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Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes
While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we r...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7501288/ https://www.ncbi.nlm.nih.gov/pubmed/32948758 http://dx.doi.org/10.1038/s41467-020-18543-0 |
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author | Delogu, F. Kunath, B. J. Evans, P. N. Arntzen, M. Ø. Hvidsten, T. R. Pope, P. B. |
author_facet | Delogu, F. Kunath, B. J. Evans, P. N. Arntzen, M. Ø. Hvidsten, T. R. Pope, P. B. |
author_sort | Delogu, F. |
collection | PubMed |
description | While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 10(2)–10(4) for bacterial populations and 10(3)–10(5) for an archaeon, which is more comparable to Eukaryotic representatives’ humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA/protein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function. |
format | Online Article Text |
id | pubmed-7501288 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-75012882020-10-01 Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes Delogu, F. Kunath, B. J. Evans, P. N. Arntzen, M. Ø. Hvidsten, T. R. Pope, P. B. Nat Commun Article While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 10(2)–10(4) for bacterial populations and 10(3)–10(5) for an archaeon, which is more comparable to Eukaryotic representatives’ humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA/protein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function. Nature Publishing Group UK 2020-09-18 /pmc/articles/PMC7501288/ /pubmed/32948758 http://dx.doi.org/10.1038/s41467-020-18543-0 Text en © The Author(s) 2020 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Delogu, F. Kunath, B. J. Evans, P. N. Arntzen, M. Ø. Hvidsten, T. R. Pope, P. B. Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes |
title | Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes |
title_full | Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes |
title_fullStr | Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes |
title_full_unstemmed | Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes |
title_short | Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes |
title_sort | integration of absolute multi-omics reveals dynamic protein-to-rna ratios and metabolic interplay within mixed-domain microbiomes |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7501288/ https://www.ncbi.nlm.nih.gov/pubmed/32948758 http://dx.doi.org/10.1038/s41467-020-18543-0 |
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