A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development

Masahiro Yamamoto, Rui Yamaguchi, Kaori Munakata, Kiyoe Takashima, Mitsue Nishiyama, Kyoji Hioki, Yasuyuki Ohnishi, Masao Nagasaki, Seiya Imoto, Satoru Miyano, Atsushi Ishige, Kenji Watanabe

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Background: Epidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal development of the host immune system. Basic research involving gnotobiotic mice has demonstrated that colonization at the age of 5 weeks is too late to reconstitute normal immune function. In this study, we examined the transcriptome profiles of the large intestine (LI), small intestine (SI), liver (LIV), and spleen (SPL) of 3 bacterial colonization models-specific pathogen-free mice (SPF), ex-germ-free mice with bacterial reconstitution at the time of delivery (0WexGF), and ex-germ-free mice with bacterial reconstitution at 5 weeks of age (5WexGF)-and compared them with those of germ-free (GF) mice.Results: Hundreds of genes were affected in all tissues in each of the colonized models; however, a gene set enrichment analysis method, MetaGene Profiler (MGP), demonstrated that the specific changes of Gene Ontology (GO) categories occurred predominantly in 0WexGF LI, SPF SI, and 5WexGF SPL, respectively. MGP analysis on signal pathways revealed prominent changes in toll-like receptor (TLR)- and type 1 interferon (IFN)-signaling in LI of 0WexGF and SPF mice, but not 5WexGF mice, while 5WexGF mice showed specific changes in chemokine signaling. RT-PCR analysis of TLR-related genes showed that the expression of interferon regulatory factor 3 (Irf3), a crucial rate-limiting transcription factor in the induction of type 1 IFN, prominently decreased in 0WexGF and SPF mice but not in 5WexGF and GF mice.Conclusion: The present study provides important new information regarding the molecular mechanisms of the so-called "hygiene hypothesis".

Original languageEnglish
Article number335
JournalBMC Genomics
Volume13
Issue number1
DOIs
Publication statusPublished - 2012 Jul 23

Fingerprint

Germ-Free Life
Microarray Analysis
Immune System
Specific Pathogen-Free Organisms
Large Intestine
Interferon Type I
Toll-Like Receptors
Small Intestine
Spleen
Hygiene Hypothesis
Interferon Regulatory Factor-3
Gene Ontology
Transcriptome
Chemokines
Genes

Keywords

  • Germ-free
  • Hygiene hypothesis
  • Metagene profiler
  • Toll-like receptor
  • Type 1 interferon

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. / Yamamoto, Masahiro; Yamaguchi, Rui; Munakata, Kaori; Takashima, Kiyoe; Nishiyama, Mitsue; Hioki, Kyoji; Ohnishi, Yasuyuki; Nagasaki, Masao; Imoto, Seiya; Miyano, Satoru; Ishige, Atsushi; Watanabe, Kenji.

In: BMC Genomics, Vol. 13, No. 1, 335, 23.07.2012.

Research output: Contribution to journalArticle

Yamamoto, M, Yamaguchi, R, Munakata, K, Takashima, K, Nishiyama, M, Hioki, K, Ohnishi, Y, Nagasaki, M, Imoto, S, Miyano, S, Ishige, A & Watanabe, K 2012, 'A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development', BMC Genomics, vol. 13, no. 1, 335. https://doi.org/10.1186/1471-2164-13-335
Yamamoto, Masahiro ; Yamaguchi, Rui ; Munakata, Kaori ; Takashima, Kiyoe ; Nishiyama, Mitsue ; Hioki, Kyoji ; Ohnishi, Yasuyuki ; Nagasaki, Masao ; Imoto, Seiya ; Miyano, Satoru ; Ishige, Atsushi ; Watanabe, Kenji. / A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. In: BMC Genomics. 2012 ; Vol. 13, No. 1.
@article{b0bb4ea5c15f4819b9e9c892418bc8d1,
title = "A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development",
abstract = "Background: Epidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal development of the host immune system. Basic research involving gnotobiotic mice has demonstrated that colonization at the age of 5 weeks is too late to reconstitute normal immune function. In this study, we examined the transcriptome profiles of the large intestine (LI), small intestine (SI), liver (LIV), and spleen (SPL) of 3 bacterial colonization models-specific pathogen-free mice (SPF), ex-germ-free mice with bacterial reconstitution at the time of delivery (0WexGF), and ex-germ-free mice with bacterial reconstitution at 5 weeks of age (5WexGF)-and compared them with those of germ-free (GF) mice.Results: Hundreds of genes were affected in all tissues in each of the colonized models; however, a gene set enrichment analysis method, MetaGene Profiler (MGP), demonstrated that the specific changes of Gene Ontology (GO) categories occurred predominantly in 0WexGF LI, SPF SI, and 5WexGF SPL, respectively. MGP analysis on signal pathways revealed prominent changes in toll-like receptor (TLR)- and type 1 interferon (IFN)-signaling in LI of 0WexGF and SPF mice, but not 5WexGF mice, while 5WexGF mice showed specific changes in chemokine signaling. RT-PCR analysis of TLR-related genes showed that the expression of interferon regulatory factor 3 (Irf3), a crucial rate-limiting transcription factor in the induction of type 1 IFN, prominently decreased in 0WexGF and SPF mice but not in 5WexGF and GF mice.Conclusion: The present study provides important new information regarding the molecular mechanisms of the so-called {"}hygiene hypothesis{"}.",
keywords = "Germ-free, Hygiene hypothesis, Metagene profiler, Toll-like receptor, Type 1 interferon",
author = "Masahiro Yamamoto and Rui Yamaguchi and Kaori Munakata and Kiyoe Takashima and Mitsue Nishiyama and Kyoji Hioki and Yasuyuki Ohnishi and Masao Nagasaki and Seiya Imoto and Satoru Miyano and Atsushi Ishige and Kenji Watanabe",
year = "2012",
month = "7",
day = "23",
doi = "10.1186/1471-2164-13-335",
language = "English",
volume = "13",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development

AU - Yamamoto, Masahiro

AU - Yamaguchi, Rui

AU - Munakata, Kaori

AU - Takashima, Kiyoe

AU - Nishiyama, Mitsue

AU - Hioki, Kyoji

AU - Ohnishi, Yasuyuki

AU - Nagasaki, Masao

AU - Imoto, Seiya

AU - Miyano, Satoru

AU - Ishige, Atsushi

AU - Watanabe, Kenji

PY - 2012/7/23

Y1 - 2012/7/23

N2 - Background: Epidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal development of the host immune system. Basic research involving gnotobiotic mice has demonstrated that colonization at the age of 5 weeks is too late to reconstitute normal immune function. In this study, we examined the transcriptome profiles of the large intestine (LI), small intestine (SI), liver (LIV), and spleen (SPL) of 3 bacterial colonization models-specific pathogen-free mice (SPF), ex-germ-free mice with bacterial reconstitution at the time of delivery (0WexGF), and ex-germ-free mice with bacterial reconstitution at 5 weeks of age (5WexGF)-and compared them with those of germ-free (GF) mice.Results: Hundreds of genes were affected in all tissues in each of the colonized models; however, a gene set enrichment analysis method, MetaGene Profiler (MGP), demonstrated that the specific changes of Gene Ontology (GO) categories occurred predominantly in 0WexGF LI, SPF SI, and 5WexGF SPL, respectively. MGP analysis on signal pathways revealed prominent changes in toll-like receptor (TLR)- and type 1 interferon (IFN)-signaling in LI of 0WexGF and SPF mice, but not 5WexGF mice, while 5WexGF mice showed specific changes in chemokine signaling. RT-PCR analysis of TLR-related genes showed that the expression of interferon regulatory factor 3 (Irf3), a crucial rate-limiting transcription factor in the induction of type 1 IFN, prominently decreased in 0WexGF and SPF mice but not in 5WexGF and GF mice.Conclusion: The present study provides important new information regarding the molecular mechanisms of the so-called "hygiene hypothesis".

AB - Background: Epidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal development of the host immune system. Basic research involving gnotobiotic mice has demonstrated that colonization at the age of 5 weeks is too late to reconstitute normal immune function. In this study, we examined the transcriptome profiles of the large intestine (LI), small intestine (SI), liver (LIV), and spleen (SPL) of 3 bacterial colonization models-specific pathogen-free mice (SPF), ex-germ-free mice with bacterial reconstitution at the time of delivery (0WexGF), and ex-germ-free mice with bacterial reconstitution at 5 weeks of age (5WexGF)-and compared them with those of germ-free (GF) mice.Results: Hundreds of genes were affected in all tissues in each of the colonized models; however, a gene set enrichment analysis method, MetaGene Profiler (MGP), demonstrated that the specific changes of Gene Ontology (GO) categories occurred predominantly in 0WexGF LI, SPF SI, and 5WexGF SPL, respectively. MGP analysis on signal pathways revealed prominent changes in toll-like receptor (TLR)- and type 1 interferon (IFN)-signaling in LI of 0WexGF and SPF mice, but not 5WexGF mice, while 5WexGF mice showed specific changes in chemokine signaling. RT-PCR analysis of TLR-related genes showed that the expression of interferon regulatory factor 3 (Irf3), a crucial rate-limiting transcription factor in the induction of type 1 IFN, prominently decreased in 0WexGF and SPF mice but not in 5WexGF and GF mice.Conclusion: The present study provides important new information regarding the molecular mechanisms of the so-called "hygiene hypothesis".

KW - Germ-free

KW - Hygiene hypothesis

KW - Metagene profiler

KW - Toll-like receptor

KW - Type 1 interferon

UR - http://www.scopus.com/inward/record.url?scp=84865339630&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84865339630&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-13-335

DO - 10.1186/1471-2164-13-335

M3 - Article

C2 - 22823934

AN - SCOPUS:84865339630

VL - 13

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 335

ER -