Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

Abstract Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets ca...

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Autores principales:	Anna Paola Carrieri, Niina Haiminen, Sean Maudsley-Barton, Laura-Jayne Gardiner, Barry Murphy, Andrew E. Mayes, Sarah Paterson, Sally Grimshaw, Martyn Winn, Cameron Shand, Panagiotis Hadjidoukas, Will P. M. Rowe, Stacy Hawkins, Ashley MacGuire-Flanagan, Jane Tazzioli, John G. Kenny, Laxmi Parida, Michael Hoptroff, Edward O. Pyzer-Knapp
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cb1dd98e135247c4b14f7dc863db1e07
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spelling	oai:doaj.org-article:cb1dd98e135247c4b14f7dc863db1e072021-12-02T13:30:50ZExplainable AI reveals changes in skin microbiome composition linked to phenotypic differences10.1038/s41598-021-83922-62045-2322https://doaj.org/article/cb1dd98e135247c4b14f7dc863db1e072021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83922-6https://doaj.org/toc/2045-2322Abstract Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome’s role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.Anna Paola CarrieriNiina HaiminenSean Maudsley-BartonLaura-Jayne GardinerBarry MurphyAndrew E. MayesSarah PatersonSally GrimshawMartyn WinnCameron ShandPanagiotis HadjidoukasWill P. M. RoweStacy HawkinsAshley MacGuire-FlanaganJane TazzioliJohn G. KennyLaxmi ParidaMichael HoptroffEdward O. Pyzer-KnappNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anna Paola Carrieri Niina Haiminen Sean Maudsley-Barton Laura-Jayne Gardiner Barry Murphy Andrew E. Mayes Sarah Paterson Sally Grimshaw Martyn Winn Cameron Shand Panagiotis Hadjidoukas Will P. M. Rowe Stacy Hawkins Ashley MacGuire-Flanagan Jane Tazzioli John G. Kenny Laxmi Parida Michael Hoptroff Edward O. Pyzer-Knapp Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
description	Abstract Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome’s role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.
format	article
author	Anna Paola Carrieri Niina Haiminen Sean Maudsley-Barton Laura-Jayne Gardiner Barry Murphy Andrew E. Mayes Sarah Paterson Sally Grimshaw Martyn Winn Cameron Shand Panagiotis Hadjidoukas Will P. M. Rowe Stacy Hawkins Ashley MacGuire-Flanagan Jane Tazzioli John G. Kenny Laxmi Parida Michael Hoptroff Edward O. Pyzer-Knapp
author_facet	Anna Paola Carrieri Niina Haiminen Sean Maudsley-Barton Laura-Jayne Gardiner Barry Murphy Andrew E. Mayes Sarah Paterson Sally Grimshaw Martyn Winn Cameron Shand Panagiotis Hadjidoukas Will P. M. Rowe Stacy Hawkins Ashley MacGuire-Flanagan Jane Tazzioli John G. Kenny Laxmi Parida Michael Hoptroff Edward O. Pyzer-Knapp
author_sort	Anna Paola Carrieri
title	Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
title_short	Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
title_full	Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
title_fullStr	Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
title_full_unstemmed	Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
title_sort	explainable ai reveals changes in skin microbiome composition linked to phenotypic differences
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cb1dd98e135247c4b14f7dc863db1e07
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Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

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