cultures were all negative, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) indicated a high abundance of CMV (16635 reads), leading to a diagnosis of CMV pneumonia. Notably, no typical resistant mutations were identified in the CMV genome. Targeted treatment with sodium phosphonoformate and letermovir was administered. As a result, the patient's condition improved remarkably with the abundance of CMV decreasing to only 12 reads. After one-year of monitoring, the primary disease was well-controlled, and no CMV reactivation was observed.

CONCLUSION: The diagnosis, treatment, and monitoring of pneumonia is crucial in post-HSCT patients. This case highlights the utility of mNGS in diagnosing and monitoring CMV pneumonia in post - HSCT patient and the effectiveness of targeted therapy in managing such infections.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
Child
Female
*Cytomegalovirus Infections/diagnosis/drug therapy
Antiviral Agents/therapeutic use
*Cytomegalovirus/isolation & purification/genetics
*Pneumonia, Viral/diagnosis/drug therapy/virology
Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy/complications
Bronchoalveolar Lavage Fluid/virology
Acetates/therapeutic use
Quinazolines/therapeutic use

@article {pmid41393784,
year = {2025},
author = {Longhi, G and Tarracchini, C and Angelini, L and Anzalone, R and Viappiani, A and Ventura, M and Milani, C and Turroni, F},
title = {Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100516},
pmid = {41393784},
issn = {2666-5174},
abstract = {Traditional dry-cured hams host diverse microbial communities; however, their taxonomic composition, functional capacity, and potential interactions with the human gut remain poorly understood. This study aimed to provide a comprehensive characterization of the microbiota associated with Italian Protected Designation of Origin (PDO) dry-cured hams and to investigate their functional relevance in the food matrix and under simulated intestinal conditions. A total of 96 samples, representing different geographical origins and maturation stages, were analyzed using metagenomics approaches. A conserved microbial core dominated by Staphylococcus equorum (prevalence 80 %) was identified, accompanied by accessory taxa such as Tetragenococcus halophilus (62 %) and Leuconostoc carnosum (10 %). Cluster analyses revealed substantial variability across samples, with community structures influenced more by producer-specific factors than by product type or ripening stage. Functional metagenomics investigation highlighted the presence of metabolic pathways associated with amino acid degradation, carbohydrate metabolism, and lipid transformation, supporting a role for ham-associated microbes in flavor and texture development. Furthermore, cultivation in a simulated gut environment showed a marked reshaping of the microbial community, with low-abundance taxa, including Bacillus spp. and Lactococcus lactis, proliferating under intestinal-like conditions, while the dominance of S. equorum was reduced. Our findings showed that the microbiota of dry-cured ham not only drives key sensory qualities of the product but also comprises a reservoir of live microorganisms capable of tolerating the gut-like conditions. These results highlight the dual role of foodborne microbiota in shaping both food properties and potential interactions with the human host, underscoring the need for further in vivo investigations.},
}

@article {pmid41393342,
year = {2025},
author = {Nishimura, Y and Omae, K and Tominaga, K and Iwasaki, W},
title = {CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf182},
pmid = {41393342},
issn = {2631-9268},
mesh = {Phylogeny ; *Evolution, Molecular ; *Genome, Bacterial ; Databases, Genetic ; },
abstract = {The recent expansion of prokaryotic genomes reveals many ortholog groups (OGs) whose function cannot be inferred from conventional, sequence similarity-based annotation methods, especially in metagenome-assembled genomes. Phylogenetic profiling is one of the promising methods to annotate these OGs, by identifying functional relationships of OGs using co- or anti-occurrence of OG distributions, not sequence similarity. Here, we proposed two new phylogenetic methods for large-scale data, Ancestral State Adjustment (ASA) and Simultaneous EVolution test (SEV), which consider the ancestral state of OG presence/absence. In evaluations using three distinct prokaryotic datasets, ASA and SEV showed better or comparable performance to both established and recently proposed methods for large-scale data. We compared the functionally related OGs detected by each method and found that SEV and its predecessor can identify slowly evolving OGs, such as housekeeping genes. In contrast, ASA and its predecessors can detect functionally related OGs that tend to be gained or lost in a fixed order, indicating a strong evolutionary constraint that provides clues for functional prediction. Using matrix multiplication, we also showed that SEV is scalable in the latest genome databases.},
}

Phylogeny
*Evolution, Molecular
*Genome, Bacterial
Databases, Genetic

@article {pmid41393220,
year = {2026},
author = {Brown, NK and Depuydt, L and Zakeri, M and Alhadi, A and Allam, N and Begleiter, D and Kabilan Karpagavalli, NB and Khajjayam, SS and Wahed, H and Gagie, T and Langmead, B},
title = {KeBaB: k-mer based breaking for finding long MEMs.},
journal = {International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)},
volume = {16073},
number = {},
pages = {10-17},
pmid = {41393220},
abstract = {Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can often ignore much of its input, skipping matching steps which are redundant to the final output. In this paper we propose KeBaB, a fast and space efficient k-mer filtration step using a Bloom filter. This approach speeds up MEM-finders such as ropebwt3 even further by letting them ignore even more, breaking the input into substrings called "pseudo-MEMs" which are guaranteed to contain all long MEMs. We also show experimentally that KeBaB can accelerate metagenomic classification without significantly reducing accuracy, either by finding all long MEMs or by leveraging the filter to find only the long MEMs present in the t longest pseudo-MEMs.},
}

@article {pmid41392764,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}

@article {pmid41392335,
year = {2025},
author = {Zheng, X and Luo, X and Zhang, Y and Zou, Z and Yang, J and Liu, H and Lu, Z and Cao, F and Wang, X and Ge, X and Li, X and Wang, J},
title = {Inflammation in Diabetic Kidney Disease Is Linked to Gut Dysbiosis and Metabolite Imbalance.},
journal = {Journal of diabetes},
volume = {17},
number = {12},
pages = {e70175},
doi = {10.1111/1753-0407.70175},
pmid = {41392335},
issn = {1753-0407},
support = {XHZDZK019//Mianyang Central Hospital/ ; 2020FH09//Mianyang Central Hospital/ ; 2022HYX005//Mianyang Central Hospital/ ; 2023YFS0470//Science and Technology Department of Sichuan Province/ ; 2023ZYDF073//Mianyang Science and Technology Bureau/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/immunology ; *Diabetic Nephropathies/microbiology/metabolism/immunology ; Male ; Middle Aged ; Female ; *Inflammation/metabolism/microbiology ; Cytokines/blood ; Case-Control Studies ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is characterized by a sustained pro-inflammatory response of the immune system, which leads to renal failure progression and related complications. Emerging evidence suggests that gut microbiota dysregulation may be a pathogenic mediator in DKD, while mechanisms remain unclear. This study aimed to identify differences in the gut microbiota of the DKD group and healthy controls (HC).

METHODS: Gut microbiota composition was determined using shotgun metagenomic sequencing on fecal samples; serum cytokines were measured via ELISA, immune phenotypes were detected using flow cytometry.

RESULTS: Significant differences in gut microbiota diversity and richness were observed between patients with DKD and HC, with higher abundances of Enterobacteriaceae, Serratia, and Shigella in the DKD group than in the HC group. Additionally, CD3+ (especially CD4+) T cells were significantly higher in the renal tissue of the DKD group than the HC group. Flow cytometry identified significantly higher circulating levels of NKT cells and CD8+ T cells and lymphocyte ratio in HC than in DKD. CD4+ cells, CD4+ TCM cells, CD8+ TCM cells, and the CD4+/CD8+ cell ratio were significantly higher in the DKD group than in the HC group, as were levels of pro-inflammatory mediators, including IL-6, TNF-α, and sCD14, and expression of the gut barrier dysfunction marker ZO-1.

CONCLUSIONS: Gut barrier dysfunction and gut microbiota imbalance may mediate the pro-inflammatory immune phenotype observed in patients with DKD and thereby contribute to DKD progression. These findings underscore the important role of the microbiota-immune axis in the development of DKD.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism/immunology
*Diabetic Nephropathies/microbiology/metabolism/immunology
Male
Middle Aged
Female
*Inflammation/metabolism/microbiology
Cytokines/blood
Case-Control Studies
Aged
Adult
Feces/microbiology

@article {pmid41392160,
year = {2025},
author = {Jamy, M and Huber, T and Antoine, T and Ruscheweyh, HJ and Paoli, L and Pelletier, E and O Delmont, T and Burki, F},
title = {Identification of a deep-branching lineage of algae using environmental plastid genomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67401-4},
pmid = {41392160},
issn = {2041-1723},
support = {2022-00351//Vetenskapsrådet (Swedish Research Council)/ ; 2021-04055//Vetenskapsrådet (Swedish Research Council)/ ; ERC consolidator grant 101044505//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Marine algae underpin entire ocean ecosystems. Yet algae in culture poorly represent their large environmental diversity, and we have a limited understanding of their convoluted evolution by endosymbiosis. Here, we perform a phylogeny-guided plastid genome-resolved metagenomic survey of Tara Oceans expeditions. We present a curated resource of 660 new non-redundant plastid genomes of environmental marine algae, vastly expanding plastid genome diversity within major algal groups, including many without closely related reference genomes. Notably, we recover four plastid genomes, including one near-complete, forming a deep-branching plastid lineage of nano-size algae that we informally name leptophytes. This group is globally distributed and generally rare, although it can reach relatively high abundance in the Arctic. A near-complete mitochondrial genome showing strong co-occurrence with leptophyte plastids is also recovered and assigned to this group. Leptophytes encompass the enigmatic plastid group DPL2, one of the very few known plastid groups not clearly belonging to major algal groups and previously known only from 16S rDNA sequences. Comparative organellar genomics and phylogenomics indicate that leptophytes are sister to haptophytes, and raise the intriguing possibility that cryptophytes acquired their plastids from haptophytes. Collectively, our study demonstrates that metagenomics can reveal hidden organellar diversity, and improve models of plastid evolution.},
}

@article {pmid41392116,
year = {2025},
author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H},
title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31280-y},
pmid = {41392116},
issn = {2045-2322},
support = {81860142//National Natural Science Foundation of China/ ; },
abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.},
}

@article {pmid41392048,
year = {2025},
author = {Liu, X and Chen, Y and Shi, Z and Shi, Z and Pu, T and Zhang, Y and He, F and Li, X and Wang, Y and Jia, J and He, B and Yang, P},
title = {Macrogenomic analysis of the previous crops effects on tobacco soil microbiomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-08640-9},
pmid = {41392048},
issn = {2045-2322},
support = {2024530700242003, 2023530700242002//the special funds for the Scientific Research Program of Yunnan Tobacco Company/ ; 2024530700242003, 2023530700242002//the special funds for the Scientific Research Program of Yunnan Tobacco Company/ ; (XDYC CYCX-2022-0071)//the "Xingdian Talent" Industry Innovation Talent Program in Yunnan Province/ ; },
abstract = {Crop rotation serves as a valuable agronomic practice for addressing succession barriers in crops, particularly in tobacco growing. The effect of different previous crops on the microbiology of soils planted with tobacco is an area that deserves further study.This study investigated the chemical properties, microbial community composition, and functional genes related to nutrient cycling in tobacco-planted soils with no preceding crop (CK), garlic (T1), or faba bean (T2) as preceding crops. The results indicated that the T1 treatment significantly decreased the contents of soil organic matter (SOM, 11.32%), total phosphorus (TP, 29.41%), total potassium (TK, 3.33%), and available potassium (AK, 46.88%), whereas the T2 treatment notably increased the content of hydrolyzable nitrogen (HN, 34.88%). Furthermore, the T2 treatment significantly enhanced the diversity of soil bacteria and fungi, particularly the bacterial Shannon index (1.49%) and fungal Chao1 (24.11%) and Shannon (7.73%) indices. In terms of microbial composition, compared to the CK, the T2 treatment enriched the relative abundance of beneficial bacterial genera (e.g., Sphingomonas, Methyloceanibacter, Rhizophagus) and reduced the relative abundance of pathogenic fungi (e.g., Fusarium). Additionally, T2 treatment increased the abundance of functional genes associated with nitrogen, phosphorus, and potassium, thereby promoting the cycling of soil nutrients. Overall, faba bean as a preceding crop was more beneficial for subsequent tobacco cultivation than fallow periods or garlic.},
}

@article {pmid41292709,
year = {2025},
author = {Quiñones-Sanchez, CL and Bilbao-Del Valle, JL and Urdaneta-Colon, MA and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in the Drosophila melanogaster Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41292709},
issn = {2692-8205},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; R25 HG012702/HG/NHGRI NIH HHS/United States ; },
abstract = {The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two commercial DNA extraction kits (Qiagen and Zymo) and two lysis methods (manual pestle homogenization and bead-beating) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and Drosophila melanogaster gut samples, a tractable model for host-microbe interactions. Full-length 16S rRNA sequencing was performed using Oxford Nanopore Technologies, followed by bioinformatic analysis using EPI2ME for taxonomic classification and standard diversity pipelines. Our data revealed that extraction and lysis methods significantly influence microbial composition, with some protocols resulting in inflated richness in MCS samples. Pestle homogenization with the Qiagen kit yielded the highest bacterial species richness while maintaining consistent representation of both Gram-positive and Gram-negative taxa. These findings demonstrate that extraction methodology strongly affects microbial diversity estimates and emphasize the need for standardized protocols to ensure reproducibility across microbiome studies, particularly those using model systems.},
}

@article {pmid41248092,
year = {2025},
author = {Richie, T and Lee, STM},
title = {Decoding the Gut Microbiota: Mechanisms of Host-Microbe Interactions and Inflammatory Pathologies.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-18},
doi = {10.1159/000549457},
pmid = {41248092},
issn = {1421-9867},
abstract = {BACKGROUND: Microbes residing in the gastrointestinal tract are intertwined with the immune development and overall health of the host throughout stages of life. It is well established that these microbes can have both positive and negative impacts on host health. Having foundational knowledge of these interactions with the host is critical in understanding gastrointestinal health.

SUMMARY: This review discusses the importance of high-resolution study of the gut microbiota, which includes potential modern approaches for analyzing the gut microbiota and considers the challenges and aspects necessary for robust investigation of the gut microbiota. Here, we highlight the complex and highly individualized relationship of microbes interacting within the host results in an ever-changing landscape in the gastrointestinal tract, whether due to host conditions or microbial conditions including microbe-microbe and microbe-host interactions. The vastness and complexity of the gut microbiota contribute to the challenge of quantifying not only a community of microbes in the gut environment, but also maintaining resolution to investigate individual microbes, capturing the network of interactions coinciding in the gastrointestinal tract. Furthermore, the review emphasizes the importance of microbial functions and products to host health outcomes in the context of inflammatory diseases.

KEY MESSAGES: Consideration for microbial functions and interactions with the gut immune system is critical for developing effective treatment strategies of inflammatory disorders. Employing high-resolution microbial techniques to investigate microbes with environmental relevance and community functions are a major challenge in the microbiome field. With new techniques and improvements on existing methodologies, investigating microbes at various community levels is feasible and becoming critical in understanding the community interactions with the host influencing the immune status and overall health outcomes.},
}

@article {pmid41391873,
year = {2025},
author = {Shen, Q and Mao, L and Shi, W and Wang, J and Ndjekadom, A and Bao, Y and Wang, X and Liu, Y and Yang, S and Ji, L and Shan, T and Zhang, W},
title = {Viral communities and identification of a parvovirus and two picornaviruses in geese with gout.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0456},
pmid = {41391873},
issn = {1347-7439},
abstract = {In recent years, an emerging infectious disease characterized by urate deposition in viscera and joints has outbreak in the goose farms of China, causing substantial economic losses. Although goose astrovirus (GoAstV) was believed to be the main causative pathogen, several studies have shown that co-infection with other viruses, such as goose parvovirus, alongside astrovirus, may exacerbate the disease condition. In our previous research, we isolated a goose astrovirus with a novel type of recombination that causes fatal gout in geese in Shanghai, China. By analyzing the viral community using viral metagenomics data of fecal, kidney and liver samples of geese with gout, we found that parvoviruses and picornaviruses occupied a substantial proportion, suggesting their potential involvement in the etiology of goose gout. To determine if there were other causative viruses present in these geese, fecal, kidney, and liver samples were deeply sequenced using viral metagenomics. The results indicated that goose parvovirus and picornavirus constituted the predominant part of all or partial viral communities. Subsequently, the genomes and genomic structures of two picornaviruses, as well as a parvovirus, were determined. Phylogenetic analysis revealed that this parvovirus, named dependoparvovirus_CH_SH01, belongs to the Parvovirinae subfamily within the family Parvoviridae, while the two picornaviruses were classified within the Megrivirus (megrivirus_CH_SH01) or Ludopivirus (ludopivirus_CH_SH01) genus within the Kodimesavirinae subfamily, respectively. Recombination analysis suggested that megrivirus_CH_SH01 was a potential recombinant virus between two megriviruses. Our study suggested that infections with viruses other than astrovirus may be associated with the occurrence of goose gout. Additionally, this work has enriched the virus sequence information for Megrivirus and picornaviruses.},
}

@article {pmid41391818,
year = {2025},
author = {Zhou, H and Gao, and Wu, B and Xu, G and Tian, L and Sun, Y and Yang, F and Ni, K},
title = {Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.017},
pmid = {41391818},
issn = {2090-1224},
abstract = {INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored.

OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources.

METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs).

RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61 % of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97 % of the BGCs and 99.76 % of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean = 14.76, P = 0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean = 7.13, P = 6.1e-05), Lamiaceae (mean = 7, P = 0.015), Ranunculaceae (mean = 8.22, P = 0.0053), and Rosaceae (mean = 7.75, P = 0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain.

CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.},
}

@article {pmid41391639,
year = {2025},
author = {Yuan, F and Wang, L and Nguyen, SM and Shu, XO and Shrubsole, MJ and Wen, W and Cai, Q and Yu, D and Zheng, W},
title = {Plant-based diets, gut microbiota, blood metabolome, and risk of colorectal, liver and pancreatic cancers: results from a large prospective cohort study of predominantly low-income Americans.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101135},
doi = {10.1016/j.ajcnut.2025.101135},
pmid = {41391639},
issn = {1938-3207},
abstract = {BACKGROUND: Plant-based diets have been advertised for environmental and health benefits. Their effects on cancer risk, gut microbial and blood metabolomic profiles remain unclear.

OBJECTIVE: We investigated plant-based diets in relation to cancer incidence as well as gut microbial composition and blood metabolites in the Southern Community Cohort Study.

METHODS: Included in the analysis were 71,533 participants. Habitual dietary intake assessed at baseline (2002-2009) was used to derive overall plant-based diet index (PDI), healthy plant-based diet index (hPDI), and unhealthy plant-based diet index (uPDI). Incident cancer cases were ascertained via linkage to state cancer registries and the National Death Index. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated from Cox proportional hazards models after adjusting for potential confounders. We examined associations of the three indices with gut microbiota and blood metabolites using fecal metagenomic and blood metabolomic data from two subsets of 417 and 1,581 participants, respectively.

RESULTS: During a median follow-up time of 11.6 years, 783, 316, and 295 incident colorectal, liver, and pancreatic cancer cases were identified. High hPDI was related to a lower liver cancer risk (HR=0.67, 95% CI=0.45, 0.99 comparing extreme quartiles, Ptrend=0.03). No apparent association was observed for colorectal cancer (CRC) in the whole cohort. However, among 49,132 CRC screening-naïve participants at baseline, PDI was inversely associated (HR=0.74, 95% CI=0.58, 0.96, Ptrend=0.01), while uPDI was positively associated (HR=1.39, 95% CI=1.06, 1.82, Ptrend=0.02) with CRC risk. No index was associated with pancreatic cancer. These diet indices were associated with microbial taxa and blood metabolites that have been implicated in the tumorigenesis of colorectum and liver.

CONCLUSIONS: A diet high in healthy plant foods and low in animal foods was inversely associated with liver cancer risk and with CRC risk among screening-naïve participants. These associations may be partly mediated through gut microbiota and systemic metabolism.},
}

@article {pmid41391314,
year = {2025},
author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J},
title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140802},
doi = {10.1016/j.jhazmat.2025.140802},
pmid = {41391314},
issn = {1873-3336},
abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.},
}

@article {pmid41391220,
year = {2025},
author = {Xu, QY and Habib, T and Gao, L and Wu, D and Li, XY and Khieu, TN and Chen, YH and Zhang, Y and Liu, YH and She, TT and Fang, BZ and Li, WJ},
title = {Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126683},
doi = {10.1016/j.syapm.2025.126683},
pmid = {41391220},
issn = {1618-0984},
abstract = {Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus Wenzhouxiangella are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305[T] and EGI_FJ10409[T], which show low 16S rRNA gene sequence identities to other validly published Wenzhouxiangella species (< 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus Wenzhouxiangella. Two halotolerant strains are grown at 0-10.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10305[T]) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409[T]), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305[T] and EGI_FJ10409[T] are Wenzhouxiangella psychrophile sp. nov. and Wenzhouxiangella indolica sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family Wenzhouxiangellaceae, for which we propose the name Halotectona sediminis gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}

@article {pmid41391055,
year = {2025},
author = {An, X and Niu, S and Al, MA and Su, E and Chen, L and He, H and Wang, Y and Zhang, S and Yang, Y and Wang, S and Wen, Z and Xu, B and Ming, Y and Zhu, W and Zhao, Z and Wu, K and Yang, Y and Xie, W and He, Z and Yan, Q},
title = {Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella).},
journal = {Advanced biotechnology},
volume = {3},
number = {4},
pages = {36},
pmid = {41391055},
issn = {2948-2801},
support = {2320004002504//Zhuhai Industry-University-Research Cooperation Project/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP002//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {The gut microbiome plays pivotal roles in the host's metabolic response to dietary interventions. Dietary macroalgae supplementation represents a promising strategy for enhancing animal growth and health via microbiome modulation. However, the underlying mechanism of how macroalgae supplementation regulates microbiome-host interactions in aquatic species remains unclear. This study investigated the effects of three dietary macroalgae-Sargassum hemiphyllum (S), Asparagopsis taxiformis (A), and Gracilaria lemaneiformis (G)-each supplemented at 5% in feed, on the gut microbiome and metabolism of grass carp (Ctenopharyngodon idella), using integrated approaches of 16S rRNA sequencing, metagenomics, and metabolomics. While all three macroalgae influenced host growth, supplementation of S provided the most comprehensive benefits, with significant enhancement of body weight and hepatic superoxide dismutase activity. Integrated multi-omics analysis revealed that dietary macroalgae supplementation increased the relative abundance of the key gut bacterial genus Shewanella, with the most notable effect observed in the supplementation of S. Subsequent analysis of a metagenome-assembled genome (MAG) of Shewanella (MAG C3_bin52) demonstrated its considerable potential for amino acid biosynthesis and metabolism. This genomic potential was further supported by metabolomic profiling, which indicated significant upregulation of amino acid-related metabolites, particularly in the supplementation S. Pathway analysis confirmed enrichment in processes associated with protein digestion and absorption, amino acid biosynthesis, and related metabolic pathways. These findings highlight the modulation of a macroalgae-microbiome-metabolite axis in grass carp, primarily mediated by the enrichment of Shewanella in gut ecosystem for enhancing host amino acid metabolism. This study advances understanding of dietary modulation of the gut microbiome and provides insights for the sustainable development of aquaculture.},
}

@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30907-4},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
}

@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00858-9},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; R01 AI151075/AI/NIAID NIH HHS/United States ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}

@article {pmid41390665,
year = {2025},
author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , },
title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66567-1},
pmid = {41390665},
issn = {2041-1723},
support = {P30 ES007033/ES/NIEHS NIH HHS/United States ; R01AI162867//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2127509//American Society for Engineering Education (ASEE)/ ; },
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.},
}

@article {pmid41390664,
year = {2025},
author = {Cao, Q and Deng, Z and Li, M and Zhu, S and Huo, Y and Dong, H and Aernouts, B and Psifidi, A and Xu, C},
title = {Integrated metagenomic and metabolomic analyses reveal tenacissoside G as a potential non-antimicrobial treatment for bovine endometritis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02264-x},
pmid = {41390664},
issn = {2049-2618},
support = {No. 2024B02016//the Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; 32125038//the National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; CARS-36//China Agriculture Research System/ ; },
abstract = {BACKGROUND: Bovine endometritis is a prevalent uterine disease that directly curtails reproductive performance and indirectly reduces milk production by increasing calving intervals. Postpartum uterine bacterial infection is the primary cause of bovine endometritis, which is typically treated with prostaglandin F2α and antimicrobials. However, abuse of antimicrobials has led to the emergence of multidrug-resistant bacteria, threatening both human and animal health. To explore alternatives to antimicrobial therapy for bovine endometritis, we integrated uterine metagenomic and metabolomic analyses and identified a novel bioactive metabolite with therapeutic potential. The potential antibacterial and anti-inflammatory effects of this metabolite against bovine endometritis were evaluated by assessing its inhibitory effect on the growth of F. necrophorum in vitro, and by quantifying histopathological scores and inflammatory cytokine expression levels in an in vivo mouse model of endometritis, respectively.

RESULTS: A total of 40 Holstein dairy cows at 21 days to 30 days postpartum were assigned into heathy cows (n = 15), subclinical endometritis cows (n = 12) and clinical endometritis cows (n = 13) according to clinical signs and laboratory tests for bovine endometritis. The uterine fluid was collected aseptically for metagenomics and metabolomics sequencing to identify bacterial species associated with bovine endometritis and metabolites that could potentially be used for treatment of bovine endometritis. A total of 17 bacterial species were significantly associated with bovine endometritis, with Fusobacterium necrophorum as the most significantly enriched in cows with clinical endometritis compared to healthy counterparts. In total, 391 metabolites were significantly differentially abundant between healthy and clinical endometritis cows. Among these, a plant-derived compound, tenacissoside G was significantly enriched in healthy cows. Notably, the abundance of F. necrophorum was significantly negatively associated with the concentration of tenacissoside G in clinical endometritis cows. Moreover, tenacissoside G significantly inhibited the growth of F. necrophorum in vitro and ameliorated inflammation in endometritis caused by F. necrophorum in a mice model.

CONCLUSION: This study provides new insights into the relationship between uterine microbiome and metabolites in bovine endometritis, potentially leading to novel strategies for treating bovine endometritis. Furthermore, tenacissoside G exhibits therapeutic effects against endometritis induced by F. necrophorum, and could serve as a potential alternative to antimicrobials for treating endometritis. Video Abstract.},
}

@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07513-z},
pmid = {41390654},
issn = {1479-5876},
}

@article {pmid41387797,
year = {2025},
author = {Fu, W and Deng, ZW and Wang, P and Zhu, ZW and Xie, ZB and Li, YZ and Zhang, HQ and Yu, HY},
title = {HIV infection complicated with talaromyces marneffei, tuberculosis, hemophagocytic lymphohistiocytosis and non-Hodgkin lymphoma: a complex case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1714},
pmid = {41387797},
issn = {1471-2334},
support = {2023JJ50447//the Natural Science Foundation of Hunan Province, CN/ ; 2024JJ7349//the Natural Science Foundation of Hunan Province, CN/ ; 2022YLT002//Hunan Provincial People's Hospital Medical Association Special Scientific Research Fund Project, CN/ ; QNJJ202503//Hunan University of Medicine General Hospital Youth Scientific Research Fund/ ; },
abstract = {BACKGROUND: Due to severe immunosuppression, human immunodeficiency virus (HIV) infected individuals are prone to multiple opportunistic infections and malignancies. This report presents a complex case of a 62-year-old male HIV patient who was diagnosed with co-infections of Talaromyces marneffei, tuberculosis, hemophagocytic lymphohistiocytosis (HLH), and ultimately non-Hodgkin B-cell lymphoma. This case provides valuable insights for clinical diagnosis and treatment.

CASE SUMMARY: The patient was admitted with complaints of “poor appetite, weight loss, and diarrhea for two weeks, accompanied by fever for four days.” Upon admission, the patient was diagnosed with HIV infection, with a CD4 + T-cell count of only 25/µL. Pathological examination of cervical lymph node aspiration and metagenomic next-generation sequencing (mNGS) confirmed infections with Talaromyces marneffei, Mycobacterium tuberculosis, and Aspergillus species. During treatment, the patient developed persistent high fever, pancytopenia, decreased fibrinogen, and significantly elevated ferritin levels. Abdominal computed tomography (CT) revealed splenomegaly. Further bone marrow examination confirmed HLH, and symptoms improved after treatment with glucocorticoids and immunoglobulin. However, the patient’s condition further deteriorated, and positron emission tomography computed tomography (PET-CT) along with repeat lymph node biopsy confirmed the diagnosis of non-Hodgkin B-cell lymphoma. Under combined antifungal, anti-tuberculosis, antiretroviral therapy (ART), and chemotherapy, the patient showed clinical improvement.

CONCLUSION: This case highlights the complexity and challenges in diagnosing and managing multiple opportunistic infections and malignancies in advanced HIV patients. It underscores the importance of multidisciplinary collaboration and provides valuable experience for the clinical management of HIV-related opportunistic infections and malignancies.},
}

@article {pmid41390498,
year = {2025},
author = {Freel, KC and Tucker, SJ and Freel, EB and Stingl, U and Giovannoni, SJ and Eren, AM and Rappé, MS},
title = {New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67043-6},
pmid = {41390498},
issn = {2041-1723},
abstract = {The bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.},
}

@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07175-9},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.

METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906 million paired-end reads per specimen.

RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.

CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}

@article {pmid41389850,
year = {2025},
author = {Petrov, VA and Schade, S and Laczny, CC and Hallqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids and a reduction of opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}

@article {pmid41389417,
year = {2025},
author = {Gong, L and Yao, L and Gu, L and Qu, Y and Gao, X and Wang, W and Huang, W and Peng, Y},
title = {Beyond traditional biological nutrient removal limits: achieving ultra-low effluent nitrogen via an anaerobic/Oxic/Anoxic (AOA) process in a pilot-scale system treating municipal wastewater.},
journal = {Water research},
volume = {290},
number = {},
pages = {125123},
doi = {10.1016/j.watres.2025.125123},
pmid = {41389417},
issn = {1879-2448},
abstract = {Developing low-cost and high-efficiency biological nutrient removal (BNR) process remains a major challenge in wastewater treatment plants (WWTPs). In this study, a pilot-scale anaerobic/oxic/anoxic (AOA) process with a treatment capacity of 100 m[3]/day was established and operated continuously for 335 days using real municipal wastewater. Without external carbon addition, the system achieved an average effluent total nitrogen (TN) concentration of 1.2 mg/L, with 90 % of values below 1.8 mg/L. Total phosphorus (TP) and chemical oxygen demand (COD) removal efficiencies reached 92.8 % and 94.1 %, respectively. A sufficient influent organic load (C/N ratio of 8.6) and extremely low nitrate concentrations enabled effective carbon storage in the anaerobic zone. Precise aeration control in the aerobic zone maintained low residual ammonium concentration, minimizing the consumption of internal carbon sources. Therefore, the anoxic zone in the AOA system fully utilized internal carbon sources for denitrification, resulting in ultra-low effluent total nitrogen concentrations. Metagenomic analysis revealed that multiple unclassified microorganisms, such as Unclassified Saccharimonadales, Unclassified Saprospiraceae, and Unclassified Myxococcales, encoded complete Gly and polyhydroxyalkanoate (PHA) metabolism as well as denitrification genes, and potentially contributed to endogenous denitrification. The AOA system overcame the nitrogen removal limitations of conventional processes by eliminating internal nitrate recirculation, while simultaneously reducing chemical dosing and energy consumption. This finding providing a scalable, energy-efficient, and economically viable strategy for next-generation WWTPs aiming to meet increasingly stringent discharge standards.},
}

@article {pmid41390369,
year = {2025},
author = {Yuan, X and Fang, M and Lan, W and Zhou, X and Yang, S and Wang, T},
title = {From urinary tract infection to deafness: community-acquired meningitis in an adult caused by hypervirulent Klebsiella pneumoniae-a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12340-0},
pmid = {41390369},
issn = {1471-2334},
abstract = {BACKGROUND: Hypervirulent Klebsiella pneumoniae (hvKP) is an emerging pathogen capable of causing lethal metastatic infections in healthy individuals. While liver abscesses are well-described, the urinary tract is increasingly recognized as a primary portal for hematogenous dissemination.

CASE PRESENTATION: A 46-year-old man with previously undiagnosed diabetes mellitus presented with community-acquired urinary tract infection (CA-UTI) that rapidly progressed to bilateral sensorineural deafness and meningitis. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) identified K. pneumoniae harboring hypervirulence genes rmpA and iucA. Blood, urine, and CSF cultures yielded an ESBL-negative, pansensitive hvKP strain. Brain MRI revealed septic emboli, consistent with hematogenous dissemination.

CONCLUSIONS: This case highlights the urinary tract as an underrecognized but lethal source of hvKP dissemination, particularly in diabetic patients. The rapid neurologic decline and permanent deafness highlight the need for early recognition and aggressive management. Virulence gene profiling should complement routine susceptibility testing. mNGS enabled rapid pathogen identification and guided targeted therapy. Clinicians must remain vigilant for CNS complications in diabetic patients with CA-UTI.},
}

@article {pmid41389890,
year = {2025},
author = {Xu, D and Zhang, W and Tao, XR and Gao, K and Zhao, MN and Wang, JW},
title = {Shenqi funeng xingnao prescription regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121035},
doi = {10.1016/j.jep.2025.121035},
pmid = {41389890},
issn = {1872-7573},
abstract = {BACKGROUND: Central fatigue is a phenomenon in which changes in the function of the central nervous system lead to decreased athletic ability and increased fatigue symptoms. Shenqi Funeng Xingnao Prescription (SQFNXNP) is a traditional Chinese medicine prescription applied to alleviate exercise-induced fatigue; however, the molecular mechanism underlying its effects on central fatigue remain elusive.

PURPOSE: This study explored the therapeutic effects and potential molecular mechanisms of SQFNXNP on central fatigue.

METHODS: A chronic fatigue model was constructed to evaluate the therapeutic effects of SQFNXNP at alleviating central fatigue, including pathological changes in the hippocampus and intestine, as well as abnormal levels of neurotransmitters and inflammation. Transcriptomic analysis revealed core gene targets, which were further validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, metagenomics was applied to explore changes in gut microbial composition and associated signaling pathways. Further validation of key proteins was conducted using western blotting (WB). Correlation analysis was further applied to identify differentially abundant metabolites related to the core targets. Compounds with prototype structures in the brain tissue after SQFNXNP administration were identified by ultra-high performance liquid chromatography-mass spectrometry analysis. A virtual screening procedure was used to screen for potential ingredients of SQFNXNP that could alleviate central fatigue.

RESULTS: SQFNXNP alleviated exercise-induced histopathological damage and mitochondrial injury in the hippocampi of mice, decreased cell apoptosis and necrosis, increased cell proliferation, and restored abnormal levels of monoamine neurotransmitters. Moreover, SQFNXNP treatment decreased inflammatory levels in the body, alleviated histopathological damage to the intestine, reduced cell apoptosis in the intestine, increased the expression of key intestinal barrier proteins, restored the goblet cell density and mucus layer integrity in the intestine, and regulated the imbalance in the gut microbiota and central fatigue-related signaling pathways. RT-qPCR and WB further revealed that SQFNXNP regulated the TNF and NOD-like receptor (NLR) signaling pathways by targeting MMP9, PTGS2, MAPK14, BCL2, TLR4, TNF, IL1B, P-AKT1, NIKBIA, and IL6 proteins. The virtual screening procedure revealed that the potential components of SQFNXNP for alleviating central fatigue were oleanolic acid and ginsenoside re.

CONCLUSION: SQFNXNP regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue, thus providing a traditional Chinese medicine strategy for treating central fatigue in the clinic.},
}

@article {pmid41389554,
year = {2025},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}

@article {pmid41389146,
year = {2025},
author = {Vorobeva, M and iAkushev, A and Chen, CC and Orihara, M and Akbar, N and Colley, P and Sehanobish, E and Chung, CHY and Scott, A and O'Brien, E and Chang, CB and Kita, H and Voyich, J and Knoop, K and Jerschow, E},
title = {Impact of Sinus Surgery on Bacteriome Composition in Patients With Chronic Rhinosinusitis With Nasal Polyps.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70082},
pmid = {41389146},
issn = {2042-6984},
support = {R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; },
}

@article {pmid41389008,
year = {2025},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics Alter Duodenal Immune Populations Upon Gluten Exposure in Mice: Implications for Non-Coeliac Gluten Sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
abstract = {A growing proportion of the non-celiac population experience adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesised that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5mg/kg) or PBS-vehicle daily for 5-days. Mice were then treated with a 3mg wheat-gluten suspension, or vehicle, on days 4 and 5 before sacrifice on day 7. Duodenal immune cells were analysed by histology and flow cytometry, while the duodenal MAM and faecal microbiome were characterised via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in faeces, and resulted in altered microbial carbohydrate and lipid metabolism, compared to vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared to vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.},
}

@article {pmid41388903,
year = {2025},
author = {Wutkowska, M and Nweze, JA and Tláskal, V and Nweze, JE and Daebeler, A},
title = {Uncovering hidden phylo: and ecogenomic diversity of the widespread methanotrophic genus Methylobacter.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf127},
pmid = {41388903},
issn = {1574-6941},
abstract = {The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterise the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulphur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognised species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.},
}

@article {pmid41388659,
year = {2025},
author = {Wallbank, JA and Kingsbury, JM and Pantos, O and Weaver, L and Smith, DA and Barbier, M and Theobald, B and Gambarini, V and Lear, G},
title = {Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70214},
doi = {10.1111/1462-2920.70214},
pmid = {41388659},
issn = {1462-2920},
support = {C03X1802//Ministry of Business, Innovation and Employment/ ; },
mesh = {*Biofilms/drug effects/growth & development ; *Seawater/microbiology ; *Plastics ; Fungi/genetics/classification/drug effects/isolation & purification ; *Bacteria/genetics/classification/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/drug effects ; },
abstract = {The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.},
}

*Biofilms/drug effects/growth & development
*Seawater/microbiology
*Plastics
Fungi/genetics/classification/drug effects/isolation & purification
*Bacteria/genetics/classification/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
*Microbiota/drug effects

@article {pmid41388485,
year = {2025},
author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL},
title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70210},
pmid = {41388485},
issn = {2993-7175},
support = {AA029925/AA/NIAAA NIH HHS/United States ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.

METHODS: B6 mice were given ethanol (EtOH; 5 g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24 h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96 h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12 h, 24 h, and 192 h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-α, IL-1β, P2Y12, ITGβ2, and α7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.

RESULTS: Data revealed increased TNF-α expression in the Amg, Hyp, and NAc and increased IL-1β expression in the Amg and NAc, 12 h after the first EtOH injection. α7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24 h after the third EtOH dose, compared to the control group. α7nAChR expression in the Hyp was observed at 2 min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24 h after the third EtOH dose. ITGβ2 showed an increasing trend in the Amg at 12 h after the first dose, followed by a significant reduction at 24 h, and 192 h after the third dose. 16S rRNA sequencing revealed a significant difference in β-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.

CONCLUSION: This study showed that brain inflammation, indicated by α7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.},
}

@article {pmid41388438,
year = {2025},
author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M},
title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02272-x},
pmid = {41388438},
issn = {2049-2618},
support = {24-12912M//Grantová Agentura České Republiky/ ; 22-03662S//Grantová Agentura České Republiky/ ; 22-33245S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; 21-21990S//Grantová Agentura České Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut für Gewässerökologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercetării şi Inovării/ ; },
abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.

RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.

CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.},
}

@article {pmid41388019,
year = {2025},
author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA},
title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67388-y},
pmid = {41388019},
issn = {2041-1723},
support = {K08 AI123494/AI/NIAID NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; },
abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.},
}

@article {pmid41387926,
year = {2025},
author = {Ma, X and Wang, B and Xu, M and Zhang, Y and Liu, N and Teng, L and Li, Z and Yang, H and Xie, X and Zhang, B and Wang, Z and Wang, Y and Liu, J and Bao, J and Luo, H},
title = {Multiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02200-z},
pmid = {41387926},
issn = {2049-2618},
support = {32192463//The Major Program of National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility of forage produced by rumen microorganisms. Thus, the interaction between grass intake and rumen microbial fermentation is a key driver of both ruminant productivity and grassland ecosystem health. However, interactions between grass species, supplementary feeding, rumen microbiome, and rumen epithelium function, remain poorly understood.

RESULTS: We employed metagenomic and metatranscriptomic analyses, coupled with single-cell RNA sequencing (scRNA-seq) of rumen wall and serum metabolomics, to investigate how the rumen microbiome regulates grass intake and host metabolism. In a two-factor (grazing intensity and concentrate supplementation) experiment with 72 lambs, supplementary feeding under moderate grazing increased dry matter intake but decreased grass consumption of Artemisia tanacetifolia. These shifts correlated with contrasting trends between metagenomic and metatranscriptomic profiles of Lachnospiraceae. scRNA-seq revealed an increased abundance of basal cells (BCs), terminally differentiated keratinocytes (TDKs), and differentiated keratinocytes (DKs) in the supplemented group, with solute carrier genes (e.g., SLC16A1) involved in short chain fatty acids (SCFAs) transport enriched in basal cells. We also identified interactions between the rumen microbiome and host epithelial cells, influencing gene expression and localization, which in turn mediated the animal serum nutrient metabolism, particularly in B vitamin, bile acids, and amino acids.

CONCLUSIONS: Our study identified key microbiome and epithelial cell subtypes involved in grass digestion and SCFAs metabolism in the rumen. This novel link between ruminal microbial function, epithelial cell cluster-based genes, and host metabolism provides critical insights into mechanisms underlying the interaction between grass intake and supplementary feeding for optimizing ruminant management strategies in sustainable grazing systems. Video Abstract.},
}

@article {pmid41387788,
year = {2025},
author = {Zhu, H and Wu, W and Ran, Y and Cai, J and Wu, W and Zhao, Y and Zeng, Y and Hou, C and Tian, Y and Shen, H and Zhang, Y and Peng, B and Zheng, K and Gao, Y and Li, X},
title = {Central nervous system infection by Angiostrongylus cantonensis in children: experience from Guangdong, China.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1713},
pmid = {41387788},
issn = {1471-2334},
mesh = {Humans ; *Angiostrongylus cantonensis/genetics/isolation & purification ; Male ; Female ; China/epidemiology ; *Strongylida Infections/diagnosis/parasitology/epidemiology/cerebrospinal fluid ; Infant ; Retrospective Studies ; Child, Preschool ; Animals ; Child ; High-Throughput Nucleotide Sequencing ; Adolescent ; *Central Nervous System Infections/parasitology/epidemiology/diagnosis/cerebrospinal fluid ; Metagenomics ; },
abstract = {BACKGROUND: Angiostrongylus cantonensis (A. cantonensis)-induced central nervous system (CNS) infection is a rare parasitic disease. Although global incidence is rising, pediatric cases remain underrecognized. This study aimed to characterize clinical features and evaluate the diagnostic utility of metagenomic next-generation sequencing (mNGS) in children.

METHODS: We retrospectively analyzed pediatric CNS angiostrongyliasis cases admitted to a national neurology center in Guangdong, China, between 2017 and 2024.

RESULTS: A total of 22 pediatric patients were enrolled (median age 1.8 years; male: female = 14:8). Most cases (68.2%) began between June and October; 45.5% had confirmed or probable exposure. Fever was the most common symptom (77.2%), followed by somnolence or lethargy (63.6%) and vomiting (59.1%). No patients reported neck stiffness or hyperesthesia. All patients showed peripheral eosinophilia (median peak 24.0%, IQR 16.0%-36.0%) and cerebrospinal fluid (CSF) pleocytosis. The initial CSF eosinophil percentage exceeded 10% in 10/22 patients (45.5%), and this increased in 7/22 patients (31.8%) during follow-up. Median peak CSF eosinophil percentage was 17.2% at day 18. Among 10 patients tested for CSF cytokines, 90.0% had elevations, with IL-6 being the most common and associated with higher CSF eosinophil percentages. Serum and CSF IgG against A. cantonensis were positive in 44.4% and 46.7%, respectively. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid was performed in 18 of the 22 patients, and A. cantonensis was identified in all tested cases (18/18, 100%), including four who were seronegative. The median mNGS read counts of A. cantonensis were 2,453 (IQR 353.5-28,641.75), which were not significantly correlated with CSF eosinophil percentages, white blood count, or protein levels. Brain magnetic resonance imaging abnormalities (81.8%) included leptomeningeal enhancement (45.5%), ventricular enlargement (40.9%), and cortical lesions (31.8%). Electroencephalogram was abnormal in 54.5%, mainly showing slowing (50.0%) or epileptiform activity 9.1%. Albendazole was used alone in 13.6% of patients, while 86.4% received combined therapy with corticosteroids. Of the 20 patients with follow-up (median 2.5 months), all recovered clinically and radiologically without relapse or sequelae.

CONCLUSION: Pediatric CNS angiostrongyliasis in Guangdong primarily affects rural children during summer-autumn. Clinical signs may be nonspecific. mNGS outperformed serology, especially in early or seronegative cases. Most patients had favorable short-term outcomes.},
}

Humans
*Angiostrongylus cantonensis/genetics/isolation & purification
Male
Female
China/epidemiology
*Strongylida Infections/diagnosis/parasitology/epidemiology/cerebrospinal fluid
Infant
Retrospective Studies
Child, Preschool
Animals
Child
High-Throughput Nucleotide Sequencing
Adolescent
*Central Nervous System Infections/parasitology/epidemiology/diagnosis/cerebrospinal fluid
Metagenomics

@article {pmid41387706,
year = {2025},
author = {Bonnet, N and Capeding, MR and Siegwald, L and Garcia-Garcera, M and Desgeorges, T and Tytgat, HLP and Krattinger, LF and Lebumfacil, J and Phee, LC and Moll, JM and Gudjonsson, A and Rodriguez-Garcia, P and Baruchet, M and Feige, JN and Jankovic, I and Chen, Y and Egli, D and Horcajada, MN},
title = {A young child formula with Limosilactobacillus reuteri and GOS modulates gut microbiome and enhances bone and muscle development: a randomized trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66930-2},
pmid = {41387706},
issn = {2041-1723},
abstract = {In this randomized, double-blind controlled trial, 182 Filipino children aged 2-3 years received either an experimental young child formula (EYCF) containing a combination of Limosilactobacillus reuteri DSM 17938 and galacto-oligosaccharides (GOS; n = 91) or a minimally fortified milk (CM; n = 91) for 6 months. Primary outcome was tibia speed of sound and secondary outcomes were muscle strength, blood vitamin D levels, bone turnover markers, gut microbiota, fecal calcium fatty acid soaps and gastro-intestinal tolerance. Compared to CM, those in the EYCF group showed increased tibia speed of sound after 3 and 6 months. The intervention remodeled the stool microbiome composition, assessed by shotgun metagenomics, with enrichment of L. reuteri and higher bifidobacteria presence in the EYCF group. Increased L. reuteri abundance after 6 months of EYCF consumption associates with higher bone quality and muscle strength. Stool metabolomics show 45 metabolites modulated by EYCF consumption and associated to microbiome compositional changes, leading to enrichment of tryptophane and indole metabolism. In summary, consumption of EYCF containing a L. reuteri + GOS synbiotic improves musculoskeletal development in toddlers via modulation of microbiota composition and function. These results provide insights on gut-musculoskeletal crosstalk during early life. Clinicaltrial.gov NCT04799028.},
}

@article {pmid41387678,
year = {2025},
author = {Xin, G and Wang, D and Zhang, X and Cen, Q and Peng, M and Liao, Y and Wang, J and Le, S and Cheng, J and Wu, WC and Hou, X and Luo, G and Gou, Q and Kong, J and Pan, Z and Li, D and Gan, S and Chen, A and Zhao, H and Shi, P and Ren, Z and Zhao, W and Liu, J and Jia, P and Sun, C and Lin, W and Wu, J and Kuang, G and Chen, J and Li, J and Holmes, EC and Deng, Z and Shi, M},
title = {Infectome analysis of small mammals in Southern China reveals pathogen ecology and emerging risks.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66462-9},
pmid = {41387678},
issn = {2041-1723},
support = {2022A1515011854//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 82341118 and 32270160//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Small mammals harbor a diverse array of potentially zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viruses, with limited attention directed to bacterial and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome-defined as the set of microorganisms infecting the host-across 2408 individual samples, representing lung, spleen, and gut from 858 animals in Guangdong province, China, considering the impact of host species, tissue, season, and geographic location on pathogen diversity. We identified 76 potential pathogen species, comprising 29 RNA viruses, 12 DNA viruses, five bacteria, and 30 eukaryotic pathogens, including 33 that are newly discovered. Distinct tissue tropisms were identified, suggesting varied transmission routes. Individual animals carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Total pathogen richness was largely influenced by geographic region, followed by host species and season, while zoonotic pathogen richness was primarily driven by host species. Collectively, these data provide insights into the structure of the pathogen infectome and the drivers of pathogen diversity and transmission in these key mammalian disease reservoirs.},
}

@article {pmid41387551,
year = {2025},
author = {Kelsey, C and Moulder, R and Yancey, H and Prescott, S and McCulloch, JA and Trinchieri, G and Dreisbach, C and Alhusen, J and Grossmann, T},
title = {Bidirectional relations between the maternal and infant gut microbiome and behavior.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41387551},
issn = {1530-0447},
abstract = {BACKGROUND: An infant's mother is one of the first sources of neonatal microbial colonization, and infant-maternal dyad microbial variations have been linked to childhood behavioral traits and mental health outcomes. However, how the gut microbiome influences mental health, including potential bidirectional relations between mother and child, remains poorly understood.

METHOD: Using metagenomic sequencing and behavioral questionnaires, we examined within-person and between-person (mother-infant dyad) associations between the gut microbiota and behavior across the first year of postnatal life (N = 121 dyads; N = 514 stool samples).

RESULTS: There were rapid changes in taxa diversity and gut microbiota composition for infants, whereas the maternal microbiome remains relatively constant. Gut microbes and functional terms (e.g., antibiotic resistance genes and virulence factors) were associated with infant temperament but not maternal depression symptoms. Whereas maternal depression was not associated with any maternal taxa or functional terms.

CONCLUSIONS: Our findings provide evidence for complex within- and between-person relations between maternal and infant gut microbiomes and behavioral traits.

IMPACT: How the gut microbiome influences maternal mental health and infant behavior remains poorly understood. We measured mothers' and infants' gut microbiota composition and behavior across the first year of the infant's life. Individual taxa from the infant, but not the maternal, gut were associated with infant behavioral temperament. Our findings provide evidence for complex bidirectional gut-behavior associations between mothers and infants.},
}

@article {pmid41387397,
year = {2025},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11003},
pmid = {41387397},
issn = {2041-1723},
support = {2020-03545//Vetenskapsrådet (Swedish Research Council)/ ; 2024-04942//Vetenskapsrådet (Swedish Research Council)/ ; 2022-06250//Vetenskapsrådet (Swedish Research Council)/ ; ALTF 740-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Phylogeny ; *Caulobacter crescentus/genetics/classification ; *Phototrophic Processes/genetics ; Biological Evolution ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Model bacteria are fundamental for research, but knowledge about their ecology and evolution is often limited. Here, we establish an evolutionary and ecological context for the model organism Caulobacter crescentus-an alphaproteobacterium intensively studied for its dimorphic lifecycle. By analyzing the phylogenetic relatedness and genetic potential of hundreds of Caulobacterales species, we reveal substantial diversity regarding their environmental distribution, morphology, cell development, and metabolism. Our work provides insights into the evolutionary history of morphological features such as the cell curvature determinant crescentin and uncovers a striking case of convergent loss of traits for cellular dimorphism among close relatives of C. crescentus. Moreover, we find that genes for phototrophy are widespread across Caulobacterales and that the new genus Acaudatibacter, described here, includes the first reported Caulobacterales lineage with photoautotrophic potential. Our study advances our understanding of an environmentally widespread bacterial order and sheds light on the evolution of fundamental prokaryotic features.},
}

Phylogeny
*Caulobacter crescentus/genetics/classification
*Phototrophic Processes/genetics
Biological Evolution
Bacterial Proteins/genetics/metabolism

@article {pmid41386833,
year = {2025},
author = {Sarkar, A and Patra, RK and Muthaiyan, M and Mallik, A},
title = {A metagenomic exploration of microbial distribution among the pond sediment, shrimp (Penaeus monodon) tissue and pond water: A special focus on nutrient cycling and shrimp viral pathogens.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {4},
pages = {100568},
doi = {10.1016/j.jgeb.2025.100568},
pmid = {41386833},
issn = {2090-5920},
abstract = {Penaeus monodon, a major shrimp species cultivated in Eastern Asia, has faced setbacks in aquaculture due to disease outbreaks. Metagenomic studies offer insights into the pond microbiome, revealing its critical roles in nutrient cycling, water quality, and disease control. This study investigated microbial communities in sediment, water, and shrimp samples from an aquaculture pond in Chaital, West Bengal, India. Shotgun metagenomic sequencing and bioinformatics analyses were used to assess taxonomic and functional profiles, focusing on nutrient cycling genes and viral populations. Sediments showed the highest microbial diversity, contributing to organic matter decomposition and ecological stability. Water microbes played roles in oxygenation and pathogen suppression, while shrimp tissues hosted microbes aiding digestion and immunity. Pathogenic viruses, especially Whispovirus (White Spot Syndrome Virus), dominated shrimp tissues. Functional gene analysis identified key pathways in carbon, nitrogen, and sulfur cycling. Integrating water quality data with microbiome profiles could help identify bioindicators and predict pathogen risks.},
}

@article {pmid41386129,
year = {2025},
author = {Bai, H and He, LY and Yadav, S and Gao, FZ and Liu, YS and Smidt, H and Ying, GG},
title = {Phages and plasmids mediate antibiotic resistance gene transfer in urban airborne bacteria.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140779},
doi = {10.1016/j.jhazmat.2025.140779},
pmid = {41386129},
issn = {1873-3336},
abstract = {Airborne antibiotic resistance genes (ARGs) pose emerging public health risks, particularly in urban settings, yet their dissemination mechanisms remain unclear. Here we cultured airborne bacteria from diverse urban environments and performed metagenomic sequencing to reconstruct 931 non-redundant metagenome-assembled genomes (MAGs), integrating horizontal gene transfer (HGT) detection, machine learning, and causal inference analyses. We identified hospitals, pharmaceutical factories, and railway stations as major sources of mobile ARGs. Both plasmids and phages actively mediate ARG transfer, promoting gene dissemination across broad phylogenetic distances. Machine learning revealed key phage functional modules related to structure, host attachment, lysis, DNA entry, and regulation that facilitate virus-mediated HGT, with synergistic interactions observed between plasmids and phages. These findings elucidate the dynamic resistome and mobility potential of metabolically active airborne bacteria, informing environmental surveillance and mitigation strategies to address airborne antimicrobial resistance within the One Health framework.},
}

@article {pmid41387308,
year = {2025},
author = {Zhao, Z and Li, Q and Bai, X and Zhai, E and Dai, W and Qian, Y and Zhang, T and Huang, Z and Huang, Z and Meng, F and Chen, J and Zuo, T and Cai, S and Zhao, R},
title = {Gut Bacterium Lysinibacillus Sphaericus Exacerbates Aspirin-induced Intestinal Injury by Production of Carboxylesterase EstB.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17747},
doi = {10.1002/advs.202517747},
pmid = {41387308},
issn = {2198-3844},
support = {82100626//National Natural Science Foundation of China/ ; 82173239//National Natural Science Foundation of China/ ; 32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 823B2010//National Natural Science Foundation of China/ ; 202206010014//Special Project of Guangzhou Science and Technology Innovation Development/ ; },
abstract = {Aspirin provides long-term health benefits but can cause gastrointestinal toxicity, and the role of gut microbiota in aspirin metabolism and enterotoxicity remains unclear. In this study, the contribution and mechanisms of microbiota-aspirin interactions in intestinal injury are investigated. In a mouse model, aspirin-induced enteropathy is found to be more severe in microbiota-replete than in microbiota-depleted mice, implicating a detrimental role of gut microbiota. Co-cultivation experiments revealed that gut microbes facilitated the biotransformation of aspirin into salicylic acid, a metabolite more harmful than aspirin itself in disrupting epithelial cell integrity and renewal, both in vitro and in vivo. Through metagenomic screening, selective bacterial interrogation, and functional validation, Lysinibacillus sphaericus is identified as the culprit bacterium, and its secreted carboxylesterase EstB as the key enzyme catalyzing aspirin hydrolysis to salicylic acid. Importantly, inhibition of microbial EstB with the dietary compound flavanomarein abrogated aspirin biotransformation and prevented intestinal injury. Together, these findings reveal L. sphaericus and EstB as central drivers of aspirin enterotoxicity, highlight the functional importance of gut microbiota in drug metabolism, and suggest microbiota- and metabolite-guided precision prevention strategies.},
}

@article {pmid41387121,
year = {2025},
author = {Ji, Y and Liu, X and Zhao, S and Zhou, S and Yang, Y and Zhang, P and Shi, Y and Qin, W and Zhu, G and Zhu, Y and Gao, Y and Jiang, J and Wang, B},
title = {Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e09416},
doi = {10.1002/advs.202509416},
pmid = {41387121},
issn = {2198-3844},
support = {U22A20590//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; 42477318//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; 2025YFE0103900//National Key R&D Program of China/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; BX20240168//China National Postdoctoral Program for Innovative Talents/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
abstract = {Patescibacteriota, also known as Candidate Phyla Radiation (CPR), is a diverse clade of ultra-small bacteria with an epibiotic lifestyle. Despite their ubiquity across diverse ecosystems and ecological importance in microbial networks, the global distribution of Patescibacteriota and functional interactions with their host organisms remain largely unknown. Here, by leveraging comprehensive Patescibacteriota genomic resources and global multi-habitat metagenomic datasets, it is demonstrated that ribosomal protein S3 (rpS3) as a reliable phylogenetic marker, enabling accurate recovery of Patescibacteriota diversity from short-read metagenomes. Using this framework, extensive taxonomic diversity and pronounced community heterogeneity are uncovered across eight ecosystems. Through network analysis and genome-wide functional screening, habitat-specific co-occurrence patterns are also revealed between Patescibacteriota and host-associated bacteria, especially potential functional synergies mediated by metabolic pathway cascades. Notably, Patescibacteriota-encoded NirK may assist sulfate-reducing bacteria in resisting nitrite stress, while NorB can mitigate nitric oxide toxicity for complete ammonia-oxidizing bacteria. Taken together, this study highlights the underappreciated diversity of Patescibacteriota and elucidates its important role in supporting host metabolism through complementary biochemical functions, offering new insights into its ecological significance and evolutionary adaptations in the global ecosystem.},
}

@article {pmid41386031,
year = {2025},
author = {Shu, M and Xue, H and Yang, Y and Zhang, X and Li, S and Bian, T and Yuan, K and Xu, C},
title = {Microbial-enzyme co-fermentation of low-grade tobacco: Metagenomics and metabolomic insights into flavor formation.},
journal = {Enzyme and microbial technology},
volume = {194},
number = {},
pages = {110803},
doi = {10.1016/j.enzmictec.2025.110803},
pmid = {41386031},
issn = {1879-0909},
abstract = {Microbial-enzyme co-fermentation effectively enhances the quality of low-grade tobacco leaves quality, but the underlying mechanisms of flavor formation remain unclear. This study investigated the dynamics and relationships of microbial communities and volatile aroma metabolites during low-grade tobacco leaves fermentation through metagenomics and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results showed that during microbial-enzyme co-fermentation, the tobacco leaves fermented for four days (D4) exhibited the highest levels of total sugars and reducing sugars, the peak total content of aroma metabolites, and the best sensory quality. Pseudomonadota, Bacillota, and Ascomycota were dominant microorganisms during fermentation. During the initial stage (D1-D4), Saccharomyces was the dominant genus, which was subsequently displaced by Pantoea at D5. This microbial succession coincided with a decline in sensory quality, indicating its crucial role in shaping flavor evolution during co-fermentation. During microbial-enzyme co-fermentation process, a total of 46 volatile metabolites were detected in low-grade tobacco leaves. Among them, seven esters with high variable important in projection values and strong microbial correlations were identified as characteristic aroma metabolites, including ethyl phenylacetate, benzyl acetate, phenylethyl acetate, ethyl myristate, ethyl palmitate, ethyl oleate, and methyl linolenate. Gene function annotation revealed carbohydrate metabolism was the most abundant, followed by amino acid metabolism. Spearman correlation analysis elucidated the formation mechanism of characteristic ester metabolites. Specifically, short-chain esters correlated with glycerolipid and amino acid metabolism, while long-chain esters linked to glycolysis and fatty-acid biosynthetic pathways.},
}

@article {pmid41385957,
year = {2025},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
doi = {10.1016/j.psj.2025.106177},
pmid = {41385957},
issn = {1525-3171},
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}

@article {pmid41385764,
year = {2025},
author = {Yang, H and Yu, Y and Cui, R and Zhang, Q and Chen, B and Zhang, Z and Xu, N and Sun, L and Lu, T and Qian, H},
title = {Environmental and Microbial Drivers of Global Rhizosphere Resistome Assembly.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11060},
pmid = {41385764},
issn = {1520-5118},
abstract = {Soil serves as a critical reservoir for antibiotic resistance genes (ARGs); however, the ecological mechanisms driving ARG assembly at the plant-soil interface remain poorly understood. In this study, we analyzed 383 metagenomic samples and identified 4803 predicted ARGs, which were classified into two distinct clusters. The ARG-abundant cluster exhibited higher rhizospheric ARG abundance and diversity but posed a relatively lower health risk compared to the ARG-scarce cluster. Warm and nutrient-rich soils promote diverse resistomes shaped by complex microbial interactions, whereas humid environments promote more homogeneously predicted ARG compositions. Environmental variables such as the temperature and nitrogen were found to indirectly influence resistome composition by modulating microbial diversity. Notably, relatively high proportions of high-risk predicted ARGs were detected in grains and raw-eat vegetables, highlighting a potential threat to public health. Our findings underscore the importance of incorporating both environmental and microbial perspectives into agricultural practices to mitigate ARG dissemination in soil.},
}

@article {pmid41385625,
year = {2025},
author = {Kohtz, AJ and Nupp, S and Hatzenpichler, R},
title = {Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota.},
journal = {Science advances},
volume = {11},
number = {50},
pages = {eaea0936},
doi = {10.1126/sciadv.aea0936},
pmid = {41385625},
issn = {2375-2548},
mesh = {*Methane/metabolism ; *Archaea/metabolism/genetics/growth & development/classification ; Phylogeny ; Metagenomics ; Genome, Archaeal ; },
abstract = {Methane is a potent greenhouse gas, largely produced by methanogenic archaea, contributing to Earth's dynamic climate and biogeochemical cycles. In the past decade, metagenomics revealed that lineages outside of the Euryarchaeota superphylum encode genes for methanogenesis. This was recently confirmed through the cultivation of two classes of methanogenic Thermoproteota. Thus far, all methanogens within the Thermoproteota are predicted or were shown to be methylotrophic. The only exception to this are the Nezhaarchaea, for which metagenomic predictions suggest they are CO2-reducing methanogens. Here, we demonstrate methanogenic activity in a third class of Thermoproteota, the Methanonezhaarchaeia. Contrary to genomic predictions for this class, we cultivated a methylotrophic species, Candidatus Methanonezhaarchaeum fastidiosum YNP3N, highlighting the importance of testing metagenomic hypotheses through experimentation. We investigate the metabolic diversity of Methanonezhaarchaeia, including metabolic modifications accompanying frequent loss of methanogenesis in this class. This highlights gaps in our understanding of the biochemistry, diversity, and evolution of thermoproteotal methanogens and their contributions to carbon cycling.},
}

*Methane/metabolism
*Archaea/metabolism/genetics/growth & development/classification
Phylogeny
Metagenomics
Genome, Archaeal

@article {pmid41385173,
year = {2025},
author = {Othman, AA and Mohamed Zain, NI and Eshak, Z and Adman, MA and Abd Latif, Z and Aboshanab, KM and Ahmad, A},
title = {Diversity of necrophagous flies and microbiome profiling of Phumosia promittens as a rainforest health indicator.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01994-3},
pmid = {41385173},
issn = {2191-0855},
abstract = {Necrophagous flies play a critical role in decomposition and serve as bioindicators of environmental health and pollution. Malaysia's tropical rainforest ecosystems may host many necrophagous fly species, including unique blowflies and their associated bacteria. However, in many forest reserve areas, the diversity of these flies remains poorly studied. This study examines the diversity of necrophagous flies and their associated surface bacteria community, with a particular focus on Phumosia promittens (Walker in J Proc Linn Soc Lond Zool 4:90-96, 1859) in the Bangi Forest Reserve, Universiti Kebangsaan Malaysia. Sampling was conducted across three plots using baited traps, and collected flies were morphologically identified and processed under sterile conditions. Surface bacteria from P. promittens were isolated and analysed through metagenomic analysis targeting the 16S rRNA (V3-V4) amplicon sequencing gene to characterise their microbial communities comprehensively. Among 2,528 individuals collected, Chrysomya megacephala (Fabricius) was the most dominant species overall, while P. promittens was the most abundant among native forest species, suggesting their ecological adaptability and potential as a bioindicator of healthy rainforest. Shannon-Wiener and Simpson's diversity of flies in the study location were 0.67 ± 0.11 and 0.29 ± 0.06, respectively. Meanwhile, the Shannon-Wiener and Simpson's diversity of bacteria from P. promittens were 5.64 ± 0.70 and 0.96 ± 0.02, respectively. Bacterial microbiome analysis revealed the presence of core genera, including Wohlfahrtiimonas, Dysgonomonas, Vagococcus, and Ignatzschineria, which are implicated in both ecological symbiosis and public health concerns. These bacteria may contribute to nutrient cycling, such as heavy metals and antibiotics. Notably, several of these genera are emerging zoonotic pathogens with antimicrobial resistance, highlighting the dual role of necrophagous flies as ecosystem contributors and disease vectors. The findings underscore the importance of monitoring native fly species and their microbiota to assess the integrity of forest ecosystems and potential public health risks.},
}

@article {pmid41385155,
year = {2025},
author = {Nazaktabar, A and Khosravi, M},
title = {First detection and characterization of Bovine parvovirus 2 and Bopivirus A in a neonatal calf with diarrhea in Iran through metagenomic RNA-seq.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {41385155},
issn = {1572-994X},
abstract = {Bovine parvovirus 2 (BoPV-2), officially classified as Ungulate copiparvovirus 1 by the ICTV, and Bopivirus A, a recently recognized picornavirus, are poorly characterized viruses sporadically reported in cattle worldwide. Here, we describe the first detection of BoPV-2 and Bopivirus A in Iran-and potentially the Middle East-through RNA-seq analysis of a diarrheic neonatal calf. Four BoPV-2 contigs (82-85% nucleotide identity; 91-100% amino acid identity) were identified, clustering within the Ungulate copiparvovirus 1 clade, while the Bopivirus sequence grouped with Chinese strains BoP8 and BoP9, supporting its classification within lineage A2. Both viruses were confirmed by phylogenetic analyses based on partial RdRp (3Dpol) and ORF regions. The concurrent detection of these viruses in a single calf suggests possible co-circulation in early-life gastrointestinal infections, highlighting the complexity of the calf virome. Notably, RNA detection of the DNA virus BoPV-2 in fecal material indicates potential intestinal replication and shedding, raising questions about its transmission dynamics. These findings expand the geographic range of BoPV-2 and Bopivirus A and underscore the value of metagenomic surveillance for uncovering under-characterized viral agents contributing to neonatal calf diarrhea.},
}

@article {pmid41384994,
year = {2025},
author = {Zhang, J and Liu, J and Bayani, A},
title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.},
journal = {Journal of cancer research and clinical oncology},
volume = {152},
number = {1},
pages = {8},
pmid = {41384994},
issn = {1432-1335},
mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.},
}

Humans
*Hematologic Neoplasms/therapy/microbiology/immunology
*Phage Therapy/methods
Animals
*Bacteriophages
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41384986,
year = {2025},
author = {Le, TT and Nguyen, HD and Dao, TK and Nguyen, HT and Nguyen, TQ and Do, TH and Truong, NH},
title = {Identification of endoglucanase-encoding genes from goat rumen bacterial metagenomes using homology- and motif-based approaches.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {70},
pmid = {41384986},
issn = {1432-072X},
support = {CSCL08.04/25-26//Institute of Biology/ ; },
mesh = {*Goats/microbiology ; *Rumen/microbiology ; *Cellulase/genetics/metabolism/chemistry ; Animals ; *Metagenome ; *Bacteria/genetics/enzymology/classification/isolation & purification ; *Bacterial Proteins/genetics/metabolism/chemistry ; Phylogeny ; Open Reading Frames ; Cellulose/metabolism ; Escherichia coli/genetics ; },
abstract = {The goat rumen harbors a dense and diverse microbial community that produces enzymes for degrading plant cell wall polysaccharides, representing a potential source of valuable enzymes for applications. In this study, we explored the diversity of endoglucanases from goat rumen bacterial metagenomes using homology- and motif-based approaches. HMM profiling identified 5,182 endoglucanase-encoding ORFs, whereas KEGG annotation (EC 3.2.1.4) detected 7,368 ORFs, with 2,902 shared between the two methods. Taxonomic assignment revealed Firmicutes and Bacteroidetes as the dominant phyla, followed by Fibrobacteres, Spirochaetes, and Lentisphaerae. At the genus level, Ruminococcus (Firmicutes) and Prevotella (Bacteroidetes) were dominant, followed by Butyrivibrio, Fibrobacter, and Treponema. Pfam domain analysis further revealed that the common endoglucanase domains, GH5 and GH9, exhibited a high degree of overlap (> 80%) between the two approaches. Notably, GH26 and GH8 were more frequently identified by HMM profiling, whereas KEGG-based mining revealed greater domain diversity. A candidate endoglucanase-encoding ORF was subsequently expressed in E. coli, and the recombinant protein was characterized. The enzyme displayed bifunctional activity on both cellulose (CMC, filter paper) and hemicellulose (xylan), with the highest activity toward CMC, and showed optimal activity at 50 °C and pH 4.0. Its activity was differentially affected by metal ions and chemical agents, and kinetic analysis revealed strong substrate affinity and high catalytic efficiency (Km = 0.8 mg/mL, Vmax = 186.12 U/mg). Overall, this study demonstrates complementary strategies for mining functional proteins from metagenomes and highlights the potential of goat rumen-derived endoglucanase for lignocellulose degradation in sustainable industrial applications.},
}

*Goats/microbiology
*Rumen/microbiology
*Cellulase/genetics/metabolism/chemistry
Animals
*Metagenome
*Bacteria/genetics/enzymology/classification/isolation & purification
*Bacterial Proteins/genetics/metabolism/chemistry
Phylogeny
Open Reading Frames
Cellulose/metabolism
Escherichia coli/genetics

@article {pmid41384736,
year = {2025},
author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A},
title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0136425},
doi = {10.1128/msystems.01364-25},
pmid = {41384736},
issn = {2379-5077},
abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.

IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.},
}

@article {pmid41384462,
year = {2025},
author = {Arfken, A and Mercante, J and Mattioli, M},
title = {Improved Sensitivity of Quantitative Polymerase Chain Reaction and Next Generation Sequencing for Detection of Salmonella spp. in Mixed Environmental Communities Using Whole Genome Amplification.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70194},
doi = {10.1002/mbo3.70194},
pmid = {41384462},
issn = {2045-8827},
mesh = {*Salmonella/genetics/isolation & purification/classification ; *High-Throughput Nucleotide Sequencing/methods ; Genome, Bacterial ; *Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; *Environmental Microbiology ; *Nucleic Acid Amplification Techniques/methods ; DNA, Bacterial/genetics ; },
abstract = {Detecting pathogens in environmental samples using molecular-based technologies can be challenging, particularly in low biomass environments or where pathogens represent a low percentage of the community. Multiple displacement amplification (MDA) is a whole genome amplification (WGA) method that has been developed for low biomass samples. However, there is a lack of information on how MDA could improve PCR and sequence-based detection and genomic characterization of pathogens in challenging environmental samples. In this study, MDA was evaluated on low template samples of the Salmonella LT2 isolate, a foodborne and waterborne environmental pathogen. MDA was also evaluated on a variety of low template mixed-microbial mock, environmental communities containing a range of Salmonella genome percentages to simulate different levels of Salmonella in the environment. Using MDA starting inputs of 1.8 × 10[4]-1.8 × 10[1] Salmonella LT2 genome copies, > 99% of the Salmonella genome was recovered following MDA at > 16X depth of coverage from as few as 500,000 merged, 250 bp paired-end reads. For the mock microbial communities, moderately high levels of genome abundance distortion were evident following MDA across all communities when compared to the expected compositions, which could not be attributed to either genome size or GC content alone. Overall, MDA may provide a useful method for increasing Salmonella detection sensitivity in low target environmental samples where downstream selective targeted applications such as real-time PCR or targeted amplicon sequencing are used, but MDA may not be appropriate for identification and detection of Salmonella when using untargeted, metagenomic sequencing.},
}

*Salmonella/genetics/isolation & purification/classification
*High-Throughput Nucleotide Sequencing/methods
Genome, Bacterial
*Real-Time Polymerase Chain Reaction/methods
Sensitivity and Specificity
*Environmental Microbiology
*Nucleic Acid Amplification Techniques/methods
DNA, Bacterial/genetics

@article {pmid41384120,
year = {2025},
author = {Li, X and Guo, G and Shi, Q and Chen, Q and Li, L},
title = {Association study between intestinal microbiota dysbiosis in inflammatory bowel disease and the global disease burden growth trend.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1635242},
pmid = {41384120},
issn = {2296-858X},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, is a group of chronic intestinal inflammatory diseases. Its incidence and prevalence have been on the rise globally, imposing a heavy burden on patients' health and social medical resources. Intestinal microbiota dysbiosis is believed to play a crucial role in the occurrence and development of IBD, but the association between them and the global disease burden growth trend remains unclear.

METHODS: By searching the Global Burden of Disease (GBD) study database, we collected IBD disease burden data from 180 countries and regions between 1990 and 2023, including key indicators such as incidence, prevalence, mortality, and disability-adjusted life years (DALYs). Intestinal microbiota data were sourced from two parts: (1) Independent collection: A total of 20,000 healthy individuals and IBD patients were selected as research subjects from 180 countries and regions using a stratified random sampling method. Fecal samples (2-5 grams per person) were collected and immediately stored in a -80 °C ultra-low temperature refrigerator to avoid changes in the microbial community structure; (2) Supplementary data from public databases: Published intestinal microbiota sequencing data of corresponding regions from 1990 to 2023 were extracted from the MGnify (https://www.ebi.ac.uk/metagenomics/), Human Microbiome Project (HMP), and GMrepo (https://gmrepo.humangut.info/) databases. The sample size for each country and region was no less than 500 to cover populations of different ages (18-70 years), genders (male/female ratio approximately 1:1), and dietary habits (high-fiber diet, high-sugar and high-fat diet). Technologies like metagenomic sequencing and 16S rRNA gene sequencing were used to obtain data on the composition, abundance, and diversity of the intestinal microbiota of the corresponding regional populations. For metagenomic sequencing, the Illumina HiSeq or NovaSeq platform was used. Linear regression models, time-series analysis, and causal inference methods were applied to evaluate the correlation between intestinal microbiota dysbiosis and the growth trends of various disease burden indicators, and to explore the potential impact mechanisms.

RESULTS: The global incidence of IBD increased from 12.3 per 100,000 in 1990 to 25.6 per 100,000 in 2023, the prevalence rose from 396 per 100,000 to 523 per 100,000, and the DALY value also increased significantly (from 230 per 100,000 in 1990 to 380 per 100,000 in 2023). The average annual growth rates of the above indicators were 2.8% (95% CI: 2.5-3.1%, p < 0.001), 1.0% (95% CI: 0.8-1.2%, p < 0.001), and 1.5% (95% CI: 1.3-1.7%, p < 0.001), respectively. Further analysis showed that intestinal microbiota dysbiosis was closely related to the growth of the disease burden. In regions with severe microbiota dysbiosis, the annual growth rate of the IBD incidence was 3.2 times higher than that in balanced regions (β = 3.2, 95% CI: 2.8-3.6, p < 0.001); when the average abundance of beneficial bacteria such as Bifidobacterium and Lactobacillus in the intestine decreased by 40% (relative to the average abundance of healthy populations) and the abundance of harmful bacteria such as Escherichia coli increased by 60%, the annual growth rate of IBD incidence in this region was as high as 8.5% (95% CI: 7.9-9.1%, p < 0.001); in regions where the Shannon index decreased by 10%, the incidence of IBD increased by an average of 15% (β = 0.15, 95% CI: 0.12-0.18, p < 0.001). A positive correlation was observed between the degree of intestinal microbiota dysbiosis and disease severity (measured by DALYs): in regions where the intestinal F/B ratio deviated from the normal range by more than 30%, DALYs were 40% higher than those in regions with a normal ratio (β = 0.40, 95% CI: 0.35-0.45, p < 0.001); in regions where the content of short-chain fatty acids (SCFAs) decreased by 20%, DALYs increased by approximately 25% (β = 0.25, 95% CI: 0.21-0.29, p < 0.001). Among IBD patients with different severity levels in the Asian region, the abundance of specific bacterial genera related to inflammation regulation (e.g., Faecalibacterium) in the intestines of severe patients decreased by more than 50% compared with healthy populations, and their DALY values were 60% higher than those of mild patients (95% CI: 55-65%, p < 0.001). Additionally, the SCFA levels of severe patients were significantly lower than those of mild patients and healthy populations (median SCFA level: 2.1 mmol/L in severe patients; 4.5 mmol/L in mild patients; 6.8 mmol/L in healthy populations, p < 0.001).

CONCLUSION: This study confirms a close association between intestinal microbiota dysbiosis in inflammatory bowel disease and the global disease burden growth trend. Intestinal microbiota dysbiosis can be used as a key indicator to predict the growth of the IBD disease burden, providing an important theoretical basis for formulating targeted prevention, control strategies, and treatment methods.},
}

@article {pmid41384118,
year = {2025},
author = {Bautista, J and Cardona-Maya, WD and Gancino-Guevara, K and López-Cortés, A},
title = {Reprogramming prostate cancer through the microbiome.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1690498},
pmid = {41384118},
issn = {2296-858X},
abstract = {Prostate cancer (PCa) is a major global public health challenge, driven by a multifactorial interplay of genetic, epigenetic, hormonal and environmental determinants. In recent years, the human microbiome has emerged as a critical and previously underappreciated contributor to PCa initiation, progression, and therapeutic response. Emerging high-resolution multi-omics studies have demonstrated that microbial communities across the gut, urinary tract and prostate form a functional axis that shapes immune surveillance, hormonal metabolism, inflammatory tone and epigenetic regulation. Dysbiosis in these compartments promotes chronic inflammation, modulates androgen receptor signaling, and produces bioactive metabolites, including short-chain fatty acids, that activate oncogenic IGF-1/MAPK/PI3K and NF-κB/JAK/STAT pathways. Cross-compartmental trafficking of bacterial taxa and metabolites reinforces tumor-promoting circuits, while specific commensals such as Akkermansia muciniphila enhance antitumor immunity and improve responses to androgen deprivation therapy. Importantly, microbiota-derived factors also modulate microRNA (miRNAs) expression and epigenetic signatures, thereby affecting tumor plasticity and resistance to therapy. These mechanistic insights have catalyzed interest in microbiome-based therapeutic approaches, including probiotics, prebiotics, fecal microbiota transplantation, dietary modulation and bacteriophage therapy, which hold promise for restoring eubiosis and enhancing treatment efficacy. Nevertheless, clinical translation remains limited by inter-individual variability and the need for well-designed, longitudinal studies integrating shotgun metagenomics, metabolomics and host-microbe interactomics. Overall, the prostate, urinary and gut microbiomes represent interconnected targets that may inform precision diagnostics and novel therapeutic strategies in PCa.},
}

@article {pmid41383742,
year = {2025},
author = {Bian, X and Xu, H and Li, J and Kuang, J and Shi, F and Li, X and Li, J},
title = {Integrated multi-omics reveals distinct maternal and neonatal gut microbial and metabolic signatures associated with small for gestational age status.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668148},
pmid = {41383742},
issn = {1664-302X},
abstract = {INTRODUCTION: Children born small for gestational age (SGA) have an elevated risk of developing metabolic disorders in later life. However, the underlying gut microbiota and metabolomic alterations in SGA mother-infant dyads remain poorly understood.

METHODS: We performed an integrated analysis of fecal metagenomics, metabolomics, and short-chain fatty acids (SCFAs) profiling in 10 SGA and 10 appropriate for gestational age (AGA) mother-infant dyads at term. Taxonomic composition, microbial functional pathways, carbohydrate-active enzyme (CAZyme) profiles, differential metabolites, and metabolite pathway enrichment were systematically evaluated.

RESULTS AND DISCUSSION: SGA neonates exhibited reduced microbial richness (Chao1 index), distinct beta-diversity, and differential abundance of key bacterial species including increased Enterococcus faecalis and Escherichia coli. Functionally, SGA maternal subjects showed divergent profiles in CAZyme genes, with lower abundance of glycoside hydrolase family 13 subfamily 16, glycosyl transferase family 66, and carbohydrate-binding module family 6, and altered structural polysaccharide degradation capacity. Metabolomic profiling revealed significant perturbations in tryptophan metabolism pathways, notably enriched in kynurenine and taurine derivatives in SGA mother and neonates. Notably, SCFA profiles were disrupted, with increased butyrate in SGA mother and reduced propionate and isobutyrate in SGA neonates. Microbe-metabolite correlation networks revealed strong associations between SGA-specific bacterial taxa and fecal metabolites. In conclusion, our analysis identifies distinct features of the early fecal microbiome and metabolome within 48 h of birth in SGA neonates compared with AGA peers, reflecting differences in initial colonization and metabolism that warrant longitudinal follow-up.},
}

@article {pmid41383739,
year = {2025},
author = {Ni, B and Gong, Y and Li, B and Qiu, L and He, K and Guo, J and Fang, H and Gao, M and Chen, M and Wei, C and Sun, W and Liu, B and Li, M and Wang, S and Xu, L},
title = {Mesenchymal stem cells alleviate pulmonary fibrosis and gut microbiota dysbiosis in systemic sclerosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1635809},
pmid = {41383739},
issn = {1664-302X},
abstract = {INTRODUCTION: Mesenchymal stem cells (MSCs) have shown the potential to alleviate systemic sclerosis (SSc) tissue fibrosis. However, our knowledge of the effects of MSCs on gut microbiota remains limited.

METHODS: In this study, we employed a bleomycin induced SSc model to investigate the effects of MSCs on pulmonary fibrosis and gut microbiota in SSc using transcriptomic, microbial metagenomic, and metabolomic analyses.

RESULTS: Our results indicated that MSCs treatment alleviated lung injury in SSc mice. Transcriptomic analysis suggested that the therapeutic effects of MSCs were primarily associated with fatty acid metabolism, PPAR signaling pathway, and AMPK signaling pathway. Furthermore, MSCs restored the relative abundance of microbial taxa, including Bacteroidota, Actinomycetota, and Akkermansia muciniphila, and improved the gut microbiota dysbiosis induced by SSc. Metabolomic data showed that MSCs modulated the dysregulation of trimethyllysine, cholesteryl sulfate expression, and nicotinate and disturbances in nicotinamide metabolism caused by SSc. Correlation analysis demonstrated significant associations among transcriptomic, microbiomic, and metabolomic datasets.

DISCUSSION: Collectively, our findings indicate that MSCs may alleviate SSc pulmonary fibrosis by reshaping the gut microbiota, thereby offering novel scientific insights for the investigation of clinical treatment targets for SSc.},
}

@article {pmid41383738,
year = {2025},
author = {Chen, G and Wiegand, C and Willett, A and Herr, C and Müller, R and Bals, R and Kalinina, OV},
title = {Comparative metagenomic analysis on COPD and health control samples reveals taxonomic and functional motifs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1636322},
pmid = {41383738},
issn = {1664-302X},
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive lung condition marked by persistent respiratory symptoms and airflow limitation and significantly affects global health. The intricate relationship between COPD and the lung microbiome has garnered attention, with metagenomic analyses revealing critical insights into microbial community dynamics and their functional roles. In this study, we conducted a comprehensive metagenomic analysis comparing throat samples from COPD patients (n = 26) and healthy controls (n = 32) derived from a large cohort analyzed at the Saarland University Hospital. Taxonomic profiling and differential abundance analysis indicated a significant reduction of the microbial diversity in COPD patients, with notable overrepresentation of pathogenic bacteria, such as Veillonella parvula (NCBI:txid29466), Streptococcus gordonii (NCBI:txid1302), Scardovia wiggsiae (NCBI:txid230143), as well as a less stable microbiome composition than in healthy individuals. Functional profiling identified alterations in metabolic pathways implicating microbial dysbiosis in disease progression. The study also highlighted enrichment of inflammation-related pathways in COPD samples, emphasizing the microbiome's role in inflammatory processes. Comparative analysis of bronchoalveolar lavage (BAL) and throat samples collected from the same 11 individuals further underscored distinct microbial compositions across respiratory tract regions, suggesting spatial variability in microbial communities. Metagenomic approaches including analysis of metabolic pathways showed significant alteration of the microbiome of the lung in COPD.},
}

@article {pmid41383638,
year = {2025},
author = {Zhao, Z and Li, J and Peng, Z and Luo, X and Duan, L and Lin, Z and Wang, P and Li, W and Jiang, H},
title = {Light-driven diel oscillations in microbial metabolism underpin estuarine biogeochemical resilience.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf216},
pmid = {41383638},
issn = {2730-6151},
abstract = {Diel light cycles profoundly influence estuarine biogeochemical processes, yet the mechanistic responses of planktonic prokaryotic communities to these rhythmic cues remain incompletely understood. This study employed an integrative multi-omics approach-combining high-frequency sampling, 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-to elucidate diel dynamics in microbial diversity, interaction networks, and metabolic functions in the Pearl River Estuary. The results revealed significant temporal partitioning in microbial organization: nocturnal communities exhibited higher α-diversity and formed more densely connected co-occurrence networks, indicative of enhanced heterotrophic processes, whereas daytime assemblages were dominated by Cyanobacteria (particularly Synechococcales) with enriched pathways for photoautotrophic carbon fixation and nitrogen assimilation. Metabolic profiling further demonstrated distinct diel oscillations in key biogeochemical processes, including daytime enhancement of Calvin cycle-mediated CO2 fixation and nocturnal upregulation of dissimilatory sulfate reduction. Network topology analysis showed that nighttime communities displayed increased clustering coefficients and reduced path lengths, suggesting more efficient resource utilization under dark conditions. Through reconstruction of 786 metagenome-assembled genomes, we identified Cyanobiaceae as key mediators of diel carbon and nitrogen transformations, while diverse heterotrophic taxa facilitated nighttime nutrient remineralization. This study provides mechanistic insights into how light-driven diel oscillations shape microbial metabolic partitioning and ecological interactions, advancing our understanding of the temporal dynamics that underpin biogeochemical resilience in estuarine ecosystems.},
}

@article {pmid41383636,
year = {2025},
author = {Laperriere, SM and Minch, B and Weissman, JL and Hou, S and Yeh, YC and Ignacio-Espinoza, JC and Ahlgren, NA and Moniruzzaman, M and Fuhrman, JA},
title = {Phylogenetic proximity is a key driver of temporal succession of marine giant viruses in a five-year metagenomic time-series.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf217},
pmid = {41383636},
issn = {2730-6151},
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs), also called giant viruses, are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding "rules" underpinning their community dynamics over time. We leveraged a five-year monthly coupled metagenomic-viromic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize their temporal population dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and nonseasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic, showing strong seasonal signals. The Imitervirales group had the highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is an important driver of the temporal niche partition of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. We also identified distinct functional content and possible interactions of two major NCLDV orders with diverse eukaryotes in the study environment- revealing their putative hosts that include both primary producers and heterotrophic grazers. Together, our multiannual time-series study captures diverse temporal patterns among marine giant viruses and demonstrates that evolutionary history plays a key role in shaping their temporal niche partitioning.},
}

@article {pmid41383301,
year = {2025},
author = {Gauthier, J and Mohammadi, S and Kukavica-Ibrulj, I and Boyle, B and Landgraff, C and Goodridge, L and White, K and Chapman, B and Levesque, RC},
title = {Leveraging artificial intelligence community analytics and nanopore metagenomic surveillance to monitor early enteropathogen outbreaks.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1675080},
pmid = {41383301},
issn = {2296-2565},
mesh = {Humans ; Quebec/epidemiology ; *Metagenomics/methods ; *Disease Outbreaks ; *Artificial Intelligence ; Wastewater/microbiology ; *Nanopores ; *Salmonella Infections/epidemiology ; *Foodborne Diseases/epidemiology ; },
abstract = {Foodborne enteric infections are a major public health and economical burden, yet their surveillance often relies on latent indicators that delay containment efforts by several days and weeks. Conversely, whole metagenome shotgun sequencing of communal wastewater allows continuous monitoring of enteric pathogens. Spikes in abundance can be observed several weeks before the first case reports emerge. In addition, AI-driven social media mining, already in use for public opinion analytics, could be repurposed for predicting outbreaks at the community level by predicting the number of people experiencing symptoms in the population given their social media activity. Here we report how AI-driven community analytics and high-throughput long-read metagenomic surveillance of communal wastewater microbiota were combined to monitor non-typhoidal salmonellosis in Quebec City, Canada, from August 2023 to February 2024. Both approaches indicated similar fluctuations over time for: (i) people experiencing salmonellosis symptoms, and (ii) Salmonella enterica relative abundance in wastewater, with predicted cases leading metagenomic peaks by a week. Moreover, both approaches detected a maximum around September 13th, 2023, 5 weeks before a Salmonella food recall for the Quebec and Ontario provinces was made by the Public Health Agency of Canada. We therefore suggest that continuous AI-driven analytics and wastewater metagenomics monitoring could become part of a nationwide surveillance pipeline from the community scale to the molecular level.},
}

Humans
Quebec/epidemiology
*Metagenomics/methods
*Disease Outbreaks
*Artificial Intelligence
Wastewater/microbiology
*Nanopores
*Salmonella Infections/epidemiology
*Foodborne Diseases/epidemiology

@article {pmid41382244,
year = {2025},
author = {Bae, IH and Kim, H and Kim, SM and Lee, YH},
title = {Multi-meta-omics reveal unique symbiotic synchronization between ectomycorrhizal fungus and soil microbiome in Tricholoma matsutake habitat.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02292-7},
pmid = {41382244},
issn = {2049-2618},
support = {RS-2022-NR072199//National Research Foundation of Korea/ ; RS-2025-00512558//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Ectomycorrhizal (ECM) fungi establish symbiotic relationships with plant roots, enhancing nutrient uptake, improving plant health, and boosting ecosystem resilience. Although previous studies reported molecular interactions among plant-ECM fungi-surrounding microbes near plant roots, microbiome-wide metabolic shifts and associations with the fungi remain unclear.

RESULTS: Using Tricholoma matsutake as a model, we initially found that T. matsutake induced remarkable microbial community turnover linked to altered soil moisture, nitrogen, and phosphorus levels. Parallel with the compositional alteration, microbiome-wide metabolic capacities, including glutamate metabolism, oligopeptide transport, and siderophore activity, were enriched in the T. matsutake-colonizing soil compared to the soils where the fungus was not colonized. From metatranscriptome data, we found that T. matsutake induced functional remodeling in nitrogen metabolism. Notably, the fungus and soil microbiome were metabolically synchronized with the upregulation of nitrate reduction, glutamate biosynthesis, tryptophan biosynthesis, and indole-3-acetic acid (IAA) biosynthesis. Metabarcoding and metatranscriptome-guided microbial associations revealed potential T. matsutake helper bacteria consisting of Conexibacter and Paraburkholderia. Phage community analyses further showed that the colonization of the ECM fungus influenced phage distributions along with the increase in temperate phage populations. The differential expression of auxiliary metabolic genes also demonstrated that phages could influence bacterial fitness in response to T. matsutake colonization.

CONCLUSION: Our multi-meta-omics-based approaches revealed unique environmental changes by T. matsutake compared to other mycorrhizal systems, as well as metabolic synchronization between the ECM fungus and surrounding microbiomes. These findings will expand our understanding of ECM symbiotic frameworks by highlighting integrated microbial and viral metabolic dynamics. Video Abstract.},
}

@article {pmid41382192,
year = {2025},
author = {Xue, R and Li, Z and Qin, W and Wang, Y and Zhao, K and Liu, L and Bai, Y},
title = {Prolonged grazing reduces the diversity and weakens virus-host links of metagenome-assembled viral community in acidic karst soil.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-025-02489-0},
pmid = {41382192},
issn = {1741-7007},
support = {41907025//National Natural Science Foundation of China/ ; 32160337//National Natural Science Foundation of China/ ; 2025ZNSFSC0202//Natural Science Foundation of Sichuan Province/ ; },
abstract = {BACKGROUND: Soil viruses are fundamental yet often overlooked components of terrestrial ecosystems, where they profoundly influence microbial diversity, community assembly, and biogeochemical cycling through predator-prey dynamics and the carriage of auxiliary metabolic genes (AMGs). However, the impact of human-driven land use change on viral communities and their functional potential remains poorly understood.

RESULTS: In this study, we analyzed viral diversity, virus-host linkage, and functional profiles of AMGs across different land management regimes in acidic karst soil after reclamation. The results showed that both bacterial and viral communities significantly differ across the four land management regimes, which are unused land, grazing pastureland, abandoned pastureland, and fertilized grazing pastureland. Grazing led to a lower viral diversity, a decrease in lysogenic viral abundance, and fewer virus-host linkages. The diversity and function of AMGs were also significantly affected by land management regimes, with grazing leading to a reduction in both AMGs diversity and relative abundance. Furthermore, both the bacterial community and soil physiochemical properties were essential factors that shaped viral diversity and lifestyle.

CONCLUSIONS: Overall, our findings indicate that inappropriate land use (long-term grazing) disrupts the virus-host balance, thereby altering the functional profiles of the soil viral community.},
}

@article {pmid41381916,
year = {2025},
author = {Li, R},
title = {Metagenomic editing integrates large DNA sequences into gut bacteria in vivo.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41587-025-02966-5},
pmid = {41381916},
issn = {1546-1696},
}

@article {pmid41381751,
year = {2025},
author = {Tabe, C and Motooka, D and Fujita, T and Makiguchi, T and Taima, K and Tanaka, H and Itoga, M and Ishioka, Y and Akita, T and Ishidoya, M and Chubachi, K and Fukushima, T and Tanaka, Y and Odagiri, H and Kameyama, Y and Kobori, Y and Tasaka, S and Fujii, H},
title = {The gut microbiota as a potential biomarker in patients with EGFR-mutant lung cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31225-5},
pmid = {41381751},
issn = {2045-2322},
abstract = {Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are highly effective against EGFR-mutant non-small cell lung cancer (NSCLC); however, identifying biomarkers that predict prognosis and adverse events is necessary. Although the gut microbiota is considered to be a biomarker for NSCLC without mutations, no studies have examined its potential as a biomarker for EGFR-mutant NSCLC. Here, we investigated the association between gut microbiota composition and diarrhea, a common side effect caused by EGFR-TKIs. In addition, we examined the association between the efficacy of EGFR-TKIs and the gut microbiota. A total of 21 NSCLC patients with EGFR mutations were enrolled. Fecal samples were collected prior to EGFR-TKI treatment and 16S rRNA metagenome sequencing was performed to evaluate the microbiota profile. In addition, α-diversity, β-diversity, and Linear discriminant analysis Effect Size (LEfSe) analyses were performed. The α-diversity of the gut microbiota was higher in patients with grade 0-1 diarrhea than in those with grade 2-3 diarrhea (Shannon, p = 0.0367). In terms of β-diversity, there was a significant difference in the best overall response between patients with a partial response (PR) to EGFR-TKIs and those with stable disease (SD)/progressive disease (PD) (weighted p = 0.041). Analysis of microbial composition revealed an increased abundance of Ruminococcus in the PR group. In patients taking EGFR-TKIs, a higher α-diversity may be associated with less severe diarrhea. In addition, a high abundance of Ruminococcus may be a potential biomarker for predicting favorable efficacy of EGFR-TKIs.},
}

@article {pmid41381546,
year = {2025},
author = {Trubl, G and Roux, S and Borton, MA and Varsani, A and Li, YF and Sun, CL and Jang, HB and Woodcroft, BJ and Tyson, GW and Wrighton, KC and Saleska, SR and Eloe-Fadrosh, EA and Sullivan, MB and Rich, VI},
title = {Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67057-0},
pmid = {41381546},
issn = {2041-1723},
support = {DE-SC0010580, DE-SC0016440, DE-SC0248445, DE-SC0023307//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1632//DOE | SC | Biological and Environmental Research (BER)/ ; 3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; SCGSR//DOE | Office of Science (SC)/ ; 21-LW-060//DOE | LDRD | Lawrence Livermore National Laboratory (LLNL)/ ; },
abstract = {Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.},
}

@article {pmid41381437,
year = {2025},
author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J},
title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11067},
pmid = {41381437},
issn = {2041-1723},
mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth & development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; },
abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.},
}

*Nitrogen/metabolism
*Triticum/metabolism/microbiology/growth & development
Soil Microbiology
*Crops, Agricultural/metabolism/microbiology
Plant Roots/metabolism/microbiology
*Agriculture/methods
Climate Change
Soil/chemistry
Nitrification
Nitrates/metabolism
*Conservation of Natural Resources
Metabolomics
Microbiota
Metagenomics
Bacteria/metabolism/genetics

@article {pmid41381092,
year = {2025},
author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM},
title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70261},
doi = {10.1111/1758-2229.70261},
pmid = {41381092},
issn = {1758-2229},
support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; },
mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; },
abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.},
}

*Copper/metabolism/chemistry
*Bacteria/metabolism/genetics/classification/isolation & purification
*Archaea/metabolism/genetics/classification/isolation & purification
*Sulfides/metabolism/chemistry
*Microbial Consortia
Metagenomics
*Minerals/metabolism/chemistry
*Microbiota
Plasmids/genetics

@article {pmid41380982,
year = {2025},
author = {Wei, B and Zhang, L and Zhang, H and Gui, B and Deng, Q and Chang, X and Yu, P and Dong, X and Zou, B and Zhang, X and Zhao, Y and Zhao, Z and Chen, J},
title = {An integrated ultrasonic and cellulase pretreatment strategy: simultaneously enhancing medium-chain fatty acid production and reducing antibiotic resistance genes in anaerobic digestion of animal manure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133780},
doi = {10.1016/j.biortech.2025.133780},
pmid = {41380982},
issn = {1873-2976},
abstract = {Rapid expansion of animal husbandry poses significant environmental challenges, including waste management and pollution. While medium-chain fatty acid (MCFA) production from livestock manure via chain elongation (CE) process in anaerobic digestion (AD) offers a promising and economically valuable waste management strategy, the associated risks of antibiotic resistance genes (ARGs) propagation through AD products are often overlooked. Additionally, the impact of substrate pretreatments on MCFA production and ARGs abundances in livestock manure during CE process remains unclear. This study assessed synergistic effects of cellulase and ultrasonic pretreatments on MCFA yield, microbial community, and ARGs during CE process of co-digesting lignocellulosic goat manure and corn straw. The results demonstrated that cellulase pretreatment increased caproate yield by 46.72 % (from 6.93 to 10.17 g of chemical oxygen demand (COD)/L). Combined cellulase and ultrasonic pretreatments decreased ARGs relative abundance by 25.28 %. The underlying mechanism was further explored through metagenome, revealing the roles of microbial community shifts and gene regulation in the beneficial outcomes. Specifically, we found that cellulase pretreatment enriched Clostridia and modulated genes related to reverse β-oxidation and ethanol oxidation, contributing to enhanced MCFA production. The reduction in ARGs abundance, particularly with combined pretreatments, was linked to a decrease in Massilibacterium abundance. Additionally, co-occurrence analysis indicated Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota as primary ARG hosts. This study demonstrates the viability of lignocellulosic goat manure for MCFA production via CE. Pretreatments effectively boost MCFA yield and mitigate ARGs, providing a basis for comprehensive biorefinery systems integrating resource valorization and ARGs control in lignocellulosic animal waste management.},
}

@article {pmid41380668,
year = {2025},
author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM},
title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.},
journal = {Cell host & microbe},
volume = {33},
number = {12},
pages = {2148-2166.e8},
doi = {10.1016/j.chom.2025.11.011},
pmid = {41380668},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; },
abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.},
}

Humans
*Microbiota/genetics
*Lung/microbiology
Disease Progression
RNA, Ribosomal, 16S/genetics
*Pneumonia/microbiology/pathology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Male
Female
Bacterial Load
Middle Aged
Aged

@article {pmid41380611,
year = {2025},
author = {Xie, C and Li, Y and Wulijia, B and Dong, X and Wang, L and Song, Y and Liao, X},
title = {Centennial Pb-Zn mining pollution: Spatial distance impacts on agricultural soil microbiota stress response.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119550},
doi = {10.1016/j.ecoenv.2025.119550},
pmid = {41380611},
issn = {1090-2414},
abstract = {Mining activities pose significant threats to agricultural ecosystems through heavy metals (HMs) contamination, particularly in acidic red soils. Since there was limited research on the response mechanisms of agricultural microorganisms at different distances within typical mining areas to HMs stress, This study investigated HMs pollution patterns, microbial community dynamics, and functional gene responses in farmland surrounding a century-old Pb-Zn mine in Shuikoushan, Hengyang City, China. Soil samples were collected from three zones: Short-Distance (SD, 0-10 km), Medium-Distance (MD, 10-15 km), and Long-Distance (LD, 15-25 km) from the mine. Results revealed a pronounced distance-dependent decline in composite HMs pollution, with Cd (R[2]=0.61) and As (R[2]=0.51) showing the strongest correlations to proximity. SD zone exhibited severe contamination, with Cd (8.25 ± 5.74 mg kg[-1]) and As (58.58 ± 49.63 mg kg[-1]) concentrations exceeding regulatory limits by 27.5 and 1.95 fold, respectively. Bacterial diversity demonstrated significant spatial stratification, with Shannon indices increasing from SD to LD zones (6.8→7.2), while β-diversity decreased, indicating reduced ecological heterogeneity at lower pollution levels. High HMs stress in SD zone favored anaerobic taxa like Thermomarinilinea and acid-tolerant phyla like Acidobacteriota, whereas aerobic taxa like Gaiella dominated less-polluted areas. Metagenomic analysis revealed upregulation of HMs resistance genes (czcABCD, cadCD, arsABCJR) in SD zone. Correlation network analysis highlighted intensified positive interactions among bacterial genus under HMs stress, suggesting cooperative survival strategies. These findings elucidate the dual pressure of HMs toxicity and soil acidification on microbial ecosystems, providing critical insights for ecological risk assessment and bioremediation strategies in mining-impacted agricultural lands. The study underscores the need for distance-based pollution control measures and highlights microbial genetic adaptation as a potential tool for rehabilitating heavy metal-contaminated red soils.},
}

@article {pmid41380516,
year = {2025},
author = {Geng, Y and Lian, CA and Yang, L and Pavlostathis, SG and Qiao, X and Qiu, Z and Wang, Y and Dong, N and Li, A and Luo, X and Yu, K},
title = {Unlocking microbial synergy in mcroalgae-bcteria gnules: RSM -driven optimization and lifecycle microbial metagenomics for high-ammonia wastewater treatment.},
journal = {Water research},
volume = {290},
number = {},
pages = {125098},
doi = {10.1016/j.watres.2025.125098},
pmid = {41380516},
issn = {1879-2448},
abstract = {Landfill leachate is challenging to treat biologically due to high ammonia toxicity and low C/N ratio, while suspended co-cultures, despite easing carbon limitations, show poor settleability and instability under high-strength conditions. This work focuses on investigating microbial synergy in microalgae-bacteria granules through RSM-driven optimization and lifecycle microbial metagenomics for high-ammonia leachate treatment. Initially, granules removed Total inorganic nitrogen (TIN) at 167.5 mg/L/d, outperforming algae-only systems. 16S rRNA analysis showed 25 % more Halomonas sp. and enriched Proteobacteria, linked to improved pollutant removal. Subsequent RSM optimization elevated TIN removal to 193.3 mg/L/d, with synchronous improvement in chemical oxygen demand (COD) removal, flocculation, Extracellular Polymeric Substances (EPS) production, and granule stability. In addition, reactor operation over 8 cycles sustained TIN removal above 193.4 mg/L/d until Cycle IV and then dropped by 5.0 %, displaying a typica granule life cycle from growth to decline. Metagenomic analysis of 326 metagenome-assembled genomes (MAGs) revealed dynamic microbial synergy that shifted from nutrient assimilation to stress adaptation, explaining the system's resilience. During assimilation-dominated stages, synergy focused on coordinated nutrient utilization, supporting energy-intensive nitrogen assimilation. As metabolism shifted to dissimilation, synergy reoriented toward stress adaptation: assimilation genes decreased to 44.3 % of their peak levels, while stress genes hcp and cah increased by 11.2-fold. This dynamic synergy provides a blueprint for lifecycle management. These findings highlight the great potential of microalgae-bacteria granules as a resilient, low-footprint approach for nitrogen removal and circular wastewater treatment.},
}

@article {pmid41380282,
year = {2025},
author = {Xu, X and Wang, J and Deng, C and Yu, X and Nie, R and Wang, S and Huang, W},
title = {Metagenomic insights into rhizosphere microbiome dynamics of Oenanthe javanica in ecological floating beds under different hydrodynamic regimes.},
journal = {Journal of contaminant hydrology},
volume = {277},
number = {},
pages = {104795},
doi = {10.1016/j.jconhyd.2025.104795},
pmid = {41380282},
issn = {1873-6009},
abstract = {Ecological floating beds (EFBs) are a cost-effective and sustainable technology that utilizes macrophyte to remove nutrients from aquatic ecosystems, where rhizosphere bacterial degradation and assimilation play a key role in nutrient removal. However, the current knowledge about how hydrodynamic regimes impact the rhizosphere bacterial community on EFB systems remains limited. Here, we investigated the effects of different hydrodynamic regimes (i.e., stagnant water, pulsed water, and flowing water conditions) on the rhizosphere bacterial community structure and function of Oenanthe javanica in an experimental EFB system based on metagenomic sequencing. We observed that bacterial community compositions on the roots of O. javanica were significantly differed across the three hydrodynamic regimes, with the highest bacterial biodiversity captured from the flowing water condition. Moreover, a total of 65 nitrogen functional genes (NFGs) were identified in the rhizosphere bacterial community, with nitrate reduction pathways dominating the nitrogen cycling processes. In contrast, totally 139 phosphorus functional genes (PFGs) were detected, primarily involved in purine metabolism, which drove the phosphorus cycling dynamics. We found the distinct nitrogen and phosphorus metabolic strategies of rhizosphere bacterial communities in response to hydrodynamic regime changes. Specifically, the relative abundances of NFGs like nasB, narl, and ansB were significantly increased under the pulsed water condition, whereas gdh_K00262 were relative abundant under the flowing condition. Moreover, pulsed water condition promoted the relative abundances of PFGs such asas phnC, phoD, and pgtP in rhizosphere bacterial communities, in contrast to the stagnant condition, which favored genes like ugpC, purK, phoH, and purA. Our study offers technical support for regulating plant degradation of pollutants to improve EFB's performance in engineering applications.},
}

@article {pmid41380256,
year = {2025},
author = {Yu, W and Zhang, J and Shi, Z and Wang, S and Lai, S and Huang, X and Zhang, J and Cai, Z and Zhao, J},
title = {Reductive soil disinfestation mitigates antibiotic resistance gene risk in the soil-lettuce continuum by restructuring dominant bacterial taxa and improving soil properties.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140745},
doi = {10.1016/j.jhazmat.2025.140745},
pmid = {41380256},
issn = {1873-3336},
abstract = {Reductive soil disinfestation (RSD) and chemical fumigation serve as effective methods for controlling soil-borne pathogens, yet their effects on soil antibiotic resistome remain poorly understood. This study combined high-throughput qPCR (HT-qPCR) and metagenomic sequencing to evaluate the impacts of dazomet fumigation (DZ) and RSD amended with alfalfa (AL) and molasses (MO) on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in an ARG-contaminated soil. Results demonstrated that both DZ and RSD treatments significantly altered the soil resistome and bacterial community. HT-qPCR revealed that DZ significantly increased the relative abundance of total ARGs, MGEs and high-risk ARGs (Rank I and Rank II) by 86.59 %, 43.12 %, 36.81 %, and 40.88 %, respectively, while RSD treatments effectively reduced MGEs by 53.96-63.30 % and significantly suppressed Rank II high-risk ARGs. Metagenomic sequencing further indicated that RSD, particularly AL, outperformed DZ in reducing most ARGs classes, with pronounced effects on predominant ARGs such as macB (16.32 %), tetA(58) (24.14 %), and TxR (29.31 %). Correlation analyses suggested that RSD mitigates ARGs contamination by modulating the dominant bacterial community, especially suppressing ARG hosts while enriching antagonists, and improving soil physicochemical properties. Variance partitioning analysis attributed greater explanatory power to bacterial community than to physicochemical properties in shaping high-risk (18.44 % vs. 3.72 %) and high-abundance (11.90 % vs. 2.79 %) ARG profiles. Moreover, RSD considerably reduced the ARGs transmission risk from soil to lettuce. These findings establish RSD as an effective strategy to curb ARGs dissemination in soil-plant system and support its adoption for safer agricultural production.},
}

@article {pmid41379797,
year = {2025},
author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D},
title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337322},
doi = {10.1371/journal.pone.0337322},
pmid = {41379797},
issn = {1932-6203},
mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation & purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.

METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n = 37; 66.1%), IBD-Unclassified (n = 9; 16.1%), ulcerative proctitis (n = 7; 12.5%), and Crohn's disease (n = 3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.

RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).

CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.},
}

Humans
*Virome/genetics
Female
Male
*Inflammatory Bowel Diseases/virology/pathology
Biopsy
High-Throughput Nucleotide Sequencing
Adult
Middle Aged
*Herpesviridae/genetics/isolation & purification
Retrospective Studies
Aged
Intestinal Mucosa/virology/pathology
*Intestines/virology/pathology
Colitis, Ulcerative/virology
Metagenomics
Young Adult

@article {pmid41379644,
year = {2025},
author = {Capoferri, G and Battegay, R and Hamelin, B and Keller, PM and Mertz, KD and Weisser, M},
title = {Borrelia afzelii Hepatitis in Patient Treated with Venetoclax and Obinutuzumab, Switzerland.},
journal = {Emerging infectious diseases},
volume = {31},
number = {11},
pages = {2167-2171},
doi = {10.3201/eid3111.250584},
pmid = {41379644},
issn = {1080-6059},
mesh = {Humans ; *Sulfonamides/adverse effects/therapeutic use ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use ; Switzerland ; *Borrelia burgdorferi Group/genetics ; *Bridged Bicyclo Compounds, Heterocyclic/adverse effects/therapeutic use ; *Lyme Disease/diagnosis/microbiology/drug therapy ; Male ; *Hepatitis/diagnosis/etiology/microbiology ; Immunocompromised Host ; *Antineoplastic Agents/adverse effects/therapeutic use ; Aged ; Female ; },
abstract = {We report Borrelia afzelii hepatitis in an immunosuppressed patient in Switzerland receiving anti-CD20 therapy and venetoclax. Diagnosis was made by metagenomic sequencing and PCR. This case underscores the need to consider Lyme borreliosis in unexplained hepatitis cases and highlights the value of molecular diagnostics in immunosuppressed patients when serologic test results are negative.},
}

Humans
*Sulfonamides/adverse effects/therapeutic use
*Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use
Switzerland
*Borrelia burgdorferi Group/genetics
*Bridged Bicyclo Compounds, Heterocyclic/adverse effects/therapeutic use
*Lyme Disease/diagnosis/microbiology/drug therapy
Male
*Hepatitis/diagnosis/etiology/microbiology
Immunocompromised Host
*Antineoplastic Agents/adverse effects/therapeutic use
Aged
Female