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The human gut virome: composition, colonization, interactions, and impacts on human health

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 colon...

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Autores principales: Pargin, Evan, Roach, Michael J., Skye, Amber, Papudeshi, Bhavya, Inglis, Laura K., Mallawaarachchi, Vijini, Grigson, Susanna R., Harker, Clarice, Edwards, Robert A., Giles, Sarah K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10244655/
https://www.ncbi.nlm.nih.gov/pubmed/37293229
http://dx.doi.org/10.3389/fmicb.2023.963173
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author Pargin, Evan
Roach, Michael J.
Skye, Amber
Papudeshi, Bhavya
Inglis, Laura K.
Mallawaarachchi, Vijini
Grigson, Susanna R.
Harker, Clarice
Edwards, Robert A.
Giles, Sarah K.
author_facet Pargin, Evan
Roach, Michael J.
Skye, Amber
Papudeshi, Bhavya
Inglis, Laura K.
Mallawaarachchi, Vijini
Grigson, Susanna R.
Harker, Clarice
Edwards, Robert A.
Giles, Sarah K.
author_sort Pargin, Evan
collection PubMed
description 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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spelling pubmed-102446552023-06-08 The human gut virome: composition, colonization, interactions, and impacts on human health Pargin, Evan Roach, Michael J. Skye, Amber Papudeshi, Bhavya Inglis, Laura K. Mallawaarachchi, Vijini Grigson, Susanna R. Harker, Clarice Edwards, Robert A. Giles, Sarah K. Front Microbiol Microbiology 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. Frontiers Media S.A. 2023-05-24 /pmc/articles/PMC10244655/ /pubmed/37293229 http://dx.doi.org/10.3389/fmicb.2023.963173 Text en Copyright © 2023 Pargin, Roach, Skye, Papudeshi, Inglis, Mallawaarachchi, Grigson, Harker, Edwards and Giles. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Pargin, Evan
Roach, Michael J.
Skye, Amber
Papudeshi, Bhavya
Inglis, Laura K.
Mallawaarachchi, Vijini
Grigson, Susanna R.
Harker, Clarice
Edwards, Robert A.
Giles, Sarah K.
The human gut virome: composition, colonization, interactions, and impacts on human health
title The human gut virome: composition, colonization, interactions, and impacts on human health
title_full The human gut virome: composition, colonization, interactions, and impacts on human health
title_fullStr The human gut virome: composition, colonization, interactions, and impacts on human health
title_full_unstemmed The human gut virome: composition, colonization, interactions, and impacts on human health
title_short The human gut virome: composition, colonization, interactions, and impacts on human health
title_sort human gut virome: composition, colonization, interactions, and impacts on human health
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10244655/
https://www.ncbi.nlm.nih.gov/pubmed/37293229
http://dx.doi.org/10.3389/fmicb.2023.963173
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