Su1893 UNCOVERING THE ALTERATIONS AND CORRELATIONS OF GUT VIROME, BACTERIA, AND METABOLITES IN PATIENTS WITH DIARRHEAPREDOMINANT IRRITABLE BOWEL SYNDROME: MULTI-OMICS ANALYSES
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The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.
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Various animal and cell culture models of diabetes mellitus (DM) have been established and utilized to study diabetic peripheral neuropathy (DPN). The divergence of metabolic abnormalities among these models makes their etiology complicated despite some similarities regarding the pathological and neurological features of DPN. Thus, this study aimed to review the omics approaches toward DPN, especially on the metabolic states in diabetic rats and mice induced by chemicals (streptozotocin and alloxan) as type 1 DM models and by genetic mutations (MKR, db/db and ob/ob) and high-fat diet as type 2 DM models. Omics approaches revealed that the pathways associated with lipid metabolism and inflammation in dorsal root ganglia and sciatic nerves were enriched and controlled in the levels of gene expression among these animal models. Additionally, these pathways were conserved in human DPN, indicating the pivotal pathogeneses of DPN. Omics approaches are beneficial tools to better understand the association of metabolic changes with morphological and functional abnormalities in DPN.
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Summary Background The human virome consists of animal‐cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High‐throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus‐like particles make to the human virome, and in particular the intestinal virome. Aim To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. Methods Relevant virome‐related articles were selected for review following extensive language‐ and date‐unrestricted, electronic searches of the literature. Results The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. Conclusions Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome‐disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales ). The stability of the virome’s regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile . Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed ‘viral dark matter’, is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
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The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease 9 states, but it is not yet known to what extent the gut virome impacts everyday human health. New 10 experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome 11 colonisation begins at birth, becoming temporally stable over a 30-month period. The stable virome is highly 12 specific to each individual and is modulated by varying factors such as age, gender, diet, and disease state. 13 The gut virome is primarily composed of bacteriophages—predominantly crAssphage, and other 14 Caudovirales. The stability of the virome’s regular constituents is disrupted by disease. Transferring the 15 faecal microbiome and its viruses from a healthy individual can restore the functionality of the gut, and 16 alleviates the symptoms of some chronic illnesses. Investigation of the virome is a relatively novel field with 17 new genetic sequences being published at an increasing rate. Many of these present with a large percentage 18 of unknown proteins, this ‘viral dark matter’ is one of the major questions facing virologists and 19 bioinformaticians. Bioinformatics tools can be used to explore both new and existing publicly available viral 20 sequence datasets to quantify and classify viral species, but not all these tools are created equal, with some 21 being more precise, effective, and efficient than others. Here, we review the literature surrounding the gut 22 virome, how it is established, how it impacts human health, the methods used to investigate it, and the viral 23 dark matter veiling the understanding of the gut virome.
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Polycystic ovary syndrome (PCOS) is the most common gynecological endocrine disease, involving multiple genes, multiple pathways, and complex hormone secretion processes. Hence, the pathogenesis of PCOS cannot be explained by a single factor. Omics analysis includes genomics, transcriptomics, and proteomics, which are fast and effective methods for studying the pathogenesis of diseases. PCOS is primarily characterized by androgen excess, and reproductive and metabolic dysfunctions. The application of omics analysis in the body fluids, blood, cells or tissues of women with PCOS offers the potential for unexpected molecular advantages in explaining new mechanisms of PCOS etiology and pathophysiology, and provides new perspectives for identifying potential biomarkers and developing new therapeutic targets. At present, several omics analyses have been applied to produce complex datasets. In this manuscript, the recent advances in omics research on PCOS are summarized, aiming at an important and parallel review of the newly published research.
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Purpose of review The purpose of this review is to recapture recent advances in cachexia-related diseases, mainly cancer cachexia, and treatment using genomic, transcriptomics, proteomic, and metabolomics-related techniques. Recent findings From recent studies in the cancer cachexia field it is clear that the tumor has a direct effect on distant organs via its secretome. The affected pathways on the other hand were largely known from earlier studies with changes in energy-related pathways (mainly lipid metabolism) and the protein degradation pathways. Treatment-oriented studies use mostly rodent models and in-vivo cultures and it is too early for human studies. Summary Omics tools are powerful if used in the right way. Omics research has identified the tumor as an important player in cancer cachexia and some interesting novel treatments have been found in experimental models.
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