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DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.
Sci Rep
December 2024
KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Traditional prediction methods, dependent on homology and sequence similarity, often fail to predict functions for novel proteins and proteins without known homologs.
View Article and Find Full Text PDFFecal microbiota transplantation as a potential therapeutic approach to improve impaired glucose tolerance via gut microbiota modulation in rat model.
J Diabetes Metab Disord
June 2025
Institute of Science, Nirma University, Ahmedabad, Gujarat 382481 India.
Objectives: To investigate the impact of diet-induced gut microbiota alterations on type 2 diabetes and assess the therapeutic potential of Fecal Microbiota Transplantation (FMT) in restoring a balanced gut microenvironment.
Methods: To induce type 2 diabetes, rats were fed a high-sugar high-fat diet (HSFD) for 90 days. After diabetes induction, animals were divided into an HSFD control group, a metformin group (100 mg/kg), and an FMT group (100 mg/kg), receiving treatment for an additional 90 days.
Growth-promoting effects of self-selected microbial community on wheat seedlings in saline-alkali soil environments.
Front Bioeng Biotechnol
December 2024
Shandong Key Laboratory of Agricultural Microbiology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.
Saline-alkali land is a type of soil environment that causes poor crop growth and low yields. Its management and utilization are, therefore of great significance for increasing arable land resources, ensuring food security, and enhancing agricultural production capacity. The application of plant growth-promoting rhizobacteria (PGPR) is an effective way to promote the establishment of symbiotic relationships between plants and the rhizosphere microenvironment, plant growth and development, and plant resistance to saline-alkali stress.
View Article and Find Full Text PDFDiagnostic performance of metagenomic next-generation sequencing among hematological malignancy patients with bloodstream infections after antimicrobial therapy.
J Infect
December 2024
Department of Hematology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, 210008, PR China. Electronic address:
Background: Metagenomic next-generation sequencing (mNGS) is an effective method for detecting pathogenic pathogens of bloodstream infection (BSI). However, there is no consensus on whether the use of antibiotics affects the diagnostic performance of mNGS. We conducted a prospective clinical study aiming to evaluate the effect of antimicrobial treatment on mNGS.
View Article and Find Full Text PDFMetagenomic next-generation sequencing and galactomannan testing for the diagnosis of invasive pulmonary aspergillosis.
Sci Rep
December 2024
Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No. 7, Zhengzhou, 450003, Henan, China.
To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) and galactomannan (GM) testing in invasive pulmonary aspergillosis (IPA) and to compare mNGS with other diagnostic approaches (serum/bronchoalveolar lavage fluid (BALF)-GM and conventional microbiological tests (CMTs) including sputum smears and culture, BALF fungal culture, and bronchial brushing). In all, 237 patients were enrolled in this retrospective study, including 120 patients with IPA and 117 with non-IPA pulmonary infections treated at Henan Provincial People's Hospital between June 2021 and February 2024. The diagnostic performance of mNGS was compared to conventional diagnostic methods including serum GM, BALF-GM, sputum smear microscopy, sputum culture, bronchial brushings, and BALF culture.
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