Is there a stable core microbiota in the equine hindgut ?

The microbial population in the hindgut plays a key role in the health and welfare of the horse: an active and functional fibrolytic bacterial population in the hindgut will convert fibrous feeds into volatile fatty acids which make a significant contribution to the energy requirements of the host, whilst an unbalanced fermentation leading to the proliferation of lactic acid producing bacteria will decrease fibre breakdown and lead to the accumulation of toxic by-products which can have wide ranging effects on the animal's metabolism including but not limited to the onset of laminitis. In the wider area of gut microbiology there is an active debate concerning the existence of a core stable microbial microbiota. It is estimated that there are perhaps 5000 unique bacterial phylotypes in the human gut when considered over a range of individuals under different spatial and temporal conditions. However, it is speculated that there are perhaps 300 phylotypes that make up a core stable microbial population in a healthy individual. This population is unique to individuals and changes only slightly as people age being resistant to modification and resilient to antibiotics. In addition, to the core group, there also are 'passengers' or transients, sometimes in great numbers, sometimes undetectable. The size of the transitory population may depend on external or coincidental influences such as diet, travelling or infections. Our recent observations have suggested that equine hindgut might not fit this model, in grazing horses the faecal microbiota (as relieved by TFRLP) was as different between individual horses on consecutive days as it was between individual horses on the same day. Whilst in horses being fed a commercial compounded feed there appear to be some stability in the faecal microbiota of individual horses during an intensive sampling regime over 72 hours, but when the same animals were sampled some 11 weeks later (having been on the same diet throughout) although again a stable population was determined over an intensive 72 hour sampling period the new population had little or no relationship to the orginal population, suggesting that the population was not stable over this 11 week period (Newbold et al unpublished observations). What is not clear from these studies is whether this represents a true instability in the equine microbiota and thus a striking departure from the human gut or merely that the equine gut contains a large volatile transient population. Unfortunately there is only very limited characterisation of the equine hindgut bacterial population either at the level of genomic or phenotypic diversity and we are unable to speculate on either the core microbiota nor its associated microbiome. High throughput pyrosequencing approaches such as 454 sequencing have allowed high density sequencing of environmental 16s rDNA transcriptomes providing previously unobtainable insights into bacterial diversity and population dynamics. Here we propose to combine highly controlled equine feeding trials using practically applicable diets and 454 based 16S rDNA transcriptomics to define the core microbiota in the equine hindgut and to provide information on it stability in comparison to other gut ecosystems. We wish to establish not only the stability of the equine hindgut microbiota but also the extent to which it is affected by diet and animal characteristics.