The Death Phase in Microbiome Dynamics

Two approaches exist for developing microbiome therapeutics: top-down (which typically involves sequencing microbiomes from different physiological or pathological states and determining correlations between the microbial composition and their state) and bottom-up (which typically involves determining the role of individual microbes and interactions between these microbes for establishing causal relationships). The amount of data produced from sequencing (top-down) has increased tremendously in recent years. However, the inferences that researchers can make from these datasets have been largely limited to correlations—determining causation remains challenging or impossible. As such, microbiome research is unable to determine whether shifts in microbiome caused a pathological state or if a pathological state caused a shift in the microbiome. In contrast, because of the control they offer, bottom-up approaches have the potential to establish clearer insights about causation. Recent advances in culturing techniques and measurement have led to improved prediction of the behavior of complex communities. However, most model systems do not account for the death of microbes; since death of certain microbes could serve as nutrients for other microbes, it is an important component of microbiome dynamics. Here, I will share the effect of different monosaccharides and disaccharides on the growth and death of Bacteroides fragilis and Escherichia coli as two model organisms in a chemically defined medium. Quantifying the growth and death behavior has the potential to enable better modulation of microbiome therapeutics.