@article {pmid40316568,
year = {2025},
author = {Joshi, P and Bhattacharjee, R and Sahu, M and Gajjar, D},
title = {Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15375},
pmid = {40316568},
issn = {2045-2322},
mesh = {*Biofilms/growth & development ; Humans ; *Urinary Catheters/microbiology ; *Candida/physiology/isolation & purification/growth & development ; Urinary Tract Infections/microbiology ; *Bacteria/growth & development/isolation & purification/genetics ; Catheter-Related Infections/microbiology ; Coinfection/microbiology ; Metagenomics ; Pseudomonas aeruginosa ; Escherichia coli ; Klebsiella pneumoniae ; },
abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.},
}

*Biofilms/growth & development
Humans
*Urinary Catheters/microbiology
*Candida/physiology/isolation & purification/growth & development
Urinary Tract Infections/microbiology
*Bacteria/growth & development/isolation & purification/genetics
Catheter-Related Infections/microbiology
Coinfection/microbiology
Metagenomics
Pseudomonas aeruginosa
Escherichia coli
Klebsiella pneumoniae

@article {pmid40315933,
year = {2025},
author = {Cheng, Z and Wang, J and Liu, X and Cao, S},
title = {Accelerated sludge granulation of novel complete ammonium and nitrate removal via denitratation anammox over nitrite process at elevated loading rates.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132610},
doi = {10.1016/j.biortech.2025.132610},
pmid = {40315933},
issn = {1873-2976},
abstract = {The Complete Ammonium and Nitrate Removal via Denitratation Anammox Over Nitrite (CANDAN) process was evaluated for rapid sludge granulation in a lab-scale sequencing batch reactor. Over 119 days under increasing nitrogen loading rates (NLRs), the system finally achieved average 89.2 % total nitrogen removal at 1.93 kg N/m[3]/d NLR, with sludge particle sizes increasing from 215.6 μm to 924.5 μm. Higher NLRs significantly increased extracellular polymeric substances, especially hydrophobic proteins, enhancing sludge hydrophobicity and aggregation. Metagenomic analysis identified Candidatus Brocadia and Thauera as predominant and key microbial genera for nitrogen removal. Furthermore, the upregulation of carbon metabolism under heightened NLRs facilitated the synthesis of hydrophobic amino acids, promoting sludge granulation. These findings demonstrate NLR-driven granulation mechanisms, highlight optimizing NLR as key for accelerating granulation, providing insights to improve start-up and operational efficiency of CANDAN systems.},
}

@article {pmid40315837,
year = {2025},
author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD},
title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.010},
pmid = {40315837},
issn = {1934-6069},
abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.},
}

@article {pmid40315739,
year = {2025},
author = {Ma, G and Yang, P and Lu, T and Deng, X and Meng, L and Xie, H and Zhou, J and Xiao, X and Tang, X},
title = {Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.},
journal = {Journal of reproductive immunology},
volume = {169},
number = {},
pages = {104535},
doi = {10.1016/j.jri.2025.104535},
pmid = {40315739},
issn = {1872-7603},
abstract = {AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.

METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.

RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.

CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.},
}

@article {pmid40315479,
year = {2025},
author = {Kharey, G and Palace, V and Whyte, L and Greer, C},
title = {Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2023-0099},
pmid = {40315479},
issn = {1480-3321},
abstract = {A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of 3 environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.},
}

@article {pmid40315414,
year = {2025},
author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ},
title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012268},
doi = {10.1371/journal.pcbi.1012268},
pmid = {40315414},
issn = {1553-7358},
abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.},
}

@article {pmid40315131,
year = {2025},
author = {Donvil, L and Housmans, JAJ and Peeters, E and Vranken, W and Orlando, G},
title = {In-silico identification of archaeal DNA-binding proteins.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf169},
pmid = {40315131},
issn = {1367-4811},
abstract = {MOTIVATION: The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, this data is unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms.

RESULTS: To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions.

AVAILABILITY: Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at xenusia.ipynb.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40314681,
year = {2025},
author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q},
title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.},
journal = {The new microbiologica},
volume = {48},
number = {1},
pages = {46-59},
pmid = {40314681},
issn = {1121-7138},
mesh = {Humans ; *Microbiota ; *Biomedical Research ; Bibliometrics ; Gastrointestinal Microbiome ; },
abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.},
}

Humans
*Microbiota
*Biomedical Research
Bibliometrics
Gastrointestinal Microbiome

@article {pmid40314024,
year = {2025},
author = {Malwe, AS and Longwani, U and Sharma, VK},
title = {XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf037},
pmid = {40314024},
issn = {2631-9268},
mesh = {*Machine Learning ; *Metagenome ; *Xenobiotics/metabolism ; Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; *Bacteria/enzymology/genetics ; Metagenomics/methods ; },
abstract = {Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141 200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38 000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.},
}

*Machine Learning
*Metagenome
*Xenobiotics/metabolism
Biodegradation, Environmental
*Environmental Pollutants/metabolism
*Bacteria/enzymology/genetics
Metagenomics/methods

@article {pmid40313842,
year = {2025},
author = {Lu, X and Du, X and Zhong, D and Li, R and Cao, J and Huang, S and Wang, Y},
title = {Nanopore Environmental Analysis.},
journal = {JACS Au},
volume = {5},
number = {4},
pages = {1570-1590},
pmid = {40313842},
issn = {2691-3704},
abstract = {As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.},
}

@article {pmid40313750,
year = {2025},
author = {Ndione, MHD and Ndiaye, EH and Dieng, M and Diouf, B and Sankhé, S and Diallo, D and Kane, M and Sene, NM and Mbanne, M and Sy, FA and Diop, SMBS and Doukanda, SFM and Sall, AA and Faye, O and Dia, N and Weaver, SC and Faye, O and Diallo, M and Fall, G and Gaye, A and Diagne, MM},
title = {Mosquito-Based Detection of Endogenous Jaagsiekte Sheep Retrovirus in Senegal: Expanding the Scope of Xenosurveillance.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5951454/v1},
pmid = {40313750},
issn = {2693-5015},
abstract = {Background Mosquitoes are well-known vectors for arthropod-borne viruses, yet their role as passive carriers of non-arthropod-borne viruses remains underexplored. Xenosurveillance, a method that utilizes blood-feeding arthropods to sample host and pathogen genetic material, has emerged as a valuable tool in viral ecology. In this study, we report the first identification of Jaagsiekte Sheep Retrovirus (JSRV)-related sequences in blood-fed mosquitoes collected in Senegal. JSRV, a betaretrovirus responsible for ovine pulmonary adenocarcinoma, is typically found in sheep, but its genetic trace in mosquitoes offers a novel perspective on host-vector contact and surveillance. Our study aimed to investigate whether mosquitoes can serve as sentinels for detecting both pathogens and host-derived markers in complex ecosystems. Methods Mosquitoes were collected between 2016 and 2019 from three ecologically significant regions in Senegal (Louga, Barkedji, and Kedougou). Blood-fed mosquitoes were pooled and subjected to RNA extraction and metagenomic sequencing using Illumina NextSeq550. Sequencing data were analyzed with CZ-ID and BLAST for viral identification. RT-qPCR assays were designed to validate the presence of JSRV-related sequences, targeting conserved regions of the envelope gene and 3' untranslated region. Phylogenetic analysis was conducted using MAFFT and IQ-TREE to compare the detected sequence with global exogenous and endogenous JSRV references. Results A diverse array of viruses across mosquito species, including both arboviruses and non-arthropod-borne viruses. A JSRV-related sequence was detected in a single blood-fed mosquito pool collected in Barkedji (2019). The RT-qPCR assay confirmed JSRV presence, validating the sequencing results. Phylogenetic analysis revealed strong similarity to known endogenous JSRV (enJSRV) sequences integrated in the sheep genome, indicating that the detected material likely originated from host DNA ingested during blood feeding. Discussion This study presents the first report of endogenous retroviral sequences detected in mosquitoes, alongside the identification of actively circulating viruses, highlighting the broader potential of mosquitoes as environmental sentinels. While mosquitoes are not biological vectors for JSRV, their ability to capture both host-derived retroviral material and pathogenic viral genomes through bloodmeals reinforces the value of xenosurveillance for monitoring livestock-vector-environment interactions. These findings contribute to broader efforts in integrated disease surveillance and underscore the utility of combining metagenomics with molecular diagnostics to detect diverse viral signals in high-risk ecological settings.},
}

@article {pmid40313611,
year = {2025},
author = {Ren, X and Sun, H and Cheng, Y and Zhang, Y and Gao, D},
title = {Neurocysticercosis detected by targeted next-generation sequencing of cerebrospinal fluid: a case report.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1504348},
pmid = {40313611},
issn = {1664-2295},
abstract = {The patient, a middle-aged male with a long history of the disease, had experienced recurrent headaches for 26 years and episodic shaking of the right limb with slurred speech for the past month. He was previously diagnosed with cerebral cysticercosis and had shown improvement after anthelmintic treatment. In recent years, he noted a resurgence of headaches. One month prior, he developed right limb shaking and occasional slurred speech. A clinical neurological examination was unremarkable, but cranial MRI and cerebrospinal fluid sequencing confirmed a diagnosis of cerebral cysticercosis. Anthelmintic treatment was administered, resulting in symptom improvement.},
}

@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}

@article {pmid40313600,
year = {2025},
author = {Tang, M and Zhang, Z and Lin, L and Niu, J and Meng, G and Wang, W and Wang, J and Wang, Y},
title = {Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {65-75},
pmid = {40313600},
issn = {2730-5848},
abstract = {UNLABELLED: Although the compositional alterations of gut bacteria in ketogenic diet (KD) have been intensively investigated, the causal relationship between this extreme diet and the microbiota changes is not fully understood. Here, we studied the growth dynamics of intestinal bacteria in KD. We used the CoPTR method to calculate the peak-to-trough ratio (PTR) based on metagenomic sequencing data, serving as an indicator of bacterial growth rates. Notably, Akkermansia muciniphila, a bacterium strongly linked to the therapeutic benefits of KD, exhibited one of the highest growth rates, aligning with its markedly elevated abundance. Our findings also revealed discrepancies in the change patterns of CoPTR values and relative abundances for various bacteria across different diet groups, some of which might be attributed to the exceptionally high or low growth rates of specific species. For some of the species demonstrating obvious differences in growth rates between KD and standard diet, we conducted in vitro culture experiments, supplementing them with diverse nutritional sources to elucidate the underlying mechanisms. The integrative analysis of bacterial abundance and growth dynamics can help deepen our understanding of the gut microbiota changes caused by KD and the therapeutic effects of this special diet.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00228-7.},
}

@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}

Humans
*Peri-Implantitis/microbiology
*Saliva/microbiology
Pilot Projects
Cross-Sectional Studies
*Microbiota
*Dental Implants/microbiology
Male
Female
Biofilms/growth & development
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid40313410,
year = {2025},
author = {Liu, J and Zhou, Y and Feng, J and Cai, C and Zhang, S},
title = {Comparative metagenomic analysis reveals the adaptive evolutionary traits of siboglinid tubeworm symbionts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533506},
pmid = {40313410},
issn = {1664-302X},
abstract = {Tubeworms flourish in marine cold seeps and hydrothermal vents through the establishment of symbiotic relationships with chemosynthetic bacteria. However, the environmental adaptations and evolutionary relationships of tubeworm symbionts across diverse habitats and hosts remain largely unknown. In this study, we characterized the genomes of 26 siboglinid tubeworm symbionts collected from deep-sea hydrothermal vents, cold seeps, and deep-sea mud, including two sequenced in this study and 24 previously published. Phylogenetic analysis classified the 26 symbiont genomes into five distinct clusters at the genus level. The findings highlight the remarkable diversity in symbiont classification, influenced by the habitat and species of tubeworm, with the symbiont genome characteristics of various genera revealing unique evolutionary strategies. Siboglinid symbionts exhibit functional metabolic diversity, encompassing chemical autotrophic capabilities for carbon, nitrogen, and sulfur metabolism, hydrogen oxidation, and a chemoorganotrophic ability to utilize various amino acids, cofactors, and vitamins. Furthermore, the symbiont's homeostatic mechanisms and CRISPR-Cas system are vital adaptations for survival. Overall, this study highlights the metabolic traits of siboglinid symbionts across different genera and enhances our understanding of how different habitats and hosts influence symbiont evolution, offering valuable insights into the strategies that symbionts use to adapt and thrive in extreme environments.},
}

@article {pmid40313389,
year = {2025},
author = {Yu, D and Liu, Y and Cai, H and Huang, W and Wu, H and Yang, P},
title = {Metagenomic investigation of bacterial laccases in a straw-amended soil.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19327},
pmid = {40313389},
issn = {2167-8359},
mesh = {*Laccase/genetics/metabolism ; *Metagenomics ; *Soil Microbiology ; Phylogeny ; *Bacteria/enzymology/genetics ; *Soil/chemistry ; Escherichia coli/genetics ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.

METHODS: Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.

RESULTS: A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.

IMPLICATIONS: These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.},
}

*Laccase/genetics/metabolism
*Metagenomics
*Soil Microbiology
Phylogeny
*Bacteria/enzymology/genetics
*Soil/chemistry
Escherichia coli/genetics
*Bacterial Proteins/genetics/metabolism

@article {pmid40313234,
year = {2025},
author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N},
title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/19390211.2025.2498127},
pmid = {40313234},
issn = {1939-022X},
abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.},
}

@article {pmid40313154,
year = {2025},
author = {Abiola, C and Gwak, JH and Lee, UJ and Adigun, AO and Rhee, SK},
title = {Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2502002},
doi = {10.71150/jm.2502002},
pmid = {40313154},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; 2021R1A2C3004015//Ministry of Science and ICT/ ; RS-2023-00213601//Ministry of Science and ICT/ ; 2020R1A6A1A06046235//Ministry of Education/ ; //Korea Institute of Marine Science & Technology Promotion/ ; RS-2024-00436293//Ministry of Oceans and Fisheries/ ; },
mesh = {*Soil Microbiology ; Phylogeny ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Ammonia/metabolism ; Oxidation-Reduction ; Soil/chemistry ; Metagenomics ; Filtration ; Nitrites/metabolism ; },
abstract = {Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera "Candidatus Nitrosocosmicus" and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.},
}

*Soil Microbiology
Phylogeny
*Nitrification
*Archaea/genetics/classification/metabolism/isolation & purification
*Bacteria/genetics/classification/metabolism/isolation & purification
Ammonia/metabolism
Oxidation-Reduction
Soil/chemistry
Metagenomics
Filtration
Nitrites/metabolism

@article {pmid40313146,
year = {2025},
author = {Jeong, H and Choe, Y and Nam, J and Ban, YH},
title = {A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2409026},
doi = {10.71150/jm.2409026},
pmid = {40313146},
issn = {1976-3794},
support = {//Ministry of Science and ICT/ ; IITP-2025-RS-2023-00260267//Institute for Information & communications Technology Planning & Evaluation/ ; 202305080001//Kangwon National University/ ; //National Research Foundation of Korea/ ; 2021R1C1C2006260//Ministry of Science and ICT/ ; RS-2023-00301850//Ministry of Education/ ; },
mesh = {*Streptomyces/genetics/metabolism ; *Multigene Family ; *Biosynthetic Pathways/genetics ; *Genome, Bacterial ; Secondary Metabolism/genetics ; Biological Products/metabolism ; *Genomics/methods ; },
abstract = {Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.},
}

*Streptomyces/genetics/metabolism
*Multigene Family
*Biosynthetic Pathways/genetics
*Genome, Bacterial
Secondary Metabolism/genetics
Biological Products/metabolism
*Genomics/methods

@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*Urinary Bladder Neoplasms/microbiology/urine
*DNA, Bacterial/isolation & purification/urine
Male
Female
Middle Aged
*Urine/microbiology
Aged
RNA, Ribosomal, 16S
Reproducibility of Results

@article {pmid40312727,
year = {2025},
author = {Wang, L and Wu, Y and Zhao, ZB and Jia, T},
title = {Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {45},
pmid = {40312727},
issn = {2524-6372},
support = {52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.

RESULTS: In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30 cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30 cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.

CONCLUSIONS: Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.},
}

@article {pmid40312673,
year = {2025},
author = {Qin, X and Song, Y and Ding, J and Qin, X and Chen, K and Wang, H},
title = {Symptomatic central nervous system infections in kidney transplant recipients: a 20-years multicenter observational study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {641},
pmid = {40312673},
issn = {1471-2334},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; *Central Nervous System Infections/epidemiology/microbiology/etiology/diagnosis/mortality/cerebrospinal fluid ; Retrospective Studies ; Middle Aged ; Adult ; *Transplant Recipients/statistics & numerical data ; China/epidemiology ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections in kidney transplant recipients (KTRs) remain poorly characterized, with current evidence largely derived from isolated case reports over the past two decades. This multicenter study aims to systematically delineate the epidemiology, clinical profiles, and outcomes of CNS infections in a large KTR cohort.

METHODS: We conducted a retrospective analysis of 3,602 KTRs across three transplant centers in China (May 2004-July 2024). CNS infections were defined by: 1) neurological symptoms/signs, and 2) microbiological confirmation via cerebrospinal fluid (CSF) analysis, including metagenomic next-generation sequencing (mNGS) and routine microbiologic testing (bacterial and fungal cultures).

RESULTS: CNS infections were diagnosed in 0.53% of KTRs (19/3602), with symptom onset occurring 2-121 months post-transplantation. Etiologies included bacterial (47%, 9/19), viral (32%, 6/19), and fungal (21%, 4/19) pathogens. Notably, 79% of cases (15/19) were exclusively identified by mNGS, whereas conventional cultures failed detection. Presenting symptoms included headache (79%) and altered mental status (42%). Mortality reached 42% (8/19) within 9-22 days of diagnosis; among survivors, 73% (8/11) exhibited neurological sequelae.

CONCLUSIONS: CNS infections in KTRs are rare but characterized by rapid progression and high fatality rate. While the risk of CNS infections persists throughout the post-transplant period, 1-6 months after transplantation is a higher-incidence period of CNS infections. KTRs with neurological symptoms (particularly headache and elevated CSF pressure) should undergo CSF mNGS which is critical in diagnosing such infections.},
}

Humans
*Kidney Transplantation/adverse effects
Male
Female
*Central Nervous System Infections/epidemiology/microbiology/etiology/diagnosis/mortality/cerebrospinal fluid
Retrospective Studies
Middle Aged
Adult
*Transplant Recipients/statistics & numerical data
China/epidemiology
Aged
Young Adult

@article {pmid40312516,
year = {2025},
author = {Kim, DD and Swarthout, JM and Worby, CJ and Chieng, B and Mboya, J and Earl, AM and Njenga, SM and Pickering, AJ},
title = {Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40312516},
issn = {2058-5276},
support = {n/a//Tufts University/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.},
}

@article {pmid40312036,
year = {2025},
author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C},
title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-15},
doi = {10.1163/18762891-bja00075},
pmid = {40312036},
issn = {1876-2891},
abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.},
}

@article {pmid40311978,
year = {2025},
author = {Wang, YX and Dong, BX and Liu, YJ and Tan, YQ and An, YT and Lin, LH and Li, G},
title = {Molecular cloning, characterization, and structural stability analysis of a rare acidic catechol 2,3-dioxygenase from the metagenome of coal-polluted soil.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {143652},
doi = {10.1016/j.ijbiomac.2025.143652},
pmid = {40311978},
issn = {1879-0003},
abstract = {Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous environmental pollutants that pose substantial health hazards, especially in coal-mining areas. This study presented the metagenomic identification and comprehensive characterization of a novel acidic catechol 2,3-dioxygenase, C23O927, derived from a coal-contaminated soil metagenome. Optimal enzymatic activity for C23O927 was observed at pH 4.0 and 55 °C, with remarkable stability across a wide pH spectrum (2.0-10.0) and temperature range (30 °C-60 °C). The enzyme displayed robust tolerance to various organic solvents and salts, and its activity was notably activated by diverse metal ions. Distinct from other catechol 2,3-dioxygenases, C23O927 exhibited oxygen tolerance and maintained robust activity after purification at 4 °C for up to three days. The structural stability of C23O927 is attributed to its unique extended β-sheet structure and increased α-helices. These characteristics help enhance rigidity and reduce the exposure of the hydrophobic core, thereby conferring greater stability on C23O927. The unique properties of C23O927, which include an optimal pH for acidic environments, salt tolerance, resistance to metal ions and organic solvents, and thermal stability, render it a promising candidate for industrial waste management and soil bioremediation.},
}

@article {pmid40311618,
year = {2025},
author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N},
title = {Global genetic structure of human gut microbiome species is related to geographic location and host health.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.014},
pmid = {40311618},
issn = {1097-4172},
abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.},
}

@article {pmid40311598,
year = {2025},
author = {Hong, Y and Cui, J and Xu, G and Li, N and Peng, G},
title = {Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156656},
doi = {10.1016/j.phymed.2025.156656},
pmid = {40311598},
issn = {1618-095X},
abstract = {BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.

PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.

METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.

RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.

CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.},
}

@article {pmid40311430,
year = {2025},
author = {Chen, Z and Hu, Y and Qiu, G and Liang, D and Cheng, J and Chen, Y and Wang, G and Zhu, X and Xie, J},
title = {Inoculation with Acinetobacter indicus CZH-5 in internal circulation airlift zeolite spheres sequencing batch reactor to augment simultaneous removal of nitrogen, phosphorus, and tetracycline.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138384},
doi = {10.1016/j.jhazmat.2025.138384},
pmid = {40311430},
issn = {1873-3336},
abstract = {Inoculating functional bacterial strains is a cost-effective strategy for enhancing treatment of anaerobic digestion liquids in swine wastewater. This study systematically evaluated inoculation of heterotrophic nitrification aerobic denitrification strain Acinetobacter indicus CZH-5 in an internal circulation airlift zeolite sphere-based sequencing batch reactor (IR) for aerobic removal of nitrogen (N), phosphorus (P), and tetracycline (TEC). Inoculation with CZH-5 promoted secretion of quorum sensing signaling molecules, specifically N-acyl-homoserine lactones (C6-HSL and C10-HSL). These signaling molecules enhance quorum sensing and reinforce cooperation among functional bacteria. Under optimal conditions, average removal efficiencies of total nitrogen, total phosphate, and TEC were 92.8 %, 88.4 %, and 93.1 %, respectively. The removal performance in IR exceeded that of the control by 26 %-71 %. N removal involved complete nitrification-denitrification, while accumulated P was transformed into phosphate monoesters within biofilm. Metagenomic analysis identified Thauera and Acinetobacter as the dominant genera, and Acinetobacter indicus as predominant species. Inoculation enhanced microbial richness and diversity to improve system operational stability. The abundance of functional genes associated with N, P, and TEC transformations significantly increased compared to the control. This study aimed to investigate the characteristics and mechanisms of inoculating a heterotrophic nitrification aerobic denitrification strain into an aerated biofilm system for swine wastewater remediation.},
}

@article {pmid40311350,
year = {2025},
author = {Monge-Olivares, L and Peñalva, G and Pulido, MR and Garrudo, L and Ángel Doval, M and Ballesta, S and Merchante, N and Rasero, P and Cuberos, L and Carpes, G and López-Cerero, L},
title = {Quantitative study of ESBL and carbapenemase producers in wastewater treatment plants in Seville, Spain: a culture-based detection analysis of raw and treated water.},
journal = {Water research},
volume = {281},
number = {},
pages = {123706},
doi = {10.1016/j.watres.2025.123706},
pmid = {40311350},
issn = {1879-2448},
abstract = {Antibiotics can modify populations of multidrug-resistant microorganism (MDRO) in urban wastewater. Our objectives were to quantify the differences in MDR Gram-negative bacteria between influents and effluents of WWTPs of a Spanish city and to evaluate the influence of human antibiotic prescriptions, as well as the persistence of these bacteria after treatment and their genetic relatedness to clinical isolates. The mean count of ESBL producers and carbapenemase producers were 3.77 and 2.74 log 10 CFU/ml, respectively. The reduction achieved by water treatment of ESBL-producing organisms was 1.4-log (96.11 %), whereas a 1.8-log reduction (98.36 %) was obtained regarding carbapenemase producing organisms. Aeromonas spp. predominated among MDROs and blaKPC-2 was the main carbapenemase detected in the influent wastewater samples. Among Escherichia coli and Klebsiella pneumoniae influent isolates, 44 % and 30 %, respectively, belonged to high-risk clones. Regarding Enterobacteriaceae, 10.6 % matched clinical isolates and one strain from an ongoing hospital outbreak was identified among raw samples. New MDROs and persistence of certain strains were detected in effluent samples. Quinolone and third-generation cephalosporin prescriptions, flow rate and population density were associated with higher OXA-48 producer counts. Despite reductions, additional technologies should be implemented in WWTPs receiving hospital discharges. Given the prevalence of environmental species, culture-based and metagenomic approaches should be combined to distinguish between human and sewage sources for antibiotic resistance monitoring. Overall, this study shows that WWTPs with secondary treatment are effective at removing MDRO, and antibiotic stewardship is a potential strategy to reduce the release of MDROs.},
}

@article {pmid40311348,
year = {2025},
author = {Liu, C and Yan, S and Luo, X and Zheng, Y and Zhen, G},
title = {Iron-based materials maintain biofilm equilibrium and function as external capacitors to minimize electron loss under intermittent power supply in MEC-AD methane production.},
journal = {Water research},
volume = {281},
number = {},
pages = {123677},
doi = {10.1016/j.watres.2025.123677},
pmid = {40311348},
issn = {1879-2448},
abstract = {Microbial electrolysis cell-anaerobic digestion (MEC-AD) is a cost-effective approach for methane (CH4) recovery from food waste, but its CH4 conversion efficiency requires improvement. To address this, a MIL-100(Fe)-modified carbon cloth anode was developed to enhance anodic biofilm formation and CH4 bioconversion efficiency. At an applied voltage of 0.8 V, the highest daily CH4 yield reached 141.6 mL/g COD/d, a 61 % increase, and increased further to 227.5 mL/g COD/d under intermittent power supply. By facilitating extracellular electron transfer (EET) in electrogenic bacteria, MIL-100(Fe) regulated biofilm thickness and maintained dynamic biofilm equilibrium. Additionally, as an external capacitor, MIL-100(Fe) functioned as a "temporary storage site" for electrons under intermittent power supply, reducing bioelectron loss. Metagenomic analysis revealed that MIL-100(Fe) significantly enriched Bacteroidia and Methanosarcina, promoting carbohydrate metabolism and CH4 production. Under intermittent power supply, MIL-100(Fe) further enriched Geobacter, enhancing electron transfer efficiency. This study demonstrates that iron-based anode modification effectively enhances CH4 production from food waste by optimizing biofilm structure and metabolic pathways, providing a promising strategy for improving MEC-AD performance.},
}

@article {pmid40310938,
year = {2025},
author = {Ma, WJ and Wang, C and Kothandapani, J and Luzentales-Simpson, M and Menzies, SC and Bescucci, DM and Lange, ME and Fraser, ASC and Gusse, JF and House, KE and Moote, PE and Xing, X and Grondin, JM and Hui, BW and Clarke, ST and Shelton, TG and Haskey, N and Gibson, DL and Martens, EC and Abbott, DW and Inglis, GD and Sly, LM and Brumer, H},
title = {Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadk7633},
doi = {10.1126/science.adk7633},
pmid = {40310938},
issn = {1095-9203},
abstract = {The gut microbiota of mammals possess unique metabolic pathways with untapped therapeutic potential. Using molecular insights into dietary fiber metabolism by the human gut microbiota, we designed a targeted drug delivery system based on bespoke glycoconjugates of a complex plant oligosaccharide called GlycoCaging. GlycoCaging of exemplar anti-inflammatory drugs enabled release of active molecules triggered by unique glycosidases of autochthonous gut bacteria. GlycoCaging ensured drug efficacy was potentiated, and off-target effects were eliminated in murine models of inflammatory bowel disease. Biochemical and metagenomic analyses of gut microbiota of individual humans confirmed the broad applicability of this strategy.},
}

@article {pmid40309222,
year = {2025},
author = {Slosser, T and Wenick, M and Markert, E and Trembath-Reichert, E and Ward, LM},
title = {Novel hot spring Thermoproteota support vertical inheritance of ammonia oxidation and carbon fixation in Nitrososphaeria.},
journal = {Access microbiology},
volume = {7},
number = {4},
pages = {},
pmid = {40309222},
issn = {2516-8290},
abstract = {Aerobic ammonia oxidation is crucial to the nitrogen cycle and is only known to be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] and a single lineage of archaea belonging to the Nitrososphaeria class of Thermoproteota [ammonia-oxidizing Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture only a limited subset of the full diversity of this clade. Here, we describe several genomes of AOA from metagenomic sequencing of a hot spring microbial mat, representing several poorly characterized basal lineages that may be important for understanding the early evolution of archaeal ammonia oxidation. These genomes include a novel genus most closely related to Nitrososphaera as well as novel species belonging to the genera Nitrosotenuis, Nitrososphaera and Nitrosotalea. Furthermore, the distributions and phylogenetic relationships of key metabolic genes support a history of vertical inheritance of ammonia oxidation and carbon fixation from the last common ancestor of crown group AOA.},
}

@article {pmid40309194,
year = {2025},
author = {Tang, CT and Wu, Y and Tao, Q and Zeng, CY and Chen, YX},
title = {Thalidomide mitigates Crohn's disease colitis by modulating gut microbiota, metabolites, and regulatory T cell immunity.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {4},
pages = {101121},
pmid = {40309194},
issn = {2214-0883},
abstract = {Thalidomide (THA) is renowned for its potent anti-inflammatory properties. This study aimed to elucidate its underlying mechanisms in the context of Crohn's disease (CD) development. Mouse colitis models were established by dextran sulfate sodium (DSS) treatment. Fecal microbiota and metabolites were analyzed by metagenomic sequencing and mass spectrometry, respectively. Antibiotic-treated mice served as models for microbiota depletion and transplantation. The expression of forkhead box P3[+] (FOXP3[+]) regulatory T cells (Tregs) was measured by flow cytometry and immunohistochemical assay in colitis model and patient cohort. THA inhibited colitis in DSS-treated mice by altering the gut microbiota profile, with an increased abundance of probiotics Bacteroides fragilis, while pathogenic bacteria were depleted. In addition, THA increased beneficial metabolites bile acids and significantly restored gut barrier function. Transcriptomic profiling revealed that THA inhibited interleukin-17 (IL-17), IL-1β and cell cycle signaling. Fecal microbiota transplantation from THA-treated mice to microbiota-depleted mice partly recapitulated the effects of THA. Specifically, increased level of gut commensal B. fragilis was observed, correlated with elevated levels of the microbial metabolite 3alpha-hydroxy-7-oxo-5beta-cholanic acid (7-ketolithocholic acid, 7-KA) following THA treatment. This microbial metabolite may stable FOXP3 expression by targeting the receptor FMR1 autosomal homolog 1 (FXR1) to inhibit autophagy. An interaction between FOXP3 and FXR1 was identified, with binding regions localized to the FOXP3 domain (aa238-335) and the FXR1 domain (aa82-222), respectively. Conclusively, THA modulates the gut microbiota and metabolite profiles towards a more beneficial composition, enhances gut barrier function, promotes the differentiation of FOXP3[+] Tregs and curbs pro-inflammatory pathways.},
}

@article {pmid40309109,
year = {2025},
author = {Zhang, Z and Sun, J and Wang, D and Lin, T and Yin, Y and Wang, W and Wang, Y and Wang, Z and Fan, L and Jiao, X},
title = {Effects of rotation corn on potato yield, quality, and soil microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1493333},
pmid = {40309109},
issn = {1664-302X},
abstract = {INTRODUCTION: Potato is an important crop that can be used both as grain and vegetable in northern China. However, the continuous cropping system of potato has led to a sharp decline in its yield and quality. As one of the effective strategies to alleviate the continuous cropping obstacle, crop rotation has received extensive attention in agricultural practices. On this basis, we have conducted an in-depth exploration of the effects of the potato-maize rotation system on the structure and diversity of the soil microbial community, aiming to analyze the internal correlation mechanism between the structure of the soil microbial community and the yield and quality of crops.

METHODS: This study was based on fields that had been under potato monoculture for five years and established six experimental treatments: potato-potato-potato (IR-A), potato-maize-potato (IR-B), potato-maize-maize (IR-C), potato-potato-potato (RF-A), potato-maize-potato (RF-B), and potato-maize-maize (RF-C).

RESULTS: The results showed that under the IR planting model, IR-B significantly increased potato yield and vitamin C content while reducing reducing sugar content compared to IR-A (p < 0.05). In the RF planting model, RF-B significantly increased potato yield, starch content, and vitamin C content compared to RF-A (p < 0.05). Microbial community structure results indicated that crop rotation significantly enhanced the relative abundance of microorganisms such as Bradyrhizobium, Pseudomonas, Sphingomonas, Purpureocillium, Streptomyces, and Halovivax (p < 0.05). These microorganisms are involved in the cycling of carbon, phosphorus, and other nutrients in the soil, playing an important role in promoting root growth, organic matter decomposition, and alleviating soil salinization. The LEfSe and RDA indicated significant differences in microbial communities between monoculture and crop rotation (p < 0.05), with soil slow-growing rhizobia, Burkholderia, and actinomycetes positively correlated with potato yield and quality. Additionally, KEGG functional annotation of different treatments revealed that K00239, K00626, K01681, and K01915 were involved in three key metabolic pathways related to carbon and nitrogen. A total of 20 significantly enriched pathways were identified (p < 0.05), among which K01681 is involved in the tricarboxylic acid cycle and is a differential gene in the RF-B treatment, suggesting that the efficient expression of K01681 during crop rotation contributes to the material cycling of the soil ecosystem. LEfSe analysis of the bins revealed that under the RF-C treatment, the relative abundance of Hyphomicrobiales was significantly higher than in other treatments (p < 0.05). Hyphomicrobiales are involved in the nitrogen fixation process and play an important role in soil nutrient cycling and plant nutrition. In summary, the potato-maize rotation significantly altered the composition of soil microbial communities (p < 0.05), increasing the relative abundance of beneficial microorganisms. This change helps maintain the health of the soil ecosystem, promotes nutrient cycling, reduces the incidence of diseases, and effectively improves both the yield and quality of potatoes.

DISCUSSION: The potato-maize rotation significantly altered the composition of soil microbial communities (p < 0.05), increasing the relative abundance of beneficial microorganisms. This change helps maintain the health of the soil ecosystem, promotes nutrient cycling, reduces the incidence of diseases, and effectively improves both the yield and quality of potatoes.},
}

@article {pmid40309103,
year = {2025},
author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F},
title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575405},
pmid = {40309103},
issn = {1664-302X},
abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.

METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.

DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.},
}

@article {pmid40308966,
year = {2025},
author = {Li, W and Zhao, M and Wu, W and Chen, G and Hang, Y and Zheng, H and Gao, Z and Liu, J and Zhao, Y},
title = {The application prospect of metagenomic next-generation sequencing technology in diagnosing suspected lower respiratory tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1494638},
pmid = {40308966},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; Aged ; Adult ; Bacteria/genetics/isolation & purification/classification ; China ; Sensitivity and Specificity ; Aged, 80 and over ; Young Adult ; Viruses/genetics/isolation & purification/classification ; Bacterial Infections/diagnosis/microbiology ; },
abstract = {OBJECTIVE: Lower respiratory tract infections present substantial diagnostic and therapeutic challenges, negatively impacting individual health. This study aims to utilize metagenomic next-generation sequencing (mNGS) technology to comprehensively explore the spectrum of pathogens, the detection of antibiotic resistance genes, and contributing factors associated with lung infections.

METHOD: The mNGS data of 217 patients with suspected lung infections attending the Respiratory Department of Nanjing Lishui People's Hospital and Gaochun People's Hospital from September 2022 to September 2023 were retrospectively analyzed. The study assessed the pathogenic spectrum of lung infections and compared the performance of patients with mNGS results from conventional microbiological techniques (CMT).

RESULTS: The overall positivity rate of mNGS was 95.20%, demonstrating superior sensitivity (97.01% vs. 41.79%) and accuracy (75.56% vs. 56.67%) compared to CMT. Bacterial infections were the most prevalent, accounting for 60.76% of cases. And the most prevalent bacteria, fungus and virus were Mycobacterium tuberculosis (14.41%), Candida albicans (15.72%), and EB virus (14.85%), respectively. The primary resistance genes detected were tetM (17, 8.29%), mel (6, 2.93%), and PC1 beta-lactamase (blaZ) (3, 1.46%). Notably, TEM-183, PDC-5 and PDC-3 were exclusively detected in the Chronic Obstructive Pulmonary Disease (COPD) group. The multivariate binary logistic regression analysis revealed that there was no significant association between gender, presence of hypertension, or COPD with the type of infection in patients (p=0.679, p=0.229, p=0.345). However, the immune status was found to be statistically significant (p=0.009).

CONCLUSION: With the guidance of mNGS, patients with suspected respiratory tract infections can rapidly and accurately establish a pathogenic basis for their conditions. mNGS effectively identify mixed infections, enrich the pathogen spectrum of lung infections, and provide a large and reliable information base for the clinical realization of targeted medication.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology/virology
Male
Female
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
*Metagenomics/methods
Retrospective Studies
Aged
Adult
Bacteria/genetics/isolation & purification/classification
China
Sensitivity and Specificity
Aged, 80 and over
Young Adult
Viruses/genetics/isolation & purification/classification
Bacterial Infections/diagnosis/microbiology

@article {pmid40308204,
year = {2025},
author = {Karalius, MC and Ramachandran, PS and Wapniarski, A and Wang, M and Zia, M and Hills, NK and Wintermark, M and Grose, C and Dowling, MM and Wilson, J and Lee, S and Chung, M and Barry, M and Xu, H and DeRisi, JL and Wilson, MR and Fullerton, HJ and , },
title = {Infection in Childhood Arterial Ischemic Stroke: Metagenomic Next-Generation Sequencing Results of the VIPS II Study.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STROKEAHA.124.050548},
pmid = {40308204},
issn = {1524-4628},
abstract = {BACKGROUND: Acute respiratory infection transiently increases risk for childhood arterial ischemic stroke (AIS). We hypothesize that this paradox of a common exposure linked to a rare outcome could be explained by either (1) the infection hypothesis: unusual or multiple pathogens or (2) the host response hypothesis: heterogeneity in the inflammatory response to infection. We leverage metagenomic next-generation sequencing (mNGS), a comprehensive microbial detection tool, to test the first hypothesis.

METHODS: The VIPS II study (Vascular Effects of Infection in Pediatric Stroke II) prospectively enrolled children with AIS at 22 international sites over 5 years (December 2016 to January 2022). Sites measured prestroke clinical infection via standardized parental interviews and chart abstraction. To assess more broadly the background spectrum of pathogens, a central research laboratory performed mNGS on plasma and oropharyngeal swabs collected within 72 hours of stroke. mNGS was also performed on biological samples from stroke-free children (June 2017 to January 2022), both without (well) and with (ill) documentation of clinical infection.

RESULTS: VIPS II enrolled 205 patients with AIS, 95 stroke-free well children, and 47 stroke-free ill children. Clinical infection, most commonly upper respiratory tract infection, was detected in 81 of 205 (40%) of patients. Both plasma and oropharyngeal swab mNGS data were available for 190 of 205 patients with AIS, 91 of 95 stroke-free well children, and 27 of 47 stroke-free ill children. mNGS detected viruses in 27 of 190 (14%) patients with AIS, 9 of 91 stroke-free well children (10%), and 9 of 27 (33%) stroke-free ill children. Most were common upper respiratory viruses. Coinfections were rare. Similar viruses were found in patients with AIS and stroke-free children.

CONCLUSIONS: mNGS detected a variety of common childhood viruses in both patients with AIS and stroke-free children, suggesting that the type of infection does not explain AIS susceptibility. Rather, the alternative hypothesis regarding an unusual host immune response to common infections in the pathogenicity of AIS should be further explored.},
}

@article {pmid40307949,
year = {2025},
author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ},
title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {108},
pmid = {40307949},
issn = {2049-2618},
support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.},
}

Humans
*Parkinson Disease/microbiology/complications
*Gastrointestinal Microbiome/genetics
Male
*REM Sleep Behavior Disorder/microbiology
Female
Aged
Middle Aged
Disease Progression
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40307838,
year = {2025},
author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C},
title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {170},
pmid = {40307838},
issn = {1466-609X},
support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Female ; Intensive Care Units/organization & administration/statistics & numerical data ; Prospective Studies ; *Health Personnel/statistics & numerical data ; China ; Adult ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?

DESIGN: Prospective, multicentre, cross-sectional study.

SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.

PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.

MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.

RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change = 1.22, 95% CI: 1.12-1.34, p < 0.001). The β-diversity of ARG between the two groups differed significantly (p = 0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall = 0.96, p for nonlinear = 0.84).

CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.

TRIAL REGISTRATION: NCT06228248.},
}

Humans
Cross-Sectional Studies
Male
Female
Intensive Care Units/organization & administration/statistics & numerical data
Prospective Studies
*Health Personnel/statistics & numerical data
China
Adult
Middle Aged
*Drug Resistance, Microbial/genetics
Gastrointestinal Microbiome/genetics
Feces/microbiology

@article {pmid40307822,
year = {2025},
author = {Huo, Y and Wu, C and Ma, D},
title = {Application of metagenomic next-generation sequencing in the diagnosis and treatment of acute pneumonia caused by Tropheryma whipplei.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {207},
pmid = {40307822},
issn = {1471-2466},
mesh = {Humans ; Male ; Female ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; Aged ; *Tropheryma/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; Adult ; Cilastatin, Imipenem Drug Combination/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Acute Disease ; Tomography, X-Ray Computed ; *Whipple Disease/drug therapy/diagnosis/microbiology ; Imipenem/therapeutic use ; },
abstract = {OBJECTIVE: The treatment plan and process for acute pneumonia caused by Tropheryma whipplei have not been clearly defined. The study aimed to conduct a retrospective analysis of the treatment for patients with acute pneumonia, caused by Tropheryma whipplei, diagnosed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF).

METHODS: All patients underwent routine blood examinations and chest CT scans. Electronic fiberoptic bronchoscopy was performed to collect BALF samples from the lesion subsegments. The BALF samples were subjected to mNGS analysis. During hospitalization, all patients were treated with imipenem-cilastatin combined with compound sulfamethoxazole (SMZ-TMP) tablets for anti-infection, and they took SMZ-TMP orally for 3 months after discharge and followed up.

RESULTS: We identified 7 cases where Tropheryma whipplei was the primary pathogen, with 3 of these cases having it as the sole detected pathogen. The clinical manifestations of acute Tropheryma whipplei pneumonia are atypical. Chest CT scans revealed that 3 cases had exudative lesions in both lungs, 4 cases had unilateral pulmonary exudative lesions, 3 cases had bilateral pulmonary nodules, 2 cases had interstitial changes, and 3 cases had pleural effusion. Following treatment, all follow-up cases showed no recurrence.

CONCLUSIONS: The mNGS examination of bronchoalveolar lavage fluid can significantly improve the early diagnosis of acute pneumonia caused by Tropheryma whipplei. The treatment involving imipenem-cilastatin combined with SMZ-TMP, followed by oral SMZ-TMP for three months, is effective.},
}

Humans
Male
Female
Retrospective Studies
Middle Aged
*High-Throughput Nucleotide Sequencing
*Anti-Bacterial Agents/therapeutic use
Aged
*Tropheryma/genetics/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology
Metagenomics
*Pneumonia, Bacterial/drug therapy/diagnosis/microbiology
Adult
Cilastatin, Imipenem Drug Combination/therapeutic use
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
Acute Disease
Tomography, X-Ray Computed
*Whipple Disease/drug therapy/diagnosis/microbiology
Imipenem/therapeutic use

@article {pmid40307239,
year = {2025},
author = {Langwig, MV and Koester, F and Martin, C and Zhou, Z and Joye, SB and Reysenbach, AL and Anantharaman, K},
title = {Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4076},
pmid = {40307239},
issn = {2041-1723},
support = {DBI-2047598//National Science Foundation (NSF)/ ; OCE-2049478//National Science Foundation (NSF)/ ; },
mesh = {*Hydrothermal Vents/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; *Ecosystem ; Metagenome ; Genome, Viral ; Pacific Ocean ; Bacteriophages/genetics/classification ; Phylogeny ; Seawater/virology ; Gammaproteobacteria/virology ; Microbiota ; Virome ; },
abstract = {Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.},
}

*Hydrothermal Vents/virology/microbiology
*Viruses/genetics/classification/isolation & purification
*Ecosystem
Metagenome
Genome, Viral
Pacific Ocean
Bacteriophages/genetics/classification
Phylogeny
Seawater/virology
Gammaproteobacteria/virology
Microbiota
Virome

@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}

*Rhizosphere
*Arsenic/metabolism
Oxidation-Reduction
*Oryza/microbiology/virology/metabolism
Soil Microbiology
*Lysogeny/genetics
Microbiota/genetics
Gene Transfer, Horizontal
Metagenome
Plant Roots/microbiology/virology
Oxidoreductases/genetics/metabolism
Metabolic Reprogramming

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

*Metagenomics/methods
Computational Biology/methods
*Software
*Gene Expression Profiling/methods
*Microbiota
Data Collection
Quality Control
Workflow
RNA, Untranslated
Molecular Sequence Annotation
Rhizosphere
Automation

@article {pmid40306604,
year = {2025},
author = {Lee, SH and Han, C and Shin, C},
title = {IUPHAR Review: Microbiota-Gut-Brain Axis and its role in Neuropsychiatric Disorders.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107749},
doi = {10.1016/j.phrs.2025.107749},
pmid = {40306604},
issn = {1096-1186},
abstract = {The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.},
}

@article {pmid40305950,
year = {2025},
author = {An, S and Li, J and Du, J and Feng, L and Zhang, L and Zhang, X and Zhuang, Z and Zhao, Z and Yang, G},
title = {Coupled nitrogen and phosphorus cycles mediated by coordinated variations of functional microbes in industrial recirculating aquaculture system.},
journal = {Water research},
volume = {280},
number = {},
pages = {123726},
doi = {10.1016/j.watres.2025.123726},
pmid = {40305950},
issn = {1879-2448},
abstract = {Industrial Recirculating Aquaculture Systems (IRAS) represent a sustainable and efficient approach to aquaculture, offering significant benefits in water conservation and environmental management. A comprehensive understanding of nitrogen (N) and phosphorus (P) cycling is essential for optimizing system design and operational strategies, enabling the maintenance of a balanced ecosystem within IRAS. Here, water microbial communities in the shrimp aquaculture pond (AP) and nitrification tank (NT) of the IRAS were investigated using a metagenomics-based approach to explore the mechanisms of N and P coupling cycles. Results showed that (1) N and P cycling genes were more abundant in AP water than in NT, with higher potentials for degrading organic N and P compounds, nitrate reduction, denitrification, and phosphate uptake in AP; and their hosts (functional bacteria) were identified as Marivivens for nitrate reduction, Polaribacter and Erythobacter for organophosphorus hydrolysis, and Fluviibacter and Sediminibacterium for phosphate uptake; (2) the coupling of N and P cycles was observed through the abundance of functional genes, likely mediated by coordinated variations in host composition, with nitrite content as a key factor influencing this variation; several bacterial species possessing both N and P cycling genes were identified, primarily engaged in the degradation of organic N and P compounds, denitrification, and phosphate uptake. This study highlights the coupling of N and P cycling in IRAS and the important role of functional bacteria in maintaining water quality. The results also have important implications for the management and improvement of IRAS for more effective aquaculture activities.},
}

@article {pmid40305569,
year = {2025},
author = {Hernandez-Valencia, JC and Gómez, GF and Correa, MM},
title = {Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320593},
doi = {10.1371/journal.pone.0320593},
pmid = {40305569},
issn = {1932-6203},
mesh = {Animals ; *Anopheles/virology ; Colombia ; *Virome/genetics ; *Metagenomics/methods ; *Mosquito Vectors/virology ; Phylogeny ; Malaria/transmission ; Metagenome ; },
abstract = {Anopheles darlingi is a main malaria vector in the neotropical region, but its viral component is not well studied, especially in the neotropics. This work aimed to analyze the virome in Anopheles darlingi from malaria endemic regions of Colombia. Specimens were collected from the Bajo Cauca, Chocoan Pacific and northwestern Amazonas regions and analyzed using an RNA-Seq approach. Results revealed a variety of RNA viral sequences with homology to those of Insect-Specific Viruses belonging to Rhabdoviridae, Partitiviridae, Metaviridae, Tymoviridae, Phasmaviridae, Totiviridae, Ortervirales and Riboviria. Despite geographical and ecological differences among regions, the An. darlingi viral composition remains consistent in different areas, with a core group of viral operational taxonomic units-vOTUs shared by the populations. Furthermore, diversity analysis uncovered greater dissimilarities in viral sequence among mosquitoes from geographically distant regions, particularly evident between populations located at both sides of the Andes Mountain range. This study provides the first characterization of the metavirome in An. darlingi from Colombia and lays the foundation for future research on the complex interactions among viruses, hosts, and microbiota; it also opens a new line of investigation on the viruses in Anopheles populations of Colombia.},
}

Animals
*Anopheles/virology
Colombia
*Virome/genetics
*Metagenomics/methods
*Mosquito Vectors/virology
Phylogeny
Malaria/transmission
Metagenome

@article {pmid40305442,
year = {2025},
author = {Cayrou, C and Silver, K and Owen, L and Dunlop, J and Laird, K},
title = {Domestic laundering of healthcare textiles: Disinfection efficacy and risks of antibiotic resistance transmission.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321467},
doi = {10.1371/journal.pone.0321467},
pmid = {40305442},
issn = {1932-6203},
mesh = {*Disinfection/methods ; *Textiles/microbiology ; Humans ; *Laundering/methods ; Microbial Sensitivity Tests ; Detergents/pharmacology ; *Cross Infection/prevention & control/microbiology ; *Drug Resistance, Microbial ; Staphylococcus aureus/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; United Kingdom ; Microbiota/drug effects ; Decontamination/methods ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Enterococcus faecium/drug effects ; },
abstract = {Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are a major public health concern, with the evidence base for the potential role of textiles as fomites in microbial transmission growing. In the UK, domestic laundering machines (DLMs) are commonly used to clean healthcare worker uniforms, raising concerns about their effectiveness in microbial decontamination and role in AMR development. This study aimed to evaluate DLMs' ability to decontaminate microorganisms and their potential impact on AMR. The performance of six DLMs was assessed using Enterococcus faecium bioindicators under various wash cycles and detergent conditions. Shotgun metagenomics was used to analyse the microbiome and resistome of DLMs. The minimum inhibitory concentrations of domestic detergents were determined for Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, and detergent tolerance and antibiotic cross-resistance were assessed. Results showed only 50% (3/6) of DLMs achieved sufficient decontamination (≥5 log10 CFU reduction) at 60°C during full-length cycles, with rapid cycles performing inconsistently. Microbiome analysis revealed the presence of potentially pathogenic bacteria (e.g., Mycobacterium sp. Pseudomonas sp. and Acinetobacter sp.) and antibiotic resistance genes, including efflux pumps and target modification genes. Detergent tolerance assays showed increased bacterial tolerance to detergents, with cross-resistance to antibiotics observed in S. aureus and K. pneumoniae, including carbapenem and β-lactam groups. Whole genome sequencing identified mutations in genes encoding efflux pumps in S. aureus (MrgA) and K. pneumoniae (AcrB) after detergent exposure, which could impact efflux pump function. Findings suggest domestic laundering of healthcare uniforms may be insufficient for decontamination, posing risks for HAI transmission and AMR. Revising laundering guidelines to ensure effective DLM performance, detergent efficacy, and considering alternatives like onsite/industrial laundering are crucial to enhancing patient safety and controlling AMR in healthcare settings.},
}

*Disinfection/methods
*Textiles/microbiology
Humans
*Laundering/methods
Microbial Sensitivity Tests
Detergents/pharmacology
*Cross Infection/prevention & control/microbiology
*Drug Resistance, Microbial
Staphylococcus aureus/drug effects/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
United Kingdom
Microbiota/drug effects
Decontamination/methods
Klebsiella pneumoniae/drug effects
Pseudomonas aeruginosa/drug effects
Enterococcus faecium/drug effects

@article {pmid40304791,
year = {2025},
author = {Bu, Y and Zhang, X and Xiong, Z and Li, K and Zhang, S and Lin, M and Zhao, G and Zheng, N and Wang, J and Zhao, S},
title = {Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {107},
pmid = {40304791},
issn = {1432-0614},
support = {2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202308//the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Fermentation/drug effects ; *Isoflavones/pharmacology/administration & dosage/metabolism ; *Trifolium/chemistry ; Genistein/pharmacology/administration & dosage ; *Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; Female ; Ammonia/metabolism ; Urease/metabolism ; Urea/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Metagenomics ; },
abstract = {Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH3-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.},
}

Animals
Cattle
*Rumen/microbiology
*Fermentation/drug effects
*Isoflavones/pharmacology/administration & dosage/metabolism
*Trifolium/chemistry
Genistein/pharmacology/administration & dosage
*Bacteria/classification/genetics/drug effects/metabolism/isolation & purification
Female
Ammonia/metabolism
Urease/metabolism
Urea/metabolism
*Gastrointestinal Microbiome/drug effects
Animal Feed/analysis
Metagenomics

@article {pmid40304704,
year = {2025},
author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J},
title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12494},
pmid = {40304704},
issn = {2041-1014},
support = {DE029612//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE028252//NIH-NIDCR/ ; },
abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.},
}

@article {pmid40304525,
year = {2025},
author = {Fernández-Quintela, A and Laveriano-Santos, EP and Portolés, T and Gual-Grau, A and Sancho, JV and Portillo, MP},
title = {Changes in Liver Metabolome Induced by Pterostilbene and Resveratrol in a Rat Model of Liver Steatosis.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70078},
doi = {10.1002/mnfr.70078},
pmid = {40304525},
issn = {1613-4133},
support = {AGL-2015-65719-R//Ministerio de Economía y Competitividad/ ; //Fondo Europeo de Desarrollo Regional (FEDER)/ ; CB12/03/30007//Instituto de Salud Carlos III (CIBERobn)/ ; IT1482-22//Government of the Basque Country/ ; },
abstract = {To gain more light on the effects of resveratrol and pterostilbene in the hepatic metabolic modifications in an in vivo model of diet-induced hepatic steatosis, and to explore their relationships with gut microbiota by untargeted metabolomics and metagenomics. Rats were divided into five groups receiving either a standard diet or a high-fat high-fructose (HFHF) diet supplemented or not with pterostilbene (15 or 30 mg/kg body weight/day; PT15 or PT30 groups, respectively) or resveratrol (30 mg/kg body weight/day; RSV30 group). Supplementation with the stilbenes reduced the hepatic steatosis induced by the HFHF diet. After the metabolomics study, 27 differentially expressed metabolites showed variable importance in projection scores > 1 and could be considered as potential biomarkers. Therefore, based on the pathway enrichment analysis, "riboflavin metabolism" and "nicotinate and nicotinamide metabolism" revealed significant enrichment. Further, riboflavin showed positive correlations to Eubacterium and Faecalibacterium, and negative correlations to Lactobacillus and Oscillospira genera. Nicotinamide mononucleotide was only positively correlated to the Ralstonia genus. The untargeted metabolomics approach showed that the actions of resveratrol or pterostilbene on the prevention of liver steatosis are mediated by specific mechanisms of action. Particularly, pterostilbene, but not resveratrol, is suggested to significantly enrich riboflavin or nicotinate and nicotinamide metabolic pathways.},
}

@article {pmid40304520,
year = {2025},
author = {Flörl, L and Meyer, A and Bokulich, NA},
title = {Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0052425},
doi = {10.1128/aem.00524-25},
pmid = {40304520},
issn = {1098-5336},
abstract = {Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.},
}

@article {pmid40303946,
year = {2024},
author = {Dakal, TC and Xu, C and Kumar, A},
title = {Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification.},
journal = {Frontiers in medical technology},
volume = {6},
number = {},
pages = {1434799},
pmid = {40303946},
issn = {2673-3129},
abstract = {The microbiome of the gut is a complex ecosystem that contains a wide variety of microbial species and functional capabilities. The microbiome has a significant impact on health and disease by affecting endocrinology, physiology, and neurology. It can change the progression of certain diseases and enhance treatment responses and tolerance. The gut microbiota plays a pivotal role in human health, influencing a wide range of physiological processes. Recent advances in computational tools and artificial intelligence (AI) have revolutionized the study of gut microbiota, enabling the identification of biomarkers that are critical for diagnosing and treating various diseases. This review hunts through the cutting-edge computational methodologies that integrate multi-omics data-such as metagenomics, metaproteomics, and metabolomics-providing a comprehensive understanding of the gut microbiome's composition and function. Additionally, machine learning (ML) approaches, including deep learning and network-based methods, are explored for their ability to uncover complex patterns within microbiome data, offering unprecedented insights into microbial interactions and their link to host health. By highlighting the synergy between traditional bioinformatics tools and advanced AI techniques, this review underscores the potential of these approaches in enhancing biomarker discovery and developing personalized therapeutic strategies. The convergence of computational advancements and microbiome research marks a significant step forward in precision medicine, paving the way for novel diagnostics and treatments tailored to individual microbiome profiles. Investigators have the ability to discover connections between the composition of microorganisms, the expression of genes, and the profiles of metabolites. Individual reactions to medicines that target gut microbes can be predicted by models driven by artificial intelligence. It is possible to obtain personalized and precision medicine by first gaining an understanding of the impact that the gut microbiota has on the development of disease. The application of machine learning allows for the customization of treatments to the specific microbial environment of an individual.},
}

@article {pmid40303154,
year = {2024},
author = {Albert, E and Kis, IE and Kiss, K and K-Jánosi, K and de Oliveira Costa, M and Tolnai, G and Biksi, I},
title = {Abortion and Lethal Septicaemia in Sows Caused by a Non-ST194 Streptococcus equi subsp. zooepidemicus.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {4008946},
pmid = {40303154},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Streptococcal Infections/veterinary/microbiology/epidemiology/mortality ; Female ; *Abortion, Veterinary/microbiology/epidemiology ; *Swine Diseases/microbiology/epidemiology/mortality ; Pregnancy ; *Sepsis/veterinary/microbiology/epidemiology ; Disease Outbreaks/veterinary ; Hungary/epidemiology ; Streptococcus ; },
abstract = {Outbreaks of zoonotic Streptococcus equi subsp. zooepidemicus (SEZ) have caused severe epidemics in the pig sector since the 1970s in Southeastern Asia, China, and more recently North America. Cases of high mortality caused by peracute septicaemia were all attributed to strains of a highly virulent clonal lineage belonging to the sequence type (ST) 194. In Europe, only two outbreaks have been reported with similar features, caused by other sequence types. In August 2023, a febrile disease followed by abortion and subsequent death was observed among sows kept in a small-scale organic pig farm in West Hungary. Symptoms, pathological lesions, and microbiological findings were suggestive of septicaemia from bacterial origin caused by SEZ. According to the results of the routine laboratory testing, no other relevant infectious agents were involved. Whole-genome sequence analysis assigned the examined strains to ST138, unrelated to any of the European isolates. It also revealed a few common SEZ virulence genes, compared to the highly virulent ST194 strains. A sudden weather change and subsequent extremely high average daily temperature before the outbreak could be identified as the only predisposing factor. The immediate antibiotic treatment and applied biosecurity measures might have helped to restrict and terminate the outbreak. To our knowledge, this is the first report on abortion and lethal septicaemia in sows from Central and Eastern Europe. The results call attention to the potential of non-ST194 SEZ strains to cause outbreaks in pig farms.},
}

Animals
Swine
*Streptococcal Infections/veterinary/microbiology/epidemiology/mortality
Female
*Abortion, Veterinary/microbiology/epidemiology
*Swine Diseases/microbiology/epidemiology/mortality
Pregnancy
*Sepsis/veterinary/microbiology/epidemiology
Disease Outbreaks/veterinary
Hungary/epidemiology
Streptococcus

@article {pmid40303144,
year = {2024},
author = {Meng, X and Sun, J and Yao, M and Sun, Y and Xu, H and Liu, C and Chen, H and Guo, J and Nie, X and He, L and Zhao, Z and Li, N and Wang, Z and Wang, J},
title = {Isolation and Identification of Severe Fever with Thrombocytopenia Syndrome Virus from Farmed Mink in Shandong, China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {9604673},
pmid = {40303144},
issn = {1865-1682},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) virus, recently named Bandavirus dabieense, belongs to the genus Bandavirus of family Phenuiviridae, and it causes SFTS in humans with clinical symptoms including fever, thrombocytopenia, gastrointestinal symptoms, and leukocytopenia. However, there are few reports on the pathogenesis of SFTSV in animals. This study first isolated the SFTSV strain SD22-2 from sick-farmed mink. Viral metagenomics was used to detect SFTSV nucleotide in the clinical specimens obtained from symptomatic minks. Then, we isolated the virus using Vero and DH82 cells, and Real-Time Quantitative PCR (RT-qPCR), indirect immunofluorescence assay, transmission electron microscopy, and Western blotting identified it. Meanwhile, phylogenetic analysis based on partial L, M, and S segment sequences indicated that the mink-origin SFTSV strain SD22-2 belonged to genotype D and was genetically close to the HB2016-003 strain isolated from humans. Taken together, we isolated and identified an SFTSV from farmed mink that may be the reservoir hosts of SFTSV. We should pay more attention to farmed minks and biosecurity practices, and active surveillance at fur farms must be reviewed and enhanced.},
}

@article {pmid40303140,
year = {2024},
author = {Song, Y and Zuo, O and Zhang, G and Hu, J and Tian, Z and Guan, G and Luo, J and Yin, H and Shang, Y and Du, J},
title = {Emergence of Lumpy Skin Disease Virus Infection in Yaks, Cattle-Yaks, and Cattle on the Qinghai-Xizang Plateau of China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {2383886},
pmid = {40303140},
issn = {1865-1682},
mesh = {Animals ; Cattle ; *Lumpy Skin Disease/epidemiology/virology ; *Lumpy skin disease virus/genetics/isolation & purification/classification ; China/epidemiology ; Phylogeny ; Tibet/epidemiology ; *Cattle Diseases/epidemiology/virology ; Genome, Viral ; },
abstract = {Lumpy skin disease (LSD) is a viral disease caused by lumpy skin disease virus (LSDV), which mainly infects cattle and can cause huge economic losses. In May 2023, yaks, cattle-yaks, and cattle in Tibet (Xizang), China, developed fever, skin nodules, and severe discharges and were suspected to be cases of LSD. Samples from these animals were analyzed using molecular biology and serological methods. The RPO30, P32, and GPCR genes were amplified by PCR and sequenced, and the whole genome of the virus was determined using viral metagenomics technology. Sequencing results showed that it was indeed an LSDV infection, and enzyme-linked immunosorbent assay results confirmed the presence of LSDV antibodies. The whole genome phylogenetic tree shows that LSDV/CHINA/Tibet/2023 is different from the previous epidemic strains in China, but clusters with India 2022 strain. This is the first report of LSD in yaks, cattle-yaks, and cattle on the highest altitude plateau in the world.},
}

Animals
Cattle
*Lumpy Skin Disease/epidemiology/virology
*Lumpy skin disease virus/genetics/isolation & purification/classification
China/epidemiology
Phylogeny
Tibet/epidemiology
*Cattle Diseases/epidemiology/virology
Genome, Viral

@article {pmid40303134,
year = {2024},
author = {Mulder, KP and Pasmans, F and van Nieuwerburgh, F and Terriere, N and Kelly, M and Bregman, S and Verbrugghe, E and Martel, A},
title = {High Prevalence of a Novel Circovirus in the European Hedgehog (Erinaceus europaeus), a Common Species in Decline.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {4670252},
pmid = {40303134},
issn = {1865-1682},
mesh = {Animals ; *Hedgehogs/virology ; *Circovirus/isolation & purification/genetics/classification ; *Circoviridae Infections/veterinary/epidemiology/virology ; Phylogeny ; Europe/epidemiology ; Prevalence ; },
abstract = {Hedgehog (Erinaceus europaeus) declines in western Europe have been associated with the emergence of Hedgehog diphtheric disease (HDD), with a probable multifactorial, yet unidentified etiology. We used metagenomic sequencing of cell-free DNA (cfDNA) in hedgehog blood to identify possible causes of HDD. We detected a novel circovirus species in the European hedgehog, providing the first record of a circovirus within the mammalian order Eulipotyphla. The novel circovirus genome exhibits the characteristic circovirus structure, including a functional replicase (REP) and capsid (CAP) gene. Phylogenetic analysis placed all four detected genomes in a monophyletic clade, most closely related to sequences isolated from dogs. Subsequent PCR-based screening of 188 hedgehog liver samples demonstrated a high prevalence (61%) of this circovirus in hedgehogs brought to wildlife rescue centers, however, without any significant association with HDD. Since circoviruses are well known to interfere with host immunity across mammalian and avian taxa, the high level of circovirus detection in hedgehogs warrants further research into the role of this novel virus in hedgehog health.},
}

Animals
*Hedgehogs/virology
*Circovirus/isolation & purification/genetics/classification
*Circoviridae Infections/veterinary/epidemiology/virology
Phylogeny
Europe/epidemiology
Prevalence

@article {pmid40303123,
year = {2024},
author = {Wang, K and Liu, S and Liang, X and Hu, W and Wen, Z and Wang, J and Wang, X and An, F and Chen, Z and Yan, H and Yan, H and Wang, L and Zhang, X and Yu, J and Wei, WK and Hua, Y},
title = {Identification and Genetic Analysis of Species D Rotaviruses in Pangolin Samples.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {1773821},
pmid = {40303123},
issn = {1865-1682},
mesh = {Animals ; *Rotavirus/genetics/isolation & purification/classification ; Phylogeny ; *Pangolins/virology ; *Rotavirus Infections/veterinary/virology ; Genome, Viral ; },
abstract = {Pangolins have been found to carry severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related coronaviruses. In light of this discovery, interest has been piqued in viromes of these heavily trafficked wild animals. In this study, we performed viral metagenomic sequencing to explore viromes of both confiscated dead pangolins and captive healthy pangolins. Sequence reads of vertebrate-associated viruses in Herpesviridae, Retroviridae, Iridoviridae, Reoviridae, Arenaviridae, and Flaviviridae were detected in confiscated dead pangolins. A novel rotavirus (RV) (Reoviridae), showing a high degree of genetic similarity to the RV species D (RVD) that was previously unreported in mammals, was further confirmed by using reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing. Three out of 18 samples from the confiscated dead pangolins were positive for genomic sequences of the novel RV. Importantly, sequence alignments and phylogenetic analyses demonstrated that these RV strains genetically belonged to the RVD. Nevertheless, these novel RVD strains were divergent from known RVD strains that have been found only in Avian. They formed a separate genetic cluster. Five serial passages were attempted to isolate the RV, but no live virus was obtained. In addition, fecal samples were collected from healthy pangolins (n = 41) in our institution and screened for RVs by viral metagenomic sequencing and RT-PCR. In these fecal samples, neither species D nor previously identified species A RVs were detected. This study reported RVDs in pangolin samples for the first time to our knowledge. Identifiability disagreements between wild and captive pangolins highlight the need for further exploration into pangolin viruses to better understand their emergence and transmission potential.},
}

Animals
*Rotavirus/genetics/isolation & purification/classification
Phylogeny
*Pangolins/virology
*Rotavirus Infections/veterinary/virology
Genome, Viral

@article {pmid40303119,
year = {2024},
author = {Lovy, J and Iwanowicz, LR and Welch, TJ and Allam, B and Getchell, RG and Geraci-Yee, S and Good, C and Snyder, J and Raines, CD and Das, N},
title = {Seasonal Mortality of Wild Atlantic Menhaden (Brevoortia tyrannus) Is Caused by a Virulent Clone of Vibrio (Listonella) anguillarum; Implications for Biosecurity along the Atlantic Coastal United States.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {8816604},
pmid = {40303119},
issn = {1865-1682},
mesh = {Animals ; *Fish Diseases/microbiology/mortality/epidemiology ; *Vibrio/pathogenicity/genetics/isolation & purification ; Seasons ; *Vibrio Infections/veterinary/mortality/microbiology/epidemiology ; Fishes ; New Jersey/epidemiology ; Atlantic Ocean/epidemiology ; New York/epidemiology ; Virulence ; },
abstract = {Atlantic menhaden are a highly migratory marine species in the Eastern United States that suffer from seasonal chronic mortality. Affected fish show neurologic signs referred to as spinning disease, including circling at the surface and erratic corkscrew swimming before death. We investigated three similar menhaden mortality events consistent with spinning disease in coastal New Jersey and New York between 2020 and 2021 to understand the cause. A unique strain of Vibrio (Listonella) anguillarum (serogroup O3) was detected regularly in high loads, particularly in the brains of moribund fish, by both metagenomics and bacterial isolation. The most common histopathological changes in moribund fish were hemorrhagic meningitis, encephalitis, pyknosis, and karyorrhexis of hematopoietic tissues in the kidney and spleen. Whole genome sequencing of isolates from moribund fish representing a wide spatial and temporal range showed that they were nearly identical clones, suggesting it to be a pathogenic strain circulating in the population. Though V. anguillarum is believed to be the main pathogen associated with spinning disease and mortality, Yersinia ruckeri (serotype O1) was isolated from smaller numbers of fish. Considering the highly migratory nature of Atlantic menhaden throughout the eastern United States and their use as bait for other fisheries, these findings identify potential biosecurity challenges that should be considered in Atlantic salmon aquaculture, fisheries, and emerging marine aquaculture in the region.},
}

Animals
*Fish Diseases/microbiology/mortality/epidemiology
*Vibrio/pathogenicity/genetics/isolation & purification
Seasons
*Vibrio Infections/veterinary/mortality/microbiology/epidemiology
Fishes
New Jersey/epidemiology
Atlantic Ocean/epidemiology
New York/epidemiology
Virulence

@article {pmid40303091,
year = {2024},
author = {Wang, YM and Deng, LS and Huang, BZ and Li, HY and Duan, JQ and Yan, YX and Lai, SY and Ai, YR and Zhou, YC and Qing, Y and Xu, ZW and Zhu, L},
title = {Whole Genome Characterization and Pathogenicity of a SC2020-1-Like PRRSV-1 Strain Emerging in Southwest China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {5627927},
pmid = {40303091},
issn = {1865-1682},
mesh = {Animals ; *Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/classification ; Swine ; *Porcine Reproductive and Respiratory Syndrome/virology/epidemiology/pathology ; China/epidemiology ; *Genome, Viral ; Phylogeny ; Virulence ; },
abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV), encompassing PRRSV-1 and PRRSV-2, significantly impacts the global pig industry by causing reproductive disorders and respiratory difficulties. In this paper, we isolated a novel PRRSV-1 strain, named SCPJ2023, from weaned piglets in Sichuan. Utilizing primary macrophages, we isolated SCPJ2023 and performed complete genome sequencing through metagenomic analysis. Phylogenetic analysis classified SCPJ2023 as pan-European subtype 1. SCPJ2023 showed a 95.3% similarity to SC2020-1. Amino acid analysis identified differences in Nsp2, GP3, and GP4 between SCPJ2023 and other representative strains. In vivo challenge experiments demonstrated that SCPJ2023 induced clinical symptoms in piglets, including coughing, fever, reduced appetite, and depression. Pathological examinations revealed hemorrhage and congestion, increased inflammatory cells, thickening of the alveolar wall, and collapse of the alveolar cavity in SCPJ2023-infected piglets. Altogether, our study identified a novel pathogenic isolate of PRRSV-1, expanding the newly named SC2020-1-like subgroup by identifying additional strains beyond the initial SC2020-1 isolate.},
}

Animals
*Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/classification
Swine
*Porcine Reproductive and Respiratory Syndrome/virology/epidemiology/pathology
China/epidemiology
*Genome, Viral
Phylogeny
Virulence

@article {pmid40303019,
year = {2024},
author = {Stadler, J and Lillie-Jaschniski, K and Zwickl, S and Zoels, S and Theuns, S and Ritzmann, M and Vereecke, N},
title = {Cross-Correlation between Biosecurity Measures and the Detection of Viral and Bacterial Agents on German Farms with Respiratory Disease.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {6205899},
pmid = {40303019},
issn = {1865-1682},
mesh = {Animals ; Germany/epidemiology ; Swine ; *Swine Diseases/microbiology/epidemiology/virology/prevention & control ; *Biosecurity ; Farms ; Animal Husbandry ; *Bacterial Infections/veterinary/epidemiology/microbiology ; Bacteria/isolation & purification/classification ; Porcine respiratory and reproductive syndrome virus/isolation & purification ; Porcine Reproductive and Respiratory Syndrome/epidemiology/virology/microbiology ; },
abstract = {Effective porcine health management relies majorly on diagnostic tests, vaccination, treatment strategies, and a proper biosecurity management plan. However, understanding the link between circulating microbes and biosecurity measures on a pig farm is not evident. Substantial progress has been made in recent years with the availability of new diagnostic tools (e.g., sequencing-based diagnostics) and extensive biosecurity management questionnaires. However, the interpretation and correlation of these results are hampered by the abundance of gained (meta)data. Therefore, we aimed to cross-correlate viral and bacterial pathogens with respiratory tropism detected by third-generation nanopore metagenomic sequencing with biosecurity measures assessed by Biocheck.UGent™. The study was conducted on 25 sow farms with attached nurseries in Germany with known respiratory distress. The biosecurity level of the study farms complied with the European averages. Interestingly, the farms with the highest biosecurity score showed the lowest overall prevalence of porcine reproductive and respiratory syndrome virus (PRRSV) and Actinobacillus sp.; the circulation of well-studied pathogenic viruses, such as PRRSV, was correlated with overall lower biosecurity scores, a higher number of stillborn piglets, and cocirculation of porcine parvovirus type 7. Moreover, potential risk factors for lesser-known agents (e.g., porcine hemagglutinating and encephalomyelitis virus, porcine respiratory coronavirus, and porcine polyomavirus) could also be addressed. For the bacterial pathogen Glaesserella sp., a correlation with increased clinical signs was observed, whereas Lactobacillus sp. and Moraxella sp. are putative biomarkers for pig farms with better biosecurity scores. In conclusion, in-depth cross-correlation of (meta)data from new diagnostic platforms with biosecurity measures on pig farms may contribute to a better understanding of new actions in adapting biosecurity measures. This will not only contribute to improved animal welfare and economic productivity but also helping to address (new) zoonotic disease threats and potential treatments.},
}

Animals
Germany/epidemiology
Swine
*Swine Diseases/microbiology/epidemiology/virology/prevention & control
*Biosecurity
Farms
Animal Husbandry
*Bacterial Infections/veterinary/epidemiology/microbiology
Bacteria/isolation & purification/classification
Porcine respiratory and reproductive syndrome virus/isolation & purification
Porcine Reproductive and Respiratory Syndrome/epidemiology/virology/microbiology

@article {pmid40302920,
year = {2025},
author = {Gao, Z and Jiang, Y and Chen, M and Wang, W and Liu, Q and Ma, J},
title = {Enhancing fever of unknown origin diagnosis: machine learning approaches to predict metagenomic next-generation sequencing positivity.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1550933},
pmid = {40302920},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Fever of Unknown Origin/diagnosis/etiology ; Female ; Male ; Middle Aged ; Algorithms ; Adult ; Aged ; },
abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) can potentially detect various pathogenic microorganisms without bias to improve the diagnostic rate of fever of unknown origin (FUO), but there are no effective methods to predict mNGS-positive results. This study aimed to develop an interpretable machine learning algorithm for the effective prediction of mNGS results in patients with FUO.

METHODS: A clinical dataset from a large medical institution was used to develop and compare the performance of several predictive models, namely eXtreme Gradient Boosting (XGBoost), Light Gradient-Boosting Machine (LightGBM), and Random Forest, and the Shapley additive explanation (SHAP) method was employed to interpret and analyze the results.

RESULTS: The mNGS-positive rate among 284 patients with FUO reached 64.1%. Overall, the LightGBM-based model exhibited the best comprehensive predictive performance, with areas under the curve of 0.84 and 0.93 for the training and validation sets, respectively. Using the SHAP method, the five most important factors for predicting mNGS-positive results were albumin, procalcitonin, blood culture, disease type, and sample type.

CONCLUSION: The validated LightGBM-based predictive model could have practical clinical value in enhancing the application of mNGS in the etiological diagnosis of FUO, representing a powerful tool to optimize the timing of mNGS.},
}

Humans
*Machine Learning
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Fever of Unknown Origin/diagnosis/etiology
Female
Male
Middle Aged
Algorithms
Adult
Aged

@article {pmid40302838,
year = {2025},
author = {Pallen, MJ and Ponsero, AJ and Telatin, A and Moss, CJ and Baker, D and Heavens, D and Davidson, GL},
title = {Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.},
journal = {Access microbiology},
volume = {7},
number = {4},
pages = {},
pmid = {40302838},
issn = {2516-8290},
abstract = {Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.},
}

@article {pmid40302016,
year = {2025},
author = {Zhou, H and Tang, L and Fenton, KA and Song, X},
title = {Exploring and Evaluating Microbiome Resilience in the Gut.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf046},
pmid = {40302016},
issn = {1574-6941},
abstract = {The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.},
}

@article {pmid40301729,
year = {2025},
author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S},
title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {39},
pmid = {40301729},
issn = {2730-7182},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.

RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200 m, with a slight increase observed above 1400 m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.

CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome
India
RNA, Ribosomal, 16S/genetics/analysis
*Altitude
*Bacteria/classification/genetics/isolation & purification

@article {pmid40301728,
year = {2025},
author = {Munoz Briones, J and Brubaker, DK},
title = {A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {115},
pmid = {40301728},
issn = {1471-2105},
support = {2120200//Directorate for Biological Sciences/ ; R01HD110367//National Institute of Child Health and Human Development/ ; },
mesh = {Humans ; *Microbiota ; *Metabolomics/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; *Computational Biology/methods ; Principal Component Analysis ; Crohn Disease/microbiology ; Multiomics ; },
abstract = {BACKGROUND: The number and size of multi-omics datasets with paired measurements of the host and microbiome is rapidly increasing with the advance of sequencing technologies. As it becomes routine to generate these datasets, computational methods to aid in their interpretation become increasingly important. Here, we present a framework for integration of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE integrates multi-omics data using single-omic latent variables (LV) organized in a structured meta-model to determine the combinations of features most predictive of a phenotype or condition.

RESULTS: We developed a supervised version of LIVE leveraging sparse Partial Least Squares Discriminant Analysis (sPLS-DA) LVs, and an unsupervised version leveraging sparse Principal Component Analysis (sPCA) principal components which both can incorporate covariate awarness. LIVE performance was tested on publicly available metagenomic and metabolomics data set from Crohn's Disease (CD) and Ulcerative Colitis (UC) status patients in the PRISM and LLDeep cohorts, and benchmarked against existing gut microbiome multi-omics approaches and vaginal microbiome datasests, achieving consistent and comparable performances. In addition to these benchmarking efforts, we present a detailed analysis and interpretation of both versions of LIVE using the PRISM and LLDeep cohorts. LIVE reduced the number of feature interactions from the original datasets for CD and UC from millions to less than 20,000 while conditioning the disease-predictive power of gut microbes, metabolites, enzymes, on clinical variables.

CONCLUSIONS: LIVE makes a distinct, complementary contribution to current methods to integrate microbiome data and offers key advantages to existing approaches in the interpretable integration of multi-omics data with clinical variables to predict to disease outcomes and identify microbiome mechanisms of disease.},
}

Humans
*Microbiota
*Metabolomics/methods
Gastrointestinal Microbiome
Metagenomics/methods
*Computational Biology/methods
Principal Component Analysis
Crohn Disease/microbiology
Multiomics

@article {pmid40301726,
year = {2025},
author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J},
title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {258},
pmid = {40301726},
issn = {1471-2180},
support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; },
mesh = {Humans ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Culture Media/chemistry ; *Biodiversity ; *Bacteriological Techniques/methods ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.},
}

Humans
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification/growth & development
*Metagenomics/methods
*Gastrointestinal Microbiome
Culture Media/chemistry
*Biodiversity
*Bacteriological Techniques/methods
Sequence Analysis, DNA
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid40300742,
year = {2025},
author = {Wang, B and Huang, T and Zhu, L and Hu, J and Ma, S and Sun, Q and Chen, K},
title = {Effect of cyanobacterial bloom proliferation on antibiotic resistance genes in the sediments of a eutrophic lake.},
journal = {Environmental research},
volume = {278},
number = {},
pages = {121717},
doi = {10.1016/j.envres.2025.121717},
pmid = {40300742},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) represent an emerging pollutant of increasing concern. In this study, we analyzed the composition and spatiotemporal variation of ARGs in the sediments of eutrophic Chaohu Lake, China, using a metagenomic method. A total of 22 ARGs and 199 ARGs subtypes were detected, with the most prevalent subtypes being multidrug (57.720 %) and rifamycin (21.781 %). A higher abundance of ARGs in Chaohu Lake was observed (p < 0.05) during winter and spring owing to multiple factors, including variations in seasonal inputs and hydraulic conditions, occurrence of cyanobacterial blooms, and changes in ARGs host bacterial communities. Spatially, a higher abundance of multidrug was observed in sediments near the Nanfei River outlet, which flows through urban areas; whereas higher levels of bacitracin were observed in sediments near the Zhao River outlet, which flows through agricultural areas. Cyanobacterial blooms and declines change the sediment physicochemical properties, endogenous phosphorus contents, microbial communities, and seasonal ARGs distribution. Correlation and collinearity analyses indicated that ARGs were transferred horizontally via mobile genetic elements (MGEs). High-risk ARGs in Chaohu Lake were observed at a very low proportion, although certain ARGs presented health risks in the western lake during spring. In this study, we highlight the interactions between cyanobacterial blooms and variations in ARGs in Chaohu Lake and provide novel insights into ARGs dynamics in eutrophic freshwater ecosystems.},
}

@article {pmid39796227,
year = {2025},
author = {Lu, Y and Li, M and Gao, Z and Ma, H and Chong, Y and Hong, J and Wu, J and Wu, D and Xi, D and Deng, W},
title = {Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
pmid = {39796227},
issn = {1422-0067},
support = {32160771//National Nature Science Foundation of China/ ; 32302707//National Nature Science Foundation of China/ ; 202101BD070001-006//Yunnan Provincial Agricultural Union Foundation/ ; 202202AE090005//Major Science and Technology Projects in Yunnan Province/ ; 202301AU070117//Yunnan Province Basic Research Program Project/ ; XDYC-CYCX-2022-0029//"Xingdian Talent" Industry Innovation Talent Program in Yunnan Province/ ; },
mesh = {Humans ; *Whole Genome Sequencing/methods ; *Genetics, Population/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Software ; *Genome, Human ; Genetic Variation ; *Metagenomics/methods ; Machine Learning ; },
abstract = {With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics. The goal is to examine the application and progress of resequencing technologies in this field and to consider future developments, including deep learning models and machine learning algorithms, which promise to enhance analytical methodologies and drive further advancements in population genomics.},
}

Humans
*Whole Genome Sequencing/methods
*Genetics, Population/methods
High-Throughput Nucleotide Sequencing/methods
*Genomics/methods
Software
*Genome, Human
Genetic Variation
*Metagenomics/methods
Machine Learning

@article {pmid40303081,
year = {2024},
author = {Yuan, Y and Li, L and Liu, Z and Yang, X and Wang, W and Xu, W and Liu, N and Sui, L and Zhao, Y and Liu, Q and Wang, Z},
title = {First Report and Genetic Characterization of Border Disease Virus in Sheep from Hulunbuir, Northeastern China.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {9924724},
pmid = {40303081},
issn = {1865-1682},
mesh = {Animals ; Sheep ; China/epidemiology ; Phylogeny ; *Border disease virus/genetics/isolation & purification/classification ; *Border Disease/epidemiology/virology ; *Sheep Diseases/virology/epidemiology ; Genome, Viral ; },
abstract = {Border disease virus (BDV), a member of the Pestivirus genus within the Flaviviridae family, is known to inflict significant economic losses on livestock farms due to its association with reproductive disorders and persistent infections in sheep and goats. However, comprehensive epidemiological investigations of BDV in China are scarce. This study examined BDV infection in sheep from Hulunbuir, Inner Mongolia, northeastern China, utilizing metagenomic sequencing and polymerase chain reaction (PCR) assay. Among the 96 serum samples analyzed, only one tested positive for BDV nucleotide sequence, yielding a prevalence rate of 1.0%. A total of 11,985 nt long genome sequences was amplified, which showed nucleotide identities ranging from 76.6% to 87.2% and amino acid identities ranging from 85.2% to 93.2% with other BDV strains worldwide. Phylogenetic analysis unequivocally placed the viral strain within genotype BDV-3, showing a close genetic affinity with strain JSLS12-01 identified in Jiangsu province, China. Furthermore, selection pressure analyses suggested that purifying selection predominantly influenced the evolutionary dynamics of BDV genomes. This study marks the inaugural detection of BDV in sheep within Inner Mongolia, northeastern China, thereby enhancing our understanding of the extensive genetic diversity and geographical distribution of BDV strains across the country. These findings hold relevance for the livestock industry and disease surveillance efforts, offering valuable insights into the prevalence and genetic characteristics of BDV in this region.},
}

Animals
Sheep
China/epidemiology
Phylogeny
*Border disease virus/genetics/isolation & purification/classification
*Border Disease/epidemiology/virology
*Sheep Diseases/virology/epidemiology
Genome, Viral

@article {pmid40303833,
year = {2023},
author = {Wang, Y and Gu, C and Han, Q and Fu, S and Wang, J and Zhuang, J and Guo, G and Liu, J and Yu, X and Qu, G and Shen, Z},
title = {A Novel Pathogen of an Emerging Infectious Disease (Large Kidney Disease) in Farmed Blue Foxes.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {6629054},
pmid = {40303833},
issn = {1865-1682},
mesh = {Animals ; *Foxes/virology ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; *Retroviridae Infections/veterinary/virology/epidemiology ; *Kidney Diseases/veterinary/virology/epidemiology ; China/epidemiology ; Phylogeny ; },
abstract = {An emerging infectious disease (EID) in foxes called "large kidney disease", characterized by enlarged kidneys, has been breaking out in fox farms in China, although its pathogenesis has not yet been elucidated. Here, we performed viral metagenomics sequencing on diseased fox tissue samples that identified a virus with 82.6% homology to the xenotropic murine leukemia virus-related virus (XMRV) PreXMRV-1 provirus strain (GenBank accession number NC_007815.2) in sick fox tissue. It was named PreXMRV-20, and its genome was verified by reverse transcription-polymerase chain reaction (PCR) and PCR product sequencing. Nonenveloped and polygonal virus-like particles consistent with the shape and size of XMRV were observed by negative staining electron microscopy. Administered subcutaneously, PreXMRV-20 infected weaned foxes, leading to growth retardation. The discovery of the PreXMRV-20 strain (the first isolation of an XMRV homolog in blue foxes) identifies a potential public health issue in blue fox breeding since XMRV has been confirmed to be a zoonotic virus.},
}

Animals
*Foxes/virology
*Communicable Diseases, Emerging/veterinary/virology/epidemiology
*Retroviridae Infections/veterinary/virology/epidemiology
*Kidney Diseases/veterinary/virology/epidemiology
China/epidemiology
Phylogeny

@article {pmid40303754,
year = {2023},
author = {Righi, C and Curini, V and Torresi, C and Cammà, C and Pirani, S and Di Lollo, V and Gobbi, P and Giammarioli, M and Viola, G and Pela, M and Feliziani, F and Petrini, S},
title = {Molecular Detection and Genetic Characterization of Bovine Kobuvirus (BKV) in Diarrhoeic Calves in a Central Italy Herd.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {6637801},
pmid = {40303754},
issn = {1865-1682},
mesh = {Animals ; Cattle ; Italy/epidemiology ; *Cattle Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Kobuvirus/genetics/isolation & purification ; *Picornaviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; *Polyomavirus Infections/veterinary/virology/epidemiology ; *Tumor Virus Infections/veterinary/virology/epidemiology ; },
abstract = {Bovine kobuvirus (BKV) is an infectious agent associated with neonatal calf diarrhoea (NCD), causing important economic losses to dairy and beef cattle herds worldwide. Here, we present the detection rate and characterize the genome of BKV isolated from diarrhoeic calves from a Central Italy herd. From January to December 2021, we collected blood samples and nasal and rectal swabs from 66 calves with severe NCD between 3 and 20 days of age. After virological (bovine coronavirus, bovine viral diarrhoea virus, and bovine rotavirus), bacteriological (Escherichia coli spp. and Salmonella spp.), and parasitological (Cryptosporidium spp., Eimeria spp., and Giardia duodenalis) investigations, we detected BKV using the metagenomic analysis. This result was confirmed using a specific polymerase chain reaction assay that revealed the number of BKV-positive nasal (24.2%) and rectal swabs (31.8%). The prevalence of BKV was higher than that of BCoV. Coinfection with BKV and BCoV was detected in 7.5% of the rectal swabs, highlighting the involvement of another infectious agent in NCD. Using next generation sequencing (NGS) approach, it was possible to obtain the complete sequence of the BKV genome from other two rectal swabs previously analysed by real-time PCR. This is the first report describing the whole genome sequence (WGS) of BKV from Italy. The Italian BKV genomes showed the highest nucleotide sequence identity with BKV KY407744.1, identified in Egypt in 2014. The sequence encoding VP1 best matched that of BKV KY024562, identified in Scotland in 2013. Considering the small number of BKV WGSs available in public databases, further studies are urgently required to assess the whole genome constellation of circulating BKV strains. Furthermore, pathogenicity studies should be conducted by inoculating calves with either only BKV or a combination with other enteric pathogens for understanding the probable role of BKV in NCD.},
}

Animals
Cattle
Italy/epidemiology
*Cattle Diseases/virology/epidemiology
*Diarrhea/veterinary/virology/epidemiology
*Kobuvirus/genetics/isolation & purification
*Picornaviridae Infections/veterinary/virology/epidemiology
Phylogeny
*Polyomavirus Infections/veterinary/virology/epidemiology
*Tumor Virus Infections/veterinary/virology/epidemiology

@article {pmid40303817,
year = {2023},
author = {Li, C and Qiu, M and Li, S and Sun, Z and Huang, Z and Qi, W and Qiu, Y and Li, J and Feng, B and Zhao, D and Lin, H and Zheng, W and Yu, X and Tian, K and Fan, K and Zhu, J and Chen, N},
title = {Metagenomic and Pathogenic Assessments Identify a Pathogenic Porcine Reproductive and Respiratory Syndrome Virus 1 with New Deletions from Adult Slaughter Pig in 2022.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {1975039},
pmid = {40303817},
issn = {1865-1682},
mesh = {Animals ; *Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/isolation & purification ; Swine ; *Porcine Reproductive and Respiratory Syndrome/virology/epidemiology ; China/epidemiology ; Phylogeny ; Metagenomics ; Genome, Viral ; Sequence Deletion ; },
abstract = {Since we first reported porcine reproductive and respiratory syndrome virus 1 (PRRSV1) wild type strains in mainland China in 2011, PRRSV1 infection has been detected in more than 20 provinces in China. During the routine investigation of PRRSV1 epidemiology in 2022, we isolated a novel PRRSV1 strain (SD1291) from an adult slaughter pig in Linyi, Shandong Province. The SD1291 could only be isolated with primary alveolar macrophages (PAMs), not with Marc-145 cells. In addition, the 2022 SD1291 isolate has higher in vitro replication efficacy than the 2014 PRRSV1 HLJB1 isolate in PAMs. Due to high genetic variation, the complete genome of SD1291 was determined by metagenomic sequencing, which showed that SD1291 shares the highest genome similarity (88.12%) with the PRRSV1 HeB47 isolate. Sequence alignment results identified a four-amino-acid deletion in nsp2 and a five-amino-acid deletion in the GP3 and GP4 overlap region of SD1291. A complete-genome-based phylogenetic tree showed that SD1291 is grouped with BJEU06-1-like PRRSV1 isolates. A piglets' challenge study showed that SD1291 can cause high fever (the highest is 41°C), reduced weight gain, mild lung consolidation, and interstitial pneumonia indicating that SD1291 is a pathogenic PRRSV1 isolate. Overall, this study first identified a novel pathogenic PRRSV1 isolate from an adult slaughter pig in China. Our findings also suggested that new PRRSV1 variants could escape the current PRRSV vaccination system and circulate in adult swine herds, which deserve more attention.},
}

Animals
*Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/isolation & purification
Swine
*Porcine Reproductive and Respiratory Syndrome/virology/epidemiology
China/epidemiology
Phylogeny
Metagenomics
Genome, Viral
Sequence Deletion

@article {pmid40303779,
year = {2023},
author = {Nelsen, A and Knudsen, D and Hause, BM},
title = {Identification of a Novel Astrovirus Associated with Bovine Respiratory Disease.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {8512021},
pmid = {40303779},
issn = {1865-1682},
mesh = {Animals ; Cattle ; *Cattle Diseases/virology ; *Astroviridae Infections/veterinary/virology ; Phylogeny ; *Astroviridae/isolation & purification/genetics/classification ; *Respiratory Tract Infections/veterinary/virology ; },
abstract = {Astroviruses (AstVs) cause gastrointestinal disease in mammals and avians. Emerging evidence suggests that some AstVs have extraintestinal tissue tropism, with AstVs detected in the liver, kidney, central nervous system, and the respiratory tract variably associated with disease. In cattle, AstV infection has been linked to gastroenteric or neurologic disease. Here, metagenomic sequencing of a lung from a bovine with respiratory disease identified a novel AstV with a predicted capsid-encoding ORF2 amino acid sequence with 66% identity to caprine astrovirus (CAstV G2.1). A quantitative reverse transcription PCR (qRT-PCR) targeting ORF2 found four out of 49 (8%) lungs and one out of 48 (2%) enteric samples obtained from bovine diagnostic submissions positive for the novel bovine astrovirus (BAstV). In two strongly qRT-PCR-positive lung samples, intense novel BAstV nucleic acid signals were mainly localized in the cytoplasm of alveolar macrophages and mononuclear cells using RNAscope® in situ hybridization (ISH). Genetic analysis of two novel BAstV genomes determined from qRT-PCR positive samples found high similarity for ORF1ab nucleotide sequence (92.1% and 93.9%) to BAstV strain BSRI-1, while ORF2 nucleotide sequence was most similar to CAstV G2.1 (74.6% and 77.6%). Phylogenetic analysis of the novel BAstV sequences found a close genetic relationship to the single BAstV (BSRI-1) previously identified from a bovine respiratory sample as well as bovine and caprine AstVs identified from various tissues. Further research is needed to determine the clinical significance of BAstV in respiratory diseases.},
}

Animals
Cattle
*Cattle Diseases/virology
*Astroviridae Infections/veterinary/virology
Phylogeny
*Astroviridae/isolation & purification/genetics/classification
*Respiratory Tract Infections/veterinary/virology

@article {pmid40300608,
year = {2025},
author = {Wirbel, J and Andermann, TM and Brooks, EF and Evans, L and Groth, A and Dvorak, M and Chakraborty, M and Palushaj, B and Reynolds, GZM and Porter, IE and Al Malki, M and Rezvani, A and Gooptu, M and Elmariah, H and Runaas, L and Fei, T and Martens, MJ and Bolaños-Meade, J and Hamadani, M and Holtan, S and Jenq, R and Peled, JU and Horowitz, MM and Poston, KL and Saber, W and Kean, LS and Perales, MA and Bhatt, AS},
title = {Accurate prediction of absolute prokaryotic abundance from DNA concentration.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101030},
doi = {10.1016/j.crmeth.2025.101030},
pmid = {40300608},
issn = {2667-2375},
abstract = {Quantification of the absolute microbial abundance in a human stool sample is crucial for a comprehensive understanding of the microbial ecosystem, but this information is lost upon metagenomic sequencing. While several methods exist to measure absolute microbial abundance, they are technically challenging and costly, presenting an opportunity for machine learning. Here, we observe a strong correlation between DNA concentration and the absolute number of 16S ribosomal RNA copies as measured by digital droplet PCR in clinical stool samples from individuals undergoing hematopoietic cell transplantation (BMT CTN 1801). Based on this correlation and additional measurements, we trained an accurate yet simple machine learning model for the prediction of absolute prokaryotic load, which showed exceptional prediction accuracy on an external cohort that includes people living with Parkinson's disease and healthy controls. We propose that, with further validation, this model has the potential to enable accurate absolute abundance estimation based on readily available sample measurements.},
}

@article {pmid40300605,
year = {2025},
author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH},
title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.03.073},
pmid = {40300605},
issn = {1879-0445},
abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.},
}

@article {pmid40300566,
year = {2025},
author = {Mahdi, ES and Komijani, M and Alaghmand, A},
title = {Metagenomics study suggests the role of vitamins and gut microbiome in autism spectrum disorder.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-20},
doi = {10.1159/000545483},
pmid = {40300566},
issn = {1421-9867},
abstract = {INTRODUCTION: Autism is a neurological disability that often appears after the age of three in children, also known as an Autism Spectrum Disorder (ASD). Several studies have examined the influence of some environmental factors, and many parameters related to the behavior of autistic patients have been measured in order to find ways to reduce ASD. This study investigates the relationship between ASD and serum levels of vitamin D3, B12, folic acid, and the gut microbiome.

METHODS: The serum levels of vitamin D3, B12, and folic acid in ASD patients were measured by the ELISA method and compared to healthy groups. DNA was extracted from stool samples of ASD patients and the control group, and then the gut microbiome was investigated via a metagenomics approach. Metagenomics sequencing was performed to analyze the 16S rRNA gene sequencing for phylum and sub phylum level microbiome.

RESULT: The result showed no significant change in the VitD3 and folate levels of ASD patients compared to the control group (p=0.157 and p=0.0505, respectively). There was a significant difference in the VitB12 level between control healthy individuals and ASD patients, in which the serum VitB12 concentration was significantly lower than the control group (p=0.0001). Our results regarding gut metagenomics showed that the abundance of the Actinobacteria by the phylum level were significantly higher in the ASD patients compared to the control group (p=0.0013). The abundance of the Firmicutes by the phylum level were significantly lower in the ASD patients compared to the control group (p=0.0016).The abundance of Bifidobacteriaceae, and Ruminococcaceae by the family level were significantly higher in the ASD patients compared to the control group (p=0.0004. and p=0.0489, respectively).Our results indicated less species richness in the ASD patients compared to the control group.

CONCLUSION: Patients with ASD have lower serum levels of vitamin B12 and different gut microbiome compared to healthy controls. Low vitamin B12 levels and altered gut microbiome are significantly associated with ASD in this study. However, further research is needed to determine whether these factors could serve as predictors of severe outcomes in ASD.},
}

@article {pmid40300499,
year = {2025},
author = {Hayes, A and Zhang, L and Feil, E and Kasprzyk-Hordern, B and Snape, J and Gaze, WH and Murray, AK},
title = {Antimicrobial effects, and selection for AMR by non-antibiotic drugs in a wastewater bacterial community.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109490},
doi = {10.1016/j.envint.2025.109490},
pmid = {40300499},
issn = {1873-6750},
abstract = {Antimicrobial resistance (AMR) is a major threat to human, animal, and crop health. AMR can be directly selected for by antibiotics, and indirectly co-selected for by biocides and metals, at environmentally relevant concentrations. Some evidence suggests that non-antibiotic drugs (NADs) can co-select for AMR, but previous work focused on exposing single model bacterial species to predominately high concentrations of NADs. There is a significant knowledge gap in understanding a range of NAD concentrations, (including lower µg/L concentrations found in the environment) on mixed bacterial communities containing a diverse mobile resistome. Here, we determined the antimicrobial effect and selective potential of diclofenac, metformin, and 17-β-estradiol, NADs that are commonly found environmental pollutants, in a complex bacterial community using a combination of culture based, metagenome, and metratranscriptome approaches. We found that diclofenac, metformin, and 17-β-estradiol at 50 µg/L, 26 µg/L, and 24 µg/L respectively, significantly reduced growth of a bacterial community although only 17-β-estradiol selected for an AMR marker using qPCR (from 7 µg/L to 5400 µg/L). Whole metagenome sequencing indicated that there was no clear selection by NADs for antibiotic resistance genes, or effects on community composition. Additionally, increases in relative abundance of some specific metal resistance genes (such as arsB) were observed after exposure to diclofenac, metformin, and 17-β-estradiol. These results indicate that environmentally relevant concentrations of NADs are likely to affect community growth, function, and potentially selection for specific metal resistance genes.},
}

@article {pmid40300492,
year = {2025},
author = {Huang, Y and Zong, S and Xu, D and He, J and Zhang, Y and Qian, M and Li, Y and Guo, B and Han, J and Qu, D},
title = {Metagenomic analysis reveals differences in antibiotic resistance and transmission risks across various poultry farming models.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179519},
doi = {10.1016/j.scitotenv.2025.179519},
pmid = {40300492},
issn = {1879-1026},
abstract = {As living standards in rural areas continue to improve, farmers are increasingly seeking to diversify their farming models beyond monoculture farming. However, the differences in bacterial resistance and the associated transmission risks between monoculture poultry farming and integrated poultry farming remain poorly understood. This study utilizes metagenomic methods to examine the distribution and transmission of antibiotic resistance across three types of farms in Zhejiang Province, as well as to investigate the horizontal transmission mechanisms of plasmid-mediated blaNDM within these agricultural systems. An analysis of 26 environmental samples and 12 saliva samples from six poultry farms with different models has revealed that integrated poultry farms exhibit a more complex microbial composition and more severe resistance compared to monoculture farms. Furthermore, a blaNDM positive plasmid pndm-CD with complex conjugation transfer region was found in the integrated farms. The insertion sequence (IS) ISCR1 present in the upstream of blaNDM has the potential to promote its spread, while the downstream complex structure IS26-blaCTX-M-IS2-qnrB-TinR-ΔISKrA14 enhances the resistance of the host to β-lactam antibiotics, and improves the competition potential of the host bacteria in the anti-antibiotic environment. This research offers the first metagenomic analysis of the differences in bacterial resistance and transmission risks between various poultry farming models. These results offer a solid theoretical basis for managing the spread of antibiotic resistance in mixed chicken and duck farming operations. Additionally, they are significant for ensuring the health of agricultural workers and the hygiene safety of the poultry meat supply chain.},
}

@article {pmid40300291,
year = {2025},
author = {Mei, J and Sheng, F and Zhang, C and Chen, X},
title = {Imaging monitoring of Balamuthia granulomatous amoebic encephalitis.},
journal = {Clinical neurology and neurosurgery},
volume = {254},
number = {},
pages = {108917},
doi = {10.1016/j.clineuro.2025.108917},
pmid = {40300291},
issn = {1872-6968},
abstract = {Balamuthia granulomatous amoebic encephalitis (GAE) is a rare and highly lethal infectious disease affecting the central nervous system, caused by the Balamuthia amoeba. This article reports the case of a child with normal immune function and no apparent epidemiological risk factors. In the initial stages, routine blood tests, cerebrospinal fluid cell tests, biochemical tests, and metagenomic next-generation sequencing (mNGS) were all normal. Surgical removal of the abscess and subsequent pathological diagnosis revealed a chronic granuloma. mNGS analysis of the brain abscess fluid identified Balamuthia mandrillaris (BM), leading to the diagnosis of Balamuthia GAE, after which antiparasitic treatment was initiated. This case underscores the importance of sustained imaging surveillance in suspected cases of Balamuthia GAE.},
}

@article {pmid40299688,
year = {2025},
author = {Chen, Y and Nian, F and Chen, J and Jiang, Q and Yuan, T and Feng, H and Shen, X and Dong, L},
title = {Metagenomic Microbial Signatures for Noninvasive Detection of Pancreatic Cancer.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13041000},
pmid = {40299688},
issn = {2227-9059},
support = {82173122, 81972234, 82273027//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with poor early detection rates owing to the limited sensitivity and specificity of the current biomarker CA19-9. Gut microbiota dysbiosis plays a key role in PDAC pathogenesis. This study aimed to evaluate the noninvasive approach we developed, combining metagenome-derived microbial signatures with CA19-9, to improve PDAC detection. Methods: This study included 50 treatment-naïve patients with PDAC and their matched controls. Fecal samples were analyzed using shotgun metagenomic sequencing. Machine learning algorithms were used to develop and validate a diagnostic panel integrating microbial signatures and CA19-9 levels. Subgroup analyses were used to confirm the robustness of the microbial markers. Results: The combined models at both species and genus levels effectively distinguished patients with PDAC from healthy individuals, and their strong diagnostic efficacy and accuracy were demonstrated through rigorous validation. Conclusions: In conclusion, the combination of gut microbiome profiling and CA19-9 improves PDAC detection accuracy compared to the use of CA19-9 alone, showing promise for early and noninvasive diagnosis.},
}

@article {pmid40299456,
year = {2025},
author = {Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Kozhakhmetova, S and Morenko, M and Duisebayeva, A and Poddighe, D and Kushugulova, A and Kozhakhmetov, S},
title = {Alterations in Gut Microbiota of Infants Born to Mothers with Obesity.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13040838},
pmid = {40299456},
issn = {2227-9059},
support = {Grant No. AP19575153 "Metagenomic predictors of childhood obesity, cross-talk with maternal mi-croflora", Grant No. AP23489538 and Grant No. BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; Grant No. 20122022CRP1602//Nazarbayev University under Collaborative Research Program/ ; },
abstract = {Background: The impact of maternal obesity on offspring health remains a major and pressing issue. We investigated its impact on the development of the infant gut microbiome during the first six months of life, examining the taxonomic composition, metabolic pathways, and antibiotic resistance genes. Methods: Twenty-four mother-infant pairs were divided into maternally obese (OB, BMI > 36) and normal weight (BM) groups. Shotgun metagenomic sequencing was performed on stool samples collected at birth and at 1, 3, and 6 months. A total of 12 maternal samples and 23 infant samples (n = 35) in the obese group and 12 maternal samples and 30 infant samples (n = 42) in the control group were sequenced. The analysis included taxonomic profiling (MetaPhlAn 4), metabolic pathway analysis (HUMAnN 3), and antibiotic resistance gene screening (CARD/ABRicate). Results: The OB group showed reduced alpha diversity in the first month (p ≤ 0.01) and an increased Firmicutes/Bacteroidetes ratio, peaking at 3 months (p ≤ 0.001). The metabolic profiling revealed enhanced carbohydrate breakdown (p ≤ 0.001) in the BM group and lipid biosynthesis (p ≤ 0.0001) in the OB group pathways. Strong correlations emerged between Lactobacillales and fatty acid biosynthesis (r = 0.7, p ≤ 0.0001) and between Firmicutes and lincosamide (r = 0.8, p ≤ 0.0001). Conclusions: The infants of obese mothers had significantly altered development of the infant gut microbiome, affecting both composition and metabolic potential. These changes may have long-term health consequences and suggest potential therapeutic targets for intervention.},
}

@article {pmid40299453,
year = {2025},
author = {Qin, L and Chen, Y and Luan, S and Yin, X and Pan, J and Wang, L and Yao, Y and Zhou, C and Bao, R and Shen, J and Miao, Q and Hu, B},
title = {Lung Microenvironment Among Patients with Nontuberculous Mycobacterial Pulmonary Disease by Metagenomic Sequencing Technique.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13040818},
pmid = {40299453},
issn = {2227-9059},
support = {NSFC82072325//National Natural Science Foundation of China/ ; },
abstract = {Background: Nontuberculous mycobacterial pulmonary disease (NTM-PD) is an increasingly prevalent chronic infection, where the host immune status plays a crucial role in disease susceptibility and progression. The complex pulmonary microenvironment, characterized by diverse microbial communities and host immune interactions, exhibits distinct features that may be fundamentally altered by the patient's underlying immune state. Methods: A total of 111 sputum specimens and 64 bronchoalveolar lavage fluid (BALF) specimens were collected from 143 patients diagnosed with NTM-PD under different immune states. Metagenomic sequencing was performed on these specimens to characterize and compare the pulmonary microenvironmental features among NTM-PD patients with a distinct immune status through comprehensive bioinformatic analyses. Results: The immunosuppressed group exhibited a lower α-diversity in sputum specimens (p < 0.05). Principal Coordinates Analysis (PCoA) of β-diversity for sputum and BALF specimens revealed significant differences between the groups (p < 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis identified species enriched in the immunosuppressed group. A co-occurrence network analysis indicated that the immunosuppressed group had more structured and actively connected networks compared to the control group. The Mantel test confirmed that the abundance of these species enriched was associated with clinical immune-inflammation-related indicators in patients. Conclusions: Our study reveals the pulmonary microenvironment in immunosuppressed patients with NTM-PD. Further work is required to explore the two-way relationship between micro-organisms and immune and inflammatory responses, with the influence on patient outcomes.},
}

@article {pmid40298885,
year = {2025},
author = {Liu, Y and Wu, R and Wu, J and Li, J and Zhang, Q and Wang, S and Sheng, G},
title = {Improving the shock resistance of anaerobic digestion under demand-oriented biogas production mode by using converter steel slag powder.},
journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {},
number = {},
pages = {734242X251333692},
doi = {10.1177/0734242X251333692},
pmid = {40298885},
issn = {1096-3669},
abstract = {Introducing flexible biogas production (FB) can result in instantaneous high-shock loads for anaerobic digestion system, posing risks to the system's stable operation. Steel slag, a typical metallurgical solid waste, has been demonstrated to enhance the buffering capacity of digestion systems, thereby increasing methane production and achieving 'waste treatment using waste'. However, its efficacy under high-shock loads in FB is uncertain. Pulse feeding experiments simulating FB were conducted to analyse the system's impact resistance with steel slag addition and investigate its enhancement mechanisms. The addition of steel slag improved the methane production rate under various shock conditions, with a particularly notable enhancement under concentration shock. This scenario also saw a significant increase in the generation of soluble chemical oxygen demand and its utilization by microorganisms. This can be attributed to the enrichment of hydrolytic bacterial phyla (Firmicutes) and genera (Gelria), with functional gene analysis revealing an increase in genes associated with Fe(III) reduction and CO2-to-methane pathways. The study results indicate that the role of steel slag as an alkaline, iron-rich material enhances system alkalinity, reduces inhibition from H2 partial pressure and boosts hydrogenotrophic methanogen activity, making it suitable as an exogenous enhancer for demand-oriented anaerobic digestion.},
}

@article {pmid40298543,
year = {2025},
author = {Bisaccia, M and Berini, F and Marinelli, F and Binda, E},
title = {Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/antibiotics14040394},
pmid = {40298543},
issn = {2079-6382},
support = {PNRA16_00105//Italian Ministry of Education, University and Research/ ; CMPT228810//Consorzio Interuniversitario per le Biotecnologie & Italian Ministry of Education, University and Research/ ; IBFM NBFC CN00000033//National Biodiversity Future Center/ ; PNRA22_0000040//Italian Ministry of Education, University and Research/ ; },
abstract = {The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.},
}

@article {pmid40298441,
year = {2025},
author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N},
title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mbio.00705-25},
pmid = {40298441},
issn = {2150-7511},
abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.},
}

@article {pmid40298422,
year = {2025},
author = {Koester, F and Myers, KS and Donohue, TJ and Noguera, DR},
title = {Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017925},
doi = {10.1128/mra.00179-25},
pmid = {40298422},
issn = {2576-098X},
abstract = {To advance the knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from four anaerobic bioreactors fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. This analysis produced 42 unique metagenome-assembled genomes (MAGs) that represent distinct taxa.},
}

@article {pmid40298412,
year = {2025},
author = {Majernik, SN and Beaver, L and Bradley, PH},
title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085724},
doi = {10.1128/msphere.00857-24},
pmid = {40298412},
issn = {2379-5042},
abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.},
}

@article {pmid40298386,
year = {2025},
author = {Chen, Z and Zhang, Z and Nie, BN and Huang, W and Zhu, Y and Zhang, L and Xu, M and Wang, M and Yuan, C and Liu, N and Wang, X and Tian, J and Ba, Q and Wang, Z},
title = {Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118824},
doi = {10.1128/msystems.01188-24},
pmid = {40298386},
issn = {2379-5077},
abstract = {UNLABELLED: The human gut microbiome's role in colorectal cancer (CRC) pathogenesis has gained increasing recognition. This study aimed to delineate the microbiome characteristics that distinguish CRC patients from healthy individuals, while also evaluating the influence of aging, through a comprehensive metagenomic approach. The study analyzed a cohort of 80 CRC patients and 80 matched healthy controls, dividing participants into a normal and a CRC group, further categorized by age into young, middle-aged, and old-aged subgroups. Extensive metagenomic sequencing of fecal samples allowed for the exploration of both the structural and functional profiles of the microbiome, with findings validated in an independent cohort to ensure robustness. Our results highlight notable differences in microbiome composition between CRC patients and healthy individuals, which exhibit age-dependent variations. Specifically, a higher prevalence of pathogenic bacteria, such as Bacteroides vulgatus, known to drive inflammation and carcinogenesis, was observed in CRC patients, alongside a reduction in beneficial microbes, including Lactobacillus. Functionally, the CRC-associated microbiome showed an increase in pathways related to DNA repair, cell cycle regulation, and metabolic activities, such as the Citrate cycle and Galactose metabolism, underscoring distinct microbial alterations in CRC patients that could influence disease onset and progression. These insights lay a foundation for future research into microbiome-based diagnostics and treatments for CRC.

IMPORTANCE: This study underscores the critical role of the gut microbiome in colorectal cancer (CRC) pathogenesis, particularly in the context of aging. By identifying age-specific microbial biomarkers and functional pathways associated with CRC, our findings provide novel insights into how microbiome composition and metabolic activities influence disease progression. These discoveries pave the way for developing personalized microbiome-based diagnostic tools and therapeutic strategies, potentially improving CRC prevention and treatment outcomes across different age groups. Understanding these microbial dynamics could also inform interventions targeting gut microbiota to mitigate CRC risk and progression.},
}

@article {pmid40298367,
year = {2025},
author = {Zhou, Z and Ma, Y and Zhang, D and Ji, R and Wang, Y and Zhao, J and Ma, C and Zhu, H and Shen, H and Jiang, X and Niu, Y and Lu, J and Zhang, B and Tu, L and Zhang, H and Ma, X and Chen, P},
title = {Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0027625},
doi = {10.1128/msystems.00276-25},
pmid = {40298367},
issn = {2379-5077},
abstract = {Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.},
}

@article {pmid40298267,
year = {2025},
author = {Cheung, S and Zhou, NA and Ruhanya, V and J Jesser, K and Nezomba, I and Musvibe, J and Manyisa, B and Nyandoro, G and Chibukira, P and Mukaratirwa, A and Muserere, ST and Masunda, K and Ong, A and Meschke, JS},
title = {Characterization of enteric pathogens in Harare, Zimbabwe using environmental surveillance and metagenomics.},
journal = {Journal of water and health},
volume = {23},
number = {4},
pages = {477-492},
pmid = {40298267},
issn = {1477-8920},
mesh = {Zimbabwe ; *Metagenomics ; *Environmental Monitoring/methods ; *Wastewater/microbiology ; Humans ; *Bacteria/isolation & purification/genetics/classification ; Drug Resistance, Bacterial ; Sewage/microbiology ; },
abstract = {High diarrheal disease burden remains an urgent concern in low- and middle-income countries, greatly affecting children under the age of 5 years and those living with HIV and AIDS. Treatment of infectious diseases has also become increasingly difficult with the rapid rise of antimicrobial resistance (AMR). Environmental surveillance of wastewater can supplement gaps in clinical surveillance as residents on a sewage system contribute to the wastewater, providing simple, composite samples that can improve understanding about both pathogens and AMR in the community. This study evaluated the effectiveness of environmental surveillance with shotgun metagenomics as a tool to characterize a broad range of enteric pathogens, antibiotic resistance genes, and virulence factor genes (VFGs) in wastewater from six neighborhoods in Harare, Zimbabwe. Alpha and beta diversity of the microbial community were similar between high-income and low-income suburbs. Enteric pathogens of high AMR and clinical concern, including Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica, were detected in all samples. The top VFGs were encoded for delivery, adherence, and motility, functions important in toxin secretion, colonization, and immune modulation. The findings provide a foundation for future studies to explore environmental surveillance and shotgun metagenomics as a public health monitoring tool for enteric diseases.},
}

Zimbabwe
*Metagenomics
*Environmental Monitoring/methods
*Wastewater/microbiology
Humans
*Bacteria/isolation & purification/genetics/classification
Drug Resistance, Bacterial
Sewage/microbiology

@article {pmid40297733,
year = {2025},
author = {Nguyen, DS and Tran, DM},
title = {Endophytic bacteriome data of Litchi chinensis established by metagenomic 16S rRNA gene sequencing.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111544},
pmid = {40297733},
issn = {2352-3409},
abstract = {This work reported the diversity profiling and predicted metabolic function of the endophytic bacteriome of lychee (Litchi chinensis S.) cultivated in Dak Lak Province of Vietnam for the first time. Roots of lychee were collected from three different fields in Krong Ana District in Dak Lak. 16S rRNA primers were used to sequence the metagenomic library. Kraken 2 was used to analyze the taxonomic distribution, while the MetaCyc database was used to predict the metabolic function. We identified 10 phyla, 14 classes, 27 orders, 30 families, and 27 genera of the endophytic bacteria from the sample. Actinomycetota was the most predominant phylum (84.49%), and biosynthesis was the bacteriome's primary function (75.42%). Data provided insight into the taxonomic distribution and metabolic function of lychee endophytic bacteria and might be helpful for the next steps concerning sustainable lychee cultivation using endophytic bacteria.},
}

@article {pmid40297591,
year = {2025},
author = {Pei, X and Liu, L and Han, Y},
title = {Advances in human microbiome and prostate cancer research.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576679},
pmid = {40297591},
issn = {1664-3224},
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology
Male
*Microbiota
*Gastrointestinal Microbiome
Tumor Microenvironment/immunology
Animals

@article {pmid40297587,
year = {2025},
author = {Dora, D and Revisnyei, P and Pasic, A and Galffy, G and Dulka, E and Mihucz, A and Roskó, B and Szincsak, S and Iliuk, A and Weiss, GJ and Lohinai, Z},
title = {Host and bacterial urine proteomics might predict treatment outcomes for immunotherapy in advanced non-small cell lung cancer patients.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1543817},
pmid = {40297587},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology ; Male ; Female ; *Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology ; Middle Aged ; *Proteomics/methods ; Aged ; Immunotherapy/methods ; Treatment Outcome ; *Proteome ; Biomarkers, Tumor/urine ; Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {INTRODUCTION: Urine samples are non-invasive approaches to study potential circulating biomarkers from the host organism. Specific proteins cross the bloodstream through the intestinal barrier and may also derive from gut microbiota. In this study, we aimed to evaluate the predictive role of the host and bacterial urine extracellular vesicle (EV) proteomes in patients with non-small cell lung cancer (NSCLC) treated with anti-PD1 immunotherapy.

METHODS: We analyzed the urine EV proteome of 33 advanced-stage NSCLC patients treated with anti-PD1 immunotherapy with LC-MS/MS, stratifying patients according to long (>6 months) and short (≤6 months) progression-free survival (PFS). Gut microbial communities on a subcohort of 23 patients were also analyzed with shotgun metagenomics. Internal validation was performed using the Random Forest (RF) machine learning (ML) algorithm. RF was validated with a non-linear Bayesian ML model. Gene enrichment, and pathway analysis of host urine proteins were analyzed using the Reactome and Gene Ontology databases.

RESULTS: We identified human (n=3513), bacterial (n=2647), fungal (n=19), and viral (n=4) proteins. 186 human proteins showed differential abundance (p<0.05) according to PFS groups, 101 being significantly more abundant in patients with short PFS and n=85 in patients with long PFS. We found several pathways that were significantly enriched in patients with short PFS (vs long PFS). Multivariate Cox regression showed that human urine proteins MPP5, IGKV6-21, NT5E, and KRT27 were strongly associated with long PFS, and LMAN2, NUTF2, NID1, TNC, IGF1, BCR, GPHN, and PPBP showed the strongest association with short PFS. We revealed that an increased bacterial/host protein ratio in the urine is more frequent in patients with long PFS. Increased abundance of E. coli and E. faecalis proteins in the urine positively correlates with their gut metagenomic abundance. RF ML model supported the reliability in predicting PFS for critical human urine proteins (AUC=0.89), accuracy (95%) and Bacterial proteins (AUC=0.74).

CONCLUSION: To our knowledge, this is the first study to depict the predictive role of the host and bacterial urine proteome in anti-PD1-treated advanced NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology
Male
Female
*Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology
Middle Aged
*Proteomics/methods
Aged
Immunotherapy/methods
Treatment Outcome
*Proteome
Biomarkers, Tumor/urine
Gastrointestinal Microbiome
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid40297511,
year = {2025},
author = {Valle, C and Parry, RH and Coutard, B and Colmant, AMG},
title = {Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf023},
pmid = {40297511},
issn = {2057-1577},
abstract = {Jingmenviruses are a distinct group of flavi-like viruses characterized by a genome consisting of four to five segments. Here, we report the discovery of three novel putative jingmenviruses, identified by mining publicly available metagenomics data from mosquito and arachnid samples. Strikingly, these novel jingmenvirus sequences contain up to six genomic segments, with pairs of homologous segments coding for putative structural proteins. Following this discovery, we found an additional homologous segment for two other jingmenvirus genomes, which had gone unnoticed in the initial publications. The presence of a single version of the segments coding for non-structural proteins suggests that we have indeed identified jingmenviruses with infectious units that contain up to six segments. We compared these novel jingmenvirus sequences to published sequences, in particular the segments with multiple open reading frames (ORFs), and we propose that the putative translation initiation mechanisms involved for these segments are ribosomal frameshift resulting in the fusion of ORFs and leaky scanning for overlapping ORFs. These putative mechanisms, conserved for all jingmenvirus sequences analysed, including in homologous segments, require biological confirmation. We also generated structural models of two putative structural proteins in the duplicated segments, and the corresponding alignments enabled us to confirm or identify the homologous relationship between sequences that shared limited nucleotide or amino acid identity. Altogether, these results highlight the fluid nature of jingmenviruses, which is a hallmark of multipartite viruses. Different combinations of segments packaged in different virus particles could facilitate the acquisition or loss of genomic segments and a segment duplication following genomic drift. Our data therefore contribute to the evidence of the multipartite nature of jingmenviruses and the evolutionary role this organization may play.},
}

@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}

*Plant Leaves/metabolism/microbiology
*Bacteria/genetics/metabolism
*Fungi/genetics/metabolism
*Rivers/microbiology
Ecosystem
Alnus
Transcriptome
RNA, Ribosomal, 16S/genetics

@article {pmid40297464,
year = {2025},
author = {Zhang, Y and Ding, G and Gao, Y and Li, Y and Zhou, P and Wu, L and Zhou, M and Wang, J and Tang, J},
title = {Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19384},
pmid = {40297464},
issn = {2167-8359},
mesh = {*Lakes/microbiology/chemistry ; China ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Chaohu Lake (CL) is one of the most polluted areas in China due to its high content of antibiotics. However, the distribution and influencing factors of antibiotic resistance genes (ARGs) in this lake are still controversial.

METHODS: To solve this problem, we used metagenomic sequencing to investigate the distribution and in-fluencing factors of ARGs in CL.

RESULTS: Our findings revealed the existence of nine kinds of ARGs, including 45 specific genes. The most abundant types were multidrug, bacitracin, polymyxin, macrolide lincosamide streptogramin, and aminoglycoside. Multiple microorganisms were undeniable ARG reservoirs, although they were not dominant species in the microbiota. Our results also showed that both the microbiota and physiochemical factors played important roles in shaping the distributions of ARGs in CL. Specifically, the levels of PO4-P (0.5927) and total phosphorus (0.4971) had a greater impact than total nitrogen (0.0515), NO3-N (0.0352), NO2-N (-0.1975), and NH3-N (-0.0952).

CONCLUSIONS: These findings provide valuable insights into the distribution and influencing factors of ARGs in lakes.},
}

*Lakes/microbiology/chemistry
China
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Genes, Bacterial
Microbiota/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40296452,
year = {2025},
author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA},
title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202500002},
doi = {10.1002/pmic.202500002},
pmid = {40296452},
issn = {1615-9861},
support = {C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; },
abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.},
}

@article {pmid40296156,
year = {2025},
author = {Fan, Y and Wang, D and Yang, JX and Ning, D and He, Z and Zhang, P and Rocha, AM and Xiao, N and Michael, JP and Walker, KF and Joyner, DC and Pan, C and Adams, MWW and Fields, MW and Alm, EJ and Stahl, DA and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J},
title = {Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {106},
pmid = {40296156},
issn = {2049-2618},
support = {DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; },
mesh = {*Groundwater/microbiology/chemistry ; Phylogeny ; *Microbiota/genetics ; Tennessee ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Nitrates/analysis ; Water Pollutants, Chemical/analysis ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; },
abstract = {BACKGROUND: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).

RESULTS: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.

CONCLUSIONS: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.},
}

*Groundwater/microbiology/chemistry
Phylogeny
*Microbiota/genetics
Tennessee
*Bacteria/classification/genetics/isolation & purification/metabolism
Nitrates/analysis
Water Pollutants, Chemical/analysis
Biodiversity
RNA, Ribosomal, 16S/genetics
Metals, Heavy/analysis

@article {pmid40295870,
year = {2024},
author = {Bell, MG and Parry, RH and Lee, TSE and Habarugira, G and McMahon, IE and Thompson, MA and Modhiran, N and Watterson, D and Batovska, J and Lynch, SE and Hall, RA and Harrison, JJ and Hobson-Peters, J},
title = {Synthetic recovery of Yada Yada virus expands insect-specific alphavirus knowledge and facilitates production of chimeric viruses.},
journal = {Npj viruses},
volume = {2},
number = {1},
pages = {45},
pmid = {40295870},
issn = {2948-1767},
support = {AQIRF067-2020-CV//Advance Queensland/ ; },
abstract = {Few insect-specific alphaviruses (ISA) have been discovered, with even fewer culturable to facilitate full characterisation. Here, we report the recovery of an infectious clone of Yada Yada virus (YYV)-a virus previously only detected by metagenomic sequencing of mosquito homogenates. Using the infectious clone, we confirmed the inability of YYV to replicate in vertebrate cells in vitro, with replication limited to only Aedes mosquito-derived cell lines. We further produced and characterised the first monoclonal antibodies (mAbs) to ISAs. Through successful replacement of the structural proteins of YYV with those of other ISAs, Eilat virus, Agua Salud (ASALV), Taï Forest (TALV) and Mwinilunga alphaviruses (MWAV), we established that a replication block for in vitro culture of TALV and MWAV in mosquito cells does not exist at virus entry. Unexpectedly, ASALV structural proteins were recognised by cross-reactive mAbs made to chikungunya (CHIKV) and Ross River viruses (RRV), suggesting a potential antigenic link between ASALV and pathogenic alphaviruses. The YYV genetic backbone was also investigated to generate chimeras displaying the structural proteins of various pathogenic vertebrate-infecting alphaviruses including CHIKV, RRV, Barmah Forest, Sindbis and Mayaro viruses. These chimeras retained the antigenic properties of the parental viruses and did not replicate in vertebrate cells, demonstrating the potential of the YYV platform for vaccine and diagnostic antigen production.},
}