A comparison of the microbiome and the metabolome of different regions of the equine hindgut

Kirsty Dougal, Patricia A Harris, Arwyn Edwards, Justin A Pachebat, Tina M Blackmore, Hilary J Worgan, C Jamie Newbold

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

The microbiome and associated metabolome of faecal samples were compared to those from the caecum and right dorsal colon of horses and ponies euthanised for nonresearch purposes by investigating the microbial population community structure as well as their functional metabolic products. Through the use of 16S rRNA gene dendrograms, the caecum microbiome was shown to cluster separately from the other gut regions. 16S rRNA gene-based quantitative PCR (q-PCR) also demonstrated differences between the caecum and the other gut regions. Metabolites as identified by Fourier transform infrared clustered in a similar way and specific metabolic products (volatile fatty acids and ammonia) also varied by region. Protozoal 18S rDNA concentration and archaeal mcrA gene concentration quantified by q-PCR were found in higher numbers in the colon than the other gut regions. Diversity calculations using Simpson and Shannon-Wiener indices demonstrated higher diversity in the right dorsal colon and faeces than in the caecum. All findings of this study suggest that faecal samples are likely to represent the microbial population of the right dorsal colon to some extent but not that of the caecum, indicating careful consideration is required when planning microbial investigations of the hindgut of the horse.

Original languageEnglish
Pages (from-to)642-652
Number of pages11
JournalFEMS Microbiology Ecology
Volume82
Issue number3
DOIs
Publication statusPrint publication - Dec 2012
Externally publishedYes

Fingerprint

Metabolome
Microbiota
Horses
Colon
horse
rRNA Genes
gene
Archaeal Genes
Polymerase Chain Reaction
Volatile Fatty Acids
Fourier Analysis
Ribosomal DNA
Ammonia
Feces
feces
Population
Fourier transform
metabolite
community structure
fatty acid

Bibliographical note

© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Keywords

  • Animals
  • Archaea
  • Bacteria
  • Cecum
  • Colon
  • DNA
  • Fatty Acids
  • Fungi
  • Horses
  • Metabolome
  • Metagenome
  • Polymerase chain reaction
  • RNA

Cite this

Dougal, Kirsty ; Harris, Patricia A ; Edwards, Arwyn ; Pachebat, Justin A ; Blackmore, Tina M ; Worgan, Hilary J ; Newbold, C Jamie. / A comparison of the microbiome and the metabolome of different regions of the equine hindgut. In: FEMS Microbiology Ecology. 2012 ; Vol. 82, No. 3. pp. 642-652.
@article{899c8e200ba14dc4b0acfef1d1b7223d,
title = "A comparison of the microbiome and the metabolome of different regions of the equine hindgut",
abstract = "The microbiome and associated metabolome of faecal samples were compared to those from the caecum and right dorsal colon of horses and ponies euthanised for nonresearch purposes by investigating the microbial population community structure as well as their functional metabolic products. Through the use of 16S rRNA gene dendrograms, the caecum microbiome was shown to cluster separately from the other gut regions. 16S rRNA gene-based quantitative PCR (q-PCR) also demonstrated differences between the caecum and the other gut regions. Metabolites as identified by Fourier transform infrared clustered in a similar way and specific metabolic products (volatile fatty acids and ammonia) also varied by region. Protozoal 18S rDNA concentration and archaeal mcrA gene concentration quantified by q-PCR were found in higher numbers in the colon than the other gut regions. Diversity calculations using Simpson and Shannon-Wiener indices demonstrated higher diversity in the right dorsal colon and faeces than in the caecum. All findings of this study suggest that faecal samples are likely to represent the microbial population of the right dorsal colon to some extent but not that of the caecum, indicating careful consideration is required when planning microbial investigations of the hindgut of the horse.",
keywords = "Animals, Archaea, Bacteria, Cecum, Colon, DNA, Fatty Acids, Fungi, Horses, Metabolome, Metagenome, Polymerase chain reaction, RNA",
author = "Kirsty Dougal and Harris, {Patricia A} and Arwyn Edwards and Pachebat, {Justin A} and Blackmore, {Tina M} and Worgan, {Hilary J} and Newbold, {C Jamie}",
note = "{\circledC} 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.",
year = "2012",
month = "12",
doi = "10.1111/j.1574-6941.2012.01441.x",
language = "English",
volume = "82",
pages = "642--652",
journal = "FEMS Microbiology Ecology",
issn = "0168-6496",
publisher = "Oxford University Press",
number = "3",

}

A comparison of the microbiome and the metabolome of different regions of the equine hindgut. / Dougal, Kirsty; Harris, Patricia A; Edwards, Arwyn; Pachebat, Justin A; Blackmore, Tina M; Worgan, Hilary J; Newbold, C Jamie.

In: FEMS Microbiology Ecology, Vol. 82, No. 3, 12.2012, p. 642-652.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A comparison of the microbiome and the metabolome of different regions of the equine hindgut

AU - Dougal, Kirsty

AU - Harris, Patricia A

AU - Edwards, Arwyn

AU - Pachebat, Justin A

AU - Blackmore, Tina M

AU - Worgan, Hilary J

AU - Newbold, C Jamie

N1 - © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

PY - 2012/12

Y1 - 2012/12

N2 - The microbiome and associated metabolome of faecal samples were compared to those from the caecum and right dorsal colon of horses and ponies euthanised for nonresearch purposes by investigating the microbial population community structure as well as their functional metabolic products. Through the use of 16S rRNA gene dendrograms, the caecum microbiome was shown to cluster separately from the other gut regions. 16S rRNA gene-based quantitative PCR (q-PCR) also demonstrated differences between the caecum and the other gut regions. Metabolites as identified by Fourier transform infrared clustered in a similar way and specific metabolic products (volatile fatty acids and ammonia) also varied by region. Protozoal 18S rDNA concentration and archaeal mcrA gene concentration quantified by q-PCR were found in higher numbers in the colon than the other gut regions. Diversity calculations using Simpson and Shannon-Wiener indices demonstrated higher diversity in the right dorsal colon and faeces than in the caecum. All findings of this study suggest that faecal samples are likely to represent the microbial population of the right dorsal colon to some extent but not that of the caecum, indicating careful consideration is required when planning microbial investigations of the hindgut of the horse.

AB - The microbiome and associated metabolome of faecal samples were compared to those from the caecum and right dorsal colon of horses and ponies euthanised for nonresearch purposes by investigating the microbial population community structure as well as their functional metabolic products. Through the use of 16S rRNA gene dendrograms, the caecum microbiome was shown to cluster separately from the other gut regions. 16S rRNA gene-based quantitative PCR (q-PCR) also demonstrated differences between the caecum and the other gut regions. Metabolites as identified by Fourier transform infrared clustered in a similar way and specific metabolic products (volatile fatty acids and ammonia) also varied by region. Protozoal 18S rDNA concentration and archaeal mcrA gene concentration quantified by q-PCR were found in higher numbers in the colon than the other gut regions. Diversity calculations using Simpson and Shannon-Wiener indices demonstrated higher diversity in the right dorsal colon and faeces than in the caecum. All findings of this study suggest that faecal samples are likely to represent the microbial population of the right dorsal colon to some extent but not that of the caecum, indicating careful consideration is required when planning microbial investigations of the hindgut of the horse.

KW - Animals

KW - Archaea

KW - Bacteria

KW - Cecum

KW - Colon

KW - DNA

KW - Fatty Acids

KW - Fungi

KW - Horses

KW - Metabolome

KW - Metagenome

KW - Polymerase chain reaction

KW - RNA

U2 - 10.1111/j.1574-6941.2012.01441.x

DO - 10.1111/j.1574-6941.2012.01441.x

M3 - Article

C2 - 22757649

VL - 82

SP - 642

EP - 652

JO - FEMS Microbiology Ecology

JF - FEMS Microbiology Ecology

SN - 0168-6496

IS - 3

ER -