A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

30562947

DOI Digital object identifier for electronic documents.

10.3390/ijms19124079

URI

Authors

Ishii C, Nakanishi Y, Murakami S, Nozu R, Ueno M, Hioki K, Aw W, Hirayama A, Soga T, Ito M, Tomita M, Fukuda S

Journal

International journal of molecular sciences

Year

2018

Keywords:

American diet, CE-TOFMS, intestinal microbiota, metabologenomics, metabolome, microbiome, multi-omics, next-generation sequencing

Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Mus musculus

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Methionine measurement Methionine measurement,methionine measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: mice fed control rodent diet.

Group 1 name Corresponds to the case (exposed) group for case-control studies: mice fed American Diet

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber

Group 0 sample size Number of subjects in the control (unexposed) group: 6

Group 1 sample size Number of subjects in the case (exposed) group: 5

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V2

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Richness Number of species: unchanged

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17

Curated date: 2021/01/10

Curator: Tahiya Begum

Revision editor(s): Claregrieve1, WikiWorks

Source: Table 2

Description: Increased abundance of microbial taxa in AD mice compared with control mice

Abundance in Group 1: increased abundance in mice fed American Diet

NCBI	Quality Control	Links
Coprococcus
Oscillospira
Ruminococcus
unclassified Prevotellaceae
unclassified Clostridiales Family XVII.
unclassified Bacillaceae
Bacillus
Lactococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/17

Curated date: 2021/01/10

Curator: Tahiya Begum

Revision editor(s): Claregrieve1, WikiWorks

Source: Table 2

Description: Decreased abundance of microbial taxa in AD mice compared with control mice

Abundance in Group 1: decreased abundance in mice fed American Diet

NCBI	Quality Control	Links
unclassified Erysipelotrichaceae
Eubacterium sp.
unclassified Clostridiaceae
Clostridium
Prevotella

Revision editor(s): Claregrieve1, WikiWorks