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An Overview of Parasite Diversity
Published in Eric S. Loker, Bruce V. Hofkin, Parasitology, 2023
Eric S. Loker, Bruce V. Hofkin
The estimates given above mostly apply to eukaryotes. If we do not restrict the definition of a parasite to just the eukaryotic realm, parasites also include some of the prokaryotes, which have been systematically underrepresented in calculations of global species diversity. They are small and easily overlooked, and many cannot be easily isolated and cultured. Currently there are only about 9,500 named species of prokaryotes (including both bacteria and archaea). Metagenomics, the characterization of genetic material recovered directly from a particular environment (soil, water and air) without the need to culture the organisms present, has revolutionized our understanding of biodiversity for prokaryotes, and for eukaryotes too as we will soon see. The genetic material being targeted is what is referred to as environmental DNA, or eDNA, that may be derived not only from unculturable microbes but also from decomposing organisms, shed skin or mucus, feces, hair, or other organismal products released into the environment. The study of eDNA has become a powerful new tool to study biodiversity.
Risk factors – Treatable traits
Published in Vibeke Backer, Peter G. Gibson, Ian D. Pavord, The Asthmas, 2023
Vibeke Backer, Peter G. Gibson, Ian D. Pavord
The area of respiratory infection undergoes a major information surge as modern molecular methods are applied to pathogen detection. There have been significant advances in the detection of individual pathogens through the use of PCR-based methods that are now applied in clinical practice, especially around respiratory viral detection. In addition, metagenomics has allowed recognition of multiple bacterial organisms at the taxa/phyla levels and is contributing to the understanding of disease pathogenesis. In patients with asthma who were not using inhaled corticosteroids, direct airway sampling identified that eosinophilic airway inflammation was associated with an altered airway microbiome. In severe asthma, patients with neutrophilic asthma have a greater frequency of pathogenic taxa at high relative abundance and reduced Streptococcus, Gemella and Porphyromonas taxa relative abundance.
A Review on L-Asparaginase
Published in Se-Kwon Kim, Marine Biochemistry, 2023
Assessing cell membrane integrity is one of the most common ways to determine the viability of the cell and its cytotoxic effects. Compounds that possess cytotoxic effects often compromise cell membrane integrity. Vital dyes, such as propidium iodide or trypan blue, are normally excluded from the inside of healthier cells; however, if the cell membrane is negotiated, they easily cross the membrane and stain the intracellular components (Riss et al., 2004). The extracellular enzyme possessed a cytotoxic effect on HL60 cell line (Hari Krishnan et al., 2016). The traditional methods of identifying the bacterial strain rely on culturing technique. Such techniques have certain limitations. In order to overcome those limitations, molecular characterization came into force. 16s rRNA sequencing can give much more information than culturing methods. Metagenomics is another field that involves the study and analysis of microbial communities from the surrounding environment without culturing. It also affords the potential to determine novel enzymes through function-based screening. Hence, metagenomics has given the scientific community with a range of novel enzymes (Zhang and Kim, 2010).
Variational Bayesian inference for association over phylogenetic trees for microorganisms
Published in Journal of Applied Statistics, 2022
Xiaojuan Hao, Kent M. Eskridge, Dong Wang
Metagenomics is a culture independent approach to survey the genetic composition of a microbial community or sample (bacteria, archaea, viruses, microbial eukaryotes, or fungi). With the application of next generation sequencing technology, it has made tremendous impact on biomedical and environmental research [see 8, 11, 13, for recent reviews and references therein]. A significant number of studies using metagenomics techniques involves the modeling of association between certain environmental factors and some characteristics of the microbial community [e.g. 5, 16]. The environment factor in this context could be that of the physical environment (properties of soil, air, water, among others), or could be regarding the host environment (nutrition; host immune response; variables concerning organs).
Strengths and caveats of identifying resistance genes from whole genome sequencing data
Published in Expert Review of Anti-infective Therapy, 2022
Brian M. Forde, David M. P. De Oliveira, Caitlin Falconer, Bianca Graves, Patrick N. A. Harris
Most clinical laboratories lack the computational infrastructure, data storage capacity and skilled personnel to perform WGS. Issues relating to data governance and management, present novel challenges for laboratories. These include the secure remote storage of genomic data to ensure patient privacy, creation of data sharing protocols for genomic and associated epidemiological/clinical metadata as well as ethical considerations arising from clinical metagenomics data containing identifiable human DNA. Furthermore, training in molecular biology and bioinformatics among clinical microbiologists and clinicians will be essential for the successful integration of this ‘disruptive technology’ into the clinical laboratory, but few jurisdictions have established processes for incorporating this into clinical infectious disease and microbiology training.
Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside
Published in Expert Review of Proteomics, 2021
Lauren C Beck, Claire L Granger, Andrea C Masi, Christopher J Stewart
Another important contributing factor to many pediatric GI diseases, as discussed, is the human gut microbiome. To study the microbiome, at a taxonomic level, metagenomics techniques are commonly employed. Unlike genomics techniques which study the genetic material of a single organism (the patient), metagenomics focuses on the study of all the genetic material present in a given environment, such as the GI tract. In a clinical context, metagenomics is very powerful for microbiome studies and enables researchers to identify specific bacteria that may be associated with disease states. Traditionally, microbiome studies have relied on culture-based techniques and more recently amplicon gene sequencing, which allows genus-level identification based on a phylogenetic marker gene, typically the 16S rRNA gene [38]. However, metagenomics offers advantages over these methods, allowing strain-level classification of both culturable and unculturable species and analysis of the functional content of samples [38]. This more granular level of information is of great benefit when studying the intestinal microbiome due to the complexity of such a community and its genetic content, as it is estimated that there are approximately 5 million unique genes, many of which contribute to host health and metabolism [39].