Open AccessA comparison of the microbiome and the metabolome of different regions of the equine hindgut
Author(s) -
Dougal Kirsty,
Harris Patricia A.,
Edwards Arwyn,
Pachebat Justin A.,
Blackmore Tina M.,
Worgan Hilary J.,
Newbold C. Jamie
Publication year - 2012
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2012.01441.x
Subject(s) - biology , hindgut , caecum , metabolome , microbiome , 16s ribosomal rna , unifrac , population , feces , metagenomics , bacteroidetes , pyrosequencing , microbiology and biotechnology , zoology , bacteria , gene , genetics , ecology , biochemistry , metabolite , midgut , medicine , demography , sociology , larva
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 16 S r RNA gene dendrograms, the caecum microbiome was shown to cluster separately from the other gut regions. 16 S r RNA gene‐based quantitative PCR (q‐ PCR ) also demonstrated differences between the caecum and the other gut regions. Metabolites as identified by F ourier transform infrared clustered in a similar way and specific metabolic products (volatile fatty acids and ammonia) also varied by region. Protozoal 18 S r DNA 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 S impson and S hannon– W iener 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.