@article {pmid40226917,
year = {2025},
author = {Lai, Q and Yao, S and Zha, Y and Zhang, H and Zhang, H and Ye, Y and Zhang, Y and Bai, H and Ning, K},
title = {Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.},
journal = {Nucleic acids research},
volume = {53},
number = {7},
pages = {},
doi = {10.1093/nar/gkaf305},
pmid = {40226917},
issn = {1362-4962},
support = {2021YFA0910500//National Key R&D Program of China/ ; 32071465//National Natural Science Foundation of China/ ; },
mesh = {*Multigene Family ; *Biosynthetic Pathways/genetics ; *Neural Networks, Computer ; *Genome, Microbial ; Phylogeny ; Metagenome ; Secondary Metabolism/genetics ; Genome, Bacterial ; },
abstract = {Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet's capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.},
}

*Multigene Family
*Biosynthetic Pathways/genetics
*Neural Networks, Computer
*Genome, Microbial
Phylogeny
Metagenome
Secondary Metabolism/genetics
Genome, Bacterial

@article {pmid40226542,
year = {2025},
author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B},
title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19260},
pmid = {40226542},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Sympatry ; Bacteroidetes/genetics/isolation & purification ; },
abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.},
}

Animals
*Gastrointestinal Microbiome/genetics
China
*Arvicolinae/microbiology
*Murinae/microbiology
*Metagenome
Metagenomics
High-Throughput Nucleotide Sequencing
Proteobacteria/genetics/isolation & purification
Firmicutes/genetics/isolation & purification
Sympatry
Bacteroidetes/genetics/isolation & purification

@article {pmid40226095,
year = {2025},
author = {Ho, JY and Koh, XQ and Kang, DY and Low, A and Hu, D and Haryono, MAS and Williams, RBH and Case, RJ and Boucher, YF},
title = {Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1437936},
pmid = {40226095},
issn = {1664-302X},
abstract = {Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41G[T] as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813[TS] (=BAABNI000000000.1[TS]) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891[T] outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.},
}

@article {pmid40225905,
year = {2025},
author = {Lambisia, AW and Mwita Morobe, J and Moraa, E and Mwarumba, S and K N Korir, F and Seif Athman, R and Kiptui, R and Mbee, M and Mugo, N and Amoth, P and Muange, P and J Houldcroft, C and Barasa, E and Mwangangi, J and Githinji, G and C Holmes, E and Isabella Ochola-Oyier, L and N Agoti, C},
title = {Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {28},
pmid = {40225905},
issn = {2398-502X},
abstract = {BACKGROUND: In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as "red eye" disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.

METHODS: Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.

RESULTS: Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV.

CONCLUSION: The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.},
}

@article {pmid40225898,
year = {2025},
author = {Liu, H and Wang, H and Sun, J and Yang, T and Mo, Z and Huang, H and Pan, Y},
title = {High-Altitude Open-Pit Coal Mining has Changed the Sulfur Cycle and Ecological Network of Plant Rhizosphere Microorganisms.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71183},
pmid = {40225898},
issn = {2045-7758},
abstract = {Ecological restoration of mining sites has a considerable effect on microbial community dynamics; however, its impact on sulfur cycling is unclear. This study explored the changes in functional genes related to sulfur cycling and microbial diversity during different stages of succession following the ecological restoration of a mining site in a cold arid area. A total of three succession stages were selected-natural, secondary, and artificial. The expression of sulfur cycle-related genes and associated microbial drivers was investigated using metagenomics and network analysis. The dominant bacteria in the secondary succession were found to be r-strategy-adopting Proteobacteria and Cyanobacteria. Natural succession primarily comprised Aspergillus and Thermus, whereas artificial succession comprised Proteobacteria, Chlorophyta, and Actinobacteria. Mining disturbances were determined to significantly reduce the abundance of sulfur-cycling archaea. Secondary succession was primarily influenced by soil total phosphorus in the sulfur-cycle gene network. The key bacteria and archaea involved in the sulfur cycle were found to be Bradyrhizobium and Nitrosopumilus, respectively. The abundance of Streptomyces was significantly higher in natural succession than in artificial or secondary succession. Burkholderia, which has biological control and bioremediation effects, was abundant during artificial succession. These results provide a theoretical basis for restoring the sulfur cycle and promoting a positive succession of ecosystems in mining areas.},
}

@article {pmid40225105,
year = {2025},
author = {He, W and Wang, S and Xiong, X and Dai, W},
title = {[18]F-FDG PET/CT Imaging of Talaromyces marneffei Infection with Bone Destruction in an HIV-Negative Patient: Case Report and Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1745-1752},
pmid = {40225105},
issn = {1178-6973},
abstract = {BACKGROUND: Talaromycosis is an opportunistic fungal infection caused by Talaromyces marneffei (T. marneffei), commonly occurs in HIV-positive individuals. While less common, it can also affect HIV-negative individuals. We reported a T. marneffei infection in an HIV-negative patient, whose imaging findings and diagnostic process offer valuable clinical insights.

CASE PRESENTATION: An HIV-negative male adult patient with an intermittent cough for more than two years and worsened for more than one month. Enhanced CT scan indicated lung cancer with rib and lymph nodes metastasis. The lower respiratory tract and bronchial lavage fluid culture of the patient were negative. He received two bronchoscopies, two biopsies and two metagenomic next-generation sequencing (mNGS) tests, which failed to find the malignant cell but sequentially identified the presence of Pasteurella multocida and the Epstein-Barr virus. His condition did not improve after anti-infective treatment for 2weeks. An 18-fluorodeoxy glucose ([18]F-FDG) PET/CT scan revealed increased radioactivity in right supraclavicular lymph node, left lung and the right tenth rib. Ultimately, a biopsy at the hypermetabolic lesion of left lung, and a third mNGS test confirmed the presence of Talaromyces marneffei. Subsequently, the patient started antifungal therapy with amphotericin B and itraconazole and showed a favorable response.

CONCLUSION: We reviewed all reported PET/CT findings of T. marneffei infection patients, suggesting that fungus T. marneffei should be considered in patients identified as infection and exhibited bone destruction and also highlight the role of PET/CT in guiding the biopsy site.},
}

@article {pmid40224142,
year = {2025},
author = {Caille, A and Connan, C and Lyon Belgy, N and Borezée, E and Cherbuy, C and Meunier, N and Meslier, V},
title = {Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103268},
pmid = {40224142},
issn = {2215-0161},
abstract = {Recent advances in the study of the gut microbiota has pointed to its under-utilized source of potentially beneficial bacteria, known as next generation probiotics, offering a promising avenue to restore or compensate impaired gut microbiota toward a healthy state. Aside from the difficulties to achieve in-lab adequate culture conditions, the use of beneficial bacterial isolates is also limited by their bioavailability in the donor itself. In the iTARGET study, we positively selected donors based on their diet enriched in fiber, that has been shown to increase the prevalence of bacterial species associated with health. The iTARGET study is a monocenter, prospective, observational study of adults with healthy lifestyle and high daily fiber consumption. We aim to recruit individuals in two phases, the first one for all individuals that will permit the identification of carriers for bacteria of interest and the second phase for a subset of individuals to allow for culture and isolation of previously identified potentially beneficial bacteria. Our primary outcome is the isolation and culture of at least one potentially beneficial isolate. The secondary outcomes comprised the high throughput metagenomic profiles of the intestinal microbiota and the characterization of the cultured isolates. The study was approved by the French Research Ethics Committees (Comité de Protection des Personnes Sud-Est I) under the National reference ID 2023-A01677-38. Study findings and results will be published in peer-reviewed Open Access journals. (Trial registration number on ClinicalTrials.gov: NCT06166810).},
}

@article {pmid40223813,
year = {2025},
author = {Alp-Baltakesmez, D and Ertürkmen, P and Bulantekin, Ö},
title = {Diversity and Functional Roles of Microorganisms in Anatolian Black Pine Cone Vinegar Fermentation.},
journal = {Food science & nutrition},
volume = {13},
number = {4},
pages = {e70155},
pmid = {40223813},
issn = {2048-7177},
abstract = {The parts of some pine species are a rich source of bioactive compounds that can be used in various food products. The current work, the physicochemical, bioactive, antimicrobial, sensory, and aromatic properties of traditional vinegar produced from Anatolian Black Pine Cones from different provinces of Turkey were determined, as well as the cultivable microbial diversity and metagenomic analysis. The total phenolic content of the vinegars ranged from 163.88 to 174.79 mg GAE/L. Antioxidant activity, measured via DPPH and ABTS assays, varied among the samples. CnB vinegar, made from Burdur province cones, stood out for its bioactive compounds, including terpenes, acetic acid, ascorbic acid, and the highest α-terpineol content (3.13%). CnB also exhibited the strongest antimicrobial activity, with the largest inhibition zone (44.91 mm) against E. coli type A, while CnM showed the lowest activity. Sensory evaluations favored CnB for its balanced flavor, while CnV was criticized for excessive sharpness, and CnM was deemed too mild. The bacterial microbiome of CnB was predominantly composed of acetic acid bacteria, with an average concentration of 7.36 log CFU/mL in the enumeration of culturable microorganisms. The dominant bacterial taxa at the phyla level included Proteobacteria (72.296%), Firmicutes (22.062%), Bacteroidota (3.665%), followed by Acetobacteraceae (71.47%), Clostridia (13.187%), Bacilli (5.066%), Bacteroidetes (3.665%), and C. negativicutes (3.737%) at the phylum level. The fungal microbiome was mainly represented by Ascomycota (78.717%) and Eukaryota Incertae sedis (15.840%). The findings demonstrate that pine cone vinegar can be employed in a multitude of applications, including food preservation and health promotion.},
}

@article {pmid40223739,
year = {2025},
author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A},
title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
doi = {10.4103/sjg.sjg_24_25},
pmid = {40223739},
issn = {1998-4049},
abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.

METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.

RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4, uncultured_crAssphage, Staphylococcus_phage_SPbeta-like, Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.

CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.},
}

@article {pmid40223703,
year = {2025},
author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H},
title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00306},
pmid = {40223703},
issn = {1520-5851},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.},
}

@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods/trends
*Metabolomics/methods
*Genomics/methods
Proteomics/methods
Precision Medicine
Host Microbial Interactions
Multiomics

@article {pmid40223231,
year = {2025},
author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S},
title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2489154},
doi = {10.1080/21505594.2025.2489154},
pmid = {40223231},
issn = {2150-5608},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; },
abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood
*Gastrointestinal Microbiome
*Feces/microbiology/chemistry
Male
Female
Middle Aged
Metagenomics
Aged
Metabolomics
Dysbiosis/microbiology
Bacteria/classification/genetics/metabolism/isolation & purification
Metabolic Networks and Pathways
Case-Control Studies
Adult

@article {pmid40223096,
year = {2025},
author = {Yang, Z and Zhou, Y and Lin, J and Wang, X and Huang, C and Gao, J and Wang, G and Yang, B and Liu, G and Duan, H and Cui, J and Zhao, J and Luo, W and Cheng, S and Liu, Y},
title = {Identification and characterization of pigeon adenovirus 1 as an emerging pathogen in pigeons from Northern and Northwest China.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {266},
pmid = {40223096},
issn = {1746-6148},
support = {BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; },
mesh = {Animals ; *Columbidae/virology ; China/epidemiology ; *Adenoviridae Infections/veterinary/virology/epidemiology/pathology ; *Bird Diseases/virology/epidemiology/pathology ; *Aviadenovirus/genetics/isolation & purification ; Phylogeny ; Genome, Viral ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; },
abstract = {BACKGROUND: In 2022, a new infectious disease characterized by severe acute hepatitis, sudden death, and high mortality among breeding pigeons, was reported in China.

RESULTS: In naturally infected pigeons, key necropsy findings comprised hepatic swelling with patchy hemorrhage and pericardial effusion. Histopathological examination further revealed degeneration, necrosis, and basophilic intranuclear inclusion bodies affecting hepatocytes, cardiomyocytes, and vascular endothelial cells. Transmission electron microscopy revealed a typical icosahedral virus structure and crystal-like arrangement of viral particles in the nucleus. Metagenomic next-generation sequencing (mNGS) of pericardial effusion samples revealed the presence of pigeon adenovirus. Sequencing analysis of the hexon and fiber-2 genes suggested that it constituted pigeon adenovirus 1 (PiAdV-1). The complete genome of CH/BJ/1/2022 was determined to be 48,071 nucleotides in length, with a 10-amino acid deletion in the fiber-2 gene at residues 627-636 and a 95-animo acid insertion in the 100 K gene at residue 75. The same disease was reproduced in pigeons by experimental infection.

CONCLUSION: Collectively, our analyses confirmed that the etiological agent was PiAdV-1, an emerging pathogen that causes severe acute hepatitis and high mortality in pigeons. This virus merits close attention because it could be catastrophic for the pigeon industry.},
}

Animals
*Columbidae/virology
China/epidemiology
*Adenoviridae Infections/veterinary/virology/epidemiology/pathology
*Bird Diseases/virology/epidemiology/pathology
*Aviadenovirus/genetics/isolation & purification
Phylogeny
Genome, Viral
*Communicable Diseases, Emerging/veterinary/virology/epidemiology

@article {pmid40222673,
year = {2025},
author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL},
title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26395},
pmid = {40222673},
issn = {1525-3198},
abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.},
}

@article {pmid40222492,
year = {2025},
author = {Xia, Y and Chen, X and Jiang, X and Shen, J},
title = {Enhanced denitrification under saline Conditions: Glycine betaine as a key osmoprotectant.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132517},
doi = {10.1016/j.biortech.2025.132517},
pmid = {40222492},
issn = {1873-2976},
abstract = {Biological denitrification is significantly inhibited by salinity, which adversely affects microbial activity and reduces efficiency. This study aimed to evaluate the impact of salinity on denitrification performance and assess the potential of glycine betaine (GB) as an osmotic pressure regulator and protective agent. Results indicated that under the optimal conditions, including an influent nitrate concentration of 51.03 mg L[-1], C/N ratio of 5.42, pH value of 8.95, and salinity of 1.05 %, the nitrate removal efficiency was predicted to reach 100 %. However, a sharp decline (56.09 ± 4.52 %) in nitrate removal efficiency occurred when salinity increased from 0 % to 3 % within the initial 6 h. This inhibition was mitigated by adding 25 mg L[-1] GB, which enhanced nitrate removal efficiency by 2.19 times. GB promoted the secretion of extracellular polymeric substances (EPS), especially polymeric protein, a critical contributor to salinity resistance. Metagenomics analysis revealed that GB improved denitrification process by upregulating key genes involved in nitrogen and carbon metabolism. Furthermore, the relative abundance of Na[+] transporter genes, K[+] transporter genes, and GB absorption and synthesis genes rose with GB addition, underscoring the indispensable role of GB in alleviating osmotic stress and accelerating microbial metabolism. These findings emphasize the detrimental effects of salinity on denitrification and demonstrate the potential of GB as an osmoprotectant, enabling efficient nitrogen removal under saline conditions.},
}

@article {pmid40222473,
year = {2025},
author = {Jing, K and Li, Y and Li, Y and Meng, Q and Guan, Q},
title = {The treated wastewater enhances the biodegradation of sulfonamide antibiotics in biofilm-sediment downstream of the receiving river outlet.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121600},
doi = {10.1016/j.envres.2025.121600},
pmid = {40222473},
issn = {1096-0953},
abstract = {Although the treated wastewater meets the discharge standards, it can still become a potential transmitted stressor that affects aquatic organisms in receiving rivers. Biofilms and sediments as the main solid-phase substances in natural aquatic environments can biodegrade micropollutants. However, most of the current studies have selected a single solid-phase material, and there are relatively few studies that comprehensively consider the effect of treated wastewater on the dissipation of micropollutants in a composite biofilm-sediment system. Therefore, this study investigated the dissipation pathways of six sulfonamide antibiotics (SAs) in biofilm-sediment and the effect of treated wastewater on SAs dissipation. The results showed that biodegradation was the main pathway for SAs dissipation in biofilm-sediment. The input of treated wastewater increased the abundance of dominant degradation bacteria Burkholderiales and Pseudomonadale, thereby improving the biodegradation rate of SAs (approximately 1.5 times higher than upstream degradation rate). These genera could also be further integrated into downstream communities to continuously mediate the biodegradation of SAs. Through mass spectrometry and metagenomic sequencing analysis, it was found that the common degradation pathways of SAs in biofilm-sediment affected by treated wastewater are acetylation, formylation, hydroxylation, and bond cleavage. Acetyltransferase played an important role in the biodegradation of SAs. In addition, the enrichment of antibiotic resistant genes during biodegradation increased the risk of their spread in the aquatic environment. These findings provide new insights into the fate of antibiotics in aquatic environments and the impact of treated wastewater on downstream bacterial communities.},
}

@article {pmid40222470,
year = {2025},
author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z},
title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121602},
doi = {10.1016/j.envres.2025.121602},
pmid = {40222470},
issn = {1096-0953},
abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2%) was higher than ammonia-oxidizing bacteria (AOB, 12.0%), but lower than ammonia-oxidizing archaea (AOA, 64.8%). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.},
}

@article {pmid40222255,
year = {2025},
author = {Bobrovska, S and Newcomer, E and Gottlieb, M and McSorley, VE and Kittner, A and Hayden, MK and Green, S and Barbian, HJ},
title = {Hospital air sampling enables surveillance of respiratory virus infections and genomes.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179346},
doi = {10.1016/j.scitotenv.2025.179346},
pmid = {40222255},
issn = {1879-1026},
abstract = {There is an urgent need for early detection and comprehensive surveillance of respiratory pathogens. Environmental surveillance may be key to timely responses for newly emerging pathogens and infections that are unreported or underreported. Here, we employed air sampling in a large urban hospital. Air samples (n = 358) were collected weekly at five locations, including two in the emergency department, two in hospital common areas and one in a storage room, for two respiratory virus seasons (November 2022 to June 2024). Air samples were tested for eight respiratory pathogens by qPCR, including RNA and DNA viruses and a bacterium. Air samples had an average of four detected pathogens per sample and 97 % samples contained SARS-CoV-2. Air sample pathogen positivity and quantity were strongly correlated with clinical surveillance for four seasonal respiratory pathogens: influenza A and B, respiratory syncytial virus, and human metapneumovirus. Targeted amplicon sequencing of SARS-CoV-2 showed that lineages detected in air samples reflected those in contemporaneous regional clinical specimens. Metagenomic sequencing with viral capture enrichment detected myriad human pathogens, including respiratory-associated viruses with recovery of full viral genomes. Detection of viral pathogens correlated well between virus capture sequencing and qPCR. Overall, this suggests air sampling can be an agile and effective tool for pathogen early warning, surveillance and genome characterization.},
}

@article {pmid40222247,
year = {2025},
author = {Suzuki, M and Hayashi, T and Takahashi, K and Nozaki, K and Kasuya, KI},
title = {Exploring biodegradation limits of n-alkanes as polyethylene models using multi-omics approaches.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179365},
doi = {10.1016/j.scitotenv.2025.179365},
pmid = {40222247},
issn = {1879-1026},
abstract = {Polyethylene (PE) is widely regarded as non-biodegradable in natural environments, despite reports suggesting partial biotic degradation. Using multi-omics analysis, this study investigated the biodegradation mechanisms of n-alkanes-structural analogs of PE-to determine the threshold carbon number in PE that allows for environmental biodegradation. n-Alkanes with 6-40 carbons (C6-C40) were biodegraded in the soil, whereas C44 and PE were not. 16S rRNA gene amplicon sequence analysis identified distinct microbial communities associated with non-degradable compounds (PEs and C44) and biodegradable alkanes (C6-C40). Notably, the microbial community composition for C40 differed from those associated with biodegradable alkanes below C36. Multi-omics analysis identified the genera Aeromicrobium, Nocardia, Nocardioides, Rhodococcus, Acinetobacter, and Fontimonas as key degraders of n-alkanes at C36 and below, utilizing alkane hydroxylases such as alkane monooxygenase (AlkB), LC-alkane monooxygenase from Acinetobacter (AlmA), and cytochrome P450 (CYP153). Conversely, the biodegradation of C40 was facilitated by taxa, including the order Acidimicrobiales and the genera, Acidovorax, Sphingorhabdus, Prosthecobacter, and Roseimicrobium using AlmA and CYP153-type hydroxylases. This difference in key degraders and alkane hydroxylases may explain the reduced biodegradability of n-alkanes above C40, including PE.},
}

@article {pmid40222078,
year = {2025},
author = {Xu, A and Gao, D and Wu, WM and Gong, X and Liang, H},
title = {Enhanced denitrification using iron modified biochar under low carbon source condition: Modulating community assembly, allocating carbon metabolism and facilitating electron transfer.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125354},
doi = {10.1016/j.jenvman.2025.125354},
pmid = {40222078},
issn = {1095-8630},
abstract = {Biochar can modulate microbial community structure to enhance denitrification but the activity is still restricted by the availability of electron transfer (ETS) under metabolic imbalance conditions. Here we developed iron (Ⅲ) modified biochar (FeBC) to substantially mitigate this electron limitation, enhance ETS and accelerate denitrification reaction via intracellular metabolism and community interaction. The results demonstrated that FeBC could significantly improve the denitrification performance, the nitrate removal rate was significantly increased by 30 % at C/N ratio of 3 (W/W) with little nitrite and nitrous oxide accumulation, attributing to the enhanced activities of the ETS and denitrifying reductases and complex microbial interactions via increased abundance of microorganisms involved in carbon and nitrogen transformations. Biochemical quantification and electrochemical analysis, revealed that FeBC activated the acceleration of the ETS process. Comparative metagenome analyses indicated that upregulating key enzymes in the tricarboxylic acid cycle was the potential respiratory enzyme associated with FeBC-mediated ETS. NADH/NAD[+] circulation stimulate the startup of carbon metabolism. This energy-linked mechanism could provide ATP for denitrification. This study revealed the functional roles of FeBC in mediating ETS and regulating the bacterial community to achieve enhanced denitrification.},
}

@article {pmid40221653,
year = {2025},
author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ},
title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {26},
pmid = {40221653},
issn = {2730-6844},
mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.

DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.},
}

*Daucus carota/microbiology
*Metagenomics/methods
*Rhizosphere
*Glycine max/microbiology/growth & development
*Microbiota
Soil Microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40221647,
year = {2025},
author = {Zhang, N and Dou, H and Guo, P and Sun, J and Zhang, F and Chen, T and Gao, C and Wang, Z},
title = {Concurrent invasive disseminated Nocardia farcinica and Candida infections in a patient undergoing long-term glucocorticoid therapy for autoimmune thrombocytopenia: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {520},
pmid = {40221647},
issn = {1471-2334},
support = {gxgnfx2022035//Domestic Visiting Training Program for Outstanding Young Backbone Teachers/ ; 2023SYKFZ05//Open project of Anhui Biochemical Drug Engineering Technology Research Center in 2023/ ; },
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/microbiology/complications ; Middle Aged ; *Nocardia/isolation & purification ; *Candidiasis/drug therapy/diagnosis/microbiology/complications ; *Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications ; *Glucocorticoids/therapeutic use/adverse effects ; Antifungal Agents/therapeutic use ; Candida albicans/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology ; Prednisone/therapeutic use/adverse effects ; Immunocompromised Host ; },
abstract = {BACKGROUND: Nocardia farcinica is a virulent organism known for its high resistance to many antibiotics and its ability to cause disseminated life-threatening infections, particularly in immunocompromised patients or those undergoing organ transplantation. Candida albicans can cause disseminated candidiasis with a mortality rate ranging from 30% to 60%. Cases involving concurrent disseminated N. farcinica and C. albicans, particularly in patients with autoimmune thrombocytopenia, are extremely rare. The presence of two disseminated pathogens complicates both diagnosis and treatment, creating substantial challenges for healthcare providers.

CASE PRESENTATION: A 50-year-old woman who had a history of autoimmune thrombocytopenia and was being treated with prednisone (60 mg qd). She presented with a 40-day history of high-grade fevers (40℃), cough, headache, and multiple abscesses in the skin structure. N. farcinica was found in her skin structure, cerebrospinal fluid, and blood, and C. albicans was cultured in cerebrospinal fluid, sputum, and urine. She was diagnosed with disseminated nocardiosis and disseminated candidiasis. The patient received a prolonged course of multiple anti-bacterial and anti-fungal medications and eventually recovered.

CONCLUSIONS: Due to the atypical clinical presentations, the diagnosis of concurrent invasive disseminated N. farcinica and C. albicans infections might be delayed. A variety of diagnostic testing, including metagenomics next-generation sequencing, can help to identify the pathogen rapidly. Drug susceptibility test can guide the selection and adjustment of antibiotics, which should be in companion with surgical interventions to save lives in affected patients.},
}

Humans
Female
*Nocardia Infections/drug therapy/diagnosis/microbiology/complications
Middle Aged
*Nocardia/isolation & purification
*Candidiasis/drug therapy/diagnosis/microbiology/complications
*Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications
*Glucocorticoids/therapeutic use/adverse effects
Antifungal Agents/therapeutic use
Candida albicans/isolation & purification
Anti-Bacterial Agents/therapeutic use
*Coinfection/microbiology
Prednisone/therapeutic use/adverse effects
Immunocompromised Host

@article {pmid40221512,
year = {2025},
author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y},
title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12568},
pmid = {40221512},
issn = {2045-2322},
support = {82104236//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; },
abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.},
}

Humans
*Tuberculosis, Pulmonary/diagnosis/microbiology
Male
Female
Middle Aged
*Lung/microbiology
*Microbiota/genetics
Adult
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Metagenomics/methods
Bronchoalveolar Lavage Fluid/microbiology
Aged

@article {pmid40221485,
year = {2025},
author = {Wu, Q and Gao, J and Sa, B and Cong, H and Deng, W and Zhang, Y and Zhong, X and Zhang, J and Wang, L and Liu, H and Yan, Y and Zhang, Y and Liu, D and Yan, W},
title = {Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {612},
pmid = {40221485},
issn = {2052-4463},
support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42293292//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Prochlorococcus/genetics ; *Synechococcus/genetics ; *Genome, Bacterial ; Nanopore Sequencing ; *Genome, Viral ; Metagenome ; Pacific Ocean ; Indian Ocean ; Seawater/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Prochlorococcus and Synechococcus are key contributors to marine primary production and play essential roles in global biogeochemical cycles. Despite the ecological importance of these two picocyanobacterial genera, current genomic datasets still lack comprehensive representation of under-sampled ocean regions, associated bacteria and viruses. To address this gap, we used a combination of second- and third-generation sequencing technologies to assemble comprehensive genomic data from 105 Picocyanobacterial enrichment cultures isolated from the Indian Ocean, the South China Sea, and the western Pacific Ocean. This dataset includes 55 Prochlorococcus and 50 Synechococcus genomes with high completeness (>98%) and low contamination (<2%), along with 308 non-redundant associated bacterial genomes derived from 1,457 medium- and high-quality non-cyanobacteria metagenome-assembled genomes (MAGs, completeness ≥50% and contamination ≤10%). Additionally, 2,113 non-redundant viral operational taxonomic units (vOTUs) were derived from a total of 7632 qualified viral contigs. This dataset provides a valuable resource for improving our understanding of the complex interactions among Prochlorococcus, Synechococcus, and their associated bacteria and viruses in marine ecosystems, offering a foundation to study their ecological roles and evolutionary dynamics.},
}

*Prochlorococcus/genetics
*Synechococcus/genetics
*Genome, Bacterial
Nanopore Sequencing
*Genome, Viral
Metagenome
Pacific Ocean
Indian Ocean
Seawater/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40221450,
year = {2025},
author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW},
title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {57},
pmid = {40221450},
issn = {2055-5008},
support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.},
}

*RNA, Ribosomal, 16S/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome
Colitis, Ulcerative/microbiology
DNA, Bacterial/genetics
Republic of Korea
Phylogeny
Feces/microbiology
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid40220806,
year = {2025},
author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q},
title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {142983},
doi = {10.1016/j.ijbiomac.2025.142983},
pmid = {40220806},
issn = {1879-0003},
abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.},
}

@article {pmid40220770,
year = {2025},
author = {Venkatesan, P},
title = {UK launch metagenomic pathogen surveillance programme.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101143},
doi = {10.1016/j.lanmic.2025.101143},
pmid = {40220770},
issn = {2666-5247},
}

@article {pmid40220715,
year = {2025},
author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X},
title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105686},
doi = {10.1016/j.ebiom.2025.105686},
pmid = {40220715},
issn = {2352-3964},
abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.

METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.

FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.

INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.

FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).},
}

@article {pmid40220662,
year = {2025},
author = {Yuan, Q and Ng, C and Goh, SG and Khor, WC and Ong, GHM and Aung, KT and Gin, KY},
title = {Evaluation of public health impact risks associated with bacterial antimicrobial resistome in tropical coastal environments.},
journal = {Water research},
volume = {282},
number = {},
pages = {123621},
doi = {10.1016/j.watres.2025.123621},
pmid = {40220662},
issn = {1879-2448},
abstract = {This study investigated antimicrobial resistance genes (ARGs) and microbial communities in Singapore's tropical coastal environments, comparing natural marine waters with aquaculture sites using metagenomic analysis. Results show consistently low ARG levels in natural ecosystems, whereas aquaculture sites exhibit elevated ARG concentrations, particularly those relevant to human pathogens, with considerably temporal fluctuations likely driven by human activities and seasonal factors. Additionally, aquaculture sites were found to host mobile genetic elements (MGEs) that may facilitate ARG spread, identifying aquaculture as a key reservoir of resistance genes with potential public health implications. These findings underscore distinct prevalence of ARG between natural and managed marine environments and highlight the need for continued surveillance to monitor ARG dynamics in coastal areas. By elucidating the potential for ARGs to transfer from aquaculture environments to the human food chain, this research emphasizes the importance of sustainable aquaculture practices and proactive ARG management strategies to mitigate antimicrobial resistance risks posed by tropical coastal ecosystem.},
}

@article {pmid40220550,
year = {2025},
author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E},
title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.},
journal = {Archives of oral biology},
volume = {175},
number = {},
pages = {106251},
doi = {10.1016/j.archoralbio.2025.106251},
pmid = {40220550},
issn = {1879-1506},
abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.},
}

@article {pmid40220395,
year = {2025},
author = {Zhu, Y and Zhang, X and Tao, W and Yang, S and Qi, H and Zhou, Q and Su, W and Zhang, Y and Dong, Y and Gan, Y and Lei, C and Zhang, A},
title = {Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138221},
doi = {10.1016/j.jhazmat.2025.138221},
pmid = {40220395},
issn = {1873-3336},
abstract = {The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.},
}

@article {pmid40219113,
year = {2025},
author = {Vinskienė, J and Tamošiūnė, I and Andriūnaitė, E and Gelvonauskienė, D and Rugienius, R and Hakim, MF and Stanys, V and Buzaitė, O and Baniulis, D},
title = {Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071045},
pmid = {40219113},
issn = {2223-7747},
support = {S-MIP-22-54//Lietuvos Mokslo Taryba/ ; },
abstract = {In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.},
}

@article {pmid40219101,
year = {2025},
author = {Fouad, N and El-Zayat, EM and Amr, D and El-Khishin, DA and Abd-Elhalim, HM and Hafez, A and Radwan, KH and Hamwieh, A and Tadesse, W},
title = {Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071033},
pmid = {40219101},
issn = {2223-7747},
abstract = {Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.},
}

@article {pmid40218354,
year = {2025},
author = {Zhu, F and Ma, J and Xue, M and Xu, W and Liu, W and Zhou, Y and Liu, M and Fan, Y},
title = {Seasonal and Regional Dynamics of the Intestinal Microbiota in Schizothorax nukiangensis from the Nujiang River.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070961},
pmid = {40218354},
issn = {2076-2615},
support = {2023TD46, 2023TD09//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (CAFS)/ ; },
abstract = {The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected samples of S. nukiangensis across different seasons and regions within the Nujiang River to comprehensively elucidate the diversity and composition of its intestinal microbiota using metagenomic technology. The results indicated that Firmicutes and Proteobacteria predominated at the phylum level, while Priestia, Bacillus, and Aeromonas were the most abundant genera identified. Notably, the relative abundance of these microorganisms varied significantly across different seasons and regions. From autumn through spring and into summer, the predominant microorganisms shifted from Firmicutes to Proteobacteria. Biomarker analysis revealed that Firmicutes (including the class bacilli and the genera Priestia and Bacillus) exhibited a higher relative abundance within the upstream group, where categories related to amino acid metabolism and carbohydrate metabolism were significantly enriched. Conversely, Proteobacteria (including several potential pathogens, such as Saezia, Pantoea, Lelliotia, and Aeromonas genera) showed an increased relative abundance within downstream groups, where disease-related categories exhibited significant enrichment. Our findings significantly enhance our understanding of how S. nukiangensis adapts to its environment, providing valuable data support for the conservation of S. nukiangensis and for ecological security assessment of the Nujiang River.},
}

@article {pmid40218343,
year = {2025},
author = {Ajmi, N and Duman, M and Coskun, B and Esen, C and Sonmez, O and Tasci, G and Coskuner-Weber, O and Ay, H and Yoyen-Ermis, D and Yibar, A and Desbois, AP and Saticioglu, IB},
title = {Unraveling Genomic and Pathogenic Features of Aeromonas ichthyocola sp. nov., Aeromonas mytilicola sp. nov., and Aeromonas mytilicola subsp. aquatica subsp. nov.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070948},
pmid = {40218343},
issn = {2076-2615},
support = {TGA-2024-1797 and 124Z735//The Research Fund of Bursa Uludag University and TÜBİTAK/ ; },
abstract = {The Gram-negative genus Aeromonas contains diverse bacterial species that are prevalent in aquatic environments. This present study describes three novel Aeromonas strains: A. ichthyocola sp. nov. A-5[T] and A. mytilicola subsp. aquatica subsp. nov. A-8[T] isolated from rainbow trout (Oncorhynchus mykiss), and A. mytilicola sp. nov. A-7[T] isolated from mussels (Mytilus galloprovincialis), respectively. Genomic analyses revealed that strains A-5[T] and A-7[T] shared the highest 16S rRNA gene sequence similarity with A. rivipollensis P2G1[T] (99.7% and 99.8%, respectively), while strain A-8[T] exhibited 99.7% identity with A. media RM[T]. Together with morphological, physiological, and biochemical data, genome-based analyses provided additional evidence for species differentiation. Digital DNA-DNA hybridization (dDDH; 56.8-65.9%) and average nucleotide identity (ANI; 94.2-95.7%) values fell below the species delineation thresholds, confirming that these isolates represent distinct taxa. Pathogenicity assays using greater wax moth (Galleria mellonella) larvae demonstrated strain-specific virulence profiles. Further genomic analyses identified biosynthetic gene clusters for nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), which often have roles in secondary metabolite production. Ecological analyses, based on genomic comparisons and metagenomic database searches, revealed the adaptability of the strains to diverse habitats, including freshwater, wastewater, and activated sludge. Based on the genetic and phenotypic data, the novel taxa Aeromonas ichthyocola sp. nov. A-5ᵀ (LMG 33534ᵀ = DSM 117488ᵀ), Aeromonas mytilicola sp. nov. A-7ᵀ (LMG 33536ᵀ = DSM 117490ᵀ), and Aeromonas mytilicola subsp. aquatica subsp. nov. A-8ᵀ (LMG 33537ᵀ = DSM 117493ᵀ) are proposed.},
}

@article {pmid40217586,
year = {2025},
author = {Komoróczy, B and Váncsa, S and Váradi, A and Hegyi, P and Vágási, V and Baradács, I and Szabó, A and Nyirády, P and Benkő, Z and Ács, N},
title = {Optimal Aspirin Dosage for the Prevention of Preeclampsia and Other Adverse Pregnancy Outcomes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072134},
pmid = {40217586},
issn = {2077-0383},
abstract = {Background/Objectives: This systematic review and meta-analysis aimed to determine the effectiveness of different aspirin dosages in preventing preeclampsia and its effect on other pregnancy-associated conditions. Methods: A comprehensive search of three databases (Pubmed, Embase, and Cochrane Library) was conducted for randomized controlled trials without time interval criteria, comparing aspirin at various doses with placebo or no specific preeclampsia prophylaxis. Eligible randomized controlled trials (RCTs) examined pregnant women receiving aspirin at any dose and time during their pregnancy, while the control group received a placebo, or placebo and a different dose of aspirin, or no specific preeclampsia prevention. No exclusion criteria were established regarding the population, study size, study site, or length of aspirin prophylaxis. Studies examining additional preventive medication (such as low-molecular-weight heparin) compared to aspirin without a placebo group were excluded. For all outcomes, the risk ratios (RRs) and mean differences (MDs) with 95% confidence intervals (CIs) were calculated. Meta-regression was performed to examine the relation between aspirin dosage and preeclampsia. Results: Based on the analysis of 31 studies involving 28,318 pregnancies and 20 studies involving 26,551 pregnancies, the early initiation of aspirin significantly reduced the overall incidence of preeclampsia (RR = 0.63, CI: 0.47-0.84) and perinatal death risk (RR = 0.82, CI: 0.72-0.93), respectively. Based on our meta-regression model, we could not establish a dose-dependent correlation between aspirin dosage and the risk of preeclampsia. Conclusions: Early-initiated aspirin prophylaxis is effective in preventing preeclampsia, without raising the incidence of placental abruption or increasing the amount of peripartum bleeding. No specific dose was superior to others; thus, further research should explore higher doses and focus on preterm preeclampsia, maternal-fetal complications, and bleeding.},
}

@article {pmid40217292,
year = {2025},
author = {Diop, K and Mbaye, B and Nili, S and Filin, A and Benlaifaoui, M and Malo, J and Renaud, AS and Belkaid, W and Hunter, S and Messaoudene, M and Lee, KA and Elkrief, A and Routy, B},
title = {Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {21},
pmid = {40217292},
issn = {1757-4749},
abstract = {BACKGROUND: The gut microbiome represents a novel biomarker for melanoma and non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Gut microbiome metagenomics profiling studies of patients treated with immunotherapy identified bacteria associated with ICI efficacy, while others have been linked to resistance. However, limitations of metagenomics sequencing, such as complex bioinformatic processing requirements, necessity of a threshold for positive detection, and the inability to detect live organisms, have hindered our ability to fully characterize the gut microbiome. Therefore, combining metagenomics with high-throughput culture-based techniques (culturomics) represents an ideal strategy to fully characterize microbiome composition to more robustly position the microbiome as a biomarker of response to ICI.

METHODS: We performed culturomics using fecal samples from 22 patients from two academic centres in Canada and the United Kingdom with NSCLC and cutaneous melanoma treated with ICI (cancer group), comparing their microbiome composition to that of 7 healthy volunteers (HV), along with matching shotgun metagenomics sequencing.

RESULTS: For culturomics results, 221 distinct species were isolated. Among these 221 distinct species, 182 were identified in the cancer group and 110 in the HV group. In the HV group, the mean species richness was higher compared to the cancer group (34 vs. 18, respectively, p = 0.002). Beta diversity revealed separate clusters between groups (p = 0.004). Bifidobacterium spp. and Bacteroides spp. were enriched in HV, while cancer patients showed an overrepresentation of Enterocloster species, as well as Veillonella parvula. Next, comparing cancer patients' clinical outcomes to ICI, we observed that among the 20 most abundant bacteria present in non-responder patients, 2 belonged to the genus Enterocloster, along with an enrichment of Hungatella hathewayi and Cutibacterium acnes. In contrast, responders to ICI exhibited a predominance of Bacteroides spp. In NSCLC patients, metagenomics analysis revealed that of the 154 bacteria species isolated through culturomics, 61/154 (39%) were also identified by metagenomics sequencing. Importantly, 94 individual species were uniquely detected by culturomics.

CONCLUSION: These findings highlight that culturomics and metagenomics can serve as complementary tools to characterize the microbiome in patients with cancer. This integrated approach uncovers specific microbiome signatures that differentiate HV from cancer patients, and identifies specific species associated with therapy response and resistance.},
}

@article {pmid40216789,
year = {2025},
author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG},
title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3469},
pmid = {40216789},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; },
abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Metagenomics/methods
*Colitis, Ulcerative/therapy/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Female
Placebos
Adult
Middle Aged

@article {pmid40216686,
year = {2025},
author = {Fan, Q and Zhang, Y and Lian, J and Liang, D and Yu, J and Liu, X and Zhang, N},
title = {Screening and community succession and functional prediction of high-efficiency degradation microbial communities for rice straw at low-temperature.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {20},
pmid = {40216686},
issn = {1433-4909},
support = {2023YFD2100803//National Key R&D Programme Project of China/ ; },
mesh = {*Oryza/microbiology/metabolism ; *Microbiota ; *Cold Temperature ; Lignin/metabolism ; },
abstract = {Traditional straw return relies on microbial degradation, but cold winters delay it, risking crops. Therefore, a microbial community adapted to rice straw degradation in cold regions was constructed by restrictive consecutively sub-cultured under low-temperature limitations. The capabilities of the microbial community, such as adaptability, stability, and degradation power, were evaluated by analyzing straw degradation features, Characterization experiments and lignocellulose enzyme activities across multiple generations. 16S amplicon sequencing was used to monitor the changes in its structure over generations. Metagenomic sequencing uses CAZy and KEGG to classify gene functions. The results showed that the highest degradation efficiencies and enzyme activities were observed in the E and F generations, dominated by Proteobacteria, Bacteroidetes, and Fungi The stable microbial community was designated as LJ-7. Metagenomic analysis showed that functional genes of LJ-7 were mainly concentrated in glycoside hydrolase (GHs) and glycosyl transferase (GTs) related genes which contained many fiber and lignin-degrading enzyme genes. It is speculated that microbial enzymes degrade straw by breaking down its complex structure into monosaccharides or metabolizing quinone compounds for energy. This experiment successfully screened a microbial community capable of degrading rice straw at low temperatures, thus offering novel research insights and pathways for straw degradation in cold conditions.},
}

*Oryza/microbiology/metabolism
*Microbiota
*Cold Temperature
Lignin/metabolism

@article {pmid40216167,
year = {2025},
author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW},
title = {Investigating the bidirectional interactions between senotherepeutic agents and human gut microbiota.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107098},
doi = {10.1016/j.ejps.2025.107098},
pmid = {40216167},
issn = {1879-0720},
abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.},
}

@article {pmid40216056,
year = {2025},
author = {Liu, S and Li, J and Zhang, Z and Tuo, J and Zhang, Q and Zhou, J and Liu, P and Zhang, XX},
title = {Exploring phylogenetic diversity of antibiotic resistance genes in activated sludge: A host and genomic location perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121588},
doi = {10.1016/j.envres.2025.121588},
pmid = {40216056},
issn = {1096-0953},
abstract = {Antibiotic resistance has emerged as a significant global public health issue. The environmental behaviors of antibiotic resistance genes (ARGs), such as their persistence and horizontal transfer, have been extensively investigated. However, the genetic diversity characteristics of ARGs remain underexplored, which limits a comprehensive analysis of their roles in the environment. In this study, we examined the genetic diversity of ARGs in activated sludge from 44 wastewater treatment plants in five countries. Most ARGs detected in activated sludge possessed multiple variants, with a median of 48. The number of variants of gd-ARGs varied among different resistance mechanisms and ARG types. The number of potential variants of ARGs was strongly correlated with host diversity. Pseudomonas spp. and Klebsiella pneumoniae, identified as pathogenic bacteria, harbored multiple ARGs and had the most variants. Most ARG subtypes on plasmids and chromosomes showed divergent evolution. Molecular docking of AdeH proteins revealed that genomic location affects tetracycline binding energy. The findings underscore the intricate interplay between genetic variation and environmental adaptation in ARGs, offering a novel perspective on the spread of antibiotic resistance.},
}

@article {pmid40215877,
year = {2025},
author = {Saeed, M and Al-Khalaifah, H and Al-Nasser, A and Al-Surrayai, T},
title = {Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105130},
doi = {10.1016/j.psj.2025.105130},
pmid = {40215877},
issn = {1525-3171},
abstract = {The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.},
}

@article {pmid40215446,
year = {2025},
author = {Allioni, GA and de Souza, GSM and Labello, JH and Torres, GSA and da Costa, DL and Casal, YR and Duarte-Neto, AN and Dorlass, EG and Amgarten, D and Malta, FM and Doi, AM and Peres Fernandes, GB and Rebello Pinho, JR and Vieira, GT and Castro, LH and Guedes, BF},
title = {Chronic Dengue Virus Encephalitis: A Case Study and Metagenomic Analysis.},
journal = {Neurology(R) neuroimmunology & neuroinflammation},
volume = {12},
number = {3},
pages = {e200394},
doi = {10.1212/NXI.0000000000200394},
pmid = {40215446},
issn = {2332-7812},
mesh = {Humans ; Male ; *Dengue/complications/diagnosis ; Young Adult ; Metagenomics ; *Dengue Virus/genetics ; *Encephalitis, Viral/virology/pathology/diagnosis/complications ; Chronic Disease ; },
abstract = {BACKGROUND AND OBJECTIVES: Dengue virus (DENV) infection can cause acute encephalitis. Chronic encephalitis with progressive dementia is rarely reported.

METHODS: We present a case of chronic encephalitis with rapidly progressive dementia, in which a potential DENV brain infection was identified with brain tissue metagenomic next-generation sequencing. Brain pathology and molecular diagnosis are also presented.

RESULTS: A 20-year-old man from SP, Brazil, presented with rapidly progressive dementia, speech apraxia, and apathy in June 2022. By January 2023, cognitive testing showed severe global impairment (MMSE score of 18/30). MRI revealed white matter abnormalities and atrophy; CSF analysis disclosed a mild lymphocytic pleocytosis, mildly elevated protein levels, and positive CSF oligoclonal bands. Despite extensive testing ruling out common infectious and inflammatory causes, the patient's condition worsened with executive dysfunction, language impairment, tremors, and myoclonus. In August 2023, a brain biopsy and next-generation sequencing identified DENV-1 genotype V, linked to Brazilian sequences from 2000 to 2022.

DISCUSSION: This case highlights a challenging instance of encephalitis with unknown etiology, where metagenomic analysis detected DENV-1 RNA in brain tissue, suggesting a possible cause.},
}

Humans
Male
*Dengue/complications/diagnosis
Young Adult
Metagenomics
*Dengue Virus/genetics
*Encephalitis, Viral/virology/pathology/diagnosis/complications
Chronic Disease

@article {pmid40215391,
year = {2025},
author = {Gómez, Á and Rodríguez-Largo, A and Pérez, E and García Freire, S and Hundehege, C and Berberich, E and Luján, L and Cortés, D},
title = {Clinicopathological progression and molecular characterization of intestinal dilatation syndrome in commercial brown layers.},
journal = {Veterinary pathology},
volume = {},
number = {},
pages = {3009858251331106},
doi = {10.1177/03009858251331106},
pmid = {40215391},
issn = {1544-2217},
abstract = {Intestinal dilatation syndrome (IDS) is a poorly described condition affecting layers and breeder hens globally. Its prevalence is increasing, particularly in free-range systems, but the cause remains unknown. This retrospective study examined 35 hens from 3 flocks: free-range flock A (n = 20) and enriched-caged flock B (n = 5), both affected by IDS, and enriched-caged flock C (n = 10), with no history of IDS. Clinicopathological studies were performed on these hens, and metagenomic analysis was conducted on the proventriculus and jejunum of hens from flock A (n = 2) and flock C (n = 2). Based on clinical signs and lesions, 3 progressive stages of IDS were identified. In the first stage, although hens were without clinical signs, proventricular dilatation and lymphoplasmacytic and heterophilic jejunitis and duodenitis were observed. The second stage was marked by cachexia, pale and small combs and wattles, and severe egg production drop. Jejunal dilatation was observed, with microscopic evidence of necrotic, lymphoplasmacytic and heterophilic jejunitis; ganglioneuritis; and mineralization of the jejunal nervous plexuses and subserosal ganglia. In the third stage, spontaneous death occurred due to jejunal volvulus and vascular involvement. Affected hens (stage 2) also exhibited elevated cloacal temperatures (>0.9°C) and marked heterophilia. Metagenomic analysis identified sequences consistent with Megrivirus C in IDS-affected hens and a disruption of the gut microbiota, with increased abundance of Fusobacterium mortiferum and Megamonas funiformis. In conclusion, this study describes in detail the clinicopathological progression of the IDS and suggests that Megrivirus C, in combination with opportunistic intestinal bacteria, could play a role in the pathogenesis of this disease.},
}

@article {pmid40214404,
year = {2025},
author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, MØ and Rudi, K},
title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12464},
pmid = {40214404},
issn = {1520-5851},
abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.},
}

@article {pmid40214102,
year = {2025},
author = {Cernooka, E and Zrelovs, N and Kazaks, A},
title = {C-terminal anchor endolysins-proposing a third class of tailed bacteriophage endolysins.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70042},
pmid = {40214102},
issn = {1873-3468},
support = {lzp-2021/1-0050//Latvijas Zinātnes Padome/ ; },
abstract = {Endolysins-enzymes produced by tailed bacteriophages to degrade bacterial cell walls-have traditionally been classified as canonical or signal-anchor-release (SAR) endolysins. However, analysis of expanding viral (meta)genomic data has revealed a third class, which we designate as C-terminal anchor (CTA) endolysins. These enzymes feature an N-terminal enzymatic domain, a C-terminal transmembrane domain, and typically lack signal sequences, distinguishing them from SAR endolysins. CTA endolysins span all known enzymatic activities and exhibit diverse architectures, though most have a single transmembrane helix and an N-out, C-in topology, consistent with periplasmic activity. While their functional mechanisms remain to be elucidated, our findings suggest that CTA endolysins are nearly as prevalent as SAR endolysins and represent a distinct, previously unrecognized branch of the endolysin world.},
}

@article {pmid40213331,
year = {2025},
author = {Wang, X and Zhao, Z and Zhao, F and Li, Y and Liang, Y and Zhou, R and Shen, S and Yu, J and Liu, W and Menghe, B},
title = {Dual-omics strategy for selecting optimal fermentation strains in traditional koumiss production.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102407},
pmid = {40213331},
issn = {2590-1575},
abstract = {Koumiss is a fermented mare's milk beverage with a long history. However, due to the current lack of specialized starters, the product quality is unstable. Therefore, we used dual-omics combined with pure culture technology to screen out strains with excellent fermentation performance for koumiss. The results showed that: (1) The dominant species in koumiss were mainly Lactobacillus and Lactococcus, and metabolites such as arachidonic acid and ascorbic acid were significantly enriched in koumiss. (2) There was a significant correlation between specific microbial species and metabolites. (3) Through preliminary screening using experiments such as milk-based curdling experiments and acid resistance tests, and then rescreening through fermentation tests, five strains with excellent fermentation characteristics were screened out. They are Lacticaseibacillus paracasei SXM-5, Lactobacillus kefianofaciens MGE42-8, Lactobacillus helveticus CFS12-11-1, Saccharomyces cerevisiae PFD-2, and Kluyveromyces marxianus PYM-1. The screened strains supply microbial resources for koumiss products and boost the development of milk beverages.},
}

@article {pmid40212922,
year = {2025},
author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H},
title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71221},
pmid = {40212922},
issn = {2045-7758},
abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.},
}

@article {pmid40212663,
year = {2025},
author = {Natasha, A and Pye, SE and Park, K and Rajoriya, S and Yang, I and Park, J and Pangestu, HS and Kim, J and Oh, Y and López, CB and Song, JW and Kim, WK},
title = {Detection and characterization of Langya virus in Crocidura lasiura (the Ussuri white-toothed shrew), Republic of Korea.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {101017},
pmid = {40212663},
issn = {2352-7714},
abstract = {Langya virus (LayV) is the only documented zoonotic agent within the shrew borne Parahenipavirus genus. Other Parahenipavirus species, including Gamak virus and Daeryeong virus, have been discovered in the Republic of Korea, highlighting the prevalence of this genus in the region. We retrospectively analyzed metagenomic next-generation sequencing of two Crocidura lasiura (the Ussuri white-toothed shrew) kidney samples from 2017, followed by paramyxovirus screening of 24 kidney samples from the same species collected in 2023. The LayV positivity rate was 12.5 % (3 of 24). Amplicon-based sequencing was subsequently developed to obtain the complete viral sequences. Five complete genomes of Langya virus Korea (LayV KOR) were identified: two from 2017 samples and three from 2023 samples. LayV KOR exhibited approximately 80 % and 95.5 % homology at the nucleotide and amino acid levels, respectively. Phylogenetic analysis underscored the close relationship between LayV KOR and LayV from China. This study represents the first detection of LayV complete sequences in shrews outside of China.},
}

@article {pmid40212081,
year = {2024},
author = {Tuerhongjiang, G and Guo, M and Qiao, X and Liu, J and Xi, W and Wei, Y and Liu, P and Lou, B and Wang, C and Sun, L and Yuan, X and Liu, H and Xiong, Y and Ma, Y and Li, H and Zhou, B and Li, L and Yuan, Z and Wu, Y and She, J},
title = {Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.},
journal = {Small science},
volume = {4},
number = {9},
pages = {2300337},
pmid = {40212081},
issn = {2688-4046},
abstract = {AIMS: Heart failure (HF) is associated with profound changes in cardiac metabolism. At present, there is still a lack of relevant research to explore the key microbiome and their metabolites affecting the progression of HF. Herein, the interaction of gut microbiota and circulating free fatty acid (FFA) in HF patients and mice is investigated.

METHODS AND RESULTS: In HF patients, by applying metagenomics analysis and targeted FFA metabolomics, enriched abundance of Clostridium sporogenes (C.sp) in early and late stage of HF patients, which negatively correlated to saturated free fatty acid (SFA) levels, is identified. KEGG analysis further indicates microbiota gene enrichment in FFA degradation in early HF, and decreased gene expression in FFA synthesis in late HF. In HF mice (C57BL/6J) induced by isoproterenol (ISO), impaired intestinal permeability is observed, and decreased fecal C.sp and increased SFA are further validated. At last, by supplementing C.sp to ISO-induced HF mice, the cardiac function, fibrosis, and myocardial size are partially rescued, together with decreased circulating SFA levels.

CONCLUSIONS: Clostridium abundance is increased in HF, compensating cardiac function deterioration via downregulation of circulating SFA levels. The results demonstrate that the gut microbiota-SFA axis plays an important role in HF protection, which may provide a strategic advantage for the probiotic therapy development in HF.},
}

@article {pmid40211978,
year = {2025},
author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ},
title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf149},
pmid = {40211978},
issn = {1477-4054},
support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China Project/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //Westlake University Industries of the Future Research Funding/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Models, Genetic ; Metagenome ; Algorithms ; },
abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.},
}

*Metagenomics/methods
Humans
*Models, Genetic
Metagenome
Algorithms

@article {pmid40211688,
year = {2025},
author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX},
title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17751},
doi = {10.1111/mec.17751},
pmid = {40211688},
issn = {1365-294X},
support = {2021YFD1400900//National Key R&D Program of China/ ; },
abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.},
}

@article {pmid40211685,
year = {2025},
author = {Kim, JW and Choi, EC and Lee, KJ},
title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.},
journal = {Osong public health and research perspectives},
volume = {},
number = {},
pages = {},
doi = {10.24171/j.phrp.2024.0319},
pmid = {40211685},
issn = {2210-9099},
abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.

METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.

RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.

CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.},
}

@article {pmid40211121,
year = {2025},
author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, É and Pombo, GDV and Santana, MHA},
title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {359},
pmid = {40211121},
issn = {1471-2164},
support = {2021/03265-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Animals
Cattle
Female
*Metabolomics/methods
Pregnancy
*Metabolic Networks and Pathways
*Metagenomics/methods
Male
Metabolome
Rumen/microbiology
Microbiota
*Prenatal Nutritional Physiological Phenomena
*Animal Nutritional Physiological Phenomena
Gastrointestinal Microbiome

@article {pmid40210868,
year = {2025},
author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA},
title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3434},
pmid = {40210868},
issn = {2041-1723},
support = {1R01DK140854//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; },
abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.},
}

Animals
*Bile Acids and Salts/metabolism
Humans
Gastrointestinal Microbiome/genetics
Mice, Knockout
Mice
Amidohydrolases/metabolism/genetics
Hydrolysis
Acyltransferases/genetics/metabolism
Taurocholic Acid/pharmacology/metabolism
Disease Models, Animal
*Colitis/metabolism/pathology/microbiology
Male
Inflammatory Bowel Diseases/metabolism/microbiology
Female
Mice, Inbred C57BL
Clostridiales/metabolism/genetics
Crohn Disease/metabolism/microbiology/genetics

@article {pmid40210629,
year = {2025},
author = {Park, JW and Yun, YE and Cho, JA and Yoon, SI and In, SA and Park, EJ and Kim, MS},
title = {Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3427},
pmid = {40210629},
issn = {2041-1723},
support = {2020R1A5A8017671//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009664//National Research Foundation of Korea (NRF)/ ; 2018R1D1A3B07050366//National Research Foundation of Korea (NRF)/ ; 2021R1F1A1064222//National Research Foundation of Korea (NRF)/ ; },
mesh = {Humans ; *Virome/genetics ; *Vegetables/virology ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Plant Leaves/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; },
abstract = {Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 10[7] viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.},
}

Humans
*Virome/genetics
*Vegetables/virology
*Gastrointestinal Microbiome/genetics
Feces/virology
*Plant Leaves/virology
Metagenome
Bacteriophages/genetics/classification/isolation & purification
Phylogeny
Metagenomics

@article {pmid40210439,
year = {2025},
author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS},
title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279543.124},
pmid = {40210439},
issn = {1549-5469},
abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.},
}

@article {pmid40210403,
year = {2025},
author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH},
title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.},
journal = {Food microbiology},
volume = {130},
number = {},
pages = {104780},
doi = {10.1016/j.fm.2025.104780},
pmid = {40210403},
issn = {1095-9998},
mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; },
abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.},
}

*Vitis/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Fungi/classification/genetics/isolation & purification
*Plant Leaves/microbiology
*Fruit/microbiology
Wine/microbiology/analysis
South Africa

@article {pmid40210162,
year = {2025},
author = {Gao, X and Yuan, S and Li, X and Xing, W},
title = {Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126213},
doi = {10.1016/j.envpol.2025.126213},
pmid = {40210162},
issn = {1873-6424},
abstract = {Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5% w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1,301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.},
}

@article {pmid40210157,
year = {2025},
author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY},
title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126209},
doi = {10.1016/j.envpol.2025.126209},
pmid = {40210157},
issn = {1873-6424},
abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58%) and Acidobacteria (6.04%) were identified as the dominant phyla and Thiobacillus (1.84%) and Lysobacter (0.99%) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r>0.7, p<0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p<0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.},
}

@article {pmid40209695,
year = {2025},
author = {Yamane, T and Masaoka, T and Ishii, C and Masuoka, H and Suda, W and Kurokawa, S and Kishimoto, T and Mikami, Y and Fukuda, S and Kanai, T},
title = {Factors contributing to the efficacy of fecal microbiota transplantation for diarrhea-dominant functional bowel disorders.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-22},
doi = {10.1159/000545183},
pmid = {40209695},
issn = {1421-9867},
abstract = {INTRODUCTION: In cases of effective fecal microbiota transplantation (FMT) for irritable bowel syndrome (IBS), donor feces have been observed to be enriched in Bifidobacterium spp., and FMT for functional bowel disease improved psychiatric symptoms. Although intestinal dysbiosis has received attention as one of the pathophysiologies of IBS, the efficacy of FMT for IBS has not yet been established. In this study, we performed a post-hoc analysis of the efficacy of FMT, focusing on metabolites in donor feces.

METHODS: FMT was performed in 12 patients, 8 with refractory diarrhea-predominant IBS and 4 with functional diarrhea (FDr), who were refractory to medical therapy. The donors were family members within the second degree of kinship and were different for each transplant. Fecal characteristics were evaluated before and 12 weeks after transplantation using the Bristol stool scale (BS). BS scores of 3-5 at 12 weeks after transplantation were considered indicative of responders, while BS scores of 6 and 7 were indicative of non-responders. Metagenomic and metabolomic analyses of all 12 donor fecal samples were performed to compare the responder and non-responder groups.

RESULTS: Before transplantation, all 12 patients had BS scores of 6-7, but 12 weeks after transplantation, 6 were in the responder group and 6 were in the non-responder group. Metagenomic analysis showed that effective donor feces contained significantly higher levels of Prevotella than ineffective donor feces. Metabolomic analysis showed that effective donor feces contained significantly higher levels of propionate and butyrate and significantly lower lactate levels than ineffective donor feces.

CONCLUSION: Propionate-, butyrate-, or Prevotella-rich donor feces may contribute to successful FMT in patients with diarrhea-dominant functional gastrointestinal disorders.},
}

@article {pmid40209677,
year = {2025},
author = {Lin, Y and Lau, HC and Liu, C and Ding, X and Sun, Y and Rong, J and Zhang, X and Wang, L and Yuan, K and Miao, Y and Wu, WK and Wong, SH and Sung, JJ and Yu, J},
title = {Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact.},
journal = {Cell host & microbe},
volume = {33},
number = {4},
pages = {589-601.e3},
doi = {10.1016/j.chom.2025.03.012},
pmid = {40209677},
issn = {1934-6069},
mesh = {Humans ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Gastrointestinal Microbiome ; Cohort Studies ; Metagenome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Aged ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor ; ROC Curve ; },
abstract = {Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.},
}

Humans
*Feces/microbiology
*Colorectal Neoplasms/microbiology/pathology/diagnosis
*Gastrointestinal Microbiome
Cohort Studies
Metagenome
Male
Female
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Aged
Fusobacterium nucleatum/isolation & purification
Biomarkers, Tumor
ROC Curve

@article {pmid40209409,
year = {2025},
author = {Cheng, Y and Zheng, X and Jiang, Y and Xiao, Q and Luo, Q and Ding, Y},
title = {Key genes and microbial ecological clusters involved in organophosphate ester degradation in agricultural fields of a typical watershed in southwest China.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138076},
doi = {10.1016/j.jhazmat.2025.138076},
pmid = {40209409},
issn = {1873-3336},
abstract = {Organophosphate esters (OPEs) are widely used as flame retardants and plasticizers, and they have raised global concern due to their persistence, bioaccumulation, and potential toxicity. However, OPE contamination characteristics and microbial degradation mechanisms in agricultural soils remain poorly understood. This study investigated agricultural soils from the riparian zone of the Anning River Basin in southwest China. The concentrations of 12 OPEs were determined using gas chromatography-tandem mass spectrometry. The results revealed that the total OPE concentration was moderate, with triethyl phosphate being the most abundant compound. Metagenomic techniques and Bayesian linear regression analysis were employed in combination with the Kyoto Encyclopedia of Genes and Genomes database to identify potential degradation pathways for triethyl phosphate and tris (2-chloroethyl) phosphate. The phoA, phoB, phoD, and glpQ genes, which encode phosphatases, catalyze ester bond cleavage, thereby facilitating the degradation of OPEs. Further microbial interaction network analysis identified core OPE-degrading microorganisms, including Pimelobacter simplex, Nocardioides sp. JS614, Nocardioides daphniae, and Methylocystis heyeri. Additionally, neutral community models indicated that environmental selection drives microbial community structure. In conclusion, this study provides an in-depth understanding of OPE contamination and its microbial degradation mechanisms in agricultural soils, offering theoretical insights for pollution management and remediation strategies.},
}

@article {pmid40209382,
year = {2025},
author = {Su, C and Kang, J and Liu, S and Li, C},
title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144192},
doi = {10.1016/j.foodchem.2025.144192},
pmid = {40209382},
issn = {1873-7072},
abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.},
}

@article {pmid40209373,
year = {2025},
author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J},
title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144178},
doi = {10.1016/j.foodchem.2025.144178},
pmid = {40209373},
issn = {1873-7072},
abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.},
}

@article {pmid40209228,
year = {2025},
author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ},
title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10888},
pmid = {40209228},
issn = {1520-5851},
abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.},
}

@article {pmid40208400,
year = {2025},
author = {Bourgon, N and Padioleau, I and Guibon, J and Fourgeaud, J and Lermine, A and Meurice, G and Guilleminot, T and Bussieres, L and Leruez-Ville, M and Dupont, JM and Ville, Y},
title = {Metagenomic analysis of NIPT raw data suggests high negative predictive value for congenital cytomegalovirus infection screening.},
journal = {Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/uog.29221},
pmid = {40208400},
issn = {1469-0705},
}

@article {pmid40207985,
year = {2025},
author = {Zhang, Q and Wang, Q and Zhang, F and Li, X and Sun, Y and Wang, L and Zhang, Z},
title = {Diagnostic value of metagenomic next-generation sequencing in patients with osteoarticular infections: a prospective study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0106424},
doi = {10.1128/spectrum.01064-24},
pmid = {40207985},
issn = {2165-0497},
abstract = {Due to the limits of traditional microbiological methods and the complexity of osteoarthritis pathogens, only a few pathogens can be detected. We evaluated metagenomic next-generation sequencing (mNGS) for detecting pathogens in osteoarthritis infection samples. We prospectively included 150 patients with osteoarthritis infection who visited the Orthopedics Department of Shandong Provincial Public Health Center from 2023 to 2024, including 124 cases of primary osteoarthritis (POI) and 26 cases of invasive osteoarthritis (IOI). The most common pathogenic bacteria were Mycobacterium tuberculosis complex, Staphylococcus aureus, and Brucella melitensis. mNGS (75.33%) significantly improved the detection of pathogens in osteoarticular infections compared to conventional tests (CT) methods (36.67%). mNGS could detect a wider spectrum of pathogens compared to CT methods, especially for mixed and rare pathogens. The treatment strategies for patients with osteoarthritis infection could be adjusted based on the results obtained from mNGS testing. Furthermore, the abundance of M. tuberculosis complex, B. melitensis, and Staphylococcus epidermidis was significantly correlated with clinical indicators.IMPORTANCEIdentifying the microorganisms responsible for osteoarthritis infection could help with early diagnosis and treatment. In this study, we compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and CT methods in patients with osteoarthritis infection and found that mNGS had a higher microbial detection rate and a broader spectrum of pathogens (especially for mixed pathogens). This study demonstrates that mNGS is an ideal tool for detecting pathogens in patients with osteoarticular infections.},
}

@article {pmid40207938,
year = {2025},
author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ},
title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.},
journal = {mBio},
volume = {},
number = {},
pages = {e0069925},
doi = {10.1128/mbio.00699-25},
pmid = {40207938},
issn = {2150-7511},
abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.},
}

@article {pmid40207877,
year = {2025},
author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W},
title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70336},
doi = {10.1002/jmv.70336},
pmid = {40207877},
issn = {1096-9071},
support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; },
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; Adult ; Aged ; Longitudinal Studies ; },
abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.},
}

Humans
*Virome
*Gastrointestinal Microbiome
*Gout/virology
Male
Middle Aged
Feces/virology
Female
*Metagenome
Metagenomics
*Viruses/classification/genetics/isolation & purification
Adult
Aged
Longitudinal Studies

@article {pmid40207279,
year = {2025},
author = {Teng, NM and Malfettone, A and Dalby, MJ and Kiu, R and Seki, D and Robinson, T and Gion, M and Bermejo, B and Pérez-García, JM and Prat, A and Vázquez, RM and Llombart-Cussac, A and Curigliano, G and Schmid, P and Barroso-Sousa, R and Mancino, M and Shimizu, E and Rodríguez-Morató, J and Mina, L and Hall, LJ and Robinson, SD and Cortés, J},
title = {Profiling the gut and oral microbiota of hormone receptor-positive, HER2-negative metastatic breast cancer patients receiving pembrolizumab and eribulin.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {4},
pmid = {40207279},
issn = {2771-5965},
abstract = {Aim: Changes in host-associated microbial communities (i.e., the microbiota) may modulate responses to checkpoint blockade immunotherapy. In the KELLY phase II study (NCT03222856), we previously demonstrated that pembrolizumab [anti-programmed cell death protein 1 (PD-1)] combined with eribulin (plus microtubule-targeting chemotherapy) showed encouraging antitumor activity in patients with hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (mBC) who had received prior treatments. Methods: A total of 58 fecal and 67 saliva samples were prospectively collected from a subset of 28 patients at baseline (BL), after three treatment cycles, and end of treatment. Shotgun metagenomics, 16S rRNA gene amplicon sequencing, and bioinformatics and statistical approaches were used to characterize fecal and oral microbiota profiles. Results: Treatment caused no substantial perturbations in gut or oral microbiota, suggesting minimal drug-related microbial toxicity. Bacteroides and Faecalibacterium were the dominant gut microbiota genera, while Prevotella and Streptococcus were present in both oral and gut samples, highlighting potential gut-oral microbial interactions. Additionally, clinical benefit (CB) appeared to be associated with gut-associated Bacteroides fragilis (B. fragilis) and a BL oral abundance of Streptococcus ≥ 30%. Notably, B. fragilis NCTC 9343 supernatant induced dose-dependent lactate dehydrogenase (LDH) release from the MCF-7 (HR-positive/HER2-negative) BC cell line. Conclusion: These findings suggest that specific gut and oral microbiota may modulate the effectiveness of combinatory anti-BC therapies, potentially through the action of microbial metabolites.},
}

@article {pmid40207161,
year = {2025},
author = {Helmi, NR},
title = {Exploring the diversity and antimicrobial potential of actinomycetes isolated from different environments in Saudi Arabia: a systematic review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568899},
pmid = {40207161},
issn = {1664-302X},
abstract = {The increasing prevalence of antimicrobial resistance (AMR) presents a significant global health challenge, underscoring the urgent need for novel antimicrobial agents. Actinomycetes, particularly Streptomyces species, are well known for synthesizing bioactive compounds with antibacterial, antifungal, and antiviral properties. This review explores the diversity and antimicrobial potential of actinomycetes from Saudi Arabia's unique ecosystems, including terrestrial (soil, rhizosphere), aquatic (marine, freshwater), extreme (deserts, caves, hot springs, mountains, and mangroves), and other unique environments. The adaptation of these microorganisms to harsh environmental conditions has driven the evolution of unique strains with enhanced biosynthetic capacities. Several studies have demonstrated their antimicrobial efficacy against multidrug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Pseudomonas aeruginosa, and Candida albicans. However, challenges in actinomycete research persist, including difficulties in culturing rare strains, limited genomic characterization, and high production costs. Recent advancements, such as genome mining, metagenomics, AI-driven bioinformatics, and CRISPR-based gene activation, offer promising avenues for unlocking novel antimicrobial compounds. Additionally, synthetic biology, advanced fermentation technologies, and nanotechnology-based drug delivery systems are enhancing the industrial scalability of actinomycete-derived antibiotics. Beyond antimicrobials, actinomycete-derived compounds show potential applications in oncology, immunotherapy, and agriculture. Alternative therapeutic strategies, including quorum sensing inhibitors, phage therapy, and combination therapies, are being explored to combat AMR. Cutting-edge analytical techniques, such as mass spectrometry, liquid chromatography, and nuclear magnetic resonance spectroscopy (NMR), are essential for structural elucidation and mechanism characterization of new bioactive compounds. To harness Saudi Arabia's microbial biodiversity effectively, interdisciplinary collaborations between microbiologists, biotechnologists, and pharmaceutical industries are crucial. Sustainable bioprospecting and advanced bioprocessing strategies will facilitate the translation of actinomycete-derived bioactive compounds into clinically viable therapeutics. Expanding research efforts into underexplored Saudi ecosystems can lead to groundbreaking discoveries in antibiotic development and beyond.},
}

@article {pmid40207154,
year = {2025},
author = {Ahn, JS and Han, EJ and Chung, HJ},
title = {Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533580},
pmid = {40207154},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous research on the gut microbiome has primarily focused on fecal microbiota, raising concerns about whether fecal samples accurately represent the entire intestinal microbiota. Studies have shown that microbial communities across the gastrointestinal (GI) tract are more diverse than those in feces, suggesting that microbial composition may vary depending on the sampling method. Additionally, analyzing the broader diversity of microbial communities in the GI tract may enhance the identification of potentially beneficial microbiota.

METHODS: In this study, we compare gut microbiome datasets obtained from fecal samples and GI samples (collected by pooling luminal contents and mucosal scrapings from the stomach to the end of the colon) of 6-month-old mice using 16S rRNA sequencing. We further investigate the associations between gut microbiota and motor, cognitive, and emotional functions in mice, examining differences between the two sample types. To assess these variations, we apply DESeq2 analysis to identify microbial species enriched in high-functioning groups and evaluate how their selection may differ depending on the sampling approach.

RESULTS: Our findings reveal notable differences in microbial composition between fecal and GI samples, suggesting that sampling methods may influence the identification of beneficial bacteria.

DISCUSSION: These results highlight the importance of selecting an appropriate sampling approach in microbiome research to ensure a comprehensive understanding of gut microbiota-host interactions.},
}

@article {pmid40207150,
year = {2025},
author = {Zhao, C and Yang, Y and Zhao, P and Bai, L},
title = {Comparative analysis of the fecal microbiota in Père David's deer and five other captive deer species.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1547348},
pmid = {40207150},
issn = {1664-302X},
abstract = {INTRODUCTION: Gut microbes are essential for host nutrition, immunity, and development. Various factors influence the composition and function of the gut microbial community. However, there is limited knowledge regarding the comparison of gut microbiota across different deer species, particularly those in the World Deer Park of Baotou (Inner Mongolia, China).

METHODS: This study utilized 16S rRNA gene amplicon sequencing to analyze the fecal microbiota and potential microbial function in Père David's Deer (Elaphurus davidianus), Sika deer (Cervus nippon), American Wapiti (Cervus canadensis), Red Deer (Cervuselaphus), Fallow Deer (Dama dama), and Reindeer (Rangifer tarandus).

RESULTS AND DISCUSSION: The findings indicated no significant differences in alpha diversity, yet there was a noteworthy distinction in beta diversity among the six deer groups. At the phylum level, the predominant bacteria in the deer populations were Firmicutes, Bacteroidetes, and Proteobacteria. At the genus level, 54 core bacterial microbiota were identified. The top four genera in AW, FD, PD, and SD were Ruminococcaceae UCG-005, Rikenellaceae RC9 gut group, RuminococcaceaeUCG-010 and Christensenellaceae R-7 group. The results of the neutral model revealed that neutral processes predominantly governed the gut microbiota community assembly in different deer species, particularly in Père David's deer. PICRUSt2 predictions showed significant enrichment of fecal bacterial functions related to fatty acid, lipid, metabolic regulator, and amino acid biosynthesis. This comparative analysis sheds light on the microbial community structure, community assembly, and potential functions, offering improved insights into the management and conservation of deer species, especially Père David's deer. Future research might focus on exploring metagenomic functions and dynamics in wild settings or across different seasons using metagenomics or metatranscriptomics.},
}

@article {pmid40206877,
year = {2025},
author = {Shi, M and Qin, T and Pu, Z and Yang, Z and Lim, KJ and Yang, M and Wang, Z},
title = {Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1473473},
pmid = {40206877},
issn = {1664-462X},
abstract = {INTRODUCTION: Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant.

METHODS: Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress.

RESULTS AND DISCUSSION: We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.},
}

@article {pmid40206699,
year = {2025},
author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS},
title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.},
journal = {Polar biology},
volume = {48},
number = {2},
pages = {62},
pmid = {40206699},
issn = {0722-4060},
abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.},
}

@article {pmid40206488,
year = {2025},
author = {He, J and Chen, Y and Jiang, Z and Li, F and Zhu, M and Xu, Z and Wang, M and Tang, M and Wu, Y and Li, Y},
title = {Diagnostic value of metagenomic next-generation sequencing in detecting Pneumocystis jirovecii pneumonia in HIV-infected patients.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1567484},
pmid = {40206488},
issn = {2296-858X},
abstract = {INTRODUCTION: Accurate diagnosis of Pneumocystis jirovecii pneumonia (PJP) in HIV patients remains challenging. This study compares metagenomic next-generation sequencing (mNGS) with PCR, GMS staining, and serum β-D-glucan (BG) assays for PJP detection and co-infection identification.

METHODS: BALF samples from 34 HIV-positive PJP patients and 50 non-PJP controls were analyzed. Diagnostic performance metrics (sensitivity, specificity, NPV, AUC) and co-pathogen profiles were evaluated for mNGS versus conventional methods.

RESULTS: mNGS and PCR both achieved 100% sensitivity. mNGS showed higher specificity (91.3% vs. 88%) and AUC (0.898 vs. 0.940 for PCR). Co-infections were detected in 67.6% of PJP cases by mNGS, including cytomegalovirus (41.2%), Epstein-Barr virus (29.4%), and non-tuberculous mycobacteria (14.7%). GMS and BG assays exhibited lower sensitivity (64.7% and 76.5%, respectively).

DISCUSSION: mNGS offers superior specificity, accuracy, and co-infection detection compared to traditional methods. Its high NPV (100%) supports clinical utility in ruling out PJP. While resource-intensive, mNGS is a promising first-line diagnostic tool for HIV-associated PJP, particularly in polymicrobial infection settings.},
}

@article {pmid40206430,
year = {2025},
author = {Zhou, Z and Sun, L and Zhou, W and Gao, W and Yuan, X and Zhou, H and Ren, Y and Li, B and Wu, Y and She, J},
title = {Probiotic Bifidobacterium reduces serum TMAO in unstable angina patients via the gut to liver to heart axis.},
journal = {Liver research (Beijing, China)},
volume = {9},
number = {1},
pages = {57-65},
pmid = {40206430},
issn = {2542-5684},
abstract = {BACKGROUND AND AIMS: Studies indicate that the gut microbiota and its metabolites are involved in the progression of cardiovascular diseases, and enterohepatic circulation plays an important role in this progression. This study aims to identify potential probiotics for the treatment of unstable angina (UA) and elucidate their mechanisms of action.

METHODS: Initially, the gut microbiota from patients with UA and control was analyzed. To directly assess the effects of Bifidobacterium supplementation, 10 patients with UA were enrolled and administered Bifidobacterium (630 mg per intake twice a day for 1 month). The fecal metagenome, serum trimethylamine N-oxide (TMAO) levels, and other laboratory parameters were evaluated before and after Bifidobacterium supplementation.

RESULTS: After supplementing with Bifidobacterium for 1 month, there were statistically significant differences (P < 0.05) in TMAO, aspartate aminotransferase, total cholesterol, and low-density lipoprotein compared to before. Additionally, the abundance of Bifidobacterium longum increased significantly, although the overall abundance of Bifidobacterium did not reach statistical significance. The gut microbiota, metabolites, and gut-liver axis are involved in the progression of UA, and potential mechanisms should be further studied.

CONCLUSIONS: Metagenomic analysis demonstrated a reduced abundance of Bifidobacterium in patients with UA. Supplementation with Bifidobacterium restored gut dysbiosis and decreased circulating TMAO levels in patients with UA. This study provides evidence that Bifidobacterium may exert cardiovascular-protective effects through the gut-liver-heart axis.

CLINICAL TRIAL NUMBER: ChiCTR2400093946.},
}

@article {pmid40205852,
year = {2025},
author = {Nowicki, M and Mroczek, M and Mukhedkar, D and Bała, P and Nikolai Pimenoff, V and Arroyo Mühr, LS},
title = {HPV-KITE: sequence analysis software for rapid HPV genotype detection.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf155},
pmid = {40205852},
issn = {1477-4054},
mesh = {Humans ; Genotype ; Algorithms ; *Software ; *Papillomaviridae/genetics/classification ; *Papillomavirus Infections/virology/diagnosis ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Human papillomaviruses (HPVs) are among the most diverse viral families that infect humans. Fortunately, only a small number of closely related HPV types affect human health, most notably by causing nearly all cervical cancers, as well as some oral and other anogenital cancers, particularly when infections with high-risk HPV types become persistent. Numerous viral polymerase chain reaction-based diagnostic methods as well as sequencing protocols have been developed for accurate, rapid, and efficient HPV genotyping. However, due to the large number of closely related HPV genotypes and the abundance of nonviral DNA in human derived biological samples, it can be challenging to correctly detect HPV genotypes using high throughput deep sequencing. Here, we introduce a novel HPV detection algorithm, HPV-KITE (HPV K-mer Index Tversky Estimator), which leverages k-mer data analysis and utilizes Tversky indexing for DNA and RNA sequence data. This method offers a rapid and sensitive alternative for detecting HPV from both metagenomic and transcriptomic datasets. We assessed HPV-KITE using three previously analyzed HPV infection-related datasets, comprising a total of 1430 sequenced human samples. For benchmarking, we compared our method's performance with standard HPV sequencing analysis algorithms, including general sequence-based mapping, and k-mer-based classification methods. Parallelization demonstrated fast processing times achieved through shingling, and scalability analysis revealed optimal performance when employing multiple nodes. Our results showed that HPV-KITE is one of the fastest, most accurate, and easiest ways to detect HPV genotypes from virtually any next-generation sequencing data. Moreover, the method is also highly scalable and available to be optimized for any microorganism other than HPV.},
}

Humans
Genotype
Algorithms
*Software
*Papillomaviridae/genetics/classification
*Papillomavirus Infections/virology/diagnosis
High-Throughput Nucleotide Sequencing
DNA, Viral/genetics
Sequence Analysis, DNA/methods

@article {pmid40205718,
year = {2025},
author = {Zhang, H and Yang, M and Ying, W and Hou, J and Zhou, Q and Sun, B and Wang, Y and Hui, X and Liu, L and Yao, H and Sun, J and Wang, W and Wang, X},
title = {Invasive fungal disease in a large cohort of hospitalized children with inborn errors of immunity in China.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {4},
pages = {e70074},
doi = {10.1111/pai.70074},
pmid = {40205718},
issn = {1399-3038},
support = {ZD2021CY001//the Shanghai Municipal Science and Technology Major Project/ ; },
mesh = {Humans ; China/epidemiology ; Male ; Female ; Retrospective Studies ; *Invasive Fungal Infections/epidemiology/drug therapy ; Child, Preschool ; Child ; Infant ; Prevalence ; *Immunologic Deficiency Syndromes/epidemiology/complications ; Adolescent ; Hospitalization ; Infant, Newborn ; },
abstract = {BACKGROUND: Invasive fungal disease (IFD) is a common complication observed in inborn errors of immunodeficiency (IEI) patients, and little is known about the overall prevalence of IFD in IEI patients. We aimed to summarize the fungal spectrum and outcomes of IFDs in a Chinese cohort of hospitalized patients with IEI.

METHODS: In this retrospective study, 607 IEI patients hospitalized from January 2018 to June 2022 were included. Demographic, clinical, and fungal infection data and IEI patient characteristics were collected and analyzed according to the IEI classification.

RESULTS: One hundred and two IEI patients were diagnosed with proven or probable IFD. The overall prevalence of IFD was 17% (102/607). There were 29 different genotypes, among which CYBB (25%), CD40LG (9%), and RAG1 (7%) mutations were the most common. Most IFD infections (87/102) were caused by one fungus. Invasive Aspergillus, Pneumocystis jirovecii pneumonia, and Penicillium infections were more commonly observed in patients with congenital defects in phagocytes, immunodeficiencies affecting cellular and humoral immunity, and defects in innate immunity, respectively. Most IFDs observed in IEI patients were single-site infections, most of which were lung infections (74%). Seventeen patients were diagnosed with disseminated IFDs, nine of which were caused by Penicillium. All patients received antifungal treatments. Eight patients (8%) died within 3 months of IFD diagnosis.

CONCLUSIONS: IFD occurrence suggests the presence of immunity impairment. The IFD fungal profile may indicate different types of IEI. Early recognition of immunodeficiency and optimal timing of antifungal therapy can reduce fatality in IEI patients.},
}

Humans
China/epidemiology
Male
Female
Retrospective Studies
*Invasive Fungal Infections/epidemiology/drug therapy
Child, Preschool
Child
Infant
Prevalence
*Immunologic Deficiency Syndromes/epidemiology/complications
Adolescent
Hospitalization
Infant, Newborn

@article {pmid40205678,
year = {2025},
author = {He, Y and Zhao, G and Ouyang, X and Wang, S and Chen, Y and Li, C and He, Y and Gao, J and Han, S and Zhao, J and Wang, J and Wang, C},
title = {Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489072},
doi = {10.1080/19490976.2025.2489072},
pmid = {40205678},
issn = {1949-0984},
mesh = {Animals ; Mice ; Gastrointestinal Microbiome/drug effects/radiation effects ; *Creatine/metabolism/pharmacology/administration & dosage ; *Ferroptosis/drug effects/radiation effects ; Mice, Inbred C57BL ; Male ; *Intestines/radiation effects/microbiology ; *Radiation-Protective Agents/metabolism/administration & dosage ; Radiation, Ionizing ; Feces/microbiology ; Enterocytes/radiation effects/metabolism ; },
abstract = {Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.},
}

Animals
Mice
Gastrointestinal Microbiome/drug effects/radiation effects
*Creatine/metabolism/pharmacology/administration & dosage
*Ferroptosis/drug effects/radiation effects
Mice, Inbred C57BL
Male
*Intestines/radiation effects/microbiology
*Radiation-Protective Agents/metabolism/administration & dosage
Radiation, Ionizing
Feces/microbiology
Enterocytes/radiation effects/metabolism

@article {pmid40205588,
year = {2025},
author = {Li, M and Wang, Z and Ma, Z and Wang, Y and Jia, H and Zhang, L and Chen, P and Mao, Y and Yang, Z},
title = {Metagenomic analysis reveals microbial drivers of heat resistance in dairy cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {35},
pmid = {40205588},
issn = {2524-4671},
support = {2022YFF1001200//National Key Research and Development Program of China/ ; },
abstract = {Heat stress poses a significant challenge to dairy cattle, leading to adverse physiological effects, reduced milk yield, impaired reproduction performance and economic losses. This study investigates the role of the rumen microbiome in mediating heat resistance in dairy cows. Using the entropy-weighted TOPSIS method, we classified 120 dairy cows into heat-resistant (HR) and heat-sensitive (HS) groups based on physiological and biochemical markers, including rectal temperature (RT), respiratory rate (RR), salivation index (SI) and serum levels of potassium ion (K[+]), heat shock protein 70 (HSP70) and cortisol. Metagenomic sequencing of rumen fluid samples revealed distinct microbial compositions and functional profiles between the two groups. HR cows exhibited a more cohesive and functionally stable microbiome, dominated by taxa such as Ruminococcus flavefaciens and Succiniclasticum, which are key players in fiber degradation and short-chain fatty acid production. Functional analysis highlighted the enrichment of the pentose phosphate pathway (PPP) in HR cows, suggesting a metabolic adaptation that enhances oxidative stress management. In contrast, HS cows showed increased activity in the tricarboxylic acid (TCA) cycle, pyruvate metabolism and other energy-intensive pathways, indicating a higher metabolic burden under heat stress. These findings underscore the critical role of the rumen microbiome in modulating heat resistance and suggest potential microbiome-based strategies for improving dairy cattle resilience to climate change.},
}

@article {pmid40205543,
year = {2025},
author = {Zou, Z and Zhao, W and Chen, Y and Liu, Z and He, G and Zhang, H},
title = {Extracorporeal membrane oxygenation in the treatment of critical Pneumocystis jirovecii pneumonia in a child with Langerhans cell histiocytosis: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {492},
pmid = {40205543},
issn = {1471-2334},
mesh = {Humans ; *Extracorporeal Membrane Oxygenation/methods ; Female ; *Pneumonia, Pneumocystis/therapy/complications/microbiology ; Child, Preschool ; *Pneumocystis carinii/genetics/isolation & purification ; *Histiocytosis, Langerhans-Cell/complications/drug therapy ; Treatment Outcome ; },
abstract = {BACKGROUND: Children with Langerhans cell histiocytosis (LCH) are particularly susceptible to infections such as Pneumocystis jirovecii pneumonia (PJP) due to the immunosuppressive effects of chemotherapy, which can progress to acute respiratory distress syndrome (ARDS) and respiratory failure. The use of Extracorporeal Membrane Oxygenation (ECMO) to manage hypoxemia secondary to PJP in LCH presents unique challenges, including the prevention of catheter-related bloodstream infections associated with arterial and venous access. This study explores a case wherein ECMO was crucial in treating severe PJP-induced respiratory failure in a pediatric patient with LCH.

CASE PRESENTATION: A 3-year-old female with a history of LCH, undergoing long-term chemotherapy and corticosteroid treatment, was admitted with fever, dyspnea, and lethargy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid confirmed Pneumocystis jirovecii (PJ). Despite aggressive management with invasive high-frequency ventilation, inhaled nitric oxide, and prone positioning, the patient's oxygenation remained critically low, with severe hypercapnia and resultant severe respiratory acidosis, necessitating vasopressor support for hemodynamic stability and venoarterial (VA) ECMO intervention. Early initiation of VA ECMO facilitated ultraprotective lung ventilation and circulatory support, effectively preventing hemodynamic collapse. The patient was successfully decannulated after 13 days of ECMO support.

CONCLUSION: While PJP is a rare and extremely serious opportunistic infection, the VA ECMO support in this pediatric case effectively managed severe PJP without ECMO-related complications. This highlights ECMO as a potentially viable, relatively effective, and safe adjunctive therapy in the management of severe PJP infections in children.},
}

Humans
*Extracorporeal Membrane Oxygenation/methods
Female
*Pneumonia, Pneumocystis/therapy/complications/microbiology
Child, Preschool
*Pneumocystis carinii/genetics/isolation & purification
*Histiocytosis, Langerhans-Cell/complications/drug therapy
Treatment Outcome

@article {pmid40205497,
year = {2025},
author = {Grønbæk, IMB and Halkjær, SI and Mollerup, S and Hansen, EH and Paulsen, SJ and Engel, S and Theede, K and Wilkens, R and Boysen, T and Petersen, AM},
title = {The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: results from a randomised, double-blind, placebo-controlled trial.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {19},
pmid = {40205497},
issn = {1757-4749},
support = {A6876//The Capital Region's Research Foundation for Health Research/ ; },
abstract = {BACKGROUND: The aetiology of Crohn's disease, a chronic inflammatory bowel disease, is multifactorial and not completely understood. However, the association with gut dysbiosis is well-established, and manipulation of the gut microbiota has gained interest as a treatment strategy. This study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (Bif195) on intestinal inflammation, symptoms, and the gut microbiome composition in patients with small intestinal Crohn's disease.

METHODS: This was a randomised, double-blind, placebo-controlled trial. Thirty-three patients with small intestinal Crohn's disease were assigned to eight weeks of treatment with Bif195 or placebo (1:1). The primary outcome was changes in bowel wall thickness measured by intestinal ultrasonography. Other outcomes were changes in symptom severity, quality of life, faecal calprotectin, fatigue, and specific inflammatory parameters on ultrasonography. Changes in the microbiome composition were also examined.

RESULTS: Bif195 did not affect the bowel wall thickness in the small intestine compared to placebo. Nor did we observe effects on secondary or clinical explorative outcomes. Analysis of the gut microbiome showed that the relative abundance of B. breve rose during the intervention in the Bif195 group, but the result was statistically non-significant. Surprisingly, we observed a clustering of baseline microbiome data into two groups that differed in several aspects including a statistically significant difference in the incidence of previous bowel resections among the participants. Furthermore, changes in symptom scores after eight weeks of intervention were significantly different across the two microbiome groups, with an interaction effect of p = 0.04.

CONCLUSIONS: Eight weeks of treatment with Bif195 did not affect clinical outcomes for Crohn's disease. However, variations in baseline microbiome data influenced the results. This underscores the importance of assessing baseline microbiome data in intervention studies in Crohn's disease.

CLINICALTRIALS: gov NCT04842149.},
}

@article {pmid40205473,
year = {2025},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V},
title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf033},
pmid = {40205473},
issn = {1574-6941},
abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.},
}

@article {pmid40205381,
year = {2025},
author = {Chen, G and Yin, L and Zhang, H},
title = {Isolation and characterization of goose astrovirus genotype 1 causing enteritis in goslings from Sichuan Province, China.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {259},
pmid = {40205381},
issn = {1746-6148},
support = {ZYN2024087//Central University Basic Scientific Research Business Expenses Special Funds/ ; },
abstract = {Since 2017, goose astrovirus (GoAstV) has been widely prevalent in various provinces of China, causing economic losses in the goose industry, with outbreak mortality rates ranging from 10 to 60%. Notably, a goose farm in Sichuan Province has faced an outbreak of infectious disease in 1-3 weeks old goslings, with a mortality rate of approximately 30%. Viral metagenomic analysis of fecal samples identified Goose astrovirus genotype 1 (GoAstV-1), and PCR analysis confirmed the presence of GoAstV-1. Furthermore, we successfully isolated a GoAstV-C1 strain using goose embryos named AAstV/Goose/CHN/2023/C1 (GenBank No. PP108251), and its viral titer was calculated as 10^4.834 ELD50/0.5 mL using the Reed-Muench method. The genome size of GoAstV-C1 was about 7,261 nucleotides through amplifying with Sanger sequencing and assembling with SeqMan software. Phylogenetic analysis revealed that GoAstV-1 strains are classified into three major subtypes: A, B, and C, with the GoAstV-C1 strain identified as a unique variant within subtype B, characterized by distinct genetic divergence features. Experimental inoculation of one-day-old goslings with the virus resulted in a mortality rate of 5 out of 15 (p-value = 0.0421) and a significant reduction in weight gain compared to controls (p-value = 0.005). Pathological examination revealed that GoAstV-C1 infection caused severe damage to the liver, spleen, and kidneys. Interestingly, unlike most GoAstV, which leads to characteristic gout symptoms, our isolates GoAstV-C1 caused obvious intestinal damage characterized by necrosis, inflammatory infiltration, and crypt architectural disruption. We indicated that GoAstV-C1 displays a unique intestinal tropism rather than characteristic gout symptoms and elucidated genomic features and evolutionary relationships of GoAstV strains. These findings help advance our knowledge of the epidemiology and pathogenicity of GoAstV-1, and the predicted structure of capsid protein could serve as a potential target for designing novel antiviral drugs or vaccines against GoAstV-1.},
}

@article {pmid40204977,
year = {2025},
author = {Deng, Z and Poulsen, JS and Nielsen, JL and Weissbrodt, DG and Spanjers, H and van Lier, JB},
title = {Identification of protein-degraders in an anaerobic digester by protein stable isotope probing and metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {87},
pmid = {40204977},
issn = {1432-0614},
support = {201708450043//China Scholarship Council/ ; },
mesh = {Anaerobiosis ; *Metagenomics ; *Acinetobacter/metabolism/genetics ; Carbon Isotopes/metabolism ; Bacterial Proteins/metabolism/genetics ; Isotope Labeling ; Metabolic Networks and Pathways ; Proteomics ; *Bioreactors/microbiology ; Proteolysis ; Glucose/metabolism ; *Proteins/metabolism ; },
abstract = {Presence of carbohydrates hampers protein degradation in anaerobic digesters. To understand this phenomenon, we used proteogenomics to identify the active protein-degraders in the presence of low and high carbohydrates concentrations. Active metabolic pathways of the identified protein-degraders were investigated using proteomics with [13]C-protein substrates (protein stable isotope probing). Results showed that 1) Acinetobacter was the active protein-degraders under both protein-fed and protein-glucose mixture-fed conditions, 2) the relative abundance of Acinetobacter was not affected by the presence of carbohydrates, 3) the incorporation of the [13]C-labelled protein substrate was predominantly observed in outer membrane-bound proteins and porin proteins, which are associated with proteinases or the transportation of amino acids across the cell wall. The Acinetobacter metabolic model and the incubation conditions suggested that glucose and proteins were degraded through anaerobic respiration. The negative impact of carbohydrates on protein biodegradation was attributed to Acinetobacter's preference for carbohydrates. This work highlights that efficient degradation of protein and carbohydrate mixtures in anaerobic digesters requires a staged or time-phased approach and enrichment of active protein-degraders, offering a new direction for process optimization in anaerobic digestion systems. KEY POINTS: • Acinetobacter identified for the first time as main anaerobic protein-degrader • Metabolic model revealed protein degradation via anaerobic respiration • Metabolic pathway analysis indicated SO4[2-] or Fe[3+] as terminal electron acceptors.},
}

Anaerobiosis
*Metagenomics
*Acinetobacter/metabolism/genetics
Carbon Isotopes/metabolism
Bacterial Proteins/metabolism/genetics
Isotope Labeling
Metabolic Networks and Pathways
Proteomics
*Bioreactors/microbiology
Proteolysis
Glucose/metabolism
*Proteins/metabolism

@article {pmid40204761,
year = {2025},
author = {Li, F and Hooi, SL and Choo, YM and Teh, CSJ and Toh, KY and Lim, LWZ and Lee, YQ and Chong, CW and Ahmad Kamar, A},
title = {Progression of gut microbiome in preterm infants during the first three months.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12104},
pmid = {40204761},
issn = {2045-2322},
support = {IF047-2021//International Funding/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; Prospective Studies ; *Bacteria/genetics/classification ; Infant ; Gestational Age ; Bifidobacterium/genetics/isolation & purification ; Meconium/microbiology ; Metagenomics ; },
abstract = {The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Infant, Premature
Infant, Newborn
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Female
Male
Prospective Studies
*Bacteria/genetics/classification
Infant
Gestational Age
Bifidobacterium/genetics/isolation & purification
Meconium/microbiology
Metagenomics

@article {pmid40204742,
year = {2025},
author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB},
title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12156},
pmid = {40204742},
issn = {2045-2322},
mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.},
}

*Gene Transfer, Horizontal
Animals
Humans
*Metagenomics/methods
Feces/microbiology
*Bacteria/genetics/drug effects
Nepal
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
Virulence Factors/genetics
Birds/microbiology
Metagenome

@article {pmid40204671,
year = {2025},
author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH},
title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00246},
pmid = {40204671},
issn = {1520-5851},
abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.},
}

@article {pmid40204030,
year = {2025},
author = {Bao, Y and Feng, S and Yu, F and Ye, W and Xing, H and Zhu, X and Bao, W and Huang, M},
title = {Self-Regulating pH Pyrite-Construction waste Biofilter: Denitrification Performance, metabolic Pathways, and clogging Alleviation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132500},
doi = {10.1016/j.biortech.2025.132500},
pmid = {40204030},
issn = {1873-2976},
abstract = {Waste-based denitrification filters face challenges like alkalinity accumulation, low efficiency, and clogging. This study proposes a novel denitrification filter using construction waste and pyrite (WPDF) to address these issues. WPDF's performance, safety, and mechanisms were evaluated by measuring effluent, filler characteristics and metagenomics. Results demonstrated a high total nitrogen removal load (88.65 g N m[-3]d[-1]) with minimal biofilm (13 %) and filler accumulation (39 %), effectively mitigating clogging. Phosphorus removal relied on chemical precipitation in construction waste. WPDF was pH self-regulating and promoted the formation and release of fulvic acid. Pyrite promotes bio-metabolism, making WPDF enriched in energy metabolism (6 %) and transporter capacity (6 %). Functional prediction indicated that WPDF was more abundant in genes related to denitrification, glycolysis, and electron transport, which promoted the heterotrophic denitrification process. This study provides a novel, efficient, and eco-friendly possible solution for wastewater and offers new insights into the molecular mechanisms of carbon and nitrogen metabolism.},
}

@article {pmid40203979,
year = {2025},
author = {Genitsaris, S and Stefanidou, N and Kourkoutmani, P and Michaloudi, E and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M},
title = {Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121563},
doi = {10.1016/j.envres.2025.121563},
pmid = {40203979},
issn = {1096-0953},
abstract = {Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.},
}

@article {pmid40203710,
year = {2025},
author = {Qv, M and Wu, Q and Wang, W and Wang, H and Zhu, L},
title = {Metagenomic insights into the response of microbial metabolic function and extracellular polymeric substances from microalgae-bacteria consortia to fluoroquinolone antibiotics.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125283},
doi = {10.1016/j.jenvman.2025.125283},
pmid = {40203710},
issn = {1095-8630},
abstract = {Microalgae-bacteria consortia (MBC) are considered a promising bioremediation technology for removing pollutants from swine wastewater. However, the overuse of antibiotics poses challenges to the effective functioning of MBC. In this study, the removal efficiency of nutrients in wastewater by MBC under different antibiotic concentrations (0, 1, 5, 10 and 50 mg/L) was evaluated. The changes of functional microbial abundance were elucidated and the response mechanism of MBC against antibiotics was investigated. Antibiotics inhibited the accumulation of MBC biomass and reduced the removal efficiency of ammonia nitrogen and total phosphorus in wastewater by 8.39 % and 8.74 % respectively. In addition, antibiotics affected the relative abundance of microorganisms (Raineyella, from 30.72 % to 15.96 %) and functional genes (glnA, gudB, NirK, NirBD, NarB, NapAB, NorBC and NosZEPS) involved in N metabolism. MBC could defend against the adverse effects of antibiotics by regulating the content of proteins in the extracellular polymeric substances.},
}

@article {pmid40203094,
year = {2025},
author = {Isobe, N and Tanaka, K and Ishii, S and Shimane, Y and Okada, S and Daicho, K and Sakuma, W and Uetani, K and Yoshimura, T and Kimoto, K and Kimura, S and Saito, T and Nakajima, R and Tsuchiya, M and Ikuta, T and Kawagucci, S and Iwata, T and Nomaki, H},
title = {Fully circular shapable transparent paperboard with closed-loop recyclability and marine biodegradability across shallow to deep sea.},
journal = {Science advances},
volume = {11},
number = {15},
pages = {eads2426},
doi = {10.1126/sciadv.ads2426},
pmid = {40203094},
issn = {2375-2548},
abstract = {To mitigate marine pollution from single-use plastics, it is crucial to transition to next-generation commodity materials that are derived from biomass and are recyclable and marine biodegradable even at abyssal depths in case of the accidental release to the ocean. Here, we develop an optically transparent millimeter-thick paperboard called transparent paperboard (tPB) through dissolution and coagulation of cellulose. The tPB is made entirely of pristine cellulose and compositionally identical to paper. A cup-shaped tPB can hold just-boiled water without an internal film coating because of its high wet tensile properties and anisotropic thermal properties. In addition, the spent tPB is material recyclable in a closed system, where all chemicals and water are also recyclable. Furthermore, the marine biodegradability of tPB across shallow to abyssal depths is confirmed by on-site degradation tests and metagenomic analyses. Hence, tPB is expected to serve as a key fully circular commodity material in sustainable societies of the future.},
}

@article {pmid40202861,
year = {2025},
author = {Singh, AK and Sathaye, SB and Rai, AK and Singh, SP},
title = {Novel Cellobiose 2-Epimerase from Thermal Aquatic Metagenome for the Production of Epilactose.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c09753},
pmid = {40202861},
issn = {1520-5118},
abstract = {Epilactose is a prebiotic molecule that exerts a bifidogenic effect and increases calcium and iron absorption in the small intestine. This study identifies a novel cellobiose 2-epimerase gene (ceM) by investigating metagenomic data generated from a thermal aquatic habitat. The computation of secondary and tertiary structure analysis, molecular docking, and MD simulation analysis indicated the protein CEM to be a novel cellobiose 2-epimerase. The gene was expressed in Escherichia coli, followed by biochemical characterization of the purified protein. CEM is capable of transforming lactose into the high-value rare sugar, epilactose, in a wide range of temperatures (4-70 °C) and pH (6.0-10.0). The enzyme was exposed to 50 °C, and hardly a 10% loss in activity was recorded after 32 h of heat treatment, suggesting that CEM is a thermostable protein. CEM is a kinetically highly efficient enzyme, with a turnover number of 9832 ± 490 s[-1] for lactose to epilactose epimerization. The maximum conversion yield of 26% epilactose was obtained in 15 min of catalytic reaction. Further, the enzyme was successfully tested to transform lactose in milk and whey samples.},
}

@article {pmid40202719,
year = {2025},
author = {Huang, Z and Liu, C and Zhao, X and Guo, Y},
title = {The effect of elevated levels of the gut metabolite TMAO on glucose metabolism after sleeve gastrectomy.},
journal = {Archives of physiology and biochemistry},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/13813455.2025.2489721},
pmid = {40202719},
issn = {1744-4160},
abstract = {Purpose：Bariatric surgery can effectively alleviate obesity and diabetes by regulation of the gut microbiota. This study aimed to investigate the change in the gut microbiota metabolite TMAO and to explore its effect on glucose metabolism after sleeve gastrectomy (SG). Materials and methods：Diet-induced obesity mouse models were established, and the mice were randomly divided into four groups: an SG group, a sham-operated group pair-fed with the SG group (PF), a sham-operated group fed ad libitum (AL), and a lean control group (C). At 10 weeks post-surgery, the changes in glycogen content of liver, gut microbiota and the level of FMO3 in the liver were evaluated, and their correlation with TMAO production was analysed. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Results：At 10 weeks post-surgery, hepatocyte glycogen levels were restored, and serum TMA and TMAO levels were significantly increased. Faecal metagenomic sequencing results showed that the abundances of Ruminococcaceae and Lachnospiraceae, which were positively correlated with TMAO production, were significantly increased after surgery. While the changes in FMO3, the key enzyme producing TMAO in the liver was found decreased significantly after SG. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Inconsistent with the changing trend of TMAO, the expression of PERK, FOXO1, PCK, and G6PC significantly decreased after SG. Conclusions：SG can significantly reduce obesity and restore glucose metabolism. After surgery, TMAO metabolites increased in a microbiota-dependent manner.},
}

@article {pmid40202375,
year = {2025},
author = {Pan, C and Xu, P and Yuan, M and Wei, S and Lu, Y and Lu, H and Zhang, W},
title = {Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70344},
doi = {10.1002/jmv.70344},
pmid = {40202375},
issn = {1096-9071},
support = {//This study was supported by the Zhenjiang Science and Technology Innovation Funds-Clinical Medicine Key Laboratory and Scientific Research Project of Health Commission of Jiangsu Province./ ; },
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Virome ; Feces/virology ; *Breast Feeding ; Female ; Male ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; *Feeding Behavior ; Bacteriophages/genetics/classification/isolation & purification ; Milk, Human/virology ; *Gastrointestinal Tract/virology ; },
abstract = {The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.},
}

Humans
Infant
*Gastrointestinal Microbiome
*Virome
Feces/virology
*Breast Feeding
Female
Male
*Viruses/classification/genetics/isolation & purification
Metagenomics
*Feeding Behavior
Bacteriophages/genetics/classification/isolation & purification
Milk, Human/virology
*Gastrointestinal Tract/virology

@article {pmid40202358,
year = {2025},
author = {Alexandre, A and Gerard, À and Sergio, I and Whim, T and Isabelle, L and Maria José, C and Lorena, I and Enrique, H and Gerardo, MA and Carolina, M and José, N and Vanessa, B and Rubén, L},
title = {Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13406},
pmid = {40202358},
issn = {1600-0765},
abstract = {AIMS: To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.

METHODS: In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.

RESULTS: The results indicated significant variation in α-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, β-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.

CONCLUSION: These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.},
}

@article {pmid40202322,
year = {2025},
author = {Scheffer, G and Chakraborty, A and Amundson, KK and Khan, R and Wilkins, MJ and Evans, P and Hubert, CRJ},
title = {Polymer biodegradation by Halanaerobium promotes reservoir souring during hydraulic fracturing.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0225324},
doi = {10.1128/aem.02253-24},
pmid = {40202322},
issn = {1098-5336},
abstract = {UNLABELLED: Hydraulically fractured shale reservoirs have facilitated studies of unexplored niches in the continental deep biosphere. In high-salinity North American shale systems, members of the genus Halanaerobium seem to be ubiquitous. Polymers like guar gum used as gelling agents in hydraulic fracturing fluids are known to be fermentable substrates, but metabolic pathways encoding these processes have not been characterized. To explore this, produced water samples from the Permian Basin were incubated both at 30°C to simulate above-ground storage conditions and at 60°C to simulate subsurface reservoir conditions. Guar metabolism coincided with Halanaerobium growing only at 30°C, revealing genes for polymer biodegradation through the mixed-acid fermentation pathway in different metagenome-assembled genomes (MAGs). Whereas thiosulfate reduction to sulfide is often invoked to explain the dominance of Halanaerobium in these settings, genes for thiosulfate metabolism were lacking in Halanaerobium genomes with high estimated completeness. Sulfide production was observed in 60°C incubations, with corresponding enrichment of Desulfohalobium and Desulfovibrionaceae that possess complete pathways for coupling mannose and acetate oxidation to sulfate reduction. These findings outline how production of fermentation intermediates (mannose and acetate) by Halanaerobium in topside settings can result in reservoir souring when these metabolites are introduced into the subsurface through produced water reuse.

IMPORTANCE: Hydraulically fractured shale oil reservoirs are ideal for studying extremophiles such as thermohalophiles. During hydraulic fracturing, reservoir production water is stored in surface ponds prior to reuse. Microorganisms in these systems therefore need to withstand various environmental changes such as the swing between warm downhole oil reservoir temperatures and cooler surface conditions. While most studies on hydraulically fractured oil reservoirs mimic the environmental conditions found in oil wells, this study follows this water cycle during fracking and the associated microbial metabolic potential during topside-produced water storage and subsurface oil reservoir conditions. Of particular interest are members of the genus Halanaerobium that have been reported to reduce thiosulfate contributing to souring of oil reservoirs. Here, we show that some Halanaerobium strains were unable to grow at hotter temperatures reflective of oil reservoir conditions and lack genes for thiosulfate reduction, despite the proposed importance of this metabolism in other studies. Rather, it is likely that these organisms metabolize complex organics in fracking fluids at lower temperatures, thereby generating substrates that support reservoir souring by thermophilic sulfate-reducing bacteria at higher temperatures. In this way, Halanaerobium promotes souring indirectly by feeding sulfate-reducing microorganisms fermentation products (e.g., acetate and hydrogen) rather than via direct sulfidogenesis via thiosulfate reduction. Therefore, the novelty of this research is not within the detection of known oil reservoir colonizing bacteria but rather in the relationship between bacteria and the indirect involvement of Halanaerobium, promoting souring throughout the produced water reuse cycle.},
}

@article {pmid40202301,
year = {2025},
author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J},
title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149624},
doi = {10.1128/msystems.01496-24},
pmid = {40202301},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.

IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.},
}