@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}

*Machine Learning
*Microbiota
Humans
Spectrometry, Fluorescence/methods
*Bacteria/isolation & purification/genetics

@article {pmid40323169,
year = {2025},
author = {Zhu, D and Galley, J and Pizzini, J and Musteata, E and Douglas, MV and Chazin, WJ and Skaar, EP and Tabor, JJ and Britton, RA},
title = {Microbial Biosensor for Sensing and Treatment of Intestinal Inflammation.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2504364},
doi = {10.1002/advs.202504364},
pmid = {40323169},
issn = {2198-3844},
support = {//Baylor College of Medicine Seed Funding/ ; //Crohn's and Colitis Foundation Litwin Pioneer Award (RAB)/ ; R01AI123278//National Institutes of Health grants/ ; U19AI157981//National Institutes of Health grants/ ; R01AI155586//National Institutes of Health grants/ ; R01AI164587//National Institutes of Health grants/ ; U19AI174999//National Institutes of Health grants/ ; },
abstract = {Synthetic biology has enabled the development of biosensors to detect intestinal inflammation, yet few target the clinically validated biomarker of intestinal inflammation calprotectin with both diagnostic and therapeutic capabilities. Here, an optimized calprotectin biosensor is presented that leverages a zinc uptake regulator (Zur) controlled promoter coupled with a memory circuit to detect and record intestinal inflammation in vivo. The level of biosensor activation strongly correlates with calprotectin levels in the colon of two independent mouse models of colitis. Coupling of the biosensor with the production of the anti-inflammatory cytokine IL10 allowed for the resolution of chemically induced colitis, demonstrating the ability of the biosensor to sense and respond to disease. This work highlights the utility of developing synthetic organisms for the diagnosis and treatment of intestinal disease using clinically validated biomarkers.},
}

@article {pmid40322835,
year = {2025},
author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C},
title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {5},
pages = {e70082},
doi = {10.1111/aji.70082},
pmid = {40322835},
issn = {1600-0897},
support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; },
abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.

METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.

RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-κB, MMP3, IκBα, IL-1β, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.

CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.},
}

Animals
Female
*Moxibustion/methods
*Gastrointestinal Microbiome/immunology
Rats
*Th17 Cells/immunology
*Interleukin-17/metabolism
*Primary Ovarian Insufficiency/therapy/immunology/chemically induced
Rats, Sprague-Dawley
*Ovary/physiology
Signal Transduction
Disease Models, Animal

@article {pmid40322711,
year = {2025},
author = {Kulsum, U and Patankar, C and Biswas, D},
title = {MOSMAP: Mosquito metagenome analysis pipeline.},
journal = {Bioinformation},
volume = {21},
number = {2},
pages = {110-112},
pmid = {40322711},
issn = {0973-2063},
abstract = {MosMAP is a bioinformatics pipeline designed for mosquito metagenome analysis. MosMAP automates essential processes like quality control, taxonomic classification, species abundance estimation and visualization by integrating tools such as Trimgalore, Kraken 2, Bracken and Krona into a user-friendly workflow. Each of these tools is integrated to ensure a smooth and efficient workflow from raw data to interpretable results. The pipeline simplifies complex bioinformatics tasks, making them accessible to researchers with limited computational expertise. MosMAP demonstrated high concordance with standard bioinformatics workflows such as Kraken and Bracken in terms of read retention, taxonomic accuracy and abundance estimation when applied to metagenomes of mosquito collected in Bhopal, India. This accessible pipeline promotes the simplification of meta-genomics, supporting research in microbiology, ecology and vector-borne diseases.},
}

@article {pmid40322468,
year = {2025},
author = {Shan, H and Wang, J and Zhang, Q and Ming, Z and Zhang, Y and He, P and Fang, P and Zhang, M and Li, W and Shi, H and Guan, Y and Yang, S},
title = {Pathogen surveillance and risk factors for pulmonary infection in patients with lung cancer: A retrospective single-center study.},
journal = {Open medicine (Warsaw, Poland)},
volume = {20},
number = {1},
pages = {20251180},
pmid = {40322468},
issn = {2391-5463},
abstract = {BACKGROUND: Early and accurate diagnosis of pulmonary infection (PI) is crucial for the timely implementation of appropriate treatment strategies in lung cancer patients.

METHODS: Metagenomic next-generation sequencing and conventional testing were performed in lung cancer patients with and without PI. The pathogen profiles were analyzed, and risk factors for PI were explored using univariate and multivariate logistic regression models.

RESULTS: A total of 55 lung cancer patients with PI and 59 non-infected lung cancer patients were included. There were 41 underlying pathogens identified by both methods in lung cancer patients with PI. The coexistence of different pathogen types was common, particularly between fungi and viruses, which was observed in 28.57% of cases. The incidence of Streptococcus pneumoniae and Pneumocystis jirovecii is significantly higher in small-cell lung carcinoma patients compared to that in non-small-cell lung carcinoma patients. Besides, cytomegalovirus, P. jirovecii, and Aspergillus were more likely to be found in advanced-stage patients. Risk factor analysis revealed that Karnofsky Performance Status <90 and chemotherapy were strongly associated with PI in lung cancer patients.

CONCLUSIONS: This study highlights the complexity of PI in lung cancer patients, emphasizing the need for tailored diagnostic and therapeutic strategies based on cancer type and stage.},
}

@article {pmid40321823,
year = {2025},
author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A},
title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19305},
pmid = {40321823},
issn = {2167-8359},
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Islands ; *Fungi/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Ecosystem ; *Microbiota ; },
abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.},
}

Brazil
*Soil Microbiology
*Biodiversity
*Bacteria/genetics/classification/isolation & purification
Islands
*Fungi/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Ecosystem
*Microbiota

@article {pmid40321713,
year = {2025},
author = {De Coninck, L and Hadermann, A and Ingletto, L and Colebunders, R and Gamnsi Njamnshi, K and Njamnshi, AK and Mokili, JL and Siewe Fodjo, JN and Matthijnssens, J},
title = {Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf024},
pmid = {40321713},
issn = {2057-1577},
abstract = {Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy-hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies have failed to detect Onchocerca volvulus in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A viral particle-based shotgun sequencing approach was used to detect viral sequences in 55 pools of 10 blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the haematophagous blackfly, which also could be present in their nematode host O. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.},
}

@article {pmid40321599,
year = {2025},
author = {Zhou, Z and Song, Y and Yan, Y and Zheng, Y},
title = {Metagenomic Next-Generation Sequencing Improves the Diagnosis Efficiency of Mixed Periprosthetic Joint Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2165-2174},
pmid = {40321599},
issn = {1178-6973},
abstract = {PURPOSE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) in the diagnosis of mixed periprosthetic joint infections (PJI).

METHODS: The data pertaining to patients suspected of PJI who underwent arthroplasty at our hospital between January 2020 and June 2024 were analyzed. Patients included in the study were subjected to microbial culture and mNGS analyses to evaluate the efficacy of mNGS in diagnosing mixed PJIs.

RESULTS: Among the 44 PJI patients included, 20 (45.45%) were culture-positive, and 35 (79.55%) were mNGS-positive. Compared to microbial culture, mNGS demonstrated significantly higher sensitivity, negative predictive value, and accuracy (79.55% vs 45.45%, 55.00% vs 35.14%, and 80.70% vs 57.89%, respectively; all P<0.05). However, the specificity of mNGS was significantly lower than culture (84.62% vs 100.00%, P<0.05). For mixed PJIs, the sensitivity of mNGS was notably higher, albeit with lower specificity and positive predictive value compared to microbial culture (72.23% vs 27.27%, 85.19% vs 100.00%, 66.67% vs 100.00%, respectively; all P<0.05). mNGS enables more sensitive detection of co-pathogens in mixed PJI, accelerating targeted therapy and reducing inappropriate broad-spectrum therapy. While its lower specificity requires clinical integration, it clarifies complex diagnoses and streamlines stewardship for improved outcomes.

CONCLUSION: mNGS is a promising technique for rapidly and accurately detecting co-pathogens in mixed PJI.},
}

@article {pmid40321269,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Cools Portier, S and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A},
title = {Profiling the human luminal small intestinal microbiome using a novel ingestible medical device.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.18.25326056},
pmid = {40321269},
abstract = {The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MD's effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness, and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct SI metabolic footprint, with bile acids and amino acids being the most abundant classes of metabolites. Host and host/microbe-derived bile acids were particularly abundant in SI samples. The application of a fast culturomics approach to two SI samples enabled species-level characterization, resulting in the identification of 90 bacterial species, including five potential novel species. The present study demonstrates the efficacy of our novel sampling MD in enabling comprehensive SI microbiome analysis through an integrative multi-omics approach, allowing the identification of distinct microbiome signatures between SI and fecal samples.},
}

@article {pmid40320901,
year = {2025},
author = {Gervasoni, KN and Iacia, MVMS and Silva, KO and Franco, LG and Mendes, MEF and Neves, TJDC and Sanches, WS and Oliveira, LB and Saito, EA and Vieira, KCO and Pereira, VC and Nai, GA and Winkelstroter, LK},
title = {Protective Effect of Piperine on Indomethacin-Induced Intestinal Damage.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70097},
doi = {10.1002/mnfr.70097},
pmid = {40320901},
issn = {1613-4133},
abstract = {Nonsteroidal antiinflammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammation and chronic pain. Chronic use of NSAIDs is associated with adverse events and organ damage, especially to the gastric mucosa and small intestine. This study evaluates the protective effect of piperine on indomethacin-induced intestinal damage. Eighteen male Mus musculus mice, aged 6-8 weeks, were used. Intestinal damage was induced with indomethacin (10 mg/mL) and cotreatment with piperine (20 mg/mL), both administered orally. After 14 days, the animals were euthanized. Biochemical serological analysis was performed. Intestinal inflammation was assessed based on macroscopic, histopathological, and metagenomic analyses. Histopathological analysis showed a reduction in small intestine inflammation (p < 0.05) and the disappearance of necrosis in the intestinal wall of the large intestine. Crypt and villus measurements showed increased values in the piperine-treated group (p < 0.05). An approximately six-fold increase in aspartate aminotransferase (AST) was observed in the Indomethacin group (p < 0.05). Regarding the intestinal microbiota, an increase in genus diversity was observed in the piperine-treated group (p < 0.05). There was a 50% reduction in micronucleus formation with the administration of piperine 20 mg/kg (p < 0.05). It was concluded that cotreatment with piperine has great potential in mitigating the side effects caused by NSAIDs.},
}

@article {pmid40320531,
year = {2025},
author = {Vidaur, L and Guridi, A and Leizaola, O and Marin, J and Rello, J and Sarasqueta, C and Sorarrain, A and Marimón, JM},
title = {Respiratory dysbiosis as prognostic biomarker of disease severity for adults with community-acquired pneumonia requiring mechanical ventilation.},
journal = {Pneumonia (Nathan Qld.)},
volume = {17},
number = {1},
pages = {10},
pmid = {40320531},
issn = {2200-6133},
support = {FIS17/01463//Instituto de Salud Carlos III/ ; FIS17/01463//Instituto de Salud Carlos III/ ; },
abstract = {OBJETIVES: To ascertain the role of the lung microbiome in the development of severe pneumonia and its potential as a biomarker for disease progression.

METHODS: BAL samples from 34 adults with severe community-acquired pneumonia (CAP) (17 viral, 8 viral coinfected with bacteria and 9 bacterial) admitted to the ICU for acute respiratory failure between 2019 and 2021 were collected within the first 48 h of admission to the ICU. The microbiome was characterized via the Ion 16S Metagenomics Kit and the Ion Torrent sequencing platform. Clinical factors, including survival, mechanical ventilation duration, blood biomarkers and organ failure in terms of acute respiratory distress syndrome (ARDS), shock or acute renal failure, were correlated with microbiome characteristics.

RESULTS: The microbiome diversity in patients with viral pneumonia was significantly greater than that in patients with bacterial or coinfected pneumonia: the Shannon diversity index was 3.75 (Q1-Q3: 2.5-4.1) versus 0.4 (Q1-Q3: 0.2-1.3) and 0.48 (Q1-Q3: 0.3-1.1), respectively (p < 0.05). The microbiome diversity index was associated with severity-of-illness (APACHE II), independent of the etiology of pneumonia (B coefficient -1.845; p < 0.01). Patients with severe viral CAP who developed ARDS had a lower presence of Proteobacteria, and those who were complicated with ventilator-associated pneumonia had a higher prevalence of Acinetobacter at admission. The mortality of patients with bacterial or coinfected pneumonia was 35%. In coinfected patients, the diversity index was associated with the development of shock.

CONCLUSION: Patients with severe CAP have low respiratory microbiome diversity, indicating that respiratory microbiome diversity is a potential biomarker of disease severity.},
}

@article {pmid40320520,
year = {2025},
author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J},
title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {111},
pmid = {40320520},
issn = {2049-2618},
support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; },
mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Droughts ; },
abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.},
}

*Microbiota/physiology
*Stress, Physiological
*Plants/microbiology
*Bacteria/classification/genetics/isolation & purification
Soil Microbiology
Droughts

@article {pmid40320100,
year = {2025},
author = {Kogoj, R and Bosilj, M and Šturm, AC and Korva, M and Smrdel, KS and Kvas, E and Pirš, M and Lepen, L and Triglav, T},
title = {Bioinformatic challenges in metagenomic next generation sequencing data analysis while unravelling a case of uncommon campylobacteriosis.},
journal = {Journal of biomedical informatics},
volume = {},
number = {},
pages = {104841},
doi = {10.1016/j.jbi.2025.104841},
pmid = {40320100},
issn = {1532-0480},
abstract = {OBJECTIVE: This study aimed to employ advanced bioinformatics and modern sequencing approaches to solve a diagnostic problem of persistent Campylobacter spp. molecular detection yet negative culture results from four consecutive stool samples of a previously healthy patient with newly diagnosed selective IgA deficiency with prolonged diarrhoea METHODS: Metagenomic next-generation sequencing (mNGS) based on short-paired end reads with basic bioinformatic read classification analysis was used at first. Due to confusing results, advanced bioinformatics involving contigs construction and classification, reference genome mappings and reads filtering with BBSplit, additionally coupled with metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding were employed to further elucidate the results. Virulence factors were analysed using the Prokka Genome Annotation tool. Modified classical bacteriology methods were finally used for further clarification.

RESULTS: Short-pair end reads analysis identified several Campylobacter species in all four samples. After advanced bioinformatic approaches were applied, candidatus C. infans was suspected as the putative pathogen. This result was further supported by metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding. Nevertheless, after modifying the culture conditions based on mNGS results, a mixed culture of candidatus C. infans and C.ureolyticus was obtained. Sequencing of the mixed culture resulted in an 87.48 % and 73.47 % genome coverage of candidatus C. infans and C. ureolyticus, respectively. In the candidatus C. infans genome more virulence factors hits were found than in the C. ureolyticus genome thus supporting the first as the most probable cause of symptoms.

CONCLUSION: This study shows the pivotal role and strengths of mNGS in unravelling an unusual case of diarrhoea and demonstrates how mNGS can guide established microbiological methods to improve on current limitations. However, it also emphasises the need for careful interpretation of sequencing data, particularly for closely related bacterial species from clinical samples that are known to support complex microbial communities.},
}

@article {pmid40320026,
year = {2025},
author = {Zheng, Y and Yue, Y and Liu, C and Pang, L and Wang, Y and Yang, Z},
title = {The role of riverbed substrates in N2O and CH4 emission: Insights from metagenomic analysis of epilithic biofilms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121772},
doi = {10.1016/j.envres.2025.121772},
pmid = {40320026},
issn = {1096-0953},
abstract = {Riverbed substrates are critical in N2O and CH4 emission with functional microbes adhering to them. However, the role of substrates remains to be fully understood. This study monitors N2O and CH4 emission and collects epilithic biofilms on riverbed substrates with various diameters and size heterogeneity from 10 sections along a mountain river. Compared with the global range, moderate water-air exchange rates of N2O (-2.34-29.2 μg/m[2]/h) and rapid CH4 emission (-2.58-35.2 mg/m[2]/h) are observed. Based on metagenomic analysis, the abundances of nirS and fmdA genes, which encode catalysts in the denitrification and the hydrogenotrophic methanogenesis process, are found to be significantly higher in the medium diameter group (2-100 mm), implying higher N2O and CH4 emission. Meanwhile, the abundance of nirS and nirK genes, which are key to N2O production, is significantly higher in the low size heterogeneity group, promoting N2O release. In contrast, the abundance of ftr, pta,ackA and ACS genes critical in the methanogenesis processes are significantly lower in the low size heterogeneity group, inhibiting CH4 emission. For N2O production, the nitrification process is found to be dominated by species of Nocardioides and Planctomycetales, denitrification process by species of Tabrizicola and Rhodobacteraceae, and dissimilatory nitrate reduction to ammonium process by Leptospiraceae species. In contrast, CH4 is mainly generated by species of Pirellula and Proteobacteria through hydrogenotrophic, acetoclastic and methylotrophic methanogenesis respectively. A structural equation model indicated that substrate physical properties are equally or even more important as/than the aquatic nutrients concentration for N2O or CH4 emission in mountain rivers.},
}

@article {pmid40319779,
year = {2025},
author = {Zhu, J and Li, X and Wang, Y and Gu, X and Wang, H and Ma, J and Huang, Y},
title = {Organic sulfur-driven denitrification pretreatment for enhancing autotrophic nitrogen removals from thiourea-containing wastewater: performance and microbial mechanisms.},
journal = {Water research},
volume = {282},
number = {},
pages = {123753},
doi = {10.1016/j.watres.2025.123753},
pmid = {40319779},
issn = {1879-2448},
abstract = {Thiourea (CH4N2S) is a widely used industrial reagent and is frequently detected in both sewage and industrial wastewater. However, treating thiourea-containing wastewater remains challenging due to its toxicity, high ammonium concentration, and low C/N ratio. In this study, a novel integrated autotrophic-heterotrophic denitrification (IAHD)- completely autotrophic nitrogen removal over nitrite (CANON) process was developed. The degradation pathway of toxic compounds, nitrogen, and sulfur release and transformation, as well as variations in functional genes were comprehensively examined. The results show that by incorporating an IAHD unit, prior to CANON, toxic thiourea was effectively degraded by the recycled nitrate from CANON. The released sulfur and organic carbon served as electron donors facilitating efficient NO3[-]-N reduction. The optimal thiourea/NO3[-]-N ratio for IAHD operation was determined to be 4:1 (m:m), achieving NO3[-] and thiourea removal efficiencies of 90 % and 99 %, respectively. Additionally, NH4[+]-N and SO4[2-]-S concentrations increased by 199.9 mg/L and 201.9 mg/L, respectively. Approximately 53.3 % of thiourea was converted into high-molecular-weight biological metabolites in the IAHD unit, which were subsequently and completely degraded in the CANON unit, where a robust nitrite-shunt and anammox process occurred. 16S rRNA amplicon sequencing revealed that Thiobacillus (with a relative abundance of 39.9 %) was the dominant genera in the IAHD unit, followed by Arenimonas (10.8 %) and norank_o_1013-28-CG33 (12.4 %), indicating that sulfur autotrophic denitrification was the primary pathway for thiourea degradation. Metagenomic analysis further confirmed that thiourea, acting as an electron donor, stimulated the expression of key functional genes involved in denitrification, sulfur oxidation, dissimilatory nitrate reduction, hydrolytic oxidation, and amino acid synthesis and transport pathways. These processes contributed to the active biological transformation of carbon, nitrogen and sulfur in the IAHD unit. This study demonstrates that implementing a prior autotrophic-heterotrophic denitrification unit effectively degrades toxic thiourea, thereby ensuring the subsequent nitrogen removal performance of CANON. This approach offers a new paradigm for the treatment of thiourea-containing wastewater, promoting a more efficient and low-carbon process.},
}

@article {pmid40319631,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Rehman, KU and Ren, Z and Jiménez, N and Zheng, L and Huang, F and Yu, Z and Yu, C and Zhang, J and Cai, M},
title = {Mitigating the transfer risk of antibiotic resistance genes from fertilized soil to cherry radish during the application of insect fertilizer.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109510},
doi = {10.1016/j.envint.2025.109510},
pmid = {40319631},
issn = {1873-6750},
abstract = {The transfer of antibiotic resistance genes (ARGs) from fertilized soil to vegetables, particularly those consumed raw, causes significant public health risks through the food chain. Black soldier fly larvae can efficiently convert animal manure into organic fertilizer with reduced antibiotic resistance. This study utilized metagenomic sequencing to investigate fields treated with control organic fertilizer (COF), black soldier fly organic fertilizer (BOF), and no fertilizer, with the aim of assessing the transfer risks of ARGs from soil to cherry radish. The results indicated that BOF significantly reduced the richness and abundance of ARGs in both soil and cherry radish compared to COF, reducing 13 ARG subtypes and a 27.6% decrease in ARG abundance in cherry radish. Moreover, a significant positive correlation was observed between mobile genetic elements (MGEs) and virulence factors (VFs) with ARGs, with BOF treatment resulting in a relative abundance reduction of 32.8% and 29.1%, respectively. The complexity of networks involving ARGs with MGEs, VFs, and microbial communities in the BOF treatment was 54.2%, 32.3%, and 32.8% lower, respectively, than the COF treatment. Further analysis of metagenomic-assembled genomes (MAGs) revealed the co-occurrence of ARGs, MGEs, and VFs in cherry radish, indicating the presence of potential pathogenic antibiotic-resistant bacteria (PARB). Notably, the abundance of these PARB in BOF radishes decreased by 45.6% compared to COF. These findings underscore the efficacy of insect fertilizer in mitigating the transfer risks of ARGs to radish, highlighting the significance of sustainable agricultural practices in managing the environmental and health risks associated with ARGs.},
}

@article {pmid40319164,
year = {2025},
author = {Fan, Y and Chen, J and Xu, S and Zhou, H and Shang, Y and Tian, X and Wang, B and Zhao, Y and Shan, G and Zhao, Y and Zhang, P and Chen, X},
title = {Bacillus cereus is a key microbial determinant of intractable otitis media with effusion.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {150},
pmid = {40319164},
issn = {2730-664X},
abstract = {BACKGROUND: Currently, the mechanisms by which otitis media with effusion (OME) progresses to intractable OME is unclear. Since crosstalk between microbiome and host contributes to many diseases, we hypothesized that similar interactions could occur in the middle ear effusion (MEE) samples from patients with OME and influence intractable OME pathogenesis. This study aimed to evaluate the microbial profile of MEE samples and to determine whether there were microbial differences between the MEE microbiota of patients with intractable OME and those with rapidly cured OME.

METHODS: MEE samples were collected from 46 OME patients, including 20 from the long course group and 26 from the short course group. Metagenomic sequencing was performed on 30 of these samples, allowing the identification of microbial differences associated with varying disease durations. The difference was verified by further experimental validation, including fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR).

RESULTS: The alpha diversity indices and overall MEE microbial structure show no significant difference between the long course and short course groups, but species such as Bacillus cereus, Nocardiopsis dassonvillei, and Rothia aeria are significantly more prevalent in the MEE of long course OME patients. qPCR analyses and FISH also confirm the difference in the abundance of Bacillus cereus between the two groups.

CONCLUSIONS: Bacillus cereus plays a role in the persistence of OME infection and serves as a potential biomarker to predict OME prognosis. Further studies are warranted to explore the value of Bacillus cereus detection in informing early intervention.},
}

@article {pmid40297421,
year = {2025},
author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA},
title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40297421},
support = {F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; },
abstract = {OBJECTIVE: The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women, and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology.

METHODS: Self-collected vaginal swabs and questionnaires on dietary and health practices were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Additionally, medication regimen and disease activity and severity were captured for the RA cohort. Vaginal swabs were subjected to full-length 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, c-reactive protein, and anti-citrullinated protein antibodies (ACPAs).

RESULTS: Vaginal microbial richness and genera Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal IL-18 and EGF levels were increased in the RA group; IL-18 correlated with multiple microbial features whereas EGF levels were not associated with bacterial composition or other host factors. Within the RA cohort, decreased relative abundance of Streptococcus was associated with joint pathologies, and Lactobacillus gasseri was lower in individuals with serum detection of ACPAs and rheumatoid factor. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines.

CONCLUSIONS: We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, disease activity and severity, and medication use. This work opens a new avenue in the multidisciplinary approach to RA patient care.},
}

@article {pmid40318372,
year = {2025},
author = {Chu, D and Zhang, H and Wang, Z and Ning, K},
title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179522},
doi = {10.1016/j.scitotenv.2025.179522},
pmid = {40318372},
issn = {1879-1026},
abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.},
}

@article {pmid40318358,
year = {2025},
author = {Karatas, M and Bloemen, M and Swinnen, J and Roukaerts, I and Gucht, SV and Van Ranst, M and Wollants, E and Matthijnssens, J},
title = {Untapped potential of wastewater for animal and potentially zoonotic virus surveillance: Pilot study to detect non-human animal viruses in urban settings.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109500},
doi = {10.1016/j.envint.2025.109500},
pmid = {40318358},
issn = {1873-6750},
abstract = {INTRODUCTION: Wastewater surveillance has become an essential tool for monitoring viral outbreaks and surveillance of human viruses. While PCR-based methods are most frequently used, more advanced techniques, such as shotgun metagenomics in combination with viral capture methods, have been developed. These capture methods significantly improve the ability to detect nearly all (known) viruses at once in complex samples, including wastewater. In this study, we focus on tracking animal specific and zoonotic viruses in city wastewater using metagenomics combined with hybrid-capture approach.

METHODS: We collected 6 wastewater samples from Leuven and Brussels, situated in the center of Belgium. Automated wastewater samplers collected 50 mL samples every 10 min resulting in a 24 h composite influent wastewater. All samples were processed using the TWIST comprehensive research panel capture, designed to target over 3,000 human and animal viruses species and 15,000 strains. Sequencing was performed on the AVITI sequencing platform, targeting an average of ten million reads per sample. The sequencing data were analyzed using the EsViritu tool.

RESULTS: Over 2294 viral genomes or segments were recovered from wastewater samples. Of these, 168 were associated with non-human vertebrate animals, including cats, dogs, pigeons, and rats, spanning 51 virus species. We identified near-complete genomes of clinically relevant animal viruses, such as pigeon circovirus, chicken anemia virus, feline bocaparvovirus 2, canine minute virus, rat coronavirus, canine parvovirus, and porcine circovirus. Additionally, we noted the presence of viruses with known cross-species transmission potential, including porcine torovirus, rosavirus, hepatitis E virus, rat hepatitis virus, and cardiovirus.

CONCLUSION: The results demonstrate the ability to track a wide range of animal viruses in urban wastewater, potentially forming an early warning system for zoonotic diseases, ultimately being a useful tool for One Health based public health approaches.},
}

@article {pmid40318224,
year = {2025},
author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ},
title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf088},
pmid = {40318224},
issn = {1751-7370},
abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.},
}

@article {pmid40316928,
year = {2025},
author = {Zhang, Y and Sun, D and Fang, Y and Feng, Y and Wu, Y and Shen, W and Wu, W and Gao, X and Sun, Y and Ma, X and Gao, F and Zhu, C and Zhou, J and Gu, C},
title = {Uncommon pulmonary manifestation of hepatitis B virus: a case report of secondary organizing pneumonia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {645},
pmid = {40316928},
issn = {1471-2334},
support = {Z-2014-06-2301//China International Medical Exchange Foundation Xiansheng Clinical Research Special Fund Research Project/ ; 2023-SSGJ-002//Key Construction Disciplines of Provincial and Municipal Co construction of Zhejiang/ ; 2021-GFXK-04//Peak Discipline of Jiaxing First Hospital/ ; 2021AD30177//Science and Technology Project of Jiaxing/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Hepatitis B virus/genetics/isolation & purification ; *Hepatitis B/complications/virology/diagnosis ; Lung/pathology/virology ; DNA, Viral/genetics ; Viral Load ; Organizing Pneumonia ; },
abstract = {BACKGROUND: Hepatitis B virus (HBV) primarily affects the liver, but increasingly, it is recognized for its potential extrahepatic manifestations. This case highlights the importance of considering viral infections in the differential diagnosis of pulmonary nodules.

CASE PRESENTATION: A 63-year-old man presented with a new mixed ground-glass nodule in the left lower lobe during a routine check-up. He had a history of liver resection for hepatocellular carcinoma, with results negative for hepatitis B virus surface antigen. The HBV viral load in the patient's serum was below the detection limit of quantitative PCR (qPCR). Immunohistological analysis of lung biopsy samples indicated chronic inflammation. However, after a course of intravenous antibiotics, the nodule increased in size, prompting further investigation. Therefore, lung biopsy tissue was subjected to metagenomic next-generation sequencing (mNGS), and HBV DNA was detected. The patient was diagnosed with secondary organizing pneumonia associated with HBV. Then he was treated with prednisone acetate and had remission.

CONCLUSION: This case underscores the potential for HBV to manifest as pulmonary complications, such as secondary organizing pneumonia. Therefore, in the stage of infectious diseases in patients with a history of hepatocellular carcinoma, HBV needs to be the focus of monitoring, so as to clarify the cause of diagnosis and treatment as soon as possible.

CLINICAL TRIAL: Not applicable.},
}

Humans
Male
Middle Aged
*Hepatitis B virus/genetics/isolation & purification
*Hepatitis B/complications/virology/diagnosis
Lung/pathology/virology
DNA, Viral/genetics
Viral Load
Organizing Pneumonia

@article {pmid40316630,
year = {2025},
author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD},
title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15356},
pmid = {40316630},
issn = {2045-2322},
support = {Small grant//Universidad del Rosario/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; },
abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metagenomics/methods
Male
*Energy Metabolism
Adult
Athletes
Young Adult
*Sports
Feces/microbiology
Female
Lipidomics

@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.},
}