Background Iron is an essential micronutrient for all living organisms, and as such, iron deficiency is the top leading cause of anaemia. Iron supplements have been shown to be detrimental to the gut microbiome and the intestinal epithelium, triggering dysbiosis and an impaired gut barrier. However, a comprehensive analysis of these two aspects have not been performed during IDA. This study aims to delve further into the analysis of the gut microbiome in an animal model of IDA and to relate microbial changes to the biological processes occurring in the colonic epithelium, with a special focus on the gut barrier. This in-depth analysis might mean a step forward minimising the negative impact of iron supplements on intestinal health during IDA. Methods IDA was experimentally induced in an animal model through the use of an iron deficient diet. Shotgun sequencing was used to gain insight into alterations of the gut microbiome in the most affected intestinal region during IDA, the colon. Histological analyses, mRNA sequencing (RNA-Seq), qPCR and immunofluorescence were used to study transcriptionally deregulated processes in the colonic epithelium. Determinations of lipopolysaccharide and bacteria-specific immunoglobulins were performed to assess microbial translocation. Results Microbial metabolism in the colon shifted towards an increased production of certain amino acids, short chain fatty acids and nucleotides, with Clostridium species being enriched during IDA. Structural alterations of the colonic epithelium were shown by histological analysis. RNA-Seq revealed a downregulation of extracellular matrix- associated genes and proteins and an overall underdeveloped epithelium. Increased levels of serum LPS in the anaemic animals and an increased immune response against IDA dysbiotic bacteria support an impairment in the integrity of the gut barrier. Conclusions IDA negatively impacts the gut microbiome and the intestinal barrier, triggering an increased microbial translocation. This study emphasizes the deterioration of gut health during IDA and the fact that it should be addressed when treating the disease.

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