The eukaryotic microbiome of the equine hindgut reveals proximal and distal ciliate faunas

The hindgut of the horse I host to the microbial community essential to the breakdown of dietary structural carbohydrates. Numerically the majority is made up of the bacteria. However, a significant proportion of the microbiota biomass is made up of ciliate protozoa. The presence or absence of ciliate species in different anatomical regions of the hindgut has been reported previously and have been proposed as proximal and distal faunas.Next generation 18S rRNA amplicon sequencing was used to characterise the eukaryotic population structure and the distribution of ciliate protozoal populations in different regions of the hindgut of the equine digestive tract. Digesta samples were taken from 10 horses from six anatomically defined hindgut regions: caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC), small colon (SC) ) with additional samples from the terminal ileum (midgut) and faecal samples (from the rectum). Total eukaryotic 18S rRNA gene amplicons were generated by PCR and sequenced using 454 pyrosequencing. Taxonomy analysis revealed the dominant phylum to be the Ciliophora (Ciliates) (57%). The remaining eukaryotic constituents were: Streptophyta (land plants) (10%), unidentified environmental eukaryotes (7%) Dikarya (4%) and Neocallimastigomycota (2%), Arthrapoda (6%), Nematoda (3%), Archamoebae (4%) and Cordata (5%). A core group of ciliate species was defined as species occurring in all horses and all gut locations. However, their relative abundance was significantly different according to gut location. UPMGA analysis showed clustering of caecum/ventral colon and dorsal/small colon gut locations, respectively suggesting the presence of distinct proximal and distal ciliate populations. Interestingly however, the ciliate population in the faeces clustered with the population present in the ileum suggesting either faecal contamination of dietary intake or coprophagy