Changes in the microbiome of a human and in the simulator of human intestinal microbial ecosystem (SHIME®) in response to a diet and probiotic supplementation

Abstract

Background. The Simulator of Human Intestinal Microbial Ecosystem (SHIME®) is used to study the behavior of a human microbiome in response to various factors. The aim of this study was to simultaneously demonstrate changes in the microbiome of a human volunteer and in the SHIME® system in response to a change in a diet and probiotic therapy due to a scarcity of published research with similar design. Results and conclusions. The probiotic therapy resulted in a decrease in fasting insulin and glucose (by 18 % and 13 %, respectively), while the increased fiber intake in the experimental diet seemed to reduce triglyceride, total and LDL cholesterol levels (by 27 %, 15 % and 14 %, respectively) in the volunteer’s blood. Due to the improvement of the volunteer’s metabolic status, changes in her microbiome were observed. Namely, the improvement of glucose homeostasis led to the occurrence of bacteria of the genus Akkermansia in the feces, while the improvement of lipid homeostasis resulted in an increase in the abundance of bacteria of the genus Bacteroides and Bifidobacterium (approx. two and four times, respectively). While changes in the microbiome diversity in the SHIME® luminal fluid (L-SHIME) and in the faeces microbiome were partially similar, the microbiome of SHIME’s intestinal wall (M-SHIME) behaved differently. The characteristic feature of both L- and M-SHIME was a microbiome that differed in its composition compared to the volunteer’s microbiome at parallel sampling points. The results of this study indicate that adjustments to the standard SHIME® experimental protocol should be made to enable the replication of the human microbiome diversity and its changes in the system.