Cargando…

Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet

Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly influencing the health and well-being of the host. In addition to the standard differential expression analysis of host genes to assess the complex cross-talk between environme...

Descripción completa

Detalles Bibliográficos
Autores principales: He, Kejun, Donovan, Sharon M., Ivanov, Ivan V., Goldsby, Jennifer S., Davidson, Laurie A., Chapkin, Robert S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766018/
https://www.ncbi.nlm.nih.gov/pubmed/33353204
http://dx.doi.org/10.3390/microorganisms8122032
_version_ 1783628618780377088
author He, Kejun
Donovan, Sharon M.
Ivanov, Ivan V.
Goldsby, Jennifer S.
Davidson, Laurie A.
Chapkin, Robert S.
author_facet He, Kejun
Donovan, Sharon M.
Ivanov, Ivan V.
Goldsby, Jennifer S.
Davidson, Laurie A.
Chapkin, Robert S.
author_sort He, Kejun
collection PubMed
description Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly influencing the health and well-being of the host. In addition to the standard differential expression analysis of host genes to assess the complex cross-talk between environment (diet), microbiome, and host intestinal physiology, data-driven integrative approaches are needed to identify potential biomarkers of both host genes and microbial communities that characterize these interactions. Our findings demonstrate that the complementary application of univariate differential gene expression analysis and multivariate approaches such as sparse Canonical Correlation Analysis (sCCA) and sparse Principal Components Analysis (sPCA) can be used to integrate data from both the healthy infant gut microbial community and host transcriptome (exfoliome) using stool derived exfoliated cells shed from the gut. These approaches reveal host genes and microbial functional categories related to the feeding phenotype of the infants. Our findings also confirm that combinatorial noninvasive -omic approaches provide an integrative genomics-based perspective of neonatal host-gut microbiome interactions.
format Online
Article
Text
id pubmed-7766018
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-77660182020-12-28 Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet He, Kejun Donovan, Sharon M. Ivanov, Ivan V. Goldsby, Jennifer S. Davidson, Laurie A. Chapkin, Robert S. Microorganisms Article Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly influencing the health and well-being of the host. In addition to the standard differential expression analysis of host genes to assess the complex cross-talk between environment (diet), microbiome, and host intestinal physiology, data-driven integrative approaches are needed to identify potential biomarkers of both host genes and microbial communities that characterize these interactions. Our findings demonstrate that the complementary application of univariate differential gene expression analysis and multivariate approaches such as sparse Canonical Correlation Analysis (sCCA) and sparse Principal Components Analysis (sPCA) can be used to integrate data from both the healthy infant gut microbial community and host transcriptome (exfoliome) using stool derived exfoliated cells shed from the gut. These approaches reveal host genes and microbial functional categories related to the feeding phenotype of the infants. Our findings also confirm that combinatorial noninvasive -omic approaches provide an integrative genomics-based perspective of neonatal host-gut microbiome interactions. MDPI 2020-12-18 /pmc/articles/PMC7766018/ /pubmed/33353204 http://dx.doi.org/10.3390/microorganisms8122032 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
He, Kejun
Donovan, Sharon M.
Ivanov, Ivan V.
Goldsby, Jennifer S.
Davidson, Laurie A.
Chapkin, Robert S.
Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet
title Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet
title_full Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet
title_fullStr Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet
title_full_unstemmed Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet
title_short Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet
title_sort assessing the multivariate relationship between the human infant intestinal exfoliated cell transcriptome (exfoliome) and microbiome in response to diet
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766018/
https://www.ncbi.nlm.nih.gov/pubmed/33353204
http://dx.doi.org/10.3390/microorganisms8122032
work_keys_str_mv AT hekejun assessingthemultivariaterelationshipbetweenthehumaninfantintestinalexfoliatedcelltranscriptomeexfoliomeandmicrobiomeinresponsetodiet
AT donovansharonm assessingthemultivariaterelationshipbetweenthehumaninfantintestinalexfoliatedcelltranscriptomeexfoliomeandmicrobiomeinresponsetodiet
AT ivanovivanv assessingthemultivariaterelationshipbetweenthehumaninfantintestinalexfoliatedcelltranscriptomeexfoliomeandmicrobiomeinresponsetodiet
AT goldsbyjennifers assessingthemultivariaterelationshipbetweenthehumaninfantintestinalexfoliatedcelltranscriptomeexfoliomeandmicrobiomeinresponsetodiet
AT davidsonlauriea assessingthemultivariaterelationshipbetweenthehumaninfantintestinalexfoliatedcelltranscriptomeexfoliomeandmicrobiomeinresponsetodiet
AT chapkinroberts assessingthemultivariaterelationshipbetweenthehumaninfantintestinalexfoliatedcelltranscriptomeexfoliomeandmicrobiomeinresponsetodiet