@article {pmid40629292,
year = {2025},
author = {Ying, L and Yuhao, W and Yafang, H and Jiao, L and Lina, D and Qinze, S and Chenghai, Y and Shaoxiong, Z and Yuexi, G and Mingwang, S and Zelin, C and Chuangchuang, W and Zihan, G and Xin, L and Lu, M and Lei, Z},
title = {Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {423},
pmid = {40629292},
issn = {1471-2180},
support = {82103868//National Natural Science Foundation of China/ ; 8191101420//National Natural Science Foundation of China/ ; 20220301//Young Talent Fund of Association for Science and Technology in Shaanxi/ ; 2023BSHTBZZ03//Shaanxi Province Postdoctoral Research Project/ ; 2023P098//Shaanxi Provincial Social Science Project/ ; 3111500001//Outstanding Young Scholars Funding/ ; xtr022019003//Xi'an Jiaotong University Basic Research and Profession Grant/ ; YX6J004//Xi'an Jiaotong University Young Talent Support Grant/ ; },
}

@article {pmid40629022,
year = {2025},
author = {Teo, JJY and Ho, EXP and Ng, AHQ and How, SHC and Chng, KR and Ateş, YC and Fau'di, MT and Aung, KT and Nagarajan, N},
title = {Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {63},
pmid = {40629022},
issn = {2731-8745},
abstract = {The distribution of microorganisms in built environments with high human traffic, such as food centres, can potentially have a significant impact on public health, particularly in the context of increasing worldwide incidence of food and fomite-related outbreaks. In many major Asian cities, public food centres are central to daily food consumption, yet there is a lack of baseline knowledge about their environmental microbiomes. We performed a city-wide metagenomic survey of food-centre microbiomes in Singapore, covering 16 centres and 240 samples, to map the abundances of microbial (bacteria, archaea, fungi, viruses) and non-microbial DNA across two timepoints. Food-centre microbiomes were found to be enriched in food-related DNA signatures compared to other environments, such as hospitals and offices, with specific food-microbe associations (e.g., Enterobacteriaceae and fish) and food DNA providing a partial explanation for the microbial profiles observed (44% of variation explained). Machine learning analysis identified a small set of microbial species (n = 22) that serve as highly accurate (>80%) location-specific signatures for various food centres, some of which persist even after 3 years. Profiling of antibiotic resistance genes (ARGs) and pathogens identified a surprising enrichment of ARGs in food centres relative to other non-healthcare environments (>2.5×), and an order of magnitude enrichment of key pathogenic species (e.g., Klebsiella pneumoniae, Enterobacter spp) even compared to hospital environments. These results highlight the contribution of diverse biotic and abiotic factors in shaping the unique microbiome profiles of different food-centre environments, and the potential for using metagenomic surveillance to understand the risk for infections and antibiotic resistance gene transmission.},
}

@article {pmid40628728,
year = {2025},
author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X},
title = {Identification of gut bacteria reductases that biotransform steroid hormones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6285},
pmid = {40628728},
issn = {2041-1723},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.},
}

*Gastrointestinal Microbiome/physiology/genetics
Humans
Phylogeny
Male
Female
*Oxidoreductases/metabolism/genetics
*Bacteria/enzymology/genetics/classification
*Steroids/metabolism
Biotransformation
Pregnenolone/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid40627884,
year = {2025},
author = {Zheng, Y and Chen, P and Wang, E and Ren, Y and Wu, X and Wei, Q and Dong, R and Guo, J},
title = {Metabolic pathway modulation for enhanced acetic acid production in acidogenic fermentation of food waste via gas self-circulation.},
journal = {Bioresource technology},
volume = {435},
number = {},
pages = {132945},
doi = {10.1016/j.biortech.2025.132945},
pmid = {40627884},
issn = {1873-2976},
abstract = {The volatile fatty acids (VFAs) produced through acidogenic fermentation of food waste can be applied as an external carbon source for denitrification in wastewater treatment. However, variations in the concentration and composition of VFAs significantly limit denitrification performance. In this study, a novel gas self-circulation strategy was investigated to enhance acetic acid production. The results indicated that gas self-circulation increased the acetic acid yield by 23.11 %, from 6.88 to 8.47 g/L. Metagenomic analyses revealed that the system reduced reliance on conventional acetogenic bacteria and significantly enriched homoacetogens. The upregulation of genes related to glycolysis and pyruvate metabolism explained the overall improvement in acidogenic metabolism. The increased abundance of key enzyme genes associated with the Wood-Ljungdahl and the acetyl coenzyme A pathways enhanced the metabolic flux toward acetate synthesis. This study presents a novel approach for enhancing selective acetic acid production and investigates the corresponding mechanistic responses.},
}

@article {pmid40627495,
year = {2025},
author = {Onohuean, H and Ogunmola, T and Adesiyan, A and Oluwamayowa Samuel, A and Oni, E and Okechukwu Paul Chima, U},
title = {Updates on cancer vaccines in brain cancer: Advances in neuroblastoma, delivery systems, and emerging technologies.},
journal = {Human vaccines & immunotherapeutics},
volume = {21},
number = {1},
pages = {2526964},
doi = {10.1080/21645515.2025.2526964},
pmid = {40627495},
issn = {2164-554X},
mesh = {Humans ; *Brain Neoplasms/therapy/immunology ; *Neuroblastoma/therapy/immunology ; *Cancer Vaccines/administration & dosage/immunology/therapeutic use ; Blood-Brain Barrier/metabolism ; *Drug Delivery Systems/methods ; Nanoparticles/administration & dosage ; COVID-19 Vaccines ; Child ; Immunotherapy/methods ; SARS-CoV-2/immunology ; COVID-19/prevention & control ; },
abstract = {Neuroblastoma stands as a major concern in pediatric oncology because it develops from neural crest cells as a neuroendocrine cancer. Nanoparticle-based vaccine delivery approaches the therapeutic activity of immune cells only toward tumor cells without inflicting damage to healthy tissues like those sustained by chemotherapy and radiation therapy. Neuroblastoma treatment faces two major barriers: penetrating the blood-brain barrier (BBB) and using nanoparticle technology. The promising developments for neuroblastoma treatment emerge from mRNA COVID-19 vaccine research and brain cancer vaccine clinical trials especially through phase I autologous dendritic cell vaccine studies. Future research needs to develop optimized nanoparticles which can trigger the release of mRNA or peptides based on tumor-specific pH and enzyme signals. The BBB can be opened temporarily through ultrasound and receptor-mediated transport approaches, which enhance vaccine delivery to brain tissues. New immunotherapeutic approaches for pediatric malignancies emerge from these recent findings to yield future success.},
}

Humans
*Brain Neoplasms/therapy/immunology
*Neuroblastoma/therapy/immunology
*Cancer Vaccines/administration & dosage/immunology/therapeutic use
Blood-Brain Barrier/metabolism
*Drug Delivery Systems/methods
Nanoparticles/administration & dosage
COVID-19 Vaccines
Child
Immunotherapy/methods
SARS-CoV-2/immunology
COVID-19/prevention & control

@article {pmid40626932,
year = {2025},
author = {Talwar, C and Guria, A and Hoffman, K and Biest, S and Jimenez, P and Kommagani, R},
title = {A role for gut mycobiome and altered fungal-bacterial interactions in women with endometriosis.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf148},
pmid = {40626932},
issn = {1529-7268},
abstract = {Endometriosis is a gynecological pathology prevalent in reproductive age women in which the inner uterine wall (endometrium) grows outside as ectopic lesions. The inflammation resulting from these growing implants closely associates with disease severity, causing chronic pain and infertility. Emerging studies have found altered bacterial communities in endometriosis and a causal role for gut bacteria in endometriosis. However, the role of the gut mycobiome i.e., the fungal component of the microbiome in endometriosis is a current knowledge gap that needs to be addressed. In this study, utilizing the stool samples from women with endometriosis, we found that the gut fungal communities are altered in women with endometriosis. By integrating the bacterial microbiota and studying the co-occurring relationships between fungi and bacteria, we identify the altered fungal-bacterial community interactions in endometriosis. In addition, we studied the microbial interactions with the host and identified the bacterial taxa as 'microbiome-associated host genetic variants' in endometriosis. By determining their interactions with fungi, we highlight the fungal taxa as underlying regulators of the disease. Experimentally, we demonstrate that the progression of endometriosis in mice is significantly impeded by the depletion of fungi, revealing a role for the gut mycobiome in endometriosis. Our results highlight the positive- and negative- co-abundance relationships shared between bacteria-fungi, bacteria-bacteria and microbes-host in the disease pathogenesis. These findings promise to stimulate future experimental research on the bacterial-fungal interactions that must be contemplated when designing microbiome-based therapeutic strategies using antifungal agents.},
}

@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf142},
pmid = {40626910},
issn = {1751-7370},
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}

@article {pmid40626735,
year = {2025},
author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA},
title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174424},
doi = {10.1128/msystems.01744-24},
pmid = {40626735},
issn = {2379-5077},
abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.

IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.},
}

@article {pmid40625833,
year = {2025},
author = {Zhou, M and Sun, S and Chen, L and Xu, H and Liu, L and Lv, J and Zhang, J and Xiong, X},
title = {The impact of bronchoalveolar lavage fluid metagenomics next-generation sequencing on the diagnosis and management of patients with suspected pulmonary infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1521641},
pmid = {40625833},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Metagenomics/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; *Pneumonia/diagnosis/microbiology/drug therapy ; Aged, 80 and over ; },
abstract = {OBJECTIVES: This study aimed to enhance the comprehension of the practical utility of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in the clinical management of patients with suspected pneumonia.

METHODS: We retrospectively analyzed 296 individuals who underwent BALF mNGS and conventional microbial tests (CMTs) for suspected pneumonia. We compared the clinical characteristics between patients with pulmonary infection (PI) and those without pulmonary infection (NPI). The detection rate of mNGS and CMTs in different groups of patients were compared. The Sankey diagram was used to present the results of the influence of mNGS on diagnosis and treatment.

RESULTS: Comparison between PI and NPI showed that individuals with fever, concurrent malignant tumors, consolidation or ground-glass opacity on chest CT(Computed tomography) images, and elevated inflammatory markers on blood tests were more likely to develop lung infections. Analysis of the rate of positive detection between CMTs and mNGS in various subgroups revealed that mNGS had a significantly higher positive detection rate in patients with pulmonary infections (87.95% vs. 71.06%, p<0.001), in immunocompetent patients (86.91% vs. 68.08%, p<0.001), and in patients with malignant tumors (92.31% vs. 69.23%, p=0.035). Furthermore, mNGS helped initiate appropriate antibiotic treatment and confirmed the effectiveness of empirical treatment. Compared to immunocompetent patients, BALF mNGS in immunocompromised individuals with suspected lung infections yielded higher rates of accurate diagnosis (62.86% vs. 42.79%, p = 0.027) and more effective treatment (71.43% vs. 58.56%, p = 0.148).

CONCLUSIONS: BALF mNGS identified a greater variety of pathogens than CMTs. Immunocompromised patients with suspected pneumonia may benefit more from BALF mNGS.},
}

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

@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}

Humans
*Periodontitis/microbiology
*Microbiota
Biofilms/growth & development
Gingiva/microbiology
Bacteria/genetics/classification

@article {pmid40625179,
year = {2025},
author = {Zhang, Y and Zong, J and Liu, Y and Zhou, K and Shi, H and Yin, WB and Liu, L and Chen, Y},
title = {Progress on targeted discovery of microbial natural products based on the predictions of both structure and activity.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5np00008d},
pmid = {40625179},
issn = {1460-4752},
abstract = {Covering: up to 2025Microbial natural products (NPs) with diverse structures and fascinating activities are a fertile source of drug discovery. Genomic and metagenomic data have revealed that there are abundant valuable resources to be explored. With the advancement in technology, methods for discovering NPs from microorganisms are undergoing notable changes. In this highlight article, we summarized different NP discovery methods into activity-guided and structure-guided categories, emphasizing the characteristics of target compounds and providing typical examples of NPs. We primarily focused on recently developed representative methods that can simultaneously predict the structure and activity features of target compounds as well as the discovery trends of NPs reflected by these cutting-edge methods.},
}

@article {pmid40624949,
year = {2025},
author = {Wu, M and Zhang, T and Han, S and Huan, S and Jiang, Y and Wang, Y and Cai, Z and Zhou, J},
title = {Structure and Function Features of Abundant and Rare Prokaryotic Communities Along Nearshore to Offshore Transitions.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70144},
doi = {10.1111/1462-2920.70144},
pmid = {40624949},
issn = {1462-2920},
support = {42476137//National Natural Science Foundation of China/ ; KCXFZ20230731093402005//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; SGDX20220530111204028//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; RCJC20200714114433069//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; ZDSYS20230626091459009//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; 2023KCXTD052//Innovation Team Project for Guangdong's Universities/ ; 2025A1515010643//Natural Science Foundation of Guangdong Province/ ; 2025A1515010519//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Biodiversity ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Microbiota ; Metagenome ; Metagenomics ; *Archaea/genetics/classification/isolation & purification ; },
abstract = {Abundant and rare taxa are crucial members of the marine microbial community. However, their biodiversity, assembly mechanisms, functional characteristics and ecological response strategies remain poorly understood. In this study, 16S rRNA and metagenomic sequencing were carried out to reveal the structural and functional features of abundant and rare taxa across the transition from nearshore to offshore. The results showed that the biodiversity of both abundant and rare taxa decreased with increasing distance from shore, with rare taxa exhibiting relatively higher diversity indices than abundant ones. Neutral model analysis revealed that the assembly process gradually changed from deterministic to stochastic from nearshore to offshore among abundant taxa. In contrast, among rare taxa, a stochastic process dominated nearshore, whereas a deterministic process was predominant in the offshore environment. Meanwhile, the proportion of variance that could be explained by environmental factors was relatively higher among abundant communities than among rare ones. A co-occurrence network analysis indicated that rare communities displayed greater complexity and a higher degree of modularity than abundant communities. Functionally, abundant communities tended to favour an r-strategy, whereas rare communities leaned towards a K-strategy. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns along coastal-to-open water transitions.},
}

Biodiversity
*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Microbiota
Metagenome
Metagenomics
*Archaea/genetics/classification/isolation & purification

@article {pmid40624695,
year = {2025},
author = {Li, Q and Huang, J and Zhou, Y and Wu, Q and Zhou, J and He, F and He, L and Shi, Y and Guo, C and Dai, J},
title = {Virome profiling of Aedes albopictus across urban ecosystems in Guangdong reveals sex-specific diversity.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {264},
pmid = {40624695},
issn = {1756-3305},
support = {2024HK037//Scientific Research Project of General Administration of Customs/ ; 2024M760629//China Postdoctoral Science Foundation/ ; 2022YFC2302700//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Aedes/virology ; *Virome/genetics ; Female ; Male ; China ; *Mosquito Vectors/virology ; Phylogeny ; Ecosystem ; Metagenomics ; Cities ; Sex Factors ; Arboviruses/genetics/isolation & purification ; },
abstract = {BACKGROUND: Aedes albopictus mosquitoes are key vectors for arboviruses such as Dengue virus, Zika virus, and Chikungunya virus, posing significant global public health risks. Guangdong Province, a densely populated subtropical region in southern China, has experienced recurrent outbreaks of mosquito-borne diseases. However, sex- and geography-specific virome profiles of Aedes albopictus populations in this area remain uncharacterized, limiting the development of targeted surveillance strategies and precise risk assessment.

METHODS: We performed a metagenomic analysis of 1269 adult Aedes albopictus collected from five cities across Guangdong Province during autumn 2021. Mosquito pools underwent viral particle enrichment followed by DNA and RNA sequencing. Bioinformatic analyses were employed to characterize viral communities, evaluate alpha/beta diversity, and conduct phylogenetic reconstruction.

RESULTS: A comparative analysis of virome profiles in male and female Aedes albopictus across five regions of Guangdong Province (Chaozhou, Guangzhou, Shaoguan, Shenzhen, Zhanjiang) revealed significant viral distribution patterns influenced by both sex and geographic location. Female mosquitoes predominantly hosted vertebrate-associated arboviruses, including Flavivirus, consistent with their blood-feeding behavior. RNA virome composition showed significant sex-specific clustering (permutational multivariate analysis of variance, PERMANOVA, P = 0.008), with coastal cities (Shenzhen, Zhanjiang) being dominated by RNA viruses, whereas inland areas (Shaoguan) exhibited a predominance of DNA viruses. DNA virome profiles displayed divergence between sexes but marked regional variation. Guangzhou emerged as an outlier, exhibiting exceptional bacteriophage diversity distinct from other regions. Phylogenetic analysis identified zoonotic pathogens with signatures of cross-species transmission and region-specific evolutionary adaptation. These findings highlight the interplay between mosquito ecology, geographic factors, and viral evolution in shaping virome diversity.

CONCLUSIONS: This study presents the inaugural comparative analysis of DNA/RNA viromes in Aedes albopictus populations across Guangdong Province, revealing distinct sex-specific and geographic patterns in viral composition. The identification of vertebrate-associated viruses in female mosquitoes reinforces their epidemiological significance as arboviral vectors, while male-specific environmental viral signatures suggest potential pathways for ecological spillover. Coastal-inland and urban-rural disparities in viral communities emphasize the need for regionally tailored surveillance. These findings provide essential baseline virome data for forecasting emerging arboviral threats and informing strategies to mitigate zoonotic spillover in subtropical urban ecosystems.},
}

Animals
*Aedes/virology
*Virome/genetics
Female
Male
China
*Mosquito Vectors/virology
Phylogeny
Ecosystem
Metagenomics
Cities
Sex Factors
Arboviruses/genetics/isolation & purification

@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Diarrhea/chemically induced/microbiology/therapy ; Mice ; *Bacteroides fragilis ; Mice, Inbred C57BL ; *Probiotics/therapeutic use ; Mice, Inbred BALB C ; *Antineoplastic Agents/adverse effects ; Middle Aged ; Fluorouracil/adverse effects ; Feces/microbiology ; Female ; Aged ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}

Animals
*Dysbiosis/chemically induced/therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects
Humans
*Diarrhea/chemically induced/microbiology/therapy
Mice
*Bacteroides fragilis
Mice, Inbred C57BL
*Probiotics/therapeutic use
Mice, Inbred BALB C
*Antineoplastic Agents/adverse effects
Middle Aged
Fluorouracil/adverse effects
Feces/microbiology
Female
Aged

@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; Male ; Middle Aged ; Female ; Metabolic Networks and Pathways ; *Dysbiosis/microbiology ; *Clostridiales/genetics/isolation & purification ; Aged ; Case-Control Studies ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}

Humans
*Cholangiocarcinoma/microbiology/metabolism
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/metabolism
*Bile Acids and Salts/metabolism
Male
Middle Aged
Female
Metabolic Networks and Pathways
*Dysbiosis/microbiology
*Clostridiales/genetics/isolation & purification
Aged
Case-Control Studies
Adult
Feces/microbiology

@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/isolation & purification/genetics/growth & development/metabolism ; *Microbial Interactions ; Coculture Techniques ; Metagenome ; Healthy Volunteers ; Feces/microbiology ; China ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bacteria/classification/isolation & purification/genetics/growth & development/metabolism
*Microbial Interactions
Coculture Techniques
Metagenome
Healthy Volunteers
Feces/microbiology
China

@article {pmid40624535,
year = {2025},
author = {Zhao, Y and Niu, X and Zhang, Y and Zhao, L and Zhang, L and He, J and Zhang, Q and Mao, Y and Wang, F and Zhao, X and Wang, R},
title = {Impact of supplementing Limosilactobacillus fermentum MN-LF23 on the eradication of Helicobacter pylori with 14-day standard quadruple therapy: a randomized, double-blind, placebo-controlled trial.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {106},
pmid = {40624535},
issn = {1475-2891},
support = {2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Male ; Female ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/therapy ; Double-Blind Method ; Middle Aged ; Adult ; *Limosilactobacillus fermentum ; Drug Therapy, Combination ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Dietary Supplements ; Dyspepsia ; },
abstract = {BACKGROUND: The effect of probiotics on Helicobacter pylori (Hp) infection demonstrates considerable heterogeneity. This study aims to elucidate the role of Limosilactobacillus fermentum MN-LF23 (MN-LF23) in Hp-infected populations.

METHODS: A total of 94 adult patients with confirmed Hp infection were enrolled in this study and randomly allocated to the placebo or MN-LF23 group. Patients initially received either placebo or probiotics along with standard quadruple therapy for 2 weeks, followed by continued administration of either placebo or probiotics for an additional 4 weeks. The eradication of Hp, serum levels of inflammatory factors, and alterations in gastrointestinal symptoms were assessed at weeks 0, 2, and 6, while fecal samples were collected for metagenomic sequencing.

RESULTS: The results showed no significant difference (P = 1) in the eradication rate between the placebo group (85.11%) and the probiotic group (82.98%). Following treatment, the incidence of constipation, dyspepsia, and Gastrointestinal Symptom Rating Scale (GSRS) scores in the probiotic group were markedly lower (P < 0.05) compared to those observed in the placebo group. Throughout the treatment process, there were no significant differences in TNF-α and IL-1β levels between the two groups. Compared to the placebo group, the probiotic group exhibited a significant increase in beneficial bacteria such as Limosilactobacillus fermentum, Lactiplantibacillus plantarum, Bifidobacterium longum, Coprococcus caltus, and Clostridium butyricum.

CONCLUSION: MN-LF23 supplementation did not improve the eradication rate of standard quadruple therapy. However, it significantly reduced the overall GSRS score, improved digestive and constipation symptoms, and promoted the proliferation of beneficial bacteria in the intestine.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
Male
Female
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/therapy
Double-Blind Method
Middle Aged
Adult
*Limosilactobacillus fermentum
Drug Therapy, Combination
Anti-Bacterial Agents/therapeutic use/administration & dosage
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome
Dietary Supplements
Dyspepsia

@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}

Humans
*Polycystic Kidney, Autosomal Dominant/microbiology/complications
*Gastrointestinal Microbiome
*Intracranial Aneurysm/microbiology/complications
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Aged
Bacteria/genetics/classification/isolation & purification

@article {pmid40624247,
year = {2025},
author = {Lin, YT and Sayols-Baixeras, S and Baldanzi, G and Dekkers, KF and Hammar, U and Nguyen, D and Nielsen, N and Eklund, AC and Varotsis, G and Holm, JB and Nielsen, HB and Lind, L and Bergström, G and Smith, JG and Engström, G and Ärnlöv, J and Sundström, J and Orho-Melander, M and Fall, T},
title = {The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {276},
pmid = {40624247},
issn = {2730-664X},
support = {ERC-STG-2018-801965, ERC-CoG-2014-649021, ERC-STG-2015-679242//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2019-01471; 2018-02784; 2018-02837; 2021-03291//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687; 20200711 (M.O-M.); 20180343, 20210357; 20200173; 20190526//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF20OC0063886//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; LUDC-IRC 15-0067//Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; },
abstract = {BACKGROUND: There is mounting evidence supporting the role of the microbiota in hypertension from experimental studies and population-based studies. We aimed to investigate the relationship between specific characteristics of the gut microbiome and 24-h ambulatory blood pressure measurements.

METHODS: The association of gut microbial species and microbial functions, determined by shotgun metagenomic sequencing of fecal samples, with 24-h ambulatory blood pressure measurements in 3695 participants and office blood pressure was assessed in multivariable-adjusted models in 2770 participants without antihypertensive medication from the Swedish CArdioPulmonary bioImage Study.

RESULTS: Gut microbiome alpha diversity was negatively associated with diastolic blood pressure variability. Additionally, four microbial species were associated with at least one of the 24-h blood pressure traits. Streptococcus sp001556435 was associated with higher systolic blood pressure, Intestinimonas massiliensis and Dysosmobacter sp001916835 with lower systolic blood pressure, Dysosmobacter sp001916835 with lower diastolic blood pressure, and ER4 sp900317525 with lower systolic blood pressure variability. Moreover, office blood pressure data from a subsample without ambulatory blood pressure measurements replicated the association of Intestinimonas massiliensis with systolic blood pressure and Dysosmobacter sp001916835 with diastolic blood pressure. Species associated with 24-h blood pressure were linked to a similar pattern of metabolites.

CONCLUSIONS: In this large cross-sectional analysis, gut microbiome alpha diversity negatively associates with diastolic blood pressure variability, and four gut microbial species associate with 24-h blood pressure traits.},
}

@article {pmid40624236,
year = {2025},
author = {Wu, D and Niu, J and Hu, J and Wang, H and Kuang, H},
title = {Metabolomics combined with metagenomics analysis reveals the potential mechanism of Zhejiang psyllium polysaccharides against hyperuricemia in rats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24180},
pmid = {40624236},
issn = {2045-2322},
mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology ; *Metagenomics/methods ; *Metabolomics/methods ; Rats ; Uric Acid/blood ; Gastrointestinal Microbiome/drug effects ; Male ; *Psyllium/pharmacology/chemistry ; *Polysaccharides/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Kidney/pathology/drug effects/metabolism ; Blood Urea Nitrogen ; Creatinine/blood ; },
abstract = {This study aimed to assess the anti-hyperuricemia efficacy of Zhejiang psyllium polysaccharides (ZPP) in rats and to explore its underlying mechanism. Hyperuricemia was induced by intragastric administration of potassium oxonate, hypoxanthine, and adenine. The serum levels of uric acid (UA), creatinine (Cr), and blood urea nitrogen (BUN) were measured, and kidney pathology was examined. Serum metabolomics was employed to monitor metabolic alterations following ZPP intervention. Metagenomic analysis was conducted to investigate the impact of ZPP on the intestinal flora of hyperuricemia rats. The results showed that ZPP could significantly reduce the serum UA level in hyperuricemia rats and exhibited a certain renal protective effect. The metabolomics results indicated that ZPP regulates uric acid levels in rats with hyperuricemia and ameliorates renal pathological changes by modulating biomarkers associated with purine metabolism, amino acid metabolism, and lipid metabolism. Metagenomic research also found that ZPP could increase the relative abundance of uric acid metabolism-related probiotics, such as Limosilactobacillus reuteri and Lactobacillus murinus, thereby improving intestinal flora imbalance in rats with hyperuricemia.},
}

Animals
*Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology
*Metagenomics/methods
*Metabolomics/methods
Rats
Uric Acid/blood
Gastrointestinal Microbiome/drug effects
Male
*Psyllium/pharmacology/chemistry
*Polysaccharides/pharmacology/therapeutic use
Rats, Sprague-Dawley
Kidney/pathology/drug effects/metabolism
Blood Urea Nitrogen
Creatinine/blood

@article {pmid40624115,
year = {2025},
author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F},
title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24242},
pmid = {40624115},
issn = {2045-2322},
support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; },
abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.},
}

Humans
Female
*Dysbiosis/microbiology
Pregnancy
Adult
Cross-Sectional Studies
Metagenomics/methods
*Microbiota/genetics
*Abortion, Spontaneous/microbiology
Mouth Mucosa/microbiology
Metagenome
*Mouth/microbiology
Young Adult

@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
*Respiratory Tract Infections/microbiology/diagnosis
Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid40623822,
year = {2025},
author = {Kwok, WC and Pates, K and Shah, A and Jackson, L and Frost, F},
title = {Antimicrobial resistance in chronic lung infection: the road to resistance.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thorax-2024-222396},
pmid = {40623822},
issn = {1468-3296},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health crisis and is particularly relevant to people living with chronic lung diseases such as bronchiectasis, cystic fibrosis and chronic obstructive pulmonary disease. These conditions frequently involve acute and chronic bacterial infections, requiring increased antibiotic usage and risk of AMR. Understanding the dynamics of AMR and emerging diagnostic and therapeutic strategies is crucial for optimising patient outcomes in this setting.

AIMS: This review explores the interplay between AMR and chronic bacterial lung infections, examining current understanding of pathogen epidemiology, diagnostic strategies, clinical implications of resistance and the impact of treatments. Future directions in research and therapeutic innovation are also outlined.

NARRATIVE: Key pathogens in chronic lung infections, such as Pseudomonas aeruginosa, Haemophilus influenzae, Staphylococcus aureus and Moraxella catarrhalis, exhibit diverse resistance mechanisms and AMR is linked to increased disease severity, exacerbation frequency and mortality, particularly with multidrug-resistant strains. Long-term antibiotic therapies, such as macrolides and inhaled agents, improve clinical outcomes but may drive resistance, necessitating ongoing efforts to understand how they can best be employed. Traditional diagnostic methods, such as culture-based antimicrobial susceptibility testing, often fail to capture the complexity of polymicrobial infections and resistomes. Although advanced techniques like next-generation sequencing and metagenomics are able to identify clinically relevant resistotypes, their development toward clinical utility is still in progress.

CONCLUSIONS: AMR in chronic lung infections represents a dynamic and multifaceted challenge. Novel antibiotics, precision medicine approaches and alternative therapies such as bacteriophages show promise but require further validation. Improved stewardship and individualised treatment strategies are critical for mitigating AMR and enhancing patient outcomes. Collaborative efforts among researchers, clinicians and policy-makers are vital to advancing care and combating this global threat.},
}

@article {pmid40623508,
year = {2025},
author = {Yang, X and Huang, J and Zeng, Z and Sun, S and Wang, J and Wang, Z},
title = {Integrated multi-omics analysis reveals the effect of glucose selenol improves rat immunity.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110023},
doi = {10.1016/j.jnutbio.2025.110023},
pmid = {40623508},
issn = {1873-4847},
abstract = {This study aimed to investigate the effects of glucose selenol (SeGlu) on the immune function of rats, with a particular focus on the spleen. Rats were randomly divided into CK (deionized water, oral), Se0.15 group (0.15 mg/L SeGlu, oral), and Se0.4 group (0.4 mg/L SeGlu, oral) for 30 days continuously. 0.15 mg/L SeGlu significantly increased the serum antioxidant levels and the levels of IgM and IgG. The Se0.4 group upregulated the inflammatory factor levels of IL-2 and IL-6, and both concentrations significantly reduced the serum TNF-α level. Transcriptome analysis indicated that the supplementation of SeGlu could affect three types of proteins: peptidases, tumor necrosis factor receptors, and transmembrane transport proteins. KEGG enrichment discovered pathway annotations directly or indirectly related to the immune process, especially phagosomes, natural killer cell-mediated cytotoxicity, and nod-like receptor signaling pathways. We identified 59 SeGlu target differentially expressed genes and 8 (NEG) and 20 (POS) co-expressed differentially expressed metabolites. Immunoglobulin-related DEGs were concentrated in the transcription factor family V-set, and were identified on chromosome 6. In addition, metagenome sequencing showed that SeGlu treatment increased abundance of Roseburia, Ruminococcus, Eubacterium, Coprobacillus, and Intestinimonas at the genus level. Spearman correlation analysis results showed that the modulatory effects of SeGlu on D-proline were related to the regulation of Roseburia, Clostridium, Eubacterium Coprobacillus, Butyricimonas, and Muribaculum. Overall, the analyses of rat physiology, transcriptome, metabolome, and metagenome offer new insights into Se on rat immunity. SeGlu provides beneficial immune protection and is a promising organic selenium enrichment additive.},
}

@article {pmid40622975,
year = {2025},
author = {Kabir, KMA and Sigera, C and Maduranga, S and Weeratunga, P and Rajapakse, S and Fernando, D and Lloyd, AR and Bull, RA and Rodrigo, C},
title = {Chikungunya masquerading as dengue infection in Sri Lanka uncovered by metagenomics.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326995},
pmid = {40622975},
issn = {1932-6203},
mesh = {Humans ; *Dengue/diagnosis/virology ; Sri Lanka ; *Chikungunya Fever/diagnosis/virology ; *Chikungunya virus/genetics ; Female ; Male ; *Metagenomics/methods ; Adult ; Middle Aged ; Phylogeny ; Dengue Virus/genetics ; Prospective Studies ; Diagnosis, Differential ; Young Adult ; High-Throughput Nucleotide Sequencing ; Adolescent ; },
abstract = {INTRODUCTION: Dengue is a significant threat to human health in South and Southeast Asia where patients are treated without diagnostic confirmation during outbreaks. This approach, though cost-effective may miss important infections especially those caused by other arboviruses (e.g., Zika, Chikungunya and West Nile virus). This study aimed to diagnose missed infections mimicking dengue by using metagenomic next generation sequencing (mNGS).

Total nucleic acid (DNA and RNA) was extracted and subjected to mNGS from acute infection plasma of 60 patients from a prospective cohort study in Sri Lanka in which patients with clinically suspected dengue fever were recruited but were later confirmed as dengue-negative by NS1 antigen testing and by dengue-specific reverse transcription and polymerase chain reaction (RT-PCR) analysis. mNGS data revealed missed chikungunya and dengue infections in five patients each, and a possible bacterial infection by Klebsiella pneumoniae in another patient. It was not possible to differentiate chikungunya infections from dengue infections based on clinical features or routine non-diagnostic laboratory tests conducted in early infection (e.g., full blood count, C-reactive protein level). Phylogenetic analysis showed that the chikungunya sequences from this study were closely related to those sequenced from Maldives, Malaysia, India and Singapore between 2015-2019.

CONCLUSIONS: Chikungunya infection may masquerade as dengue especially in low- and middle-income countries where dengue is treated based on clinical suspicion only - without confirmatory testing. As both infections are likely prevalent worldwide, but the complications and natural history of chikungunya and dengue infections are quite different, the addition of cheap and accessible diagnostics for both infections should be pursued in endemic countries.},
}

Humans
*Dengue/diagnosis/virology
Sri Lanka
*Chikungunya Fever/diagnosis/virology
*Chikungunya virus/genetics
Female
Male
*Metagenomics/methods
Adult
Middle Aged
Phylogeny
Dengue Virus/genetics
Prospective Studies
Diagnosis, Differential
Young Adult
High-Throughput Nucleotide Sequencing
Adolescent

@article {pmid40622965,
year = {2025},
author = {Adigoun, RFR and Durand, A and Aholoukpè, HNS and Tchokponhoué, DA and Achigan-Dako, EG and Bokonon-Ganta, AH and Benizri, E},
title = {Plant tissue type and mineral contents shape endophytic bacterial communities in the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] in Benin.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327715},
pmid = {40622965},
issn = {1932-6203},
mesh = {*Endophytes/genetics/classification ; Plant Leaves/microbiology/metabolism ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Benin ; *Bacteria/genetics/classification/isolation & purification ; *Minerals/metabolism/analysis ; Phylogeny ; },
abstract = {Diverse endophytic bacteria inhabit distinct tissues of a given species and are essential for plant growth and resilience to various stresses. Little information is available on bacterial endophytes associated with Synsepalum dulcificum, an opportunity fruit crop with high economic and medicinal values. Using Illumina sequencing of the bacterial 16S rRNA gene, the diversity and structure of the endophytic bacterial community in the roots and leaves of S. dulcificum were determined, considering 29 accessions from three distinct phenotypes located either in home gardens or on farms in Benin. 2,468 Operational Taxonomic Units (OTUs) were recorded in the leaf and root endosphere of S. dulcificum, affiliated with 20 bacterial phyla, 49 classes, 125 orders, 217 families and 365 genera. Actinomycetota, Pseudomonadota and Chloroflexota were the most abundant phyla in the roots. In comparison, Pseudomonadota stood out as almost the unique phylum in the leaves, suggesting a significant decrease in diversity from roots to leaves. Significant correlations (p < 0.05) were observed between the relative abundance of the endophytic bacterial taxa and the mineral contents in the leaves, roots, and soil. While bacterial communities depended highly on accession, plant phenotype and habitat discriminated them in roots and leaves, respectively. Metagenome function prediction indicated that S. dulcificum harbors bacteria with the potential to metabolize carbohydrates and amino acids, as well as synthesize secondary metabolites and antimicrobial compounds beneficial for plant growth and adaptation to environmental stresses. These findings open room for exploiting endophytic diversity to enhance the growth and sustainable production of S. dulcificum.},
}

*Endophytes/genetics/classification
Plant Leaves/microbiology/metabolism
Plant Roots/microbiology
RNA, Ribosomal, 16S/genetics
Benin
*Bacteria/genetics/classification/isolation & purification
*Minerals/metabolism/analysis
Phylogeny

@article {pmid40622630,
year = {2025},
author = {Yuan, R and Jin, X and Liu, X and Hao, K and Shi, Y and Yang, Z and Zhang, L and Chen, J and Guo, C and Wu, Y and Tang, J and Zhao, Z},
title = {Increased pathogens and reduced intestinal immune genes associated with fish diseases during the winter-spring transition.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40622630},
issn = {1618-1905},
support = {cx[23]1007//the Jiangsu Agricultural Science and Technology Independent Innovation fund/ ; },
abstract = {Global climate change has posed significant challenges to the aquaculture industry, leading to the emergence of novel diseases. A recently emerging disease, termed the overwintering syndrome, has been reported in freshwater fish aquaculture systems in China during the winter-spring transition. This syndrome is characterized by weight loss, decreased activity levels, and mass mortality. Currently, little is known about cause of the emerging disease. In this study, the gut microbiota of healthy and diseased channel catfish (Ictalurus punctatus) were analyzed using metagenomic sequencing. Diseased fish exhibited a notable reduction in bacterial diversity compared to healthy controls, while the viral richness was significantly higher. Additionally, random forest models based on gut microbiota composition revealed high accuracy in distinguishing between diseased and healthy fish. Several gut microbiota biomarkers with potential diagnostic value were identified, primarily consisting of rare taxa (relative abundance < 5%), except for Alphaproteobacteira, Siphoviridae and Podoviridae. Furthermore, an increase in the prevalence and abundance of pathogens was observed in the intestines of diseased fish compared to healthy counterparts. Notably, Vibrio cholerae and Dickeya dadantii were enriched in the intestines of fish exhibiting the overwintering syndrome. Concurrently, genes involved in the synthesis of innate immune factors was markedly diminished in the gut microbiota of diseased fish, along with a reduction in the microbial hosts of these genes. Collectively, these findings elucidate the enrichment of pathogens and the attenuation of innate immunity in fish with the overwintering syndrome, correlating with alterations in the gut microbiota.},
}

@article {pmid40622282,
year = {2025},
author = {Ni, Z and Zhou, Y and Chang, M and Xia, T and Zhou, W and Gao, Y},
title = {High-Altitude Impacts on Gut Microbiota: Accelerated Aging and the Urgency for Targeted Health Interventions.},
journal = {High altitude medicine & biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ham.2025.0016},
pmid = {40622282},
issn = {1557-8682},
abstract = {The human gut microbiota is integral to the aging process, and its composition is notably influenced by the unique environmental pressures of high-altitude plateaus, characterized by hypobaric and hypoxic conditions. This study explores the correlation between physiological aging and gut microbiota among high-altitude plateau inhabitants, an essential aspect of health preservation in such regions. We conducted a metagenomic analysis of fecal samples from 105 individuals who migrated to high-altitude areas before the age of 20. Our results demonstrate that advancing age and prolonged high-altitude living significantly modify the gut microbiota, evidenced by reduced diversity and an elevated Firmicutes to Bacteroidetes (F/B) ratio in older subjects. Notably, the abundance of the anti-aging bacterium Akkermansia muciniphila (A. muciniphila) inversely correlates with age, showing a significant decline post the age of 25. A comparative analysis of 2,007 individuals from lower altitudes revealed a similar negative correlation between A. muciniphila and age, with a decline evident from age 38. These findings indicate that the high-altitude plateau environment may accelerate the decline of A. muciniphila by 10 years, underscoring the need for targeted health strategies for high-altitude populations.},
}

@article {pmid40622149,
year = {2025},
author = {Chen, Z and Xun, L and Xia, Y and Gong, X},
title = {Overlooked role of heterotrophic prokaryotes in sulfur oxidation makes the sediment of the Bohai Sea a sufficient sink of hydrogen sulfide.},
journal = {mBio},
volume = {},
number = {},
pages = {e0172225},
doi = {10.1128/mbio.01722-25},
pmid = {40622149},
issn = {2150-7511},
abstract = {Marine sediments are the active sites for the biogeochemical cycling of sulfur. Sulfate is used as a major terminal electron acceptor for the anaerobic oxidation of organic compounds in deep sediments, and the produced sulfide is normally oxidized back to sulfate in upper sediments. However, it is unclear which microorganisms, metabolic pathways, and enzymes are mainly involved in oxidation. Here, we used metagenomics, metatranscriptomics, and the testing of sulfide, thiosulfate, and sulfite oxidation in sediment samples to figure out how sulfide is oxidized in the Bohai Sea sediments. Surprisingly, sulfur oxidation is widespread in the microbial community (>67.1%) of mostly heterotrophic prokaryotes across 44 phyla, dominated by Proteobacteria. Known chemolithotrophic sulfur oxidizers were absent. The prevalent sulfur-oxidizing pathway was sulfide to zerovalent sulfur, sulfite, and then sulfate. Thiosulfate is not a major metabolic intermediate. Genes encoding sulfide oxidation (sqr and fccAB), zerovalent sulfur oxidation (pdo, rdsrAB, and shdr), and sulfite oxidation (aprAB/sat) were abundant and upregulated after adding NaHS. Thiosulfate, which is formed between the reaction of zerovalent sulfur and sulfite, was only slowly oxidized, which was consistent with the lack of key genes encoding for direct oxidation of thiosulfate to sulfate. The findings indicate how sulfur is oxidized in the Bohai Sea sediments. The common participation in sulfur oxidation by most heterotrophic prokaryotes results in the effective oxidation of sulfide in the surface sediment, blocking the release of hydrogen sulfide into the water column.IMPORTANCESulfur cycling is tightly interwoven with other crucial element cycles, including carbon, nitrogen, and iron in marine sediments. Sulfate is the most abundant electron acceptor in marine sediments, and sulfate reduction generates a large amount of sulfide. The majority of sulfide is oxidized to sulfate via abiotic or biological transformations, mainly by sulfur oxidizers with different redox states. However, autotrophic sulfur oxidizers, considered key players for sulfur oxidation, are in low abundance in the sediment, limiting our understanding of the pivotal biogeochemical process. This study shows the prevalent distribution of sulfur oxidation among the microbial community and emphasizes the importance of heterotrophic sulfur oxidation in sediments. It evidences the importance of previously overlooked key enzymes for elemental sulfur oxidation and supports that thiosulfate is not the major intermediate during sulfur oxidation. Understanding these key processes is crucial for elucidating biogeochemical processes in marine sediments.},
}

@article {pmid40621974,
year = {2025},
author = {Chen, J and Aherfi, S and Steichen, P and Rios, G and Waldmann, R and Barbry, P},
title = {[Molecular epidemiology of viruses sequenced from wastewater].},
journal = {Medecine sciences : M/S},
volume = {41},
number = {6-7},
pages = {585-592},
doi = {10.1051/medsci/2025083},
pmid = {40621974},
issn = {1958-5381},
mesh = {*Wastewater/virology ; Humans ; *SARS-CoV-2/genetics/isolation & purification ; COVID-19/epidemiology/virology ; *Molecular Epidemiology/methods ; *Viruses/genetics/isolation & purification ; Metagenomics/methods ; Pandemics ; Genome, Viral ; },
abstract = {Virus surveillance using metagenomic analysis of sequences from wastewater appears to be a promising epidemiological tool for monitoring the spread of viruses in large populations. Its use during the COVID-19 pandemic enabled the monitoring of SARS-CoV-2 circulation without requiring the collection of multiple individual samples. This approach allows both symptomatic and asymptomatic infections to be monitored in a highly cost-effective way. Initially based on PCR detection, the introduction of nucleic acid sequencing has improved this tool by providing more detailed metagenomic information. Experience with COVID-19 pandemics suggests that this epidemiological tool should now be extended to other viruses detectable in wastewater. This review discusses the different methods used, highlighting the challenges of a rapid deployment on an international scale to better understand the global circulation of viral pathogens.},
}

*Wastewater/virology
Humans
*SARS-CoV-2/genetics/isolation & purification
COVID-19/epidemiology/virology
*Molecular Epidemiology/methods
*Viruses/genetics/isolation & purification
Metagenomics/methods
Pandemics
Genome, Viral

@article {pmid40621956,
year = {2025},
author = {Huang, X and Yang, L and Zhou, S and Zhong, L and Xu, G and Bi, M and Yang, X and Su, X and Rillig, MC},
title = {Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70329},
doi = {10.1111/gcb.70329},
pmid = {40621956},
issn = {1365-2486},
support = {42021005//National Natural Science Foundation of China/ ; U23A20145//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo Municipal Science and Technology Innovative Research Team/ ; ANSO-PA-2023-18//Alliance of International Science Organizations/ ; },
mesh = {*Biofilms/growth & development ; *Plastics ; *Nitrogen Cycle ; *Estuaries ; Transcriptome ; Nitrogen/metabolism ; Ecosystem ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; Metagenome ; },
abstract = {Biofilms represent a ubiquitous microbial lifestyle that facilitates colonization, symbiosis, and nutrient cycling, shaping environmental chemical transformations. In the Anthropocene, the proliferation of artificial surfaces, particularly plastics, has introduced novel and artificial ecological niches for microbial colonization. However, the biogeochemical potential of biofilms on these emerging artificial substrates remains largely unknown. Here, using [15]N tracing, amplicon, metagenome, and metatranscriptomic sequencing, we explore nitrogen (N) potential biogeochemistry across artificial and natural biofilms as well as the bulk seawater. Our results reveal that plastic biofilms exhibit enhanced N transformation potential, including elevated nitrification (2~45-fold), denitrification (5~44-fold), and N2O production (3~13-fold) rates, compared to natural biofilms and ambient seawater. This functional shift corresponds to distinct microbial community structures, driven by active N-cycling taxa and metabolic pathway reconfigurations on plastic surfaces. We also observe that carbohydrate metabolism pathways, such as glycolysis and the pentose phosphate pathway, were highly expressed in plastic biofilms, with transcriptional levels of glk (encoding glucokinase) and PGK (encoding phosphoglycerate kinase) increased by 6- and 2-fold, respectively. Our findings depict the role of plastic biofilms as active participants in estuarine N cycling and underscore the broader implications of plastic pollution on ecosystem biogeochemistry.},
}

*Biofilms/growth & development
*Plastics
*Nitrogen Cycle
*Estuaries
Transcriptome
Nitrogen/metabolism
Ecosystem
Seawater/microbiology
Bacteria/metabolism/genetics
Gene Expression Profiling
Metagenome

@article {pmid40621942,
year = {2025},
author = {Lefler, FW and Berthold, DE and Barbosa, M and Hu, J and Taylor, A and Moretto, J and Chaffin, JD and Raymond, H and Laughinghouse, HD},
title = {Metagenomes from cyanobacterial harmful algal blooms from lakes in Ohio (USA).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0040025},
doi = {10.1128/mra.00400-25},
pmid = {40621942},
issn = {2576-098X},
abstract = {We report two metagenomic libraries of freshwater cyanobacterial harmful algal blooms (cyanoHABs) from Ohio, USA. One sample was collected from a Planktothrix-dominated bloom in Grand Lake St. Marys, and another from a mixed Dolichospermum and Microcystis-dominated cyanoHAB in the western basin of Lake Erie.},
}

@article {pmid39253412,
year = {2025},
author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, Â and Castrillo, G and Wagner, MR},
title = {Persistent legacy effects on soil microbiota facilitate plant adaptive responses to drought.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.26.609769},
pmid = {39253412},
issn = {2692-8205},
abstract = {Both chronic and acute drought alter the composition and physiology of soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Currently, little is known about how the resulting precipitation legacy effects manifest at the molecular and physiological levels and how they influence neighboring plants, especially in the context of subsequent drought. We characterized metagenomes of six prairie soils spanning a steep precipitation gradient in Kansas, USA. By statistically controlling for variation in soil porosity and elemental profiles, we identified bacterial taxa and functional gene categories associated with precipitation. This microbial precipitation legacy persisted through a 5-month-long experimental drought and mitigated the negative physiological effects of acute drought for a wild grass species that is native to the precipitation gradient, but not for the domesticated crop species maize. In particular, microbiota with a low-precipitation legacy altered transcription of a subset of host genes that mediate transpiration and intrinsic water use efficiency during drought. Our results show how long-term exposure to water stress alters soil microbial communities with consequences for the drought responses of neighboring plants.},
}

@article {pmid40621926,
year = {2025},
author = {Samson, R and Kumar, S and Dastager, S and Khairnar, K and Dharne, M},
title = {Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0172024},
doi = {10.1128/spectrum.01720-24},
pmid = {40621926},
issn = {2165-0497},
abstract = {Glacier-fed rivers are significant ecological components of the river catchments, yet their microbial diversity and the associated antimicrobial potential remain underexplored. The Ganges is a glacier-fed river of immense cultural, religious, and ecological significance that supports over 400 million people downstream, providing essential water for agriculture, industry, and daily use. Despite its importance, the microbial community composition and antimicrobial potential, across its relatively pristine origin, remain largely underexplored. One possible explanation for this could be the lower microbial load in the upstream glacier-fed region, which likely results in a reduced DNA yield, insufficient for whole-metagenome sequencing, in contrast to the more biologically diverse and nutrient-rich lower reaches. In this study, we developed an efficient DNA extraction and amplification method using low-input DNA to sequence the microbiome from sediments of the glacier-fed Ganges River in pre-monsoon and post-monsoon over 2 years. Taxonomic and functional diversity of bacterial and viral (phage) communities were analyzed, together with the seasonal variations in their composition. Significant differences in microbial communities were observed in response to seasonal shifts (P < 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P < 0.05). The microbiome harbors potential for the biosynthesis of streptomycin, phenylpropanoid, penicillin, and cephalosporins. Bacteriophages from Podoviridae, Myoviridae, and Siphoviridae showed lytic potential against putrefying and pathogenic bacteria. This first comprehensive study on the glacier-fed Ganges River highlights significant seasonal shifts in microbial diversity. The initial insights into the functional profile of the bacterial and phage diversity offer opportunities to explore various natural compounds and enzymes to tackle antimicrobial resistance under the one-health canopy.IMPORTANCEThis study addresses a knowledge gap by exploring the microbial diversity and antimicrobial potential of the glacier-fed Ganges River across different seasons. The findings reveal various taxa with biosynthetic capabilities for antimicrobial compounds. Additionally, the presence of bacteriophages with lytic potential opens up opportunities for their exploration and application spanning various domains of one health. These findings lay a foundational basis for understanding the unique properties of this riverine ecosystem and offer valuable insights into environmental conservation and the potential to tackle antimicrobial resistance.},
}

@article {pmid40621774,
year = {2025},
author = {Albini, A and Trapani, D and Bertolini, F and Noonan, DM and Orecchia, R and Corso, G},
title = {From combination early detection to multicancer testing: shifting cancer care toward proactive prevention and interception.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-24-0558},
pmid = {40621774},
issn = {1940-6215},
abstract = {Identifying the presence of tumors at a very early stage or deciphering the process underlying their development can enable the interception of pro-malignant mechanisms underpinning cancer emergence, facilitating more effective prevention. Advances in molecular profiling allow the detection of genetic, epigenetic, immune, and microenvironmental alterations associated with cancer risk. Liquid biopsy permits non-invasive analysis of circulating tumor cells, nucleic acids, immune cells, extracellular vesicles, proteins, cytokines, and metabolites, while metagenome analysis facilitates gut microbiota profiling. Multi-cancer early detection (MCED) assays broaden this approach, capturing signals from multiple malignancies using a single blood sample. These technologies go beyond genomics, addressing immune dysregulation and metabolic shifts and may help identify gut microbiota imbalances. Clonal hematopoiesis of indeterminate potential (CHIP) gets increasing recognition of biomarker. Cardiovascular risk scores based on multiple parameters are an inspiring example The analysis of a combination of cancer drivers and enablers should provide a more sensitive and personalized measure of cancer prodromic profiles. Artificial intelligence will further support this transition by integrating molecular, immune, and metabolic data to develop individualized risk profiles. This shift from single-cancer detection to integrated, mechanism-based screening fosters a more proactive prevention model.. This combination early detection empowers cancer interception by using strategies including lifestyle modification, nutritional optimization, drug repurposing, pharmacologic interventions, and targeted chemoprevention. Moving beyond single parameters analysis and organ-specific screening, this multidimensional approach advances early detection and interception as practical clinical goals, facilitating the fundamental aim of positioning prevention at the forefront of oncology.},
}

@article {pmid40621575,
year = {2025},
author = {Gupta, S and Bhargava, V and Kaur, J and Lata, P},
title = {Adaptations, diversity, and biotechnological potential of thermophilic microorganisms: exploring culture-dependent and culture-independent approaches in extreme environments.},
journal = {3 Biotech},
volume = {15},
number = {8},
pages = {232},
pmid = {40621575},
issn = {2190-572X},
abstract = {Thermophilic prokaryotes exhibit remarkable adaptations at both physiological and molecular levels, which enables them to survive in elevated-temperature environments (35-113 °C). This review consolidates the current findings on membrane, genomic and proteomic adaptations of thermophiles, including presence of ether-linked lipids, branched-chain fatty, saturated long-chain hydrocarbons, reverse gyrase-mediated DNA supercoiling, and group II chaperonins. Although culture-independent approaches, such as metagenomics and next-generation sequencing (NGS) techniques, have expanded our understanding of thermophilic microbial diversity, which is limited by traditional culture-dependent approaches. However, these findings are largely based on the genomic predictions rather than direct experimental evidence. Therefore, the culture-dependent methods are crucial for isolating and characterizing thermophiles for both genetic and functional studies. India's geothermal spring ecosystems serve as natural laboratories for studying diverse thermophilic communities, offering a valuable resource for both ecological and biotechnological exploration. Enzymes derived from thermophiles, known as thermophiles exhibit remarkable thermal stability and catalytic efficiency at temperatures ranging from 60 to 125 °C, with applications in biofuels, pharmaceuticals, and industrial bioprocessing. Integration of both culture-based and metagenomic approach provide a comprehensive framework for understanding the thermophile biology and reveals their biotechnological potential.},
}

@article {pmid40620900,
year = {2025},
author = {Desingu, PA and Arunkumar, S and Nagarajan, K and Saikumar, G},
title = {Metagenomics identification of genetically distinct tick virome in India unveils signs of purifying selection, and APOBEC and ADAR editing.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112873},
pmid = {40620900},
issn = {2589-0042},
abstract = {Recently, several tick-borne zoonotic viruses have been identified through the application of virus metagenomics. However, the tick virome in South Asia and the factors driving the evolution of these viruses remain largely unknown. In this study, we report the complete genomes of the genetically distinct Nairobi sheep disease virus (NSDV), Jingmen tick virus (JMTV), Lihan tick virus (LTV), and Mivirus, along with nearly complete genomes of turnip mosaic virus (TMV) and turnip yellows virus (TYV). We also present partial genomes of Tamdy orthonairovirus, Nayun tick nairoviruses (NTNV), PTV-like viruses, Xinjiang tick-associated virus-1 (XTAV1), Totivirus, Kismayo viruses, Quaranjavirus, and Brown dog tick phlebovirus-2 (BDTPV-2), identified from Indian ticks through virus metagenomics. The diversity was categorized into distinct groups specific to particular host organisms and/or geographical regions. Our findings also indicated that selection pressure for codon usage in these viruses was influenced by purifying selection, which induces transition mutations potentially through apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) and adenosine deaminases acting on RNA (ADAR) editing.},
}

@article {pmid40620487,
year = {2025},
author = {Luo, W and Zhang, S and Sun, J and Xu, J and Huang, W and Hao, R and Ou, Z and Wen, Z and Wang, D and Xiao, G and Dong, H},
title = {Microbial and clinical disparities in pneumonia: insights from metagenomic next-generation sequencing in patients with community-acquired and severe pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538109},
pmid = {40620487},
issn = {1664-302X},
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is a major global cause of death, with its varying symptoms and severity complicating diagnosis and treatment. Severe pneumonia (SP), a more critical form of CAP, has higher mortality and often requires intensive care. The identification of clinical markers to differentiate CAP from SP has the potential to improve treatment protocols and patient outcomes. Concurrently, metagenomic next-generation sequencing (mNGS) demonstrates significant promise in pathogen detection and in elucidating microbiome disparities between CAP and SP.

METHODS: This retrospective study analyzed clinical and pathogen data from 204 patients diagnosed with CAP and 25 patients diagnosed with SP in the Department of Respiratory and Critical Care Medicine at the Zengcheng Branch of Nanfang Hospital, Southern Medical University, spanning the period from September 2022 to June 2023. Clinical characteristics were compared, and bronchoalveolar lavage fluid (BALF) samples underwent mNGS for microbial detection and characterization. Statistical analyses, encompassing Chi-square, Fisher's exact test, Student's t-test, and LEfSe analysis, were employed to compare clinical and microbiological data between the CAP and SP cohorts.

RESULTS: Patients with SP were significantly older and exhibited higher incidences of sepsis, hypotension, tachycardia, multilobar infiltrates, and consciousness disorders compared to those with CAP. Elevated levels of C-reactive protein (CRP) and procalcitonin (PCT) were more frequently observed in SP patients. mNGS analysis identified diagnostic microbiology profiles between groups. Diverse microbiological profiles (> 5 species) were more common in SP patients (> 30% detection rate). Beta diversity analysis demonstrated significant differences in microbial community composition between CAP and SP groups (p = 0.001), though alpha diversity metrics showed no significant differences. Both LEfSe and ANCOM-BC2 analyses consistently identified Pseudomonas as a potential biomarker for SP and Streptococcus for CAP.

CONCLUSION: The substantial differences observed in clinical characteristics, pathogen profiles, and microbiomes between patients with CAP and those with SP highlight the imperative need for comprehensive diagnostic methodologies in the management of pneumonia. mNGS has demonstrated substantial utility in informing personalized treatment strategies, with the potential to enhance clinical outcomes. Future research should prioritize elucidating the dynamics of microbial communities and their impact on pneumonia severity, with the objective of refining and optimizing therapeutic strategies.},
}

@article {pmid40619813,
year = {2025},
author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT},
title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf323},
pmid = {40619813},
issn = {1477-4054},
support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; },
abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.},
}

Humans
*Dysbiosis/microbiology
*Systems Biology/methods
*Microbiota
Metagenomics
Metabolomics
Proteomics

@article {pmid40619005,
year = {2025},
author = {Hullar, MAJ and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW},
title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.026},
pmid = {40619005},
issn = {1938-3207},
abstract = {BACKGROUND: Dietary patterns characterized by low-glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.

OBJECTIVE: Evaluate the effects of a low glycemic load (LGL) versus a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.

METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n=69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.

RESULTS: Overall community structure measured by alpha and beta diversity were not significantly different across the diets although diet did significantly increase the abundance of 13 out of 161 genera (padj<0.05) and 5 species in the LGL and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (β=-1.15, SE=0.24 with 95% CI (-1.63, -0.67); padj=0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (β =0.20, SE=0.05 with 95% CI (0.09, 0.30); padj=0.03); was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, p<0.001). CAZymes enriched in the HGL diet reflected dietary additives while CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between HOMA IR and the Coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (padj=0.035) that was positive in the HGL diet (β=0.20, SE=0.09 with 95% CI (0.02, 0.39)) and negative in the LGL diet (β =-0.23, SE=0.09 with 95% CI (-0.40, -0.06)).

CONCLUSION: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.},
}

@article {pmid40618661,
year = {2025},
author = {Gao, Y and Zhang, L and Zhang, Y and Yang, M and Ma, W},
title = {Porous Ca-doped Al2O3 with abundant basic sites for enhanced hydrolysis of fermentative antibiotics.},
journal = {Water research},
volume = {285},
number = {},
pages = {124138},
doi = {10.1016/j.watres.2025.124138},
pmid = {40618661},
issn = {1879-2448},
abstract = {Efficient elimination of antibiotics from wastewater is crucial for the stability of biological treatment systems and the safety of effluent. This study presents a heterogeneous catalytic hydrolysis system using porous calcium-doped alumina (P-Ca-Al), synthesized with ammonium chloride as a green gas template. Characterization reveals that calcium species are highly dispersed in the tetrahedral sites of alumina, forming Ca-O-Al bonds. The coexistence of surface basic sites and Lewis acid sites on P-Ca-Al was confirmed by CO2 temperature-programmed desorption spectrum and pyridine adsorption infrared spectroscopy. These sites are responsible for the highly efficient hydrolysis of Erythromycin-A (Ery-A), achieving an 18-fold increase in efficiency compared to conventional NaOH aqueous solutions, with no degradation observed on solid CaO under identical conditions. The selective hydrolysis of the antibacterial functional groups of Ery-A reduces antimicrobial activity with low energy and reagent consumption. The degradation mechanism is confirmed through solvent kinetic isotope effect (KIE) investigation and identification of hydrolysis intermediates. The macrolide ring and glycosidic bond in Ery-A are hydrolyzed by proton subtraction from surface basic sites, preventing resistance gene formation as confirmed by metagenomic analysis. This work provides a possible way to selectively remove antibiotics from complex industrial wastewater.},
}

@article {pmid40618650,
year = {2025},
author = {Wan, X and Li, Q and Li, Z and Shi, L and Pan, Y and Li, M and Liu, Z},
title = {MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109653},
doi = {10.1016/j.envint.2025.109653},
pmid = {40618650},
issn = {1873-6750},
abstract = {Antibiotic resistance (AMR) in animal agriculture represents a critical One Health challenge, with pig farms serving as major reservoirs for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). While MGEs are known drivers of ARG dissemination, their impact on actual expression of resistance in these complex microbial communities is poorly understood. This study aimed to quantify the contribution of MGE-associated ARGs to overall resistance expression and compare their transcriptional efficiency to chromosomally located ARGs in pig farm wastewater. Utilizing deep metagenomic and metatranscriptomic sequencing on wastewater from five typical Chinese pig farms, we comprehensively elucidated ARG presence, genetic context, host association, and transcriptional activity. We identified a vast dataset comprising 811 ARG types conferring resistance to 27 antibiotic classes, with 71.02 % actively transcribed, indicating significant resistance potential. MGEs were associated with 34.87 % of ARG-like ORFs. Crucially, MGE-associated ARGs were responsible for the majority (62.07 %) of total ARG transcript abundance, exhibiting an expression efficiency nearly 2.5 times higher than ARGs on chromosomal non-MGE loci. Taxonomic analysis revealed that these highly expressed MGE-associated ARGs were primarily hosted by genera known to include opportunistic pathogens, such as Enterococcus, Escherichia, and Klebsiella. Differential coverage binning further uncovered diverse draft genomes simultaneously harboring multiple highly expressed ARGs and MGEs, potentially contributing to the persistence and spread of highly resistant bacterial strains. Our findings underscore that MGEs not only propagate ARGs but critically enhance their expression, providing vital data for effective AMR surveillance and mitigation strategies within the One Health framework.},
}

@article {pmid40618153,
year = {2025},
author = {Lin, D and Zhang, X and Wang, D and Liu, T and Li, T and Zhang, Y and Li, L and Huang, Y and Guo, Y and Zhang, R and Chen, X and Feng, T},
title = {UMPlex™: a targeted next-generation sequencing primer design workflow.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {222},
pmid = {40618153},
issn = {1743-422X},
support = {2024A1515030195//Guang Dong Basic and Applied Basic Research Foundation/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; Workflow ; *Molecular Diagnostic Techniques/methods ; *DNA Primers/genetics ; Sensitivity and Specificity ; Influenza, Human/diagnosis/virology ; },
abstract = {We have developed a tailored next-generation sequencing (tNGS) panel, employing our innovative UMPlex™ primer design workflow, to enhance pathogen identification in clinical diagnostics. Through iterative experimentation and rigorous validation, we refined the primer design by excluding those with insufficient specificity or efficiency. To mitigate amplification challenges arising from pathogenic mutations, we implemented a strategy of using a minimum of two primer pairs per pathogen, ensuring redundancy and robust detection. Validation using clinical samples showcased high specificity and efficacy, with 11 cultured pathogens isolated exclusively. In a study involving 107 positive respiratory samples, tNGS outperformed the TaqMan Array, detecting a higher number of pathogens in patients with influenza-like symptoms of unknown etiology. Additionally, tNGS yielded higher read counts for potentially pathogenic microorganisms and produced results consistent with metagenomic NGS, despite generating a reduced data volume. This approach not only improves detection rates but also offers a flexible tool for both clinical diagnostics and surveillance, particularly in the context of influenza-like illnesses.},
}

*High-Throughput Nucleotide Sequencing/methods
Humans
Workflow
*Molecular Diagnostic Techniques/methods
*DNA Primers/genetics
Sensitivity and Specificity
Influenza, Human/diagnosis/virology

@article {pmid40618061,
year = {2025},
author = {Liang, H and Yang, Y and Yi, S and Cai, D and Zhou, H and Yin, H and Yuan, C and Zhou, G and Tian, D and Xia, X and Wang, Z and Chen, F},
title = {Metagenomics-based novel Caulimoviridae virus discovery and its development of identification markers in Lilium lancifolium thunb.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {221},
pmid = {40618061},
issn = {1743-422X},
support = {DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; },
mesh = {*Lilium/virology ; *Metagenomics/methods ; Genome, Viral ; *Plant Diseases/virology ; Phylogeny ; *Caulimoviridae/genetics/isolation & purification/classification ; Sequence Analysis, DNA ; Genetic Markers ; },
abstract = {Plant viruses cause considerable economic losses in the lily industry due to the emergence of diverse viral mutations and novel pathogens. Effective detection and identification of these viruses are critical for controlling their spread and mitigating infections. In this study, two novel Caulimoviridae viruses, namely Lancifolium Caulimovirus A (LCaA) and Lancifolium Caulimovirus B (LCaB), were identified for the first time in Lilium lancifolium Thunb. (tiger lily) through integrated metagenomic sequencing and Sanger sequencing. The complete genomes of LCaA and LCaB were determined to be 7,542 nt and 7,582 nt in length, respectively. Among the pooled tiger lily samples, seven LCaA isolates exhibited genome sequence identities ranging from 99.59 to 99.73%, while six LCaB isolates showed identities between 98.51% and 98.91%. Leveraging these isolates genomic variations, four sets of diagnostic markers were developed to distinguish the LCa viruses (LCaA and LCaB). Specific marker combinations were employed to identify LCa, LCaA, and LCaB strains. This study reports the discovery of two novel Caulimoviridae species and establishes a robust PCR-based methodology for their detection. The developed markers provide a valuable diagnostic tool for the early detection and management of LCa viruses in lily cultivation systems.},
}

*Lilium/virology
*Metagenomics/methods
Genome, Viral
*Plant Diseases/virology
Phylogeny
*Caulimoviridae/genetics/isolation & purification/classification
Sequence Analysis, DNA
Genetic Markers

@article {pmid40617811,
year = {2025},
author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {228},
pmid = {40617811},
issn = {2158-3188},
mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; },
abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.},
}

Humans
*Schizophrenia/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
Feces/microbiology
Case-Control Studies
Metabolic Networks and Pathways
Fungi

@article {pmid40617568,
year = {2025},
author = {Tian, G and Zhang, R and Zhao, M and Ye, Z and Dai, T and Chen, D and Zeng, Y and Yang, Y and Zhou, J and Zhang, B and Guo, X},
title = {Biogeochemical stratification governs microbial hydrocarbon degradation potential in a petrochemical contaminated site.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122286},
doi = {10.1016/j.envres.2025.122286},
pmid = {40617568},
issn = {1096-0953},
abstract = {The success of in situ bioremediation at petrochemical-contaminated sites (defined as those impacted by petrochemical production or accidental release) depends on the structure and functional capacities of indigenous microbial communities, as well as the physicochemical gradients that shape their metabolic potential. While microbial degradation mechanisms are well-documented in homogeneous environments, systematic evaluations of microbial dynamics across environmental compartments (e.g., surface/middle/deep soil vs. groundwater) remain scarce. In this study, we combined chemical profiling with shotgun metagenomic sequencing to characterize layer-specific microbial assemblages and hydrocarbon degradation pathways at a historically contaminated petrochemical site. Total petroleum hydrocarbons (TPHs) were markedly higher in the middle and deep soil layers compared to the surface. In subsurface layers, elevated organic carbon and moisture limited oxygen diffusion, and high concentrations of hydrophobic hydrocarbons imposed toxic stress, together creating a reducing environment that favored anaerobic taxa and pathways such as benzoyl-CoA reductase. In contrast, surface soils, with greater aeration and lower pollutant levels, harbored approximately 50 % greater microbial α-diversity (P < 0.05) and supported more diverse and complex metabolic capabilities. Groundwater showed an 83 % detection frequency of naphthalene, and its high solubility and toxicity selected for specialized degraders. Principal Coordinates Analysis (PCoA) revealed distinct depth-dependent community clustering of microbial communities (P < 0.001), with middle/deep soil microbiomes showing significantly reduced metabolic versatility for xenobiotics (BTEX, PAHs, and derivatives) compared to surface soils and groundwater at the community level. Functional gene annotation identified rate-limiting enzymes in aerobic/anaerobic degradation pathways (dmpK [benzene], badA [ethylbenzene], nahA [naphthalene], and fadA [fatty acid β-oxidation]), and Metagenome-Assembled Genomes (MAGs)-based reconstructions revealed a systemic bias towards anaerobic degradation. These mechanistic insights guide layer-specific in situ bioremediation, integrate environmental gradients with microbial functional potential for targeted treatments, and provide a framework for predicting community succession and functional resilience at petrochemical-contaminated sites.},
}

@article {pmid40617153,
year = {2025},
author = {Song, L and Liang, Q and Chen, Y and Wu, L and Zhou, J and Wei, Z and Xie, J and Liu, H and Meng, J},
title = {Clinical characterization and diagnosis of 14 patients with Chlamydia psittaci pneumonia.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {3},
pages = {116985},
doi = {10.1016/j.diagmicrobio.2025.116985},
pmid = {40617153},
issn = {1879-0070},
abstract = {OBJECTIVE: To investigate the clinical features, diagnostic approaches, and therapeutic strategies for Chlamydia psittaci (C. psittaci) pneumonia.

METHODS: We conducted a retrospective analysis of 14 patients diagnosed with C. psittaci pneumonia between December 2021 and February 2025 at The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China. Diagnosis was confirmed via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Clinical manifestations, laboratory findings, imaging characteristics, treatment regimens, and outcomes were systematically analyzed.

RESULTS: The cohort comprised seven males and seven females, aged 46-83 years. A documented history of avian exposure was present in 57.1 % (8/14) of patients. All patients presented with high fever. Lab tests showed increased inflammatory markers (CRP, ESR, d-dimer) in all patients. White blood cell counts were elevated in seven patients and normal in seven others. Neutrophilia occurred in 11 cases and lymphopenia in 13. Elevated procalcitonin (10 cases), LDH (12 cases), creatine kinase (8 cases), and transaminases (ALT: 7 cases; AST: 9 cases) were documented. Electrolyte disturbances included hypokalemia (6 cases), hyponatremia (9 cases), and hypochloremia(13 cases). Eight patients had renal dysfunction (high creatinine/urea), six showed hyperbilirubinemia. Chest imaging revealed varied lung infiltrations: consolidations, ground-glass opacities, nodular shadows, and patchy infiltrates. All cases were confirmed by mNGS and effectively treated with tetracyclines or fluoroquinolones.

CONCLUSION: C. psittaci pneumonia frequently presents with sepsis-like symptoms and rapid clinical deterioration. Early diagnosis using mNGS is crucial for guiding timely antimicrobial therapy, significantly improving patient outcomes, especially in cases where conventional diagnostics may be limited or delayed.},
}

@article {pmid40616852,
year = {2025},
author = {Zhu, X and Gao, X and Zhu, Y and Huang, J and Peng, F and Pang, Q and Yang, F and Xie, L and Hua, Z and Wang, L},
title = {The impact of land use on the composition of dissolved organic matter and its relationship with microbes in a river basin in Northwestern China: Insights into microbial community structure and metabolic function.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126446},
doi = {10.1016/j.jenvman.2025.126446},
pmid = {40616852},
issn = {1095-8630},
abstract = {Land use variations influence aquatic dissolved organic matter (DOM); however, the responses of relationships between DOM composition and microbial communities/metabolic genes to land use types and landscape indices remain insufficiently explored. This study conducted four field sampling sessions on the Qingshui River, northwestern China, investigated the shifts in DOM-transforming microbes and genes under distinct land use patterns (forest & grassland, urban area, and agricultural land) using metagenomics analysis, elucidated the DOM-microbe interactions in response to land use characteristics from the perspective of both basin and land use types by statistical approaches. At the basin scale, land use primarily influenced DOM quality rather than quantity. Partial least-squares path model demonstrated that landscape indices influenced DOM components predominantly by inhibiting gene abundances associated with metabolic pathways, exerting a more pronounced impact than land use area proportions. Notably, DOM composition, microbial metabolic genes, and their interactions differed significantly across land use types. Urban areas exhibited the highest levels of DOM aromaticity and the largest proportions of autochthonous sources, their fragmented landscape characteristics destabilized the microbial network, resulting in a comprehensive rather than partial suppression of genes involved in DOM transformation pathways (carbohydrate metabolism, energy metabolism, and amino acid metabolism). Compared to other land use scenarios, the downstream agricultural areas emerged as active zones for microbial utilization of DOM, maintained high microbial network stability and gene abundances similar to forest & grassland, highlighting the microbial resilience. These insights advance mechanistic understanding of how land use governs aquatic DOM-microbe interactions in arid and semi-arid watersheds.},
}

@article {pmid40616790,
year = {2025},
author = {Wen, Z and Yang, M and Lu, G and Han, M and Song, Y and Sun, Y and Tu, Q and Yin, T and Niu, K and Sun, S and Qi, J and Fazal, A and Yang, Y},
title = {Microbial Alliances: Unveiling the Effects of a Bacterial and Fungal Cross-Kingdom SynCom on Bacterial Dynamics, Rhizosphere Metabolites, and Soybean Resilience in Acidic Soils.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c12416},
pmid = {40616790},
issn = {1520-5118},
abstract = {Acidic soils, covering 40 to 50% of arable land, hinder productivity due to phosphorus limitation and aluminum toxicity. Using a synthetic community (SynCom) approach, we tested a native Rhizobium (Rh) and a non-native Ensifer fredii (Ef) strain, both combined with the mycorrhizal fungus Rhizophagus intraradices (Ri), on soybean growth in acidic soil. The native RhRi SynCom outperformed EfRi, significantly improving soybean growth, yield, and soil health. Metagenomics and metabolomics revealed that RhRi significantly enhanced beneficial microorganisms (AD3, Gemmataceae) and metabolites (putrescine, stearic acid), hence improving nutrient cycling, stress tolerance, and membrane integrity. RhRi also enhanced soil enzyme activity (urease, phosphatases), which resulted in an increase in nitrogen and phosphorus availability and a decrease in rhizosphere toxicity. These alterations enhanced plant resilience, soil structure, and microbial diversity. RhRi activated metabolic pathways (amino acids, lipids, ABC transporters, and secondary metabolites) that are involved in nutrient acquisition and stress response. Conversely, EfRi provided minimal advantages, emphasizing the significance of native microbial compatibility. Our findings show that native SynComs boost crop resilience and production in acidic soils through synergistic microbial interactions and metabolic reprogramming, thereby offering a sustainable agricultural strategy in harsh environments.},
}

@article {pmid40616449,
year = {2025},
author = {Alsanea, A and Bounaga, A and Lyamlouli, K and Zeroual, Y and Boulif, R and Zhou, C and Rittmann, B},
title = {Sulfate Reduction in the Hydrogen-Based Membrane Biofilm Reactor Receiving Calcium Reduced Phosphogypsum Water.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70015},
pmid = {40616449},
issn = {1097-0290},
support = {//This study was supported by the OCP Group's Situation Innovation within the framework of 500 [AS81]./ ; },
abstract = {Phosphogypsum (PG), a byproduct of phosphate mining, contains sulfate that can be leached and converted to elemental sulfur, thus offering a sustainable opportunity to recover sulfur (S) as a step toward a circular economy. Calcium, at ~15 mM in PG leachate, creates inorganic precipitation that interferes with biological sulfate reduction, the first step of S recovery. Here, we evaluated the effectiveness of using cation-exchange to lower the calcium concentration in water-leached PG (PG water) delivered to a H2-based membrane biofilm reactor (H2-MBfR) employed to reduce sulfate to sulfide. A high sulfate flux (1 gS/m[2]-day) and 65% sulfate reduction were achieved despite a high pH (10) resulting from base production during sulfate reduction. However, soluble sulfide was only 20% of the reduced S, possibly due to precipitation of sulfide, iron, and phosphate, and alkalinity analysis revealed possible formation of polysulfides. Shallow metagenomics of the biofilm documented that Desulfomicrobium was the dominant sulfate-reducing bacterium, while Thauera, a mixotroph capable of sulfate reduction and sulfide oxidation, also was an important genus. The metagenomics also revealed the presence of methanogens and acetogens that competed for H2 and CO2. Although calcium removal from PG water improved sulfate reduction and reduced inorganic precipitation in the H2-MBfR, soluble sulfide generation must be improved by supplying sufficient CO2 to moderate pH increase due to sulfate reduction and by controlling the H2-delivery capacity to limit methanogens and acetogens.},
}

@article {pmid40615957,
year = {2025},
author = {Durand, K and Ogier, JC and Nam, K},
title = {The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {413},
pmid = {40615957},
issn = {1471-2180},
support = {ANR-10-LABX-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-001-01//Agence Nationale de la Recherche/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche,France/ ; Resistome//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification ; *DNA-Directed RNA Polymerases/genetics ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Computational Biology/methods ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Bacterial Proteins/genetics ; High-Throughput Nucleotide Sequencing/methods ; Shotgun Sequencing ; },
abstract = {BACKGROUND: The importance of microbial community profiling has been increasingly recognized in biological and environmental research. While metabarcoding has been widely used for such analysis by targeting specific DNA sequences as markers, shotgun sequencing has been proposed as an alternative method because the analysis of whole genomes can potentially reduce biases introduced by targeted approaches. However, it is largely unknown whether shotgun sequencing may provide improved precision for qualitative taxonomic identification and quantitative abundance estimation compared with metabarcoding with housekeeping gene markers, such as the rpoB gene. Furthermore, the comparative performance of various bioinformatics pipelines for shotgun data analysis remains uncertain. In this study, we evaluated the performance of rpoB metabarcoding and shotgun sequencing coupled to various bioinformatic pipelines to describe the bacterial diversity of artificially generated mock bacterial communities, which included eukaryote gDNA intentional contamination or whole-genome amplification. For shotgun sequencing, the Assembly-Binning-Method and k-mer-based approaches were evaluated.

RESULTS: For taxonomic profiling, the Assembly-Binning-Method and rpoB metabarcoding exhibited comparable sensitivity and precision, whereas k-mer approaches produced a notably high number of false negatives. In some cases, the Assembly-Binning-Method improved taxonomic resolution compared with rpoB metabarcoding by identifying taxa at the species level rather than the genus level. Regarding the quantification of microbial composition, the Assembly-Binning-Method consistently showed a higher correlation with expected values ​​and a lower dissimilarity index than rpoB metabarcoding. The use of three sets of reference genomes to calculate depth coverage did not systematically affect the precision of the Assembly-Binning-Method.

CONCLUSIONS: These results demonstrate that although shotgun sequencing and rpoB metabarcoding have nearly equivalent accuracy in taxonomic profiling, shotgun sequencing has better taxonomic resolution and outperforms rpoB metabarcoding in quantitative estimation of microbial community abundance using the Assembly-Binning approach.},
}

*DNA Barcoding, Taxonomic/methods
*Bacteria/genetics/classification
*DNA-Directed RNA Polymerases/genetics
*Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
Computational Biology/methods
Phylogeny
*Microbiota/genetics
Metagenomics/methods
Bacterial Proteins/genetics
High-Throughput Nucleotide Sequencing/methods
Shotgun Sequencing

@article {pmid40615853,
year = {2025},
author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B},
title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {745},
pmid = {40615853},
issn = {1479-5876},
mesh = {Humans ; *Hepatic Encephalopathy/microbiology/etiology/blood ; *Liver Cirrhosis/microbiology/surgery/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; Ammonia/blood ; Aged ; },
abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.

RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.

CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.},
}

Humans
*Hepatic Encephalopathy/microbiology/etiology/blood
*Liver Cirrhosis/microbiology/surgery/complications
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Portasystemic Shunt, Transjugular Intrahepatic/adverse effects
Ammonia/blood
Aged

@article {pmid40615598,
year = {2025},
author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J},
title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23957},
pmid = {40615598},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; },
abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.},
}

*Wastewater/microbiology
*Transcriptome
Ecosystem
Fresh Water/microbiology
*Eukaryota/genetics

@article {pmid40615451,
year = {2025},
author = {Omar, HS and Hagag, MH and El-Khishin, D and Hashem, M},
title = {Expression of pathogenesis-related proteins in potato brown rot plants confers resistance to filamentous pathogens under field trials.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23927},
pmid = {40615451},
issn = {2045-2322},
mesh = {*Solanum tuberosum/microbiology/genetics ; *Plant Diseases/microbiology/genetics ; *Disease Resistance/genetics ; *Ralstonia solanacearum/pathogenicity ; Soil Microbiology ; Pseudomonas/genetics ; *Plant Proteins/genetics/metabolism ; },
abstract = {The present investigation aims to use innovative metagenomics technologies and denaturing gradient gel electrophoresis (DGGE) to compare the microbial communities of conductive and suppressive soils in connection to brown rot disease in the entire value of Egyptian potato imports. Besides evolution, the bioefficacy of two biocontrol agents, either alone or in consortium, on plant growth promotion and activation of defense responses in potato against the brown rot diseases. The soil status of collecting soil from seven different locations in different governorates was evaluated for tolerance to the artificial inoculation of the pathogen agent of R. solanacearum on potato plants. The DGGE uses 16 srRNA primers that were used to compare two extreme patterns for identifying the microbial population detected in environmental samples. Different bands were extracted from the DGGE gel and sequenced. The sequencing data results revealed that the biocontrol agent factor has a 100% gene bank similarity and belongs to the Pseudomonas species. The Pseudomonas nucleotide sequences isolates were deposited in the Gene Bank under Accession Nos. PP930812, PQ466864, and PQ470140. The findings showed that the soil from the governorates of Kerdasa exhibited a less tolerant treatment, with an estimated disease severity of 78.33%. On the other hand, ElBeheira Kom Hamada soil showed significant tolerance, with an estimated disease severity of 11.67. According to the data of gene expression analysis, both treated plants with the biocontrol agents showed a significant increase in PR-1, PR-2 and PR-Q gene expression, which accelerated the defense response and reduced brown rot disease. The evaluated potato genotype results proved to have the potential for brown rot disease resistance and higher yield production. The findings of this study recommended that biopriming with a microbial consortium enhance potato growth, productivity, and induction of defense responses against S. tuberosum through the induction of systemic resistance via expression of PR pathogenic-related protein network. The present investigation offers significant perspectives that warrant further exploration in subsequent studies to address the traceability requirements of the worldwide economics of disease control for potato plants.},
}

*Solanum tuberosum/microbiology/genetics
*Plant Diseases/microbiology/genetics
*Disease Resistance/genetics
*Ralstonia solanacearum/pathogenicity
Soil Microbiology
Pseudomonas/genetics
*Plant Proteins/genetics/metabolism

@article {pmid40615445,
year = {2025},
author = {Di Gloria, L and Casbarra, L and Lotti, T and Ramazzotti, M},
title = {Testing the limits of short-reads metagenomic classifications programs in wastewater treating microbial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23997},
pmid = {40615445},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Sewage/microbiology ; *Metagenome ; },
abstract = {Biological wastewater treatment processes, such as activated sludge (AS) and aerobic granular sludge (AGS), have proven to be crucial systems for achieving both efficient waste purification and the recovery of valuable resources like poly-hydroxy-alkanoates. Gaining a deeper understanding of the microbial communities underpinning these technologies would enable their optimization, ultimately reducing costs and increasing efficiency. To support this research, we quantitatively compared classification methods differing in read length (raw reads, contigs and MAGs), overall search approach (Kaiju, Kraken2, RiboFrame and kMetaShot), as well as source databases to assess the classification performances at both the genus and species levels using an in silico-generated mock community designed to provide a simplified yet comprehensive representation of the complex microbial ecosystems found in AS and AGS. Particular attention was given to the misclassification of eukaryotes as bacteria and vice versa, as well as the occurrence of false negatives. Notably, Kaiju emerged as the most accurate classifier at both the genus and species levels, followed by RiboFrame and kMetaShot. However, our findings highlight the substantial risk of misclassification across all classifiers and databases, which could significantly hinder the advancement of these technologies by introducing noises and mistakes for key microbial clades.},
}

*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Sewage/microbiology
*Metagenome

@article {pmid40614847,
year = {2025},
author = {Wang, R and Chen, H and Liu, Y},
title = {Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122285},
doi = {10.1016/j.envres.2025.122285},
pmid = {40614847},
issn = {1096-0953},
abstract = {The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.},
}

@article {pmid40614652,
year = {2025},
author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T},
title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105488},
doi = {10.1016/j.psj.2025.105488},
pmid = {40614652},
issn = {1525-3171},
abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.},
}

@article {pmid40614609,
year = {2025},
author = {Ogola, HJO},
title = {Wastewater-driven nutrient enrichment restructures viral community assembly, host interactions, and ecological function along the Nakivubo-Lake Victoria interface in Uganda.},
journal = {The Science of the total environment},
volume = {993},
number = {},
pages = {180002},
doi = {10.1016/j.scitotenv.2025.180002},
pmid = {40614609},
issn = {1879-1026},
abstract = {Gulf ecosystems in freshwater lakes are dynamic interfaces of microbial activity, shaped by complex interactions between natural processes and anthropogenic inputs from surrounding urban catchments. This study investigated viral community composition, functional potential, and virus-host interactions along the Nakivubo catchment-Lake Victoria interface in Murchison Bay, Uganda. Metagenomic profiling of 28 samples across four compartments: wastewater treatment plant (WWTP); a municipal channel; papyrus-dominated wetland; and Lake water, revealed spatially distinct viromes dominated by Uroviricota (45.8-94.8 %), with higher richness observed in Channel and Wetland than in WWTP and Lake samples. Community structure was strongly compartmentalized (PERMANOVA, p < 0.001), with WWTP and Channel viromes distinct from those in less impacted compartments. Human-associated viruses, including crAss-like phages (up to 29.3 %) and Picobirnaviruses (11.4 %), were enriched in WWTP samples, reflecting fecal pollution. Linear discriminant analyses and random forest modeling identified Sinsheimervirus as wetland indicator, while Fukuivirus, Bellamyvirus and Prokaryotic dsDNA virus were characteristic of lake viromes. Viral-bacterial co-occurrence networks were fragmented and less cohesive in WWTP and Channel (average path length = 3.2), but more modular and nested in Wetland (avg. path length = 1.9; modularity = 0.47), reflecting ecological structuring. Among environmental variables, ammonia-N was the strongest correlate of viral beta diversity (Mantel r = 0.67, p < 0.01). Functionally, auxiliary metabolic genes (AMGs) linked to photosynthesis, nitrogen and carbohydrate cycling were enriched in Wetland and Lake, while mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) were largely confined to WWTP, Channel, and Wetland. These patterns suggest selective viral adaptations to eutrophic, contaminated environments and their attenuation downstream. The findings demonstrate how wastewater-driven nutrient enrichment shapes viral community assembly, host associations, and ecological function along tropical freshwater continua. Viruses emerge as sensitive indicators of anthropogenic impact and offer new perspectives for water quality monitoring and ecosystem health assessment in urban-influenced lake systems.},
}

@article {pmid40614422,
year = {2025},
author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S},
title = {The invisible threats of sunscreen as a plastic co-pollutant: Impact of a common organic UV filter on biofilm formation and metabolic function in the nascent marine plastisphere.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139103},
doi = {10.1016/j.jhazmat.2025.139103},
pmid = {40614422},
issn = {1873-3336},
abstract = {Plastic debris in marine environments serves as a substrate for microbial colonisation, forming biofilms known as 'plastispheres'. Also accumulated on plastic debris are co-pollutants including UV-protective organic UV-filters from sunscreens, which likely interact with this niche through their lipophilicity. Despite their widespread use and environmental accumulation, the influence of UV-filters on plastisphere composition and function has never been investigated. This study therefore investigates, for the first time, how co-pollution - specifically by an organic UV-filter - impacts the composition and function of marine plastisphere communities. To achieve this, low-density polyethylene (LDPE) was incubated with marine microbial communities for six days to cultivate a nascent plastisphere, which was then exposed to 5 mg/L of EthylHexyl MethoxyCinnamate (EHMC); the most used organic UV-filter in sunscreens, and a prevalent marine pollutant. Metagenomic analyses revealed that EHMC favoured the growth of bacterial generalists Pseudomonas and Psychromonas while reducing pollutant-degrading genera like Marinomonas. Analysis of 3070 proteins revealed a consistent upregulation of proteins used for biofilm maintenance by Pseudomonas with EHMC exposure, including the considerable upregulation of outer membrane porin F (OprF) which regulates exopolymeric substance (EPS) production. Additionally, proteins thought to indicate a shift from aerobic to anaerobic respiration were frequently expressed after exposure to EHMC. This may have selected against the obligate aerobes Marinomonas and Pseudoalteromonas, contributing to the observed shift in community composition. These findings underscore the importance of considering chemical co-pollutants in plastisphere research as we now begin to discover how ecologically significant, and potentially harmful microbial genera are affected by this interaction.},
}

@article {pmid40614349,
year = {2025},
author = {Ma, RA and Ding, YH and Zhong, S and Jing, TT and Chen, X and Zhang, SY},
title = {A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109655},
doi = {10.1016/j.envint.2025.109655},
pmid = {40614349},
issn = {1873-6750},
abstract = {Recent studies reported an increased abundance of antibiotic resistance genes (ARGs) in urban greenspaces, yet the predictability of ARG variance along urbanization gradients remains unclear. We sampled paired soil and phyllosphere samples from the same site in wetland parks along urbanization gradients to assess the correlations of soil and phyllosphere ARG abundance with urbanization indices. Our results revealed that the abundance of phyllosphere resistomes correlated better with urbanization gradients than did that of soil resistomes and increased along urbanization gradients. Moreover, the phyllosphere presented more ARG-MGE (mobile gene element) pairs in metagenome-assembled genomes than soil, suggesting greater transmission potential than soil ARGs. Proximity to the built area and microbial diversity were the most important factors that significantly (p < 0.01) drove the variance in phyllosphere ARG abundance. By integrating population density, land use type, landscape metrics, and air quality data into machine learning models, we predicted phyllosphere ARG abundance at a 10-meter resolution. Among the five tested algorithms tested in the machine learning models (ridge regression, K-nearest neighbor, support vector machine, and neural network), the random forest algorithm achieved the highest accuracy with the lowest root mean square error (27.24 vs. 40.79-46.79 for the other models). These results demonstrate a strong association between phyllosphere ARG abundance and urbanization indices and provide predictions of the potential ARG risk along these gradients. The heightened transmission potential in urban greenspaces may facilitate the spread of antibiotic resistance spread to human pathogens, which poses significant public health threats.},
}

@article {pmid40614175,
year = {2025},
author = {Khalil, S and Paras, ML and Eichenberger, E and Sohail, MR},
title = {The Next Step: Role of Metagenomic Next Generation Sequencing for Microbial Detection in Culture-negative Cardiovascular infections.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf361},
pmid = {40614175},
issn = {1537-6591},
abstract = {Cardiovascular infections, including those involving native and prosthetic heart valves, implantable cardiac devices, mechanical circulatory assist devices, and vascular grafts, are associated with significant morbidity and mortality risks. Optimal management of these complex infections requires pathogen-directed antimicrobial therapy. However, standard culture-based methods often fail to identify causative organisms due to prior antimicrobial use, infections due to fastidious organisms, or biofilm-associated infections. Emerging evidence suggests that microbial cell-free DNA (mcfDNA) and metagenomic testing can enhance pathogen detection, particularly in culture-negative cases. However, their results require careful clinical interpretation, often necessitating input from infectious diseases specialists. In this review, we examine published evidence regarding metagenomic testing for cardiovascular infections and its impact on patient care. We propose a framework for microbiological adjudication of mcfDNA results, introduce standardized definitions for clinical impact assessment, and provide guidance on integrating mcfDNA testing into diagnostic evaluation of patients with culture-negative cardiovascular infections.},
}

@article {pmid40613917,
year = {2025},
author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M},
title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40613917},
issn = {1435-5922},
support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; },
abstract = {BACKGROUND & AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.

METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.

RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.

CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.},
}

@article {pmid40613821,
year = {2025},
author = {Saini, N and Ghosh, A and Bhadury, P},
title = {Linking Plastic Degradation Potential and Resistance Gene Abundance in Bacterioplankton Community of the Sundarbans Estuarine Ecosystem.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf067},
pmid = {40613821},
issn = {1574-6968},
abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.},
}

@article {pmid40613581,
year = {2025},
author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T},
title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf300},
pmid = {40613581},
issn = {1477-4054},
support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; },
mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; },
abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.},
}

Bayes Theorem
*Microbiota
*Neural Networks, Computer
*Metagenomics/methods
Humans
*Computational Biology/methods
Algorithms
Multiomics

@article {pmid40613164,
year = {2025},
author = {Zhang, QL and Dong, LL and Zhang, LL and Wu, YJ and Li, M and Bo, J and Wang, LL and Jing, Y and Dou, LP and Liu, DH and Gu, ZY and Gao, CJ},
title = {[Characteristics of Gut Microbiota Changes and Their Relationship with Infectious Complications During Induction Chemotherapy in AML Patients].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {3},
pages = {738-744},
doi = {10.19746/j.cnki.issn.1009-2137.2025.03.017},
pmid = {40613164},
issn = {1009-2137},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/drug therapy/microbiology ; *Induction Chemotherapy ; Feces/microbiology ; Male ; Female ; Middle Aged ; },
abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota changes in patients with acute myeloid leukemia (AML) undergoing induction chemotherapy and to explore the relationship between infectious complications and gut microbiota.

METHODS: Fecal samples were collected from 37 newly diagnosed AML patients at four time points: before induction chemotherapy, during chemotherapy, during the neutropenic phase, and during the recovery phase. Metagenomic sequencing was used to analyze the dynamic changes in gut microbiota. Correlation analyses were conducted to assess the relationship between changes in gut microbiota and the occurrence of infectious complications.

RESULTS: During chemotherapy, the gut microbiota α-diversity (Shannon index) of AML patients exhibited significant fluctuations. Specifically, the diversity decreased significantly during induction chemotherapy, further declined during the neutropenic phase (P < 0.05, compared to baseline), and gradually recovered during the recovery phase, though not fully returning to baseline levels.The abundances of beneficial bacteria, such as Firmicutes and Bacteroidetes, gradually decreased during chemotherapy, whereas the abundances of opportunistic pathogens, including Enterococcus, Klebsiella, and Escherichia coli, progressively increased.Analysis of the dynamic changes in gut microbiota of seven patients with bloodstream infections revealed that the bloodstream infection pathogens could be detected in the gut microbiota of the corresponding patients, with their abundance gradually increasing during the course of infection. This finding suggests that bloodstream infections may be associated with opportunistic pathogens originating from the gut microbiota.Compared to non-infected patients, the baseline samples of infected patients showed a significantly lower relative abundance of Bacteroidetes (P < 0.05). Regression analysis indicated that Bacteroidetes abundance is an independent predictive factor for infectious complications (P < 0.05, OR =13.143).

CONCLUSION: During induction chemotherapy in AML patients, gut microbiota α-diversity fluctuates significantly, and the abundance of opportunistic pathogens increase, which may be associated with bloodstream infections. Patients with lower baseline Bacteroidetes abundance are more prone to infections, and its abundance can serve as an independent predictor of infectious complications.},
}

Humans
*Gastrointestinal Microbiome
*Leukemia, Myeloid, Acute/drug therapy/microbiology
*Induction Chemotherapy
Feces/microbiology
Male
Female
Middle Aged

@article {pmid40613026,
year = {2025},
author = {Li, J and Zhou, Y and Zou, N and Chen, M},
title = {A Case of Nocardia cyriacigeorgica Infection and Literature Review.},
journal = {Cureus},
volume = {17},
number = {7},
pages = {e87189},
pmid = {40613026},
issn = {2168-8184},
abstract = {Nocardia bacteria primarily enter the human body through the respiratory tract or open wounds, leading to suppurative infections. These infections are more prevalent in individuals with compromised immune systems and can affect the lungs, resulting in pulmonary nocardiosis. The bacteria may also disseminate via the bloodstream to adjacent tissues or infect various organs. Clinical manifestations, physical signs, and imaging findings of nocardial pneumonia lack specificity. Additionally, Nocardia grows slowly and is often overgrown by faster-growing bacteria in sputum cultures, making it difficult to isolate. As a result, clinical misdiagnosis and missed diagnosis are common. With the growing number of immunocompromised individuals, the incidence of nocardial infections has been increasing. Improving laboratory personnel's awareness of this pathogen and enhancing their technical capabilities are crucial for accurate and timely clinical diagnosis. A 34-year-old female patient was reported to have contracted pneumonia caused by Nocardia cyriacigeorgica. The patient experienced a cough and sputum production without a clear cause 20 days prior. Despite clinical empirical treatment, the cough and sputum persisted, and there was also a high fever accompanied by chills and shivering. Metagenomic next-generation sequencing (mNGS) results of the bronchoalveolar lavage fluid showed that it was caused by Nocardia cyriacigeorgica. After four days of sputum culture, bacterial colonies were observed and subsequently identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) as Nocardia cyriacigeorgica. This patient received a combined treatment of compound sulfamethoxazole/trimethoprim and linezolid. Soon, his condition improved, and he was discharged from the hospital. During the two-month follow-up examination, it was observed that the lesion had been largely absorbed and the affected area had significantly reduced in size. The patient no longer experienced coughing or phlegm production. Following a comprehensive review of the clinical data of this case and relevant literature, we aim to improve the capacity of laboratory personnel in cultivating and identifying this rare bacterial pathogen. Furthermore, this study seeks to emphasize to clinical practitioners that bronchoalveolar lavage fluid should be collected for mNGS when pulmonary Nocardia infection is suspected, which can enhance diagnostic accuracy, facilitate early detection and timely intervention, and ultimately alleviate the burden on patients.},
}

@article {pmid40612788,
year = {2025},
author = {Veeranan Arun Giridhari, V and Uma Maheswari, T and Vanniarajan, C and Hariharan, T and Karthikeyan, S},
title = {Probing the metagenome and nutritional composition of idli batter fortified with electrolytic iron for addressing anaemia.},
journal = {Journal of food science and technology},
volume = {62},
number = {8},
pages = {1481-1490},
pmid = {40612788},
issn = {0022-1155},
abstract = {Iron deficiency affects people throughout the world, with preschoolers having the highest frequency followed by women of reproductive age and pregnant mothers. Of the different approaches to reducing iron deficiency, food fortification is a desirable and easily acceptable public health approach. Additionally, food fortification is proven to be economical and offers the benefit of reaching a larger population through current food delivery systems without necessitating significant adjustments to current consumption habits. In light of this, idli, a widely popular and commonly consumed fermented staple breakfast from Southern India, is chosen as a delivery system for addressing iron deficiency. Furthermore, because of its high nutritional content and ease of digestion, idli is eaten by people of all ages. The fortificant's bioavailability will also be successful during idli fermentation. Therefore, following the necessary dietary requirement, the readily accessible form of electrolytic iron is added to the idli batter, and its impact on the microbiological, nutritional, and sensory quality of idli was assessed. A metagenome investigation demonstrated that the fermentation microflora of idli batter was unaffected by electrolytic iron fortification with more probiotic microbiota during fermentation. It has been found that electrolytic iron at 9 mg, or 30% Recommended Dietary Allowance, has superior sensory qualities and bioavailability.},
}

@article {pmid40612471,
year = {2025},
author = {Arias, RS and Dobbs, JT and Orner, VA and Conforto, EC and Rago, AM and Cazon, LI and Sobolev, VS and Power, IL and Lamb, MC and Massa, AN},
title = {First metagenome- and metatranscriptome dataset of Thecaphora frezzii teliospores, assembly and annotation of a new bacterial genome.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111779},
pmid = {40612471},
issn = {2352-3409},
abstract = {These datasets correspond to sequencing of DNA and RNA extracted from surface-disinfected teliospores of the fungus Thecaphora frezzii Carranza and Lindquist, causal agent of smut disease in peanut (Arachis hypogaea L.). The DNA was sequenced using Pacific Biosciences (PacBio) Sequel II and RNA was sequenced in Illumina MiSeq 300 bp paired end (PE). Initial de novo assembly and Basic Local Alignment Search Tool (BLAST) of contigs to the 16S reference sequence database at NCBI had hits on seven bacterial species: Luteibacter pinisoli, Variovorax paradoxus, Rhizobium metallidurans, Caulobacter segnis, Roseateles violae, Novosphingobium rosa, Herbaspirillum seropedicae, and the fungus T. frezzii. High stringency mapping of the RNA sequences to the genomes of these organisms showed that 96% of the reads corresponded to bacteria and only 4% to T. frezzii. De novo assembly of PacBio reads revealed the whole genome of a Luteibacter sp. with 88.56% or lower similarity to those in NCBI database, whereas most RNA sequences (> 10 million reads) mapped to the new Luteibacter sp. genome assembled here. We annotated the new Luteibacter sp. genome, assessed its completeness by BUSCO, and aligned it to its closest relative, Luteibacter aegosomatissinici. We are not aware of any report that describes bacteria colonizing teliospores of T. frezzii. The DNA and RNA sequencing datasets provided here could be used to study the distribution of prokaryotes colonizing T. frezzii teliospores, and to explore the role of the microbiome of T. frezzii teliospores on the outcome of peanut smut disease.},
}

@article {pmid40612390,
year = {2025},
author = {Yu, J and Lv, X and Wang, Q and Gao, M and Li, W},
title = {Metagenomic sequencing for identification of nontuberculous mycobacteria and other pathogens in patients with mixed infection of the lung.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1592216},
pmid = {40612390},
issn = {2235-2988},
mesh = {Humans ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Middle Aged ; Male ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Female ; Retrospective Studies ; *Metagenomics/methods ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; *Coinfection/microbiology/diagnosis ; Adult ; Aged, 80 and over ; *Lung Diseases/microbiology/diagnosis ; },
abstract = {BACKGROUND: It can be difficult to distinguish lung disease caused by nontuberculous mycobacteria (NTM), Mycobacterium tuberculosis, and mixed infections (MIs) that include NTM. Metagenomic next generation sequencing (mNGS) is a highly sensitive method that can reliably identify lung pathogens. We retrospectively analyzed the records of patients who had MIs of the lungs that included NTM and received mNGS testing.

METHODS: The records of 36 patients who were diagnosed with NTM infection of the lungs at the Second Hospital of Jilin University from Nov 2023 to Jun 2024 were analyzed. Initial empirical treatments were ineffective in all patients, leading to the application of mNGS of bronchoalveolar lavage fluid (BALF).

RESULTS: The average patient age was 62.4 years, 22 patients had one or more underlying chronic disease, and all patients had at least one respiratory symptom (cough, sputum production, fever, or dyspnea). Chest CT examinations showed that patients had different degrees of pneumonia and pleural effusion. Among tested patients, there were elevated levels of erythrocyte sedimentation rate in 81.8% (18/22) and elevated C-reactive protein in 90.5% (19/21). There were variable results from acid-fast staining of bronchoalveolar lavage fluid (BALF; 3/36, 8.3%), and transbronchial lung biopsy (TBLB; 5/14, 35.7%). mNGS identified seven NTM species. Treatment based on the mNGS results led to the resolution of clinical symptoms and absorption of lung lesions in all patients.

CONCLUSIONS: Most of the 36 patients with MIs of the lungs that included NTM had underlying diseases. The results of traditional tests, including sputum or BALF culture and smear, acute phase markers, and TBLB pathological examination, were problematic. mNGS provides rapid and reliable diagnosis, allowing the rapid implementation of appropriate therapy in patients with MIs of the lungs that include NTM.},
}

Humans
*Nontuberculous Mycobacteria/genetics/isolation & purification/classification
Middle Aged
Male
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
Female
Retrospective Studies
*Metagenomics/methods
Aged
Bronchoalveolar Lavage Fluid/microbiology
Lung/microbiology/pathology
High-Throughput Nucleotide Sequencing
*Coinfection/microbiology/diagnosis
Adult
Aged, 80 and over
*Lung Diseases/microbiology/diagnosis

@article {pmid40612127,
year = {2025},
author = {Madlala, SS and Mchunu, N and Dalasile, M and Pierneef, R and Reddy, P},
title = {Metagenomic evaluation of food hygiene practices in the National School Nutrition Programme in KwaZulu Natal, South Africa.},
journal = {Health SA = SA Gesondheid},
volume = {30},
number = {},
pages = {2814},
pmid = {40612127},
issn = {2071-9736},
abstract = {BACKGROUND: The National School Nutrition Programme (NSNP) provides meals to schools in low-income areas in South Africa, implemented by the Department of Basic Education (DBE) with food safety monitored by Municipal Health Services.

AIM: To assess compliance of school kitchens with general hygiene requirements (R638 of 2018) and detect food pathogens on food contact surfaces using amplified metagenomics.

SETTING: The study was conducted in quintile 1 and 2 primary schools in Vryheid, KwaZulu-Natal.

METHODS: A quantitative cross-sectional study assessed the safety compliance of food preparation and storage areas in 33 primary schools against national legislation standards. Fifteen samples of food contact surfaces were collected from four schools and analysed using Illumina sequencing to identify prevalent bacterial genera.

RESULTS: None of the schools possessed a Certificate of Acceptability. Significant structural issues include poor pest control, inadequate sanitary facilities, a lack of food safety training and inadequate waste management. Taxonomic analysis revealed several dominant bacterial genera, including Pseudomonas, Stenotrophomonas, Acinetobacter and Pantoea, indicating potential routes for food contamination and subsequent risks for foodborne illnesses.

CONCLUSION: The study highlighted critical inadequacies in food preparation and storage areas requiring urgent intervention to ensure safe meal preparation. It emphasised the need for improved food safety monitoring and compliance in schools in low-income areas. Next-generation sequencing (NGS) techniques identified a broad spectrum of pathogens, offering a robust method for assessing environmental hygiene.

CONTRIBUTION: This study provides insights into food safety risks in the NSNP, informing policies and interventions to improve food safety and reduce foodborne illnesses in schools.},
}

@article {pmid40611965,
year = {2025},
author = {Ivanova, M and Aarestrup, FM and Otani, S},
title = {Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597804},
pmid = {40611965},
issn = {1664-302X},
abstract = {The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical importance for surveillance applications. Here, we evaluate how different multiplexing levels (four and eight samples per flowcell) on two ONT platforms, GridION and PromethION, influence the detection of ARGs, bacterial taxa and pathogens. While overall resistome and bacterial community profiles remained comparable across multiplexing levels, ARG detection was more comprehensive in the four-plex setting with low-abundance genes. Similarly, pathogen detection was more sensitive in the four-plex, identifying a broader range of low abundant bacterial taxa compared to the eight-plex. However, triplicate sequencing of the same microbiomes revealed that these differences were primarily due to sequencing variability rather than multiplexing itself, as similar inconsistencies were observed across replicates. Given that eight-plex sequencing is more cost-effective while still capturing the overall resistome and bacterial community composition, it may be the preferred option for general surveillance. Lower multiplexing levels may be advantageous for applications requiring enhanced sensitivity, such as detailed pathogen research. These findings highlight the trade-off between multiplexing efficiency, sequencing depth, and cost in metagenomic studies.},
}

@article {pmid40611959,
year = {2025},
author = {Qi, S and Qian, J and Li, Y and Li, Y and Li, W and Gao, X},
title = {Effect of acupuncture at Back-Shu points on gut microbiota in insomnia model rats based on metagenomic sequencing technology.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541958},
pmid = {40611959},
issn = {1664-302X},
abstract = {BACKGROUND: Increasing evidence indicates a bidirectional interaction between the gut microbiota and sleep regulation via the microbiota-gut-brain axis. Acupuncture is widely used to treat insomnia, and its efficacy may be mediated in part by modulation of the gut microbiota and its metabolic pathways.

METHODS: A rat model of insomnia was established by intraperitoneal injection of para-chlorophenylalanine (PCPA). Rats received acupuncture at Back-Shu points for 2 weeks. Sleep behavior was assessed using the pentobarbital-induced sleep test, and fecal samples were collected for metagenomic sequencing to analyze changes in gut microbial composition and function before and after acupuncture.

RESULTS: Compared with the model group, acupuncture significantly shortened sleep latency and prolonged sleep duration. Metagenomic analysis revealed that acupuncture partially restored the PCPA-induced decline in α-diversity and markedly altered β-diversity. Functionally, acupuncture enriched beneficial taxa such as Lactobacillus johnsonii and Ligilactobacillus murinus, and promoted pathways involved in tryptophan and glutamate metabolism as well as short-chain fatty acid (SCFA) synthesis. These changes may act by restoring neurotransmitter balance, strengthening gut barrier integrity, and modulating immune responses. Notably, SCFAs can activate G-protein-coupled receptors to suppress overactivation of the hypothalamic-pituitary-adrenal (HPA) axis, counteracting insomnia-related pathophysiology.

CONCLUSION: Acupuncture at Back-Shu points ameliorates PCPA-induced insomnia-like behavior in rats and beneficially remodels gut microbiota structure and metabolic function. These findings support a key role for the microbiota-gut-brain axis in acupuncture's regulation of sleep and provide a theoretical basis for developing microbiota-targeted adjunctive therapies for insomnia.},
}

@article {pmid40611899,
year = {2025},
author = {Pokharel, SK and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC},
title = {Establishing Conserved Biosynthetic Gene Clusters of the Phylum Myxococcota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.19.660557},
pmid = {40611899},
issn = {2692-8205},
abstract = {A surge in sequenced myxobacteria catalyzed by advancements in long read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze eleven genera and 195 sequenced genomes including ten newly reported myxobacterial isolate, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient, sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium ; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.},
}

@article {pmid40611207,
year = {2025},
author = {Wang, Q and Zhang, M and Meng, M and Luo, Z and Pan, Z and Deng, L and Qin, J and Guo, B and Zhu, D and Zhang, Y and Guo, H and Liang, Y and Su, Z},
title = {Integration bile acid metabolomics and gut microbiome to study the anti-liver fibrosis effects of total alkaloids of Corydalis saxicola Bunting.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {106},
pmid = {40611207},
issn = {1749-8546},
support = {82060763//National Natural Science Foundation of China/ ; GXFCDP-PS-2022//Guangxi First-class Discipline Project for Pharmaceutical Sciences/ ; GXQH202409//Guangxi Youth Qihuang Scholars Training Project/ ; },
abstract = {BACKGROUND: Bile acids and gut microbiota participate in the pathogenesis of liver fibrosis (LF). The total alkaloids of Corydalis saxicola Bunting (TACS) is a traditional Chinese medicine extract that has been used to treat LF, but the underlying mechanisms are not clear. This study performed integrated metabolomics and gut microbiome analysis to study the anti-LF mechanism of TACS using a rat model.

METHODS: Ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was used to identify the chemical compounds in TACS. Biochemical and histopathological analysis were performed to determine the efficacy of TACS. Bile acid-targeted metabolomics was used to assess changes in the bile acid (BA) profiles in TACS-treated LF rats. 16S rRNA gene sequencing and metagenomics were used to assess changes in the gut microbiota of the TACS-treated LF rats. Antibiotic cocktail treatment and fecal microbiota transplantation (FMT) were used to determine the relationship between the gut microbiota and the anti-LF effects of TACS. Metagenomics was used to identify significantly enriched gut microbiota after TACS treatment and its correlation with the anti-LF effects was verified by in vivo experiments.

RESULTS: TACS treatment significantly reduced the levels of serum liver enzymes, fibrosis and pro-inflammatory cytokines in the liver. TACS significantly increased the levels of chenodeoxycholic acid (CDCA) and taurochenodeoxycholic acid (TCDCA) in the cecum and decreased the levels of cholic acid (CA) and deoxycholic acid (DCA) in the liver of the LF rats. TACS significantly increased the abundances of Lactobacillus and Akkermansia in the LF rats. Antibiotic cocktail treatment and FMT have shown that the effect of TACS cure liver fibrosis depends on the gut microbiota. The abundance of Lactobacillus reuteri was significantly increased by TACS. Administration of Lactobacillus reuteri via gavage ameliorated LF.

CONCLUSIONS: TACS exerted anti-LF effects in rats by modulating bile acid metabolism and gut microbiome.},
}

@article {pmid40610423,
year = {2025},
author = {Fuhrmeister, ER and Kim, S and Mairal, SA and McCormack, C and Chieng, B and Swarthout, JM and Paulos, AH and Njenga, SM and Pickering, AJ},
title = {Context-Seq: CRISPR-Cas9 targeted nanopore sequencing for transmission dynamics of antimicrobial resistance.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5898},
pmid = {40610423},
issn = {2041-1723},
support = {OPP1129535//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; UL1TR002544//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1906957//National Science Foundation (NSF)/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; Animals ; Humans ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; Kenya ; Anti-Bacterial Agents/pharmacology ; Dogs ; *Bacteria/genetics/drug effects ; Klebsiella pneumoniae/genetics/drug effects ; Child ; Adult ; Escherichia coli/genetics/drug effects ; Poultry/microbiology ; beta-Lactamases/genetics ; Genome, Bacterial ; Haemophilus influenzae/genetics/drug effects ; },
abstract = {Precisely understanding how and to what extent antimicrobial resistance (AMR) is exchanged between animals and humans is needed to inform control strategies. Metagenomic sequencing has low detection for rare targets such as antibiotic resistance genes, while whole genome sequencing of isolates misses exchange between uncultured bacterial species. We introduce Context-Seq, CRISPR-Cas9 targeted sequencing of ARGs and their genomic context with long-reads. Using Context-Seq, we investigate genetically similar AMR elements containing the ARGs blaCTX-M and blaTEM between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing blaTEM and blaCTX-M that are shared between animals and humans within and between households. We also uncover potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumoniae, and Haemophilus influenzae in this study context. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.},
}

*CRISPR-Cas Systems/genetics
Animals
Humans
*Nanopore Sequencing/methods
*Drug Resistance, Bacterial/genetics
Kenya
Anti-Bacterial Agents/pharmacology
Dogs
*Bacteria/genetics/drug effects
Klebsiella pneumoniae/genetics/drug effects
Child
Adult
Escherichia coli/genetics/drug effects
Poultry/microbiology
beta-Lactamases/genetics
Genome, Bacterial
Haemophilus influenzae/genetics/drug effects

@article {pmid40609888,
year = {2025},
author = {Maki, T and Takami, H and Pointing, S and Kurosaki, Y and Fukui, H and Bin, C and Kai, K},
title = {Bacterial stress adaptation and antibiotic resistance in dust-transportable bioaerosols originating from the Gobi Desert.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126759},
doi = {10.1016/j.envpol.2025.126759},
pmid = {40609888},
issn = {1873-6424},
abstract = {Airborne microorganisms which dispersed from the Gobi Desert throughout East Asia via long-range dust transports, are believed to maintain their viability against atmospheric stressors that influence ecosystem dynamics and human health during deposition in downwind environments. However, the adaptative mechanisms that facilitate microbial tolerance to environmental stressor, and the persistence of factors such as antibiotic resistance relevant to human health have not been determined. Here, we described the metagenomic and physiological interrogation of airborne bacteria collected from aerosols at an altitude of 500 m using a balloon-mounted sampler and at a parallel site 3 m above the ground in the dust-source region of Gobi Desert. The shotgun metagenomic DNA sequencing which determine was performed for characterizing the taxonomic compositions of airborne bacteria and their potential functions. The communities were dominated by species in the phyla Actinobacteria, Bacillota, Bacteroidota, and Pseudomonadota (Alpha). Metabolic-pathway analysis revealed that Gobi Desert bioaerosols were enriched in functions associated with antibiotic resistance, cell-membrane transporters, and/or environmental adaptation. The antibiotic and osmotic-change resistances were confirmed among viable bacteria isolates showing higher level of resistances in the aerosols collected at 500 m than those of 3 m. These findings suggest that elevated altitudes result in environmental filtering that allows bacterial taxa to survive long-term transport to distant locations during dust events and transfer antibiotic resistance.},
}

@article {pmid40609443,
year = {2025},
author = {Lu, B and Wang, P and Hu, J and Qian, J and Liu, F and He, Y and Tang, S and Shen, J and Liu, Y},
title = {PFOS-induced alterations in phosphorus dynamics and soil microbial functions in wetlands.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126445},
doi = {10.1016/j.jenvman.2025.126445},
pmid = {40609443},
issn = {1095-8630},
abstract = {Perfluorooctanesulfonate (PFOS), a widely persistent pollutant, poses significant ecological risks, yet its impact on critical nutrient cycles, such as phosphorus (P), in wetland ecosystems remains poorly understood. Phosphorus is essential for plant growth and microbial functions, and disruptions in its cycling can have profound effects on ecosystem stability. This study investigates the influence of PFOS on P dynamics and soil microbial functions in the rhizosphere of Phragmites communis. We examined how varying PFOS concentrations affect inorganic and organic P forms and microbial gene expression associated with P transformations. High PFOS concentrations significantly reduced shoot and root P content, corresponding to declines in labile phosphorus (NaHCO3-Pi). Additionally, shifts in microbial community diversity and composition were observed, particularly under high PFOS exposure, where key phosphorus-cycling genes, such as phoD in rhizosphere soils, showed significantly reduced transcriptional levels (as quantified by qRT-PCR), despite increased gene abundance as revealed by metagenomic sequencing. These findings offer new insights into how emerging contaminants like PFOS disrupt phosphorus cycling and microbial functions in wetland ecosystems, with broader implications for ecological risk assessments.},
}

@article {pmid40609272,
year = {2025},
author = {Ji, B and Chen, Q and Song, Y and Dong, Z and Ding, J and Wang, G and Liu, G and Gao, P and Zhao, J},
title = {Distributions of pathogenic bacteria, antibiotic resistance genes, and virulence factors in pig farms in China.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118607},
doi = {10.1016/j.ecoenv.2025.118607},
pmid = {40609272},
issn = {1090-2414},
abstract = {The abundance of antibiotic resistance genes (ARGs) in pig feces can lead to their dissemination in the pig farm environment, posing a serious risk to human health through potential exposure and transmission. However, the extent of microbial contamination in pig farms, including ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and human bacterial pathogens (HBPs), is still largely unknown. In this study, metagenomics was employed to identify the composition and characteristics of microorganism communities, ARGs, VFGs, MGEs and HBPs in pig farm environments from seven different regions of China. The results showed that there were significant differences in the composition of microorganisms and Firmicutes, Bacteroides, Proteobacteriahe Spirochaetes were the dominant phyla in the pig farm environment. The abundance and composition of ARGs, VFGs, MGEs and HBPs varied significantly in pig farm environments in different regions, with the abundance in Fujian being significantly higher than that in other regions. In total, 216 ARGs, 479 VFGs, 143 MGEs and 78 HBPs were identified across all pig feces, soil, and wastewater samples. The most prominent ARGs were those related to tetracycline, aminoglycoside, and MLS resistance. Escherichia coli, Arcobacter cryaerophilus, Corynebacterium xerosis, Aerococcus viridans, and Collinsella aerofaciens were the most commonly found HBPs in the pig farm environment. Procrustes analysis and Mantel test results showed a strong correlation between ARGs and HBPs, VFGs and HBPs, and ARGs and VFGs. ARGs were mainly harbored by E. coli, Klebsiella pneumoniae, and Enterococcus faecalis in the pig farm environments. The random forest model indicated that the presence of MGEs (intI1, IS91, and tnpA) was significantly correlated with the total abundance of resistance genes, which can be utilized as an important indicator for measuring resistance genes. The study establishes a foundational understanding of the prevalence and diversity of ARGs, VFGs, and HBPs in pig farm environments, aiding in the development of effective management strategies to mitigate ecological and public health risks.},
}

@article {pmid40609120,
year = {2025},
author = {Jiang, M and Xie, Z and Fan, Q and Tang, G and Pan, N and Zeng, H and Xu, Y and Zhang, C and Luo, M and Li, F},
title = {Epidemiological characteristics of Circovirus Human infection in hospitalized patients in a representative infectious disease hospital in Guangzhou, China, from Feb 2023 to Dec 2024.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {3},
pages = {116962},
doi = {10.1016/j.diagmicrobio.2025.116962},
pmid = {40609120},
issn = {1879-0070},
abstract = {Circovirus Human reported in recent years have drawn attention as potential human pathogens in susceptible patients. However, its epidemiological characteristics are less investigated. We found 3 infected cases in 1330 hospitalized patients with suspected unidentified infections in a designated hospital for treating infectious diseases by retrospectively analyzing their metagenomic sequencing data. All three patients were HIV-positive and immunosuppressed. Liver function tests were normal at admission but showed transient acute injury during antimicrobial therapy, without hepatitis virus coinfection.},
}

@article {pmid40608709,
year = {2025},
author = {Jiang, L and Zhou, L and Huang, S and Ao, Z and Han, X},
title = {Venovenous extracorporeal membrane oxygenation in severe community-acquired Acinetobacter baumannii pneumonia.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {6},
pages = {971-976},
doi = {10.3855/jidc.19761},
pmid = {40608709},
issn = {1972-2680},
mesh = {Humans ; Male ; *Extracorporeal Membrane Oxygenation/methods ; Middle Aged ; *Acinetobacter baumannii/isolation & purification ; *Community-Acquired Infections/therapy/microbiology/diagnosis ; *Acinetobacter Infections/therapy/diagnosis/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/therapy/diagnosis/microbiology ; Treatment Outcome ; Respiratory Distress Syndrome/therapy ; Meropenem/therapeutic use ; Tigecycline ; },
abstract = {INTRODUCTION: Globally, Acinetobacter baumannii (A. baumannii) is a significant nosocomial pathogen. Community-acquired pneumonia (CAP) caused by A. baumannii is rare, but often associated with severe outcomes.

CASE PRESENTATION: A 48-year-old man was admitted to a local hospital, presenting a 14-hour history of acute fever, cough, expectoration, chest pain, and dyspnea. Owing to the development of severe acute respiratory distress syndrome (ARDS) and septic shock, the patient was promptly transferred to our institution for veno-venous extracorporeal membrane oxygenation (VV-ECMO) following intubation and mechanical ventilation. Sputum culture, digital polymerase chain reaction (dPCR) assay of blood, and metagenomic next-generation sequencing (mNGS) assay of bronchoalveolar lavage fluid (BALF) all indicated A. baumannii. The patient responded favorably to treatment with meropenem and tigecycline. The amelioration of his respiratory function allowed for the cessation of ECMO after 7 days; and subsequently, the patient was successfully weaned from ventilatory support.

CONCLUSIONS: A. baumannii should be considered as a possible causative organism of CAP based on presentation in the tropical or subtropical wet season, a very aggressive clinical course, typical chest imaging features, and the presence of A. baumannii in sputum. ECMO represents an efficacious treatment alternative for severe ARDS and septic shock complications associated with A. baumannii when conventional mechanical ventilation proves inadequate, particularly when initiated early in the clinical course.},
}

Humans
Male
*Extracorporeal Membrane Oxygenation/methods
Middle Aged
*Acinetobacter baumannii/isolation & purification
*Community-Acquired Infections/therapy/microbiology/diagnosis
*Acinetobacter Infections/therapy/diagnosis/microbiology
Anti-Bacterial Agents/therapeutic use
*Pneumonia, Bacterial/therapy/diagnosis/microbiology
Treatment Outcome
Respiratory Distress Syndrome/therapy
Meropenem/therapeutic use
Tigecycline

@article {pmid40608623,
year = {2025},
author = {Nascimento, GMD and Romano, CM and Rozanski, A and de Moura Coletti, T and Urbinatti, PR and Natal, D and Marrelli, MT and de Araújo, AB and Nardi, MS and da Costa, AC and Natal Fernandes, L},
title = {Detection of Furrundu phlebovirus in Aedes scapularis (Diptera: Culicidae) collected in urban parks, in a highly urbanized city.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {67},
number = {},
pages = {e38},
pmid = {40608623},
issn = {1678-9946},
mesh = {Animals ; *Aedes/virology ; Phylogeny ; Brazil ; *Phlebovirus/isolation & purification/genetics/classification ; Female ; *Mosquito Vectors/virology ; Parks, Recreational ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; },
abstract = {Mosquitoes (Diptera: Culicidae) are arthropods of medical importance because they can carry arboviruses. High-throughput sequencing (HTS) technology and metagenomic approaches conducted in mosquitoes have contributed to the discovery of many insect-specific viruses (ISVs), which have the potential to affect their vector competence. Mosquitoes were collected in urban parks in Sao Paulo city, Brazil and 20 pools with female mosquitoes were subjected to HTS by HiSeq 2500 sequencing system (Illumina). Long viral sequences (1,585-6,701 base pairs) were recovered from two pools of Aedes scapularis. BLASTx analyses revealed they had greater identity with segment L and S of Salarivirus and segment M of Furrundu phlebovirus, which encode, respectively, the RNA-dependent RNA polymerase (RdRd), the nucleocapsid protein, and a polyprotein. Phylogenetic tree of the segment L and S of the Phenuiviridae Family showed our sequences grouped with unverified sequences of Furrundu phlebovirus, an unclassified ISV that belongs to the Hareavirales Order and was first reported in mosquitoes in the Brazilian Pantanal, the largest natural tropical wetland worldwide. We report the second detection of Furrundu phlebovirus in mosquitoes collected in urban parks, showing it could be in mosquitoes from natural places and in green areas in urban cities. We conclude that Furrundu phlebovirus possibly occurs in Aedes scapularis in green areas, in Sao Paulo. Further studies should elucidate the role of this virus in the vector competence of Aedes scapularis and its interaction with different arboviruses.},
}

Animals
*Aedes/virology
Phylogeny
Brazil
*Phlebovirus/isolation & purification/genetics/classification
Female
*Mosquito Vectors/virology
Parks, Recreational
High-Throughput Nucleotide Sequencing
RNA, Viral/genetics

@article {pmid40608492,
year = {2025},
author = {Ozuru, R and Yamagishi, J and Takeuchi, A and Date, Y and Fujii, T and Sugimoto, C and Nakajima, C and Suzuki, Y and Aoki, K and Fujii, J and Matsuba, T},
title = {Unification of Symbiotic Bacteria During Larva-to-Adult Transition in Culicoides circumscriptus (Diptera: Ceratopogonidae).},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf069},
pmid = {40608492},
issn = {1574-6968},
abstract = {Blood-sucking midges such as Leptoconops and Culicoides are of medical importance due to their role in causing skin irritation and potentially transmitting pathogens. Investigating their bacterial communities, including possible endosymbionts, may help clarify ecological adaptations and interactions with hosts. Leptoconops nipponensis Tokunaga (Lnt) and Culicoides circumscriptus (Cc), blood-sucking midges, cause severe itching and inflammation in humans. Cc was collected from a small sample of an outbreak swarm of Lnt in the peninsula area of Yonago City, Tottori Prefecture, Japan. This study compared the bacterial flora of Lnt and Cc, revealing distinct bacterial diversity shifts in these insect species between life stages. We analyzed the bacterial communities of adult and larval females of Cc and Lnt using MiSeq sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Notably, alpha diversity in Cc adults was significantly reduced to 1.5 (n = 43), indicating that Cc adults were dominated by a single bacterial genus, compared to 14.9 in Cc larvae (n = 19). BLAST analysis identified this dominant genus in adult Cc as Rickettsia (Candidatus Tisiphisa), which is known for transovarial transmission in arthropod vectors. In contrast, the bacterial diversity of Lnt showed no significant difference between adults (18.1, n = 32) and larvae (n = 15). These findings suggest that the dominance of Rickettsia in Cc (Candidatus Tisiphisa) adults is linked to their emergence, potentially reflecting differences in reproductive biology and ecological adaptations between these two insect species. Further research is needed to elucidate the functional role of Rickettsia in the life cycle and physiology of Cc.},
}

@article {pmid40607849,
year = {2025},
author = {Zhang, H and Zhao, D and Wu, QL and Zeng, J},
title = {Environment selected microbial function rather than taxonomic species in a plateau saline-alkaline wetland.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0220624},
doi = {10.1128/aem.02206-24},
pmid = {40607849},
issn = {1098-5336},
abstract = {UNLABELLED: Comprehending the microbial community in plateau saline-alkaline wetlands, an understudied and vulnerable ecosystem, is vital for predicting ecosystem functions within the context of global climate change. Despite the rapid shrinkage and potential drying up of some of these wetlands, our knowledge of the microbial community in this ecosystem remains fragmented. Here, we utilized metagenomic sequencing to investigate the distribution of methane, nitrogen, and sulfur cycling genes/pathways and formation mechanism of microbial communities across sediment, surface rhizosphere soils (Rsurface), subsurface rhizosphere soils (Rsubsurface), surface bulk soils (Bsurface), and subsurface bulk soils (Bsubsurface) in Cuochuolong Wetland, a typical saline-alkaline wetland located in the Tibetan Plateau. The results showed that sediment exhibited relatively higher functional potentials for methanogenesis but lower potentials for methane oxidation. Denitrification and dissimilatory sulfate reduction potentials increased with decreasing salinity across the five habitats, following the trend: sediment
IMPORTANCE: Understanding the formation mechanism of microbial communities is a central goal in ecology. However, our understanding of microbial community remains fragmented in plateau saline-alkaline wetlands, despite their unique status as a vulnerable ecosystem characterized by high altitude, low disturbance, high salinity, sensitivity to global climate change, and localized shrinkage in some areas. Furthermore, previous studies on community formation mechanism have predominantly focused on microbial taxonomic structure, neglecting their functional compositions. Beyond providing a comprehensive understanding of the distribution patterns of methane, nitrogen, and sulfur cycling microbial communities within plateau saline-alkaline wetland, this study offers a novel perspective on formation mechanism of microbial community by emphasizing the deterministic selection of extreme environment on microbial function. This study also expands our comprehension of the diversity of microbes containing the nod gene, which may substantially contribute to global methane and nitrogen budgets.},
}

@article {pmid40607829,
year = {2025},
author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB},
title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0038025},
doi = {10.1128/msystems.00380-25},
pmid = {40607829},
issn = {2379-5077},
abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.},
}

@article {pmid40607500,
year = {2025},
author = {Luo, Y and Cheng, W and Ma, L and Wang, T and Shi, W},
title = {Diagnostic value of nanopore-based metagenomic third-generation sequencing in the diagnosis of Pneumocystis jirovecii infection in patients with lung cancer.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
pmid = {40607500},
issn = {1473-5644},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Pneumonia, Pneumocystis/diagnosis/microbiology/complications ; *Pneumocystis carinii/genetics/isolation & purification ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Prospective Studies ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; *Nanopore Sequencing/methods ; Adult ; Aged, 80 and over ; China ; },
abstract = {Introduction. Pneumocystis jirovecii pneumonia (PJP, formerly known as Pneumocystis carinii pneumonia), an opportunistic fungal infection caused by the fungus P. jirovecii, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung cancer. Traditional diagnostic methods for PJP, such as Grocott-Gomori's methenamine silver staining and real-time PCR, have limitations, including low positivity and high missed diagnosis rates.Gap Statement. Despite the critical need for accurate and sensitive diagnostic tools for PJP, especially in immunocompromised populations, existing methods fall short in providing the necessary reliability and efficiency.Aim. This study aims to evaluate the efficacy of nanopore-based metagenomic third-generation sequencing in diagnosing P. jirovecii infection in lung cancer patients, hypothesizing that this approach may offer superior sensitivity and specificity.Methodology. A prospective observational study was conducted on 118 lung cancer patients with suspected pulmonary P. jirovecii infection at the Sixth Hospital of Nantong City, China, from January 2021 to December 2023. The identification of pathogens in bronchoalveolar lavage fluid samples was performed using both metagenomics and traditional tests.Results. Metagenomics showed a significantly higher detection rate of P. jirovecii (33.0%) compared to methenamine silver staining (4.2%) and real-time PCR (30.5%). The sensitivity, specificity and accuracy of metagenomics detection were all 100%, which is markedly superior to traditional methods. Furthermore, metagenomics also identified mixed infections with other pathogens, such as Cytomegalovirus and Epstein-Barr virus.Conclusion. Metagenomics technology demonstrates high sensitivity and specificity in diagnosing P. jirovecii infection, including mixed infections with other pathogens, in lung cancer patients. It provides a clear direction for clinical treatment and is a powerful tool for diagnosing PJP, contributing to improved diagnostic efficiency and accuracy, reducing misdiagnosis and missed diagnosis rates and improving clinical outcomes in these patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Pneumonia, Pneumocystis/diagnosis/microbiology/complications
*Pneumocystis carinii/genetics/isolation & purification
Male
Female
Middle Aged
*Metagenomics/methods
Aged
Prospective Studies
Sensitivity and Specificity
Bronchoalveolar Lavage Fluid/microbiology
High-Throughput Nucleotide Sequencing
*Nanopore Sequencing/methods
Adult
Aged, 80 and over
China

@article {pmid40607081,
year = {2025},
author = {Zhang, Q and Teng, Z and Gong, P},
title = {A case of acute renal dysfunction and multiorgan dysfunction caused by Rickettsia japonica infection.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02283},
pmid = {40607081},
issn = {2214-2509},
abstract = {This article reports a case of acute renal dysfunction and multi-organ dysfunction syndrome caused by Rickettsia japonica infection. The patient, a 79-year-old male, presented with unexplained fever, fatigue, anorexia, vomiting, and chest tightness, followed by oliguria and a decline in mental status. Laboratory tests revealed significant abnormalities, including elevated white blood cells, thrombocytopenia, hepatic and renal dysfunction, and coagulopathy. Imaging studies showed pulmonary infection and bilateral pleural effusion. Based on the history of tick bite, clinical manifestations, and metagenomic next-generation sequencing (mNGS) results, which detected R. japonica, the patient was diagnosed with Japanese spotted fever (JSF). He received multidisciplinary comprehensive treatment, including mechanical ventilation, continuous renal replacement therapy (CRRT), antimicrobial therapy, blood transfusions, and supportive care. After 15 days of treatment, the patient's fever resolved, inflammatory markers decreased significantly, and organ functions improved gradually, leading to eventual recovery and discharge. This case highlights the importance of early recognition and treatment of R. japonica infection, especially in endemic areas, to prevent rapid deterioration and multi-organ failure.},
}

@article {pmid40606566,
year = {2025},
author = {Wang, L and Wang, L and Chen, L},
title = {NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {2},
pages = {208-211},
pmid = {40606566},
issn = {2730-5848},
abstract = {UNLABELLED: Metagenomics and metabolomics technologies have been widely used to investigate the microbe-metabolite interactions in vivo. However, the computational methods that accurately infer the microbe-metabolite interactions are lacking. We present a context-aware framework for graph representation learning, NetNiche, which predicts microbe-metabolite and microbe-microbe interactions in an accurate manner, by integrating their abundance data with prior knowledge. We applied NetNiche to datasets on gut and soil microbiome, and demonstrated that NetNiche can outperform the state-of-the-art methods, such as SParse InversE Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Sparse Correlations for Compositional data (SparCC) and microbe-metabolite vectors (mmvec). NetNiche is an effective tool with wide applicability for the multi-omics study of human microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00168-8.},
}

@article {pmid40606560,
year = {2025},
author = {Wang, H and Zhuang, Y and Hua, R and Yao, T and Lin, K and Zhang, Y and Huang, R and Wang, R and Guo, S and Shen, Q and Shao, Y and Wu, W and Fan, L and Feng, Y and Yao, Q and Ye, H and Kong, X and Zhang, Q and Wang, R and Liu, T},
title = {Multi-Omics Exploration of Obesity Biomarkers in Sedentary and Weight Loss Cohorts.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {2},
pages = {137-153},
pmid = {40606560},
issn = {2730-5848},
abstract = {UNLABELLED: Sedentary behavior for two years during the coronavirus disease 2019 (COVID-19) pandemic contributes to weight gain. Gut microbiota and blood metabolome are related to body mass index (BMI) and indicate individual metabolic changes. Surgery and exercise are effective weight-loss methods. The precise plasma metabolites and gut microbiota biomarkers involved and the underlying mechanisms are still largely unclear. To address this issue, we analyzed weight gain and weight loss cohorts to identify biomarkers associated with obesity. In the sedentary cohort, 49 subjects were recruited in year 2019. After two years of sedentary behavior during the COVID-19 pandemic, the BMI of 24 subjects significantly increased (Weight gain group), while that of the remnant 25 subjects remained constant (Maintaining weight group). At baseline and two years post baseline, the gut microbiota and blood metabolome, as well as body composition and clinical indicators, were all collected. In weight loss studies, we analyze the plasma metabolome of the two cohorts, including individuals who underwent laparoscopic sleeve gastrectomy (LSG) surgery and exercise intervention. Weight gain through sedentary behavior contributed to the variation of the gut microbiota and plasma metabolites composition. Creatine, phenylalanine and tyrosine exhibited significant positive associations with BMI and fat mass. We further confirmed the association between BMI and plasma metabolites in two weight loss cohorts. By utilizing a linear regression model, we found that 10 metabolites including creatine were correlated with BMI in weight loss individuals. Based on receiver operating characteristic (ROC) curves, creatine exhibited a satisfactory classification performance in regard to predicting weight reduction (AUCLSG = 0.890, AUCS ports = 0.840). Moreover, some gut microbiota, including Bifidobacterium angulatum DSM 20098 = JCM 7096 and Rothia dentocariosa M567I could affect BMI through the mediating factor of creatine.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00165-x.},
}

@article {pmid40606175,
year = {2025},
author = {Wang, J and Zhu, Y and Li, D and Zheng, X and Chai, C and Zhang, J and Wu, J and Hu, Q and Zhao, S},
title = {The diversity of viral community in Sogatella furcifera revealed by meta-transcriptomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1617239},
pmid = {40606175},
issn = {1664-302X},
abstract = {INTRODUCTION: Metagenomic analyses has significantly advanced our understanding of viral evolution and their functions within organismal biology. In particular, exploring the virome of agricultural pests like the white-backed planthopper (WBPH) is essential for understanding their role as potential virus vectors and developing effective pest management strategies.

METHODS: To explore viral diversity, we collected white-backed planthoppers (WBPHs) from nine sites spanning four Chinese provinces (Liaoning, Fujian, Guangxi, and Yunnan) and performed metagenomic sequencing.

RESULTS: Our analysis identified 11 novel viruses belonging to 7 viral families, encompassing positive-sense single-stranded RNA (+ssRNA), negative-sense single-stranded RNA (-ssRNA), and double-stranded RNA (dsRNA) viruses. Remarkably, eight of the southern Chinese sites, excluding one in Liaoning province, contained a previously undiscovered Sobelivirales virus. Using rapid-amplification of cDNA ends (RACE), we determined the complete genome sequence of this novel Sobelivirales virus. Subsequent analyses of its encoded proteins, potential structural domains, and phylogenetic relationships suggested that it may belong to a new genus within the Sobelivirales. Small RNA sequencing confirmed viral replication in WBPH by revealing that virus-derived small interfering RNAs (vsiRNAs) were primarily 21 and 22 nucleotides long.

DISCUSSION: Our results have important implications for understanding virus carriage in WBPHs, evaluating their role as virus vectors, and informing the development of improved pest management strategies. Furthermore, this study highlights the power of metagenomics in uncovering novel viruses and expanding our knowledge of viral diversity.},
}

@article {pmid40606163,
year = {2025},
author = {Komori, E and Kato-Kogoe, N and Imai, Y and Sakaguchi, S and Taniguchi, K and Omori, M and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Lee, SW and Ueno, T},
title = {Gastrectomy-induced alterations in gut microbiota linked to changes in oral and gastric microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599503},
pmid = {40606163},
issn = {1664-302X},
abstract = {INTRODUCTION: Gastrectomy serves as a primary treatment for gastric cancer, a leading global malignancy, and affects significant physiological and anatomical changes in the digestive tract. Recent studies highlight the critical role of gastrointestinal microbiota in postoperative health following digestive tract surgeries, including gastrectomy. These alterations possibly impact the gut microbiota and affect patient health by influencing the bacterial environment in the gastrointestinal tract. However, the relationships between the gastrointestinal tract and the oral, gastric, and gut microbiota after gastrectomy are not clear. In this study, we aimed to characterize alterations in the gut microbiota due to gastrectomy and evaluate whether these alterations are associated with the oral and gastric microbiota.

METHODS: Saliva, gastric fluid, and stool samples were collected from patients diagnosed with primary gastric cancer who underwent gastrectomy at two time points, before and 6 months after gastrectomy. Next, 16S rRNA metagenomic analysis was performed. Diversity and linear discriminant analysis effect size (LEfSe) analyses of each microbiota were conducted before and after gastrectomy to compare alterations in the gut, oral, and gastric microbiota.

RESULTS: The diversity of gut microbiota increased after gastrectomy compared to that before gastrectomy (Shannon index, p = 0.044), with LEfSe analysis showing increased abundance of Rothia and Lactobacillus in the gut microbiota. Additionally, the proportion of participants with Rothia in their gut microbiota increased, and this genus was present in the oral and gastric microbiota of almost all participants. Furthermore, a significant rise in Lactobacillus was observed in the gut, oral, and gastric microbiota of paired participants.

DISCUSSION: We characterized gut microbiota alterations caused by gastrectomy and demonstrated their relationship with changes in oral and gastric microbiota, thereby elucidating interactions between the gastrointestinal tract microbiota in response to changes in the gastric environment.},
}

@article {pmid40606158,
year = {2025},
author = {Tang, MLY and Lau, SCK},
title = {Varying effects of chlorination on microbial functional repertoire and gene expression in contrasting effluents.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593147},
pmid = {40606158},
issn = {1664-302X},
abstract = {Effluents produced from different influent sources and sewage treatment processes carry distinct microbial community compositions. These microbiomes exhibit varying degrees of resistance and resilience under chlorination; however, their survival strategies and potential risks to the public health and ecosystem have yet to be fully characterized. In view of this, we subjected microbiomes from two contrasting types of effluents with distinct influent properties (seawater/freshwater-based) and prior treatment processes (primary/secondary) to metagenomics and metatranscriptomics analyses for comparing the alterations in their functional genes and activities under chlorination. The effluents presented highly dissimilar genomic and transcriptomic profiles. The variations in these profiles were significantly correlated to physicochemical factors including salinity, DO, BOD5, TSS, and TN. We recovered novel metagenome-assembled genomes (MAGs) from each type of effluent, revealing that those recovered from the same effluent tended to share similar functional properties which aligned with the physicochemical parameters of the effluent. Notably, the type and extent of alterations in genomic and transcriptomic profiles under chlorination varied greatly between effluents. Most of the genes and transcripts with significant changes in relative abundances were exclusive to their respective effluents. Also, the number of genes and transcripts with significant increase in relative abundances after chlorination were much higher than those with reduction. These enriched genes and transcripts were responsible for a wide range of functions, including energy generation, repair of damaged components and stress responses. Furthermore, the remanent microbiomes in chlorinated effluents still harbored numerous genes related to waterborne diseases and antimicrobial resistance, suggesting the potential risks of discharging these effluents into the environment. This study revealed the diverse effects of chlorination on different types of effluent microbiomes. It suggested that the remanent microbiomes in chlorinated effluents would have great variance in genetic potential and activities, providing insights into the evaluation and regulation of chlorine disinfection in sewage treatment.},
}

@article {pmid40605980,
year = {2025},
author = {Xu, Z and Zhang, Y and Wang, D and Xuan, C and Li, Z and Xu, H},
title = {Impact of cytomegalovirus DNAemia detected by next-generation sequencing on short-term prognosis after lung transplantation.},
journal = {Infectious medicine},
volume = {4},
number = {2},
pages = {100185},
pmid = {40605980},
issn = {2772-431X},
abstract = {BACKGROUND: Cytomegalovirus (CMV) is a common opportunistic pathogen following lung transplantation, associated with post-transplant complications and adverse outcomes. This study aims to evaluate the incidence of CMV DNAemia identified through metagenomic next-generation sequencing (mNGS) during the early postoperative phase of lung transplantation and assess its effects on the short-term outcomes for recipients.

METHODS: We conducted a retrospective analysis of clinical data from 115 patients who received lung transplants at the Affiliated Wuxi People's Hospital of Nanjing Medical University between May 2020 and November 2023. Based on mNGS-detected CMV DNAemia status, patients were stratified into DNAemia group and normal group. Nonparametric tests (Mann-Whitney U/Wilcoxon signed-rank) and mixed-effects models for intergroup comparisons. Kaplan-Meier survival analysis with log-rank testing for overall survival differences. Univariate logistic regression to identify risk factors for ICU mortality and 90-day mortality. Multivariate logistic regression adjusting for confounders. Propensity score matching (1∶1 optimal nearest neighbor, caliper = 0.25) was implemented to address covariate imbalance, followed by univariate logistic regression analyses in the matched cohort.

RESULTS: In the early postoperative period following lung transplantation, CMV DNAemia was detected via mNGS with an incidence rate of 15.7%. The CMV DNAemia group demonstrated a significantly lower 90-day overall survival rate compared to the normal group, with the Log-rank test revealing statistically significant survival differences between groups (p < 0.001). Univariate and multivariate logistic regression analyses identified CMV DNAemia as an independent risk factor for ICU all-cause mortality (OR = 5.00, 95% CI: 1.37-18.27, p = 0.015), while with other pathogens infections independently predicted 90-day all-cause mortality (OR = 3.40, 95% CI: 1.10-10.44, p = 0.033). After propensity score matching, baseline characteristics were well-balanced between the CMV DNAemia and normal groups. In the matched cohort, univariate logistic regression further confirmed CMV DNAemia as an independent risk factor for ICU mortality (OR = 7.43, 95% CI: 1.23-45.00, p = 0.029). Mediation analysis demonstrated that co-pathogen infections mediated the relationship between CMV DNAemia and 90-day all-cause mortality, with a proportion mediated of 20.6% (95% CI: 1.7%-138.5%, p < 0.001).

CONCLUSIONS: mNGS revealed a higher incidence of early CMV DNAemia post-lung transplantation than previously reported. CMV DNAemia significantly correlates with poor prognosis. Despite limitations in sample size and retrospective design, this study provides novel insights into CMV monitoring and management post-transplantation. Future research should determine optimal timing for preemptive antiviral strategies guided by mNGS.},
}

@article {pmid40605848,
year = {2025},
author = {Grevskott, DH and Victor, MP and Lima, TE and Radisic, V and Nimje, PS and Marathe, NP},
title = {High-throughput sequencing data of the microbiota and antibiotic resistance genes from biofilms on polystyrene and nylon rope incubated in Bergen harbor.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111718},
pmid = {40605848},
issn = {2352-3409},
abstract = {Plastics can provide a hydrophobic surface for microorganisms to attach, colonize and form microbial biofilms, referred to as 'plastisphere.' The aim of this study was to determine the microbiota of biofilms on plastic, using field trials in Bergen harbour, Norway using metagenomics. Polystyrene (PS) and nylon ropes (PA) were submerged in sea for four weeks, biofilm communities were collected, and the extracted DNA was subjected to metagenomic sequencing (n=12). The average salinity and temperature during the experiment were 9.02 °C (8.2-10.7) and 28.85 ‰ (26.1 ‰ - 33.1 ‰). We obtained a total of ∼460 Gigabases of sequence data from our samples. Gammaproteobacteria and Alpha proteobacteria were the most prominent on these polymers with β-lactamases as the most abundant resistance gene class. The datasets will be useful for the scientific community working on plastic-associated biofilms.},
}

@article {pmid40605092,
year = {2025},
author = {Han, Y and Deng, Z and Peng, Y and Peng, J and Cao, L and Xu, Y and Yang, Y and Zhou, H and Zhang, C and Zhang, D and Wang, M and Zhang, C and Greening, C and Dong, X},
title = {Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {156},
pmid = {40605092},
issn = {2049-2618},
support = {42406109//National Natural Science Foundation of China/ ; 42406131//National Natural Science Foundation of China/ ; 42376084//National Natural Science Foundation of China/ ; 42276150//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 20250131//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 2023M734096//China Postdoctoral Science Foundation/ ; 2024M762799//China Postdoctoral Science Foundation/ ; GZC20241467//Postdoctoral Fellowship Program of CPSF/ ; 2023B0303000015//Guangdong Major Project of Basic and Applied Basic Research/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification/enzymology ; Phylogeny ; *Halogenation ; *Archaea/genetics/classification/metabolism/isolation & purification/enzymology ; *Seawater/microbiology ; Metagenomics/methods ; Bacterial Proteins/genetics/metabolism ; Metagenome ; Oxidation-Reduction ; },
abstract = {BACKGROUND: Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role is not completely understood, especially in deep-sea environments. To address this gap, we investigated the diversity and expression of genes encoding reductive dehalogenase catalytic subunits (RdhAs), and ecophysiology of potential organohalide reducers in deep-sea cold seeps, which are environments rich in halogenated compounds.

RESULTS: Through genome-resolved metagenomic analysis of 165 global cold seep sediment samples, 4 types of RdhA-like sequences were identified based on their features and phylogenetic relationships: prototypical respiratory, transmembrane respiratory, cytosolic, and a novel clade. Cold seeps were found to harbor a higher abundance of these rdhA-like genes compared to other marine sediments, highlighting their potential as microbial reductive dehalogenation hotspots. These rdhA-like genes are encoded by a wide range of microorganisms across 4 archaeal and 36 bacterial phyla, significantly expanding the known diversity of organohalide reducers. Halogen geochemistry, laboratory incubations, metatranscriptomic data, and metabolomic profiling confirmed the presence of organohalides at concentrations of up to 18 mg/g in these sediments and suggested the potential for microbial reductive dehalogenation. Our findings suggest that organohalide reducers in cold seep sediments may participate in diverse biogeochemical processes, as inferred from the presence of genes related to carbon, hydrogen, nitrogen, sulfur, and trace element cycling. Additionally, RdhA-like proteins from cold seeps have diverse N-terminal structures across different gene groups.

CONCLUSIONS: These findings collectively suggest that reductive dehalogenation is an important process in deep-sea environments, mediated by a diverse array of microbes and novel enzymes. The discovery of diverse and abundant rdhA-like genes, along with their genomic context and potential metabolic linkages, highlights the role of cold seeps as reservoirs of microbial diversity with possible implications for environmental remediation. Video Abstract.},
}

*Geologic Sediments/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification/enzymology
Phylogeny
*Halogenation
*Archaea/genetics/classification/metabolism/isolation & purification/enzymology
*Seawater/microbiology
Metagenomics/methods
Bacterial Proteins/genetics/metabolism
Metagenome
Oxidation-Reduction

@article {pmid40605035,
year = {2025},
author = {Liu, J and Zhang, Y and Xu, L and Gu, G and Dong, Z},
title = {Parabacteroides johnsonii inhibits the onset and progression of colorectal cancer by modulating the gut microbiota.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {734},
pmid = {40605035},
issn = {1479-5876},
support = {School Science [2022] No.7//Clinical Program of Air Force Medical University/ ; 22BJQN004//Fourth Military Medical University/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most prevalent malignant tumor and the second leading cause of cancer-related deaths globally. The genus Parabacteroides is an important component of the gut microbiota. P. distasonis and P. goldsteinii are reported probiotics, and their roles in CRC have been investigated in related studies. However, the association between P. johnsonii and CRC remains unknown.

METHODS: P. johnsonii (10–42) and Lactococcus formosensis (22–2) were isolated from healthy human feces. 29 mice that demonstrated normal feeding and activity were randomly assigned to four groups: normal control (NC group), CRC model (IC group), P. johnsonii (PJ group), and L. formosensis (LO group). Colonic tumor tissues from the IC, PJ, and LO groups and normal colon tissues from the NC group were then collected for HE staining and immunohistochemical staining. Fecal samples from mice during the hyperproliferative and adenoma phases were collected for Metagenomic sequencing and metabolite analysis.

RESULTS: P. johnsonii intervention reduced the number and slowed the growth of colonic tumors, improved tumor histological scores, and decreased microenvironmental inflammation levels. P. johnsonii improved the composition of intestinal flora in mice with colon cancer, increased gut microbial species diversity, and maintained gut microbiota stability. Furthermore, P. johnsonii intervention increased the abundance of Bifidobacterium pseudolongum and Lactobacillus, which play a role in ameliorating AOM/DSS-induced gut microbiota dysbiosis. P. johnsonii intervention affected the metabolic pathways, including amino sugar degradation and galactose metabolism, sphingolipid synthesis, amino acid synthesis, and polyphenol synthesis pathways, with the tryptophan metabolism pathway as the primary pathway being affected.

CONCLUSION: Our study profiled the P. johnsonii administration reduces the number of tumors and lower tumor staging in AOM/DSS-induced colon cancer mice by modulating gut microbiota and its metabolites at early stages.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-06675-0.},
}

@article {pmid40605027,
year = {2025},
author = {Yun, CS and Kim, JK and Kwon, H and Kim, Y and Her, M and Moon, JS},
title = {Conventional diagnosis and metagenomic analysis of a novel co-infection case involving Escherichia coli and immunosuppressive conditions with petechial hepatitis of broilers in South Korea: a case report.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {432},
pmid = {40605027},
issn = {1746-6148},
support = {N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; },
mesh = {Animals ; *Chickens ; *Poultry Diseases/diagnosis/microbiology/virology ; *Escherichia coli Infections/veterinary/diagnosis/microbiology/complications ; *Coinfection/veterinary/diagnosis/microbiology ; Metagenomics ; Escherichia coli/isolation & purification/genetics ; Republic of Korea ; *Hepatitis, Animal/diagnosis/microbiology/virology ; *Purpura/veterinary/diagnosis/microbiology ; Liver/pathology/microbiology ; },
abstract = {BACKGROUND: The conventional diagnosis in poultry disease enhances accuracy by combining clinical and necropsy observation with various molecular biological analysis. However, if the causative agents of a disease are not isolated and detected, accurate diagnosis and future disease management become challenging. The purpose of the present study aimed to diagnose and identify the causes of disease in broilers with novel petechial hepatitis by applying metagenomic analysis.

CASE PRESENTATION: Through the necropsy, tracheal and pericardial congestion, and severe petechia and perihepatitis in the livers were observed. Histopathological examination revealed infiltration of lymphocytes and bacterial colonies in various organs, as well as severe sinusoidal congestion, hemorrhages and hepatocyte necrosis in the livers. E. coli was isolated and identified in the liver samples. Although FAdV, CkChpV, CAstV, IBV and IBDV were detected, no viral agents were detected in the livers. Metagenomic analysis of the livers showed a predominance of bacterial composition, followed by fungal and viral agents, with E. coli being the most abundant. Analysis of virulence factors in E. coli revealed the presence of those associated with APEC, as well as other IPEC and ExPEC pathotypes.

CONCLUSION: The present study identified a novel petechial hepatitis in broilers, associated with co-infections of antigenic variant IBDV, multiple pathotypes of E. coli, and possibly various causative. The application of metagenomic analysis proved valuable in identifying diverse potential pathogens when conventional methods were limited. These findings highlight the utility of metagenomic approaches as a complementary diagnostic tool and support their continued use in advancing poultry disease management.},
}

Animals
*Chickens
*Poultry Diseases/diagnosis/microbiology/virology
*Escherichia coli Infections/veterinary/diagnosis/microbiology/complications
*Coinfection/veterinary/diagnosis/microbiology
Metagenomics
Escherichia coli/isolation & purification/genetics
Republic of Korea
*Hepatitis, Animal/diagnosis/microbiology/virology
*Purpura/veterinary/diagnosis/microbiology
Liver/pathology/microbiology

@article {pmid40604425,
year = {2025},
author = {Wang, C and Song, W and Li, C and Cao, Y and Li, X and Zhao, J and Yang, F and Yu, H and Liang, Q and Yang, KQ and Liu, JN and Fang, H},
title = {Metagenomic analysis reveals Bacillus cereus OTU8977 as a potential probiotic in promoting walnut growth.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {839},
pmid = {40604425},
issn = {1471-2229},
support = {2024LZGC025//Improved Variety Program of Shandong Province of China/ ; },
mesh = {*Bacillus cereus/genetics/physiology ; *Juglans/growth & development/microbiology ; Rhizosphere ; Metagenomics ; Soil Microbiology ; *Probiotics ; Plant Roots/microbiology/growth & development ; },
abstract = {BACKGROUND: Rhizosphere microorganisms can improve soil quality, promote plant growth, and enhance plant health. Despite the isolation of numerous plant growth-promoting rhizobacteria (PGPR) strains, research on how PGPR enhances walnut growth remains limited.

RESULTS: In this study, the metagenomic sequencing of the rhizosphere soil in 8 major walnut-producing areas in China was conducted to identify 150 shared core amplicon sequence variants. Then, we isolated a strain of Bacillus cereus OTU8977 from the walnut rhizosphere soil and evaluated its potential plant growth-promoting functions. B. cereus OTU8977 can optimize the walnut rhizosphere microecology and promote its growth through its considerable potential in nitrogen fixation, phosphorus solubilization, and potassium dissolution. Transcriptomic analysis of walnut roots revealed that B. cereus OTU8977 promotes the growth of walnuts by enhancing phenylpropanoid biosynthesis and carbohydrate metabolic processes.

CONCLUSIONS: This study identified a strain of Bacillus cereus with multiple plant growth-promoting functions, which significantly enhanced walnut growth. Moreover, the study further elucidated the mechanisms underlying its growth-promoting effects, providing a theoretical foundation for the development of walnut-specific microbial fertilizers.},
}

*Bacillus cereus/genetics/physiology
*Juglans/growth & development/microbiology
Rhizosphere
Metagenomics
Soil Microbiology
*Probiotics
Plant Roots/microbiology/growth & development

@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited.

RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market.

CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04115-z.},
}

@article {pmid40604345,
year = {2025},
author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB},
title = {Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70417},
doi = {10.1002/alz.70417},
pmid = {40604345},
issn = {1552-5279},
support = {U01AG061359/AG/NIA NIH HHS/United States ; U19AG063744/AG/NIA NIH HHS/United States ; R01AG070973/AG/NIA NIH HHS/United States ; R01AG083883/AG/NIA NIH HHS/United States ; #S10 OD026929/GF/NIH HHS/United States ; //Vilas Early-Career Investigator Award/ ; #2023-00356//Swedish Research Council/ ; #2022-01018//Swedish Research Council/ ; #2019-02397//Swedish Research Council/ ; #101053962//European Union's Horizon Europe research and innovation programme/ ; #ALFGBG-71320//Swedish State Support for Clinical Research/ ; #201809-2016862//Alzheimer Drug Discovery Foundation (ADDF)/ ; #ADSF-21-831376-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831381-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831377-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-24-1284328-C//AD Strategic Fund and the Alzheimer's Association/ ; #22HLT07//European Partnership on Metrology co-financed from the European Union's Horizon Europe Research and Innovation Programme and by the Participating States/ ; //Bluefield Project/ ; //Cure Alzheimer's Fund/ ; //Olav Thon Foundation/ ; //Erling-Persson Family Foundation/ ; #FO2022-0270//Familjen Rönströms Stiftelse, Stiftelsen för Gamla Tjänarinnor, Hjärnfonden, Sweden/ ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/ ; JPND2021-00694//European Union Joint Programme-Neurodegenerative Disease Research/ ; UKDRI-1003//NIH and Care Research University College London Hospitals Biomedical Research Centre and the UK Dementia Research Institute at UCL/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology/pathology/cerebrospinal fluid ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; Biomarkers/cerebrospinal fluid ; Feces/microbiology ; Metagenomics ; Amyloid beta-Peptides/cerebrospinal fluid ; Aged, 80 and over ; },
abstract = {BACKGROUND: The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.

METHODS: Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.

RESULTS: Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.

DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.

HIGHLIGHTS: Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) ε4 status+ vs APOE ε4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.},
}

Humans
*Alzheimer Disease/microbiology/pathology/cerebrospinal fluid
*Gastrointestinal Microbiome/physiology
Male
Female
Aged
Biomarkers/cerebrospinal fluid
Feces/microbiology
Metagenomics
Amyloid beta-Peptides/cerebrospinal fluid
Aged, 80 and over

@article {pmid40604305,
year = {2025},
author = {Li, Y and Shi, Z and Zhang, X and Ren, H and Ji, H and Yang, F and Fu, Z and Kong, X and Cheng, X and Li, J and Wu, K and Zhong, Y and Zhong, H and Ji, L},
title = {Metagenomic analysis revealing links between age, gut microbiota and bone loss in Chinese adults.},
journal = {npj metabolic health and disease..},
volume = {3},
number = {1},
pages = {18},
pmid = {40604305},
issn = {2948-2828},
support = {7222238//Beijing Natural Science Founding/ ; },
abstract = {Accumulating evidence has linked gut microbiota to bone health. However, investigations into the impacts of aging, gut microbiota, and their interactions in the development of osteoporosis remain inconclusive. We employed quantitative computed tomography to measure lumbar bone mass density (BMD) and analyzed shotgun metagenomic data in 684 Chinese adults. Our analyses revealed significant positive associations between BMD and abundances of multiple Lachnospiraceae species, including Lachnospira eligens, Blautia wexlerae, and Roseburia hominis, as well as pathways involved in L-arginine biosynthesis and butyrate production-independent of age, diet habits, and lifestyles. Moreover, we demonstrated that individuals with enterotype Bacteroides exhibited a more pronounced age-related decline in BMD compared to those with enterotype Prevotella, a pattern we validated in an independent cohort. Our findings offer valuable insights into BMD-related gut microbial features and interactions between aging, gut microbiota, and bone loss, opening potential avenues for microbiota-based prevention and treatment strategies for osteoporosis.},
}