The Long and Short Term Dynamics of the Human Gut Microbiome

Abstract

The microbiome is closely linked to human health and disease. Research has shown that the microbiome changes throughout life but studies looking at: how early life events influence the differences in the microbial composition in mid-childhood; how the microbiome changes over a long period of time; and whether microbiome transplantation can shift imbalance in the human microbiome are limited. Thus, here I explore short and long-term fluctuations in the human gut microbiome that are associated with early life-events, ageing, and an intervention. Firstly, I hypothesise that adverse early life events in preterm children change the microbial composition, functions and metabolic products of the gut microbiome in midchildhood. My results identified different active microbial species as classifiers of the preterm condition together with functional changes, altered profiles of plasma and faecal amino acids, faecal volatiles and faecal calprotectin levels. I speculate that the pretermspecific changes observed in the active gut microbiome were established in early infancy and are associated with on-going low-grade gut inflammation. Secondly, characterisation of the gut microbial composition of artist Billy Apple® from stool contaminated toilet tissues collected in 1970 and 2016 showed that the microbial composition in 2016 represents 45% of the microbial species in 1970. Moreover, components of Apple‟s microbiome were associated with the allele frequency at seven single nucleotide polymorphisms in his genome confirming that genetics contribute to the selection and maintenance of the microbiome over the artist‟s lifetime. Thirdly, I studied the short- and medium-term effects of lean donor faecal microbiota transplantation on the gut microbiota composition in a group of female adolescents with severe obesity. My results showed that the faecal microbiome transplantation is capable of shifting the recipient microbiota successfully at 6 weeks, postfaecal microbiota transplantation. The engrafted microbiota remained unchanged for half of a year in spite of subtle dietary and environmental changes.