Interactions and functionalities of the gut revealed by computational approaches

Nirupama Benis

Research output: Thesisinternal PhD, WUAcademic

Abstract

The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations.

The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response.

Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.

LanguageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Smits, M.A., Promotor
  • Martins dos Santos, Vitor, Promotor
  • Schokker, Dirkjan, Co-promotor
  • Suarez Diez, Maria, Co-promotor
Award date4 Jul 2017
Place of PublicationWageningen
Publisher
Print ISBNs9789463434546
DOIs
Publication statusPublished - 2017

Fingerprint

digestive system
gastrointestinal system
pathogens
methodology
bioinformatics
homeostasis
toxins
animal models
digestion
antibiotics
swine
organisms
mice
nutrients
diet
infection

Keywords

  • pigs
  • mice
  • digestive tract
  • digestive system
  • intestinal microorganisms
  • intestinal mucosa
  • computational science
  • immune system
  • feeds
  • animal nutrition
  • nutrition physiology
  • animal health

Cite this

Benis, Nirupama. / Interactions and functionalities of the gut revealed by computational approaches. Wageningen : Wageningen University, 2017. 247 p.
@phdthesis{36217fda430d4f12b7b645ca643587d1,
title = "Interactions and functionalities of the gut revealed by computational approaches",
abstract = "The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations. The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response. Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.",
keywords = "pigs, mice, digestive tract, digestive system, intestinal microorganisms, intestinal mucosa, computational science, immune system, feeds, animal nutrition, nutrition physiology, animal health, varkens, muizen, spijsverteringskanaal, spijsverteringsstelsel, darmmicro-organismen, darmslijmvlies, computational science, immuunsysteem, voer, diervoeding, voedingsfysiologie, diergezondheid",
author = "Nirupama Benis",
note = "WU thesis 6706 Includes bibliographical references. - With summary in English",
year = "2017",
doi = "10.18174/416470",
language = "English",
isbn = "9789463434546",
publisher = "Wageningen University",
school = "Wageningen University",

}

Benis, N 2017, 'Interactions and functionalities of the gut revealed by computational approaches', Doctor of Philosophy, Wageningen University, Wageningen. https://doi.org/10.18174/416470

Interactions and functionalities of the gut revealed by computational approaches. / Benis, Nirupama.

Wageningen : Wageningen University, 2017. 247 p.

Research output: Thesisinternal PhD, WUAcademic

TY - THES

T1 - Interactions and functionalities of the gut revealed by computational approaches

AU - Benis, Nirupama

N1 - WU thesis 6706 Includes bibliographical references. - With summary in English

PY - 2017

Y1 - 2017

N2 - The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations. The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response. Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.

AB - The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations. The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response. Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.

KW - pigs

KW - mice

KW - digestive tract

KW - digestive system

KW - intestinal microorganisms

KW - intestinal mucosa

KW - computational science

KW - immune system

KW - feeds

KW - animal nutrition

KW - nutrition physiology

KW - animal health

KW - varkens

KW - muizen

KW - spijsverteringskanaal

KW - spijsverteringsstelsel

KW - darmmicro-organismen

KW - darmslijmvlies

KW - computational science

KW - immuunsysteem

KW - voer

KW - diervoeding

KW - voedingsfysiologie

KW - diergezondheid

U2 - 10.18174/416470

DO - 10.18174/416470

M3 - internal PhD, WU

SN - 9789463434546

PB - Wageningen University

CY - Wageningen

ER -