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Commensal microbiota and its relationship to homeostasis and disease
Published in Phillip D. Smith, Richard S. Blumberg, Thomas T. MacDonald, Principles of Mucosal Immunology, 2020
Jonathan Braun, Elaine Y. Hsiao, Nicholas Powell
At a metagenomic level, the intestinal microbiome contains an enormous number of genes, more than 150 times the number of unique (nonredundant) genes found in the human genome. This metagenome spans the entire range of enzymatic functions and complements the human genome, particularly in genes contributing to nutrient uptake and digestion. In contrast to the interindividual diversity of microbial composition, the representation of genes by function is highly conserved. Although less studied, the intestinal microbiome also includes diverse fungi, higher eukaryote organisms, and virus-like organisms. Unlike the bacterial microbiota, the intestinal “virome” seems to be a stable but highly individual trait, with minimal influence of either family or environment. It may also be of particular importance because its exceptional abundance and diversity may contribute an enormous genetic repertoire to intestinal function.
Epilogue
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Concerning the basic virome problems, it is important to take into account that the advent of new biology produces tons of sequences in the terabyte range every day from sequencing centers (Bursteinas et al. 2016; Biji CL and Achuthsankar 2017). As the sequencing cost is reducing, the majority of life science laboratories can generate genomic data in terabyte scale and access a huge volume of data from public repositories, such as the European Bioinformatics Institute (EBI) or National Center for Biotechnology Information (NCBI). Therefore, the problems of data storage, compression, evaluation, and analysis are of great importance nowadays and provide additional insights to the biologist.
The Role of Fecal Microbiota Transplantation in Neurological Diseases
Published in David Perlmutter, The Microbiome and the Brain, 2019
Thomas Borody, John Bienenstock
The bacterial communities that comprise the gut microbiome represent a continuum that increases both in number and complexity as you move through the gastrointestinal (GI) tract. The largest and most diverse microbial population is found in the colon, so most of the extant research has focused on the fecal microbiota. However, it is important to remember that the composition of gut microbiota, while predominantly bacterial, also contains vast amounts of viruses (predominantly bacteriophages [virome]), fungi (mycobiome), and also archaea. Therefore, feces and fecal extracts contain diverse microbial categories and a varying amount of bacterial products and components, including products of fermentation and digestion.
Real life treatment experience and outcome of consecutively hospitalised patients with SARS-CoV-2 pneumonia by Omicron-1 vs Delta variants
Published in Infectious Diseases, 2023
Efthymia Giannitsioti, Panagiotis Mavroudis, Ioannis Speggos, Antigoni Katsoulidou, Nikos Pantazis, Theodoros Loupis, Ioannis Daniil, Nektaria Rekleiti, Sofia Damianidou, Christina Louka, Chrysanthi Sidiropoulou, Georgios Kranidiotis, Lemonia Velentza, Alexandra Stamati, Maria Kasidiaraki, Efrosini Efstratiadi, Garyfallia Linardaki, Georgios Chrysos, Olympia Zarkotou, Katerina Zoi, Kyriaki Tryfinopoulou, Styliani Gerakari
Whole genome sequencing of the virome was performed on the Illumina NovaSeq 6000. QIAseq SARS-CoV-2 Primer Panel Kit (based on the Artic Network V3 primer design) with QIAseq FX DNA Library Prep protocol was used for the construction of libraries according to the manufacturer’s instructions. Paired-end and dual-indexed 2 × 150bp sequencing was done using NovaSeq SP Reagent Kit (300 cycles). Sequences were demultiplexed and basecalls were converted to FASTQ using bcl2fastq2 v2.20. The FASTQ reads were then trimmed for adapter and primer sequences using fastp and iVar’s primer trimming tools respectively. Reads were then aligned to the Wuhan reference genome (NC_045512v2) using minimap2 and processed to consensus sequence using the iVar consensus tool. The generated Fasta files with more than 3000 missing bases (N bases) were excluded from further analysis. Variant calling was performed using GATK’s HaplotypeCaller (version 4.1.2 at default parameters) and variants with AF >90% were kept and annotated using Annovar. Following quality control, fasta files were uploaded to NextClade (https://clades.nextstrain.org) for the time-scaled phylogeny and the relevant tree was created and clades were called. Lineage identification was performed using the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN version 3.1.20) software suite (https://github.com/hCoV-2019/pangolin) with pangoLEARN updated to 2022-02-02.
Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor
Published in Gut Microbes, 2021
Jilei Zhang, Yongguo Zhang, Yinglin Xia, Jun Sun
The human microbiota is consisted of bacteria, viruses, fungi, multicellular parasites and archaea. The virome is a collection of nucleic acids. Both RNA and DNA that compose the viral community associated with a particular ecosystem of microbiota. The virome includes viruses that infect host cells, virus-derived elements in the genome, and viruses that infect the broad array of other types of microorganisms that inhabit the host.27 The virome includes eukaryotic viruses, endogenous retroviruses, bacterial viruses (i.e., bacteriophages), and archaeal viruses and is one of the least understood components of the microbiota.28,29 Fecal virome was involved in many diseases using samples from both human patients and mouse model, such as colitis and diabetes.30–34 Dysbiosis of the microbiome not only leads to intestinal inflammatory and infectious diseases but also to diseases beyond the gastrointestinal tract.5,35 Moreover, dysbiosis of intestinal microbiota could influence internally through interaction and metabolites, such as bacteriophages and bacteria.36 At present, we are beginning to understand the influence of VDR on microbial homeostasis, which is critical in various diseases.5,37–40 However, the effects and mechanisms of VDR on the virome have not been fully elucidated.
Gut non-bacterial microbiota contributing to alcohol-associated liver disease
Published in Gut Microbes, 2021
Wenkang Gao, Yixin Zhu, Jin Ye, Huikuan Chu
Furthermore, gut virome can interact with the host immune system directly. The intestinal immune system is mainly comprised of intestinal intraepithelial lymphocytes (IELs), lamina propria lymphocytes (LPLs), and Peyer’s patches (PPs),136 which could be important in the pathogenesis of ALD. Among them, commensal viruses can be recognized by retinoic acid-inducible gene 1 (RIG-1) signaling in antigen-presenting cells (APCs), and RIG-1 signaling can promote IL-15 production, prevent inflammation and tissue damage as well as maintain the homeostasis of IELs.137 Moreover, scientists found that the immune cells including CD4+ and CD8+ T cells increased in the germ-free mice treated with bacteriophages, and the increased abundance of bacteriophages can exacerbate intestinal colitis through toll-like receptor 9 (TLR9) and interferon-gamma (IFN-γ), indicating that phages can alter mucosal immunity to impact mammalian health.138 But, the mechanism of the phage recognition by the mucosal immune system needs more studies in animal models. Moreover, some studies on pathogenic enteroviruses, such as norovirus and rotavirus, have revealed several signaling pathways of intestinal recognition of viral nucleic acids.139,140 Thus, the gut virome either commensal or pathogenic viruses is a hot topic in host immune response.