Lung abscesses are one of the most common lower respiratory tract infections worldwide and can seriously endanger life. However, pathogens associated with lung abscesses still cannot be detected quickly and accurately with the current microbial detection technology. Here, the case of a 53-year-old male with a lung abscess caused by oral bacteria is reported. After metagenomic next-generation sequencing was applied to identify the pathogenic microorganism, the patient recovered with precision medicine. Metagenomic next-generation sequencing is an important tool for the clinical diagnosis of infectious diseases caused by microorganisms and in guiding precision medicine.
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http://dx.doi.org/10.2217/fmb-2022-0172 | DOI Listing |
Nat Commun
January 2025
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples.
View Article and Find Full Text PDFGut Pathog
January 2025
Microba Pty Ltd, Brisbane, Australia.
Background: Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms.
View Article and Find Full Text PDFCureus
December 2024
Psychiatry, Patton State Hospital, San Bernardino, USA.
Introduction: Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are chronic disorders of the gastrointestinal tract associated with gut microbiota dysbiosis and inflammation. Serum-derived bovine immunoglobulin (SBI) is used to manage IBS and IBD and has shown prebiotic-like effects in ex vivo models. Re-establishing a healthy gut microbiome with novel treatments like SBI could help treat the underlying causes of these diseases leading to higher and sustained patient response.
View Article and Find Full Text PDFMicrobiome
January 2025
Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Background: The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.
View Article and Find Full Text PDFFront Parasitol
August 2024
Department of Zoology and Environmental Management, Faculty of Science, University of Kelaniya, Dalugama, Kelaniya, Sri Lanka.
Dirofilariasis, caused by the nematode spp., poses significant challenges in diagnosis due to its diverse clinical manifestations and complex life cycle. This comprehensive literature review focuses on the evolution of diagnostic methodologies, spanning from traditional morphological analyses to modern emerging techniques in the context of dirofilariasis diagnosis.
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