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.

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change

“…The impact of the change of diet was marked, despite a high inter-horse variability as seen in the large mean standard errors that was found mainly in lactate concentrations in the caecum and colon. This confirmed the individual susceptibility, seen in horses fed high-starch diets as previously reported by several authors studying the equine hindgut microbial ecosystem (Julliand et al, 2001;Medina et al, 2002;Dougal et al, 2012 andSchoster et al, 2013;Sadet-Bourgeteau et al, 2014;Costa et al, 2015), and confirmed that some horses are more likely to develop digestive dysbiosis and potential intestinal diseases, such as colic. Using PCA the data showed that the two microbial ecosystems of horses clearly differed with the diet, and thus established that the hindgut microbiota was altered with the B diet.…”

“…These faecal parameters could be of particular usefulness for the diagnosis of microbial imbalances in the caecum and RV colon (the proximal hindgut). Previous studies have shown that faeces could be representative of the distal hindgut microbial composition, but not of the proximal hindgut (Da Veiga et al, 2005;Hastie et al, 2008;Dougal et al, 2012 andSchoster et al, 2013;Sadet-Bourgeteau et al, 2014;Costa et al, 2015). In this study the data demonstrated that variations in the proximal hindgut microbial ecosystem could have repercussions on the faecal one.…”

“…The accessibility to such contents is not possible routinely from nonexperimental animals, as there is no direct access to these gut regions, whereas faeces can easily be collected and could be used as suitable samples to generate biomarkers to evaluate the status of the hindgut microbiota. Several studies have compared the hindgut and the faeces in terms of microbial diversity and structure (Da Veiga et al, 2005;Hastie et al, 2008;Dougal et al, 2012 andSchoster et al, 2013;Sadet-Bourgeteau et al, 2014;Costa et al, 2015) and in terms of microbial activity (Da Veiga et al, 2005;Dougal et al, 2012). Overall, these studies concluded that the microbial communities found in the proximal region of the hindgut (caecum, right ventral (RV) colon and left ventral colon) clearly differed from those found in the distal region (left dorsal colon and right dorsal colon), with the change occurring at the pelvic flexure region of the gut.…”

Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA)

“…Indeed, it has yet to be demonstrated whether the faecal bacterial ecosystem is representative of that of the caecum and/or colon. Few studies have compared the bacterial community diversity of the equine caecum, colon and faeces (de Fombelle et al, 2003;Hastie et al, 2008;Dougal et al, 2011 and2012;Schoster et al, 2013). Of these few studies, all of them concluded that the faecal bacterial community was not representative of that of the caecum.…”

“…de Fombelle et al (2003) and Hastie et al (2008) quantified specific bacterial community in the right ventral v. left dorsal colon using culturing techniques and ventral v. dorsal colon using quantitative PCR. Recently, Dougal et al (2011 and2012) and Schoster et al (2013) assessed the impact of gut location at the level of bacterial community using terminal restriction fragment length polymorphism (TRFLP). Dougal et al (2011 and2012) found that the bacterial diversity of the right dorsal colon was similar to that of the faeces, which could be expected since, anatomically, the right dorsal colon is the closest to the rectum.…”