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The human gut microbiota, particularly the intestinal microbiota, shapes host physiology, disease risk, and therapeutic outcomes through complex metabolic and enzymatic activities. Recent advances in molecular omics, metabolomics, enzyme bioinformatics, and artificial intelligence (AI) have …
Read PDF<h4>Context</h4>Apical periodontitis (AP) is an inflammatory condition caused by root canal infection. Primary AP (PAP) arises from untreated necrotic pulp and is typically polymicrobial, whereas persistent or refractory AP (RAP) occurs after root canal treatment …
Read PDFWith ongoing biodiversity loss, a wide range of taxa are being monitored to support the implementation of conservation measures aimed at preventing their decline. Effective monitoring requires the development of robust and scalable tools and …
Read PDFAntimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to …
Read PDF<h4>Background</h4>Both type 2 diabetes mellitus (T2DM) and COVID-19 are associated with gut microbial alterations. It remains unclear whether COVID-19 causes further gut dysbiosis among individuals with T2DM.<h4>Objective</h4>This study aimed to characterize the gut microbiome of …
Read PDFBACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological …
Read PDF<h4>Summary</h4>TAGINE is a feature engineering algorithm that leverages the microbial taxonomic tree to optimize feature sets in microbiome data for predictive modeling. The algorithm starts with features at high taxonomic levels and iteratively splits them …
Read PDFGlaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences …
Read PDF<h4>Motivation</h4>Large-scale prospective cohort studies collect longitudinal biospecimens alongside time-to-event outcomes to investigate biomarker dynamics in relation to disease risk. The nested case-control (NCC) design provides a cost-effective alternative to full cohort biomarker studies while preserving …
Read PDF<h4>Motivation</h4>The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome …
Read PDF<h4>Motivation</h4>Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain …
Read PDFClimate change, population growth and the increasing demand for food and nutritional security necessitate the development of climate-resilient cereal crops. This requires first gaining mechanistic insights into the molecular mechanisms underpinning plant abiotic and biotic …
Read PDFObesity is a highly complex, multifactorial disease influenced by dynamic interactions among genetic, epigenetic, environmental, and behavioral determinants that explicitly position genetics as the core. While advances in multi-omic integration have revolutionized our understanding of …
Read PDFImmune checkpoint inhibitors (ICIs) have transformed oncology, yet durable benefit remains confined to a minority of patients, revealing the limitations of single biomarkers such as PD-L1 expression, tumor mutational burden, and microsatellite instability. Multi-omics profiling, …
Read PDFImmunotherapy has revolutionized hematologic cancer treatment, yet responses remain unpredictable due to primary resistance, relapse, and life-threatening toxicities. Conventional biomarkers fail to capture the complexity of tumor-immune interactions, necessitating integrative approaches. This review explores how …
Read PDFThis study assessed the vaginal microbiome in women with HIV undergoing cervical transformation zone treatment in Zambia. 16S rRNA sequencing showed lower microbial diversity in successful outcomes (N = 18) than those with treatment failure …
Read PDFIn recent years, the role of the gut microbiota in regulating human health has gained increasing scientific attention, particularly during early life [...].
Read PDF<h4>Background</h4>Oral dysbiosis plays an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Our study aimed to perform a pairwise comparison of the oral microbiota, especially the bacteriome, from OSCC tumoral surface vs …
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