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Causal discovery for the microbiome
Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various di...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680137/ https://www.ncbi.nlm.nih.gov/pubmed/36152674 http://dx.doi.org/10.1016/S2666-5247(22)00186-0 |
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author | Corander, Jukka Hanage, William P Pensar, Johan |
author_facet | Corander, Jukka Hanage, William P Pensar, Johan |
author_sort | Corander, Jukka |
collection | PubMed |
description | Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch’s classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere. |
format | Online Article Text |
id | pubmed-9680137 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
record_format | MEDLINE/PubMed |
spelling | pubmed-96801372022-11-22 Causal discovery for the microbiome Corander, Jukka Hanage, William P Pensar, Johan Lancet Microbe Article Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch’s classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere. 2022-11 2022-09-21 /pmc/articles/PMC9680137/ /pubmed/36152674 http://dx.doi.org/10.1016/S2666-5247(22)00186-0 Text en https://creativecommons.org/licenses/by/4.0/This is an Open Access article under the CC BY 4.0 license. |
spellingShingle | Article Corander, Jukka Hanage, William P Pensar, Johan Causal discovery for the microbiome |
title | Causal discovery for the microbiome |
title_full | Causal discovery for the microbiome |
title_fullStr | Causal discovery for the microbiome |
title_full_unstemmed | Causal discovery for the microbiome |
title_short | Causal discovery for the microbiome |
title_sort | causal discovery for the microbiome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680137/ https://www.ncbi.nlm.nih.gov/pubmed/36152674 http://dx.doi.org/10.1016/S2666-5247(22)00186-0 |
work_keys_str_mv | AT coranderjukka causaldiscoveryforthemicrobiome AT hanagewilliamp causaldiscoveryforthemicrobiome AT pensarjohan causaldiscoveryforthemicrobiome |