In an ecology everything happens at the same time
There are various examples of treatment protocols that use a phased or stepped approach. One example is the so called “5R” approach in which treating the gut health consists of five phases: remove, replace, reinoculate, repair, and rebalance (1). The first step (remove) includes removal of pathogens, whereas it is not until the third step (reinoculated) before probiotics are used.
We often get the question if pathogens should not be removed before starting with personalized probiotics. The answer is plain and simple: no. The gut microbiome is an ecology and in an ecology everything happens at the same time. If pathogens are removed, other microbes are affected as well. Even if anti-microbial treatments would only kill the undesired microbial species (which is not the case, also not with phytotherapeutics), its removal will leave an open niche and other species will fill the gap. This happens very quickly, because bacteria replicate within minutes to hours (2).
Let’s zoom in on the fact that that many protocols wait with the reinoculate-step for one or two months, knowing that bacteria replicate in minutes to hours. We can use a well-known example of an ecology as a metaphor: a forest. Waiting between removal and reinoculation for one or two months in gut microbiome treatments, is similar to burning a forest to remove undesired trees and wait with planting new trees for dozens of years. The open niches will be filled with new species long before you would start reinoculation.
Back to personalized probiotics. In addition to the fact that waiting between removal and reinoculation for one or two months does not make sense in an ecology of species that replicate in minutes to hours, it also does not makes sense when looking at probiotic effects. That is, most probiotic strains that Microbiome Center has available do not have just one effect. Often, the strains can both inhibit pathogens and improve desired microbiome functions such as butyrate production, as well as improving specific clinical outcomes. It is not one or the other.
Many protocols that use a phased or stepped approach are developed by supplement producers. Although it may help them to sell products for each phase, the biological reality does not support such a way of working. A more realistic perspective is to consider the microbiome as an ecology, and realize that in an ecology everything happens at the same time. Thus: it makes sense to also treat everything at the same time, as well as to personalized the treatment.
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