Dietary Impacts on Changes in Diversity and Abundance of the Murine Microbiome During Progression and Treatment of Cancer
Authors: Paden Holly , Kurbatfinski Nikola , Poelstra Jelmer , Ilic Sanja 
Published: May 2022

The microbiome has been recognized as being highly impactful for cancer outcomes, both with respect to the diversity and composition of the microbial population, as well as overall abundance. Presence or absence of certain microbial species has been correlated to improved cancer outcomes, in concert with specific treatments. However, little research has been performed to consider the reciprocal of this relationship: how different treatments, or the progression of disease, impact the microbiome. Further, though correlations have been demonstrated between dietary intake of both fats and carbohydrates and the composition and breadth of the microbiome, no studies have investigated the microbiome population as it is impacted by cancer and therapeutic treatments under different dietary regiments.

This study aims to investigate how dietary patterns, in concert with progression of cancer and both surgical and therapeutic interventions, impact the diversity and abundance of the murine microbiome.

A total of 116 c57BI/6 female mice (7‐8 weeks old) were randomized into four groups (n=29/group, each) one week post ovariectomy. Mice received a specific, semi‐purified diet consisting of A) low sucrose, high omega 3 fatty acid; B) low sucrose, low omega 3 fatty acid; C) high sucrose, high omega 3 fatty acid; or D) high sucrose, high omega 3 fatty acid. For high omega 3 fatty acid groups, 2% of daily calories were supplied to the mice as EPA and DHA in a 1.5:1 ratio. One week after implementation of diets all mice were inoculated with E0771 breast cancer cells. Twelve days following inoculation all mice were subject to lumpectomy. Eight days following, measurement procedures were repeated, as at baseline. Ten days following lumpectomy, half of the mice from each dietary cohort were treated with saline, while the other half were treated with a chemotherapeutic agent (9 mg/kg body weight doxorubicin and 90 mg/kg body weight cyclophosphamide). Six days later, the experiment ended, and mice were sacrificed following IACUC guidelines. Fecal samples, which had been collected at each time point noted above, were processed using QIAmp® PowerFecal® DNA isolation kit and were sent to MCIC (OSU Wooster Campus) for 16S ribosomal genetic profiling. A genomic library was generated, using previously validated primers for the V4 region. FASTQ files were filtered, trimmed, dereplicated, and denoised. Cleaned FASTQ files were then used to infer ASVs.

Over the progression of cancer, there has been a consistent decrease in the alpha diversity of the microbiome. The effect of diet was mitigated by introduction of chemotherapeutic agents, though the significance of this effect is yet to be determined. While the analysis is still ongoing, it has been determined that there is a clear dietary effect which interacts with abundance. Multiple ASVs have been shown to be positively associated with high fat consumption, though inverse effects, as well as timepoint and treatment effects, have also been noted. Akkermansia muciniphila was a highly present bacterial species in all treatments, despite it usually being noted only as a minor resident of the gut.