The population of microbes (microbiome) in the intestine is a symbiotic ecosystem conferring trophic and protective functions. Since the biochemical environment shapes the structure and function of the microbiome, we tested whether
uremia and/or dietary and pharmacologic interventions in
chronic kidney disease alters the microbiome. To identify different microbial populations, microbial
DNA was isolated from the stools of 24 patients with
end-stage renal disease (
ESRD) and 12 healthy persons, and analyzed by phylogenetic microarray. There were marked differences in the abundance of 190 bacterial operational taxonomic units (OTUs) between the
ESRD and control groups. OTUs from Brachybacterium, Catenibacterium, Enterobacteriaceae, Halomonadaceae, Moraxellaceae, Nesterenkonia, Polyangiaceae, Pseudomonadaceae, and Thiothrix families were markedly increased in patients with
ESRD. To isolate the effect of
uremia from inter-individual variations, comorbid conditions, and dietary and medicinal interventions, rats were studied 8 weeks post 5/6
nephrectomy or
sham operation. This showed a significant difference in the abundance of 175 bacterial OTUs between the uremic and control animals, most notably as decreases in the Lactobacillaceae and Prevotellaceae families. Thus,
uremia profoundly alters the composition of the gut microbiome. The
biological impact of this phenomenon is unknown and awaits further investigation.