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Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the "One Health" framework. Cefiderocol is a siderophore cephalosporin recently …
Read PDFMicrobially mediated hydrocarbon biodegradation is a cornerstone of natural attenuation and engineered bioremediation, yet the <i>in situ</i> mechanisms and key microbial players remain incompletely resolved due to the historical reliance on cultivation-based approaches. Recent advances …
Read PDF<h4>Background</h4>Live animal markets (LAMs) are recognized as hotspots for zoonotic disease emergence. Environmental surveillance (ES), particularly when paired with metagenomic sequencing, offers an advanced and actionable approach to pathogen detection in high-risk settings. However, the …
Read PDFInsect meals are promising sustainable protein sources for poultry, but comprehensive insights into their effects on gut health and growth performance are lacking. This study is the first to elucidate relationships between gut health parameters …
Read PDFRecent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments …
Read PDF<h4>Objective</h4>To systematically evaluate the application and utility of omics technologies, high-throughput methods measuring the complete or targeted set of molecules inside a biological system at a certain timepoint, in monitoring and optimizing rehabilitation interventions in …
Read PDFFunctional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool samples …
Read PDF<h4>Background/objectives</h4>Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, …
Read PDFMetagenomic next-generation sequencing (mNGS) offers a powerful, hypothesis-free approach for pathogen detection in clinical samples, allowing the identification of both known and novel microorganisms. However, the predominance of host nucleic acid in most samples poses …
Read PDFIn the intensive care unit (ICU), antibiotics often begin under extreme uncertainty. Fever, leukocytosis, hypotension, and organ dysfunction may signal bacterial infection, but the same findings are common with aspiration, post-operative inflammation, drug reactions, or …
Read PDFCurrent long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of …
Read PDFShotgun metagenomes were used to identify microbes associated with a pink discoloration of an unpasteurized blue cheese made in the United States. Taxonomic assessments of individual reads and metagenome-assembled genomes revealed that the genus <i>Virgibacillus</i> …
Read PDF<h4>Background</h4>The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome …
Read PDFThe advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its …
Read PDFTaxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive …
Read PDFThe human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant …
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