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Metagenomic assembled plasmids of the human microbiome vary across disease cohorts
We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9163076/ https://www.ncbi.nlm.nih.gov/pubmed/35654877 http://dx.doi.org/10.1038/s41598-022-13313-y |
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author | Stockdale, S. R. Harrington, R. S. Shkoporov, A. N. Khokhlova, E. V. Daly, K. M. McDonnell, S. A. O’Reagan, O. Nolan, J. A. Sheehan, D. Lavelle, A. Draper, L. A. Shanahan, F. Ross, R. P. Hill, C. |
author_facet | Stockdale, S. R. Harrington, R. S. Shkoporov, A. N. Khokhlova, E. V. Daly, K. M. McDonnell, S. A. O’Reagan, O. Nolan, J. A. Sheehan, D. Lavelle, A. Draper, L. A. Shanahan, F. Ross, R. P. Hill, C. |
author_sort | Stockdale, S. R. |
collection | PubMed |
description | We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses. |
format | Online Article Text |
id | pubmed-9163076 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-91630762022-06-05 Metagenomic assembled plasmids of the human microbiome vary across disease cohorts Stockdale, S. R. Harrington, R. S. Shkoporov, A. N. Khokhlova, E. V. Daly, K. M. McDonnell, S. A. O’Reagan, O. Nolan, J. A. Sheehan, D. Lavelle, A. Draper, L. A. Shanahan, F. Ross, R. P. Hill, C. Sci Rep Article We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses. Nature Publishing Group UK 2022-06-02 /pmc/articles/PMC9163076/ /pubmed/35654877 http://dx.doi.org/10.1038/s41598-022-13313-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Stockdale, S. R. Harrington, R. S. Shkoporov, A. N. Khokhlova, E. V. Daly, K. M. McDonnell, S. A. O’Reagan, O. Nolan, J. A. Sheehan, D. Lavelle, A. Draper, L. A. Shanahan, F. Ross, R. P. Hill, C. Metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
title | Metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
title_full | Metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
title_fullStr | Metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
title_full_unstemmed | Metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
title_short | Metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
title_sort | metagenomic assembled plasmids of the human microbiome vary across disease cohorts |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9163076/ https://www.ncbi.nlm.nih.gov/pubmed/35654877 http://dx.doi.org/10.1038/s41598-022-13313-y |
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