Cargando…

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets

BACKGROUND: Evidence is accumulating that perturbation of early life microbial colonization of the gut induces long-lasting adverse health effects in individuals. Understanding the mechanisms behind these effects will facilitate modulation of intestinal health. The objective of this study was to ide...

Descripción completa

Detalles Bibliográficos
Autores principales: Benis, Nirupama, Schokker, Dirkjan, Suarez-Diez, Maria, Martins dos Santos, Vitor AP, Smidt, Hauke, Smits, Mari A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518884/
https://www.ncbi.nlm.nih.gov/pubmed/26220188
http://dx.doi.org/10.1186/s12864-015-1733-8
_version_ 1782383417627770880
author Benis, Nirupama
Schokker, Dirkjan
Suarez-Diez, Maria
Martins dos Santos, Vitor AP
Smidt, Hauke
Smits, Mari A
author_facet Benis, Nirupama
Schokker, Dirkjan
Suarez-Diez, Maria
Martins dos Santos, Vitor AP
Smidt, Hauke
Smits, Mari A
author_sort Benis, Nirupama
collection PubMed
description BACKGROUND: Evidence is accumulating that perturbation of early life microbial colonization of the gut induces long-lasting adverse health effects in individuals. Understanding the mechanisms behind these effects will facilitate modulation of intestinal health. The objective of this study was to identify biological processes involved in these long lasting effects and the (molecular) factors that regulate them. We used an antibiotic and the same antibiotic in combination with stress on piglets as an early life perturbation. Then we used host gene expression data from the gut (jejunum) tissue and community-scale analysis of gut microbiota from the same location of the gut, at three different time-points to gauge the reaction to the perturbation. We analysed the data by a new combination of existing tools. First, we analysed the data in two dimensions, treatment and time, with quadratic regression analysis. Then we applied network-based data integration approaches to find correlations between host gene expression and the resident microbial species. RESULTS: The use of a new combination of data analysis tools allowed us to identify significant long-lasting differences in jejunal gene expression patterns resulting from the early life perturbations. In addition, we were able to identify potential key gene regulators (hubs) for these long-lasting effects. Furthermore, data integration also showed that there are a handful of bacterial groups that were associated with temporal changes in gene expression. CONCLUSION: The applied systems-biology approach allowed us to take the first steps in unravelling biological processes involved in long lasting effects in the gut due to early life perturbations. The observed data are consistent with the hypothesis that these long lasting effects are due to differences in the programming of the gut immune system as induced by the temporary early life changes in the composition and/or diversity of microbiota in the gut. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1733-8) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4518884
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-45188842015-07-30 Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets Benis, Nirupama Schokker, Dirkjan Suarez-Diez, Maria Martins dos Santos, Vitor AP Smidt, Hauke Smits, Mari A BMC Genomics Research Article BACKGROUND: Evidence is accumulating that perturbation of early life microbial colonization of the gut induces long-lasting adverse health effects in individuals. Understanding the mechanisms behind these effects will facilitate modulation of intestinal health. The objective of this study was to identify biological processes involved in these long lasting effects and the (molecular) factors that regulate them. We used an antibiotic and the same antibiotic in combination with stress on piglets as an early life perturbation. Then we used host gene expression data from the gut (jejunum) tissue and community-scale analysis of gut microbiota from the same location of the gut, at three different time-points to gauge the reaction to the perturbation. We analysed the data by a new combination of existing tools. First, we analysed the data in two dimensions, treatment and time, with quadratic regression analysis. Then we applied network-based data integration approaches to find correlations between host gene expression and the resident microbial species. RESULTS: The use of a new combination of data analysis tools allowed us to identify significant long-lasting differences in jejunal gene expression patterns resulting from the early life perturbations. In addition, we were able to identify potential key gene regulators (hubs) for these long-lasting effects. Furthermore, data integration also showed that there are a handful of bacterial groups that were associated with temporal changes in gene expression. CONCLUSION: The applied systems-biology approach allowed us to take the first steps in unravelling biological processes involved in long lasting effects in the gut due to early life perturbations. The observed data are consistent with the hypothesis that these long lasting effects are due to differences in the programming of the gut immune system as induced by the temporary early life changes in the composition and/or diversity of microbiota in the gut. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1733-8) contains supplementary material, which is available to authorized users. BioMed Central 2015-07-29 /pmc/articles/PMC4518884/ /pubmed/26220188 http://dx.doi.org/10.1186/s12864-015-1733-8 Text en © Benis et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Benis, Nirupama
Schokker, Dirkjan
Suarez-Diez, Maria
Martins dos Santos, Vitor AP
Smidt, Hauke
Smits, Mari A
Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
title Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
title_full Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
title_fullStr Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
title_full_unstemmed Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
title_short Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
title_sort network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518884/
https://www.ncbi.nlm.nih.gov/pubmed/26220188
http://dx.doi.org/10.1186/s12864-015-1733-8
work_keys_str_mv AT benisnirupama networkanalysisoftemporalfunctionalitiesofthegutinducedbyperturbationsinnewbornpiglets
AT schokkerdirkjan networkanalysisoftemporalfunctionalitiesofthegutinducedbyperturbationsinnewbornpiglets
AT suarezdiezmaria networkanalysisoftemporalfunctionalitiesofthegutinducedbyperturbationsinnewbornpiglets
AT martinsdossantosvitorap networkanalysisoftemporalfunctionalitiesofthegutinducedbyperturbationsinnewbornpiglets
AT smidthauke networkanalysisoftemporalfunctionalitiesofthegutinducedbyperturbationsinnewbornpiglets
AT smitsmaria networkanalysisoftemporalfunctionalitiesofthegutinducedbyperturbationsinnewbornpiglets