NGS vs PCR
3 min read
NGS
16S amplicon NGS based microbiome studies provide deep, insightful data into the microbial constitution of the human gut. It would not be an understatement to say that the technology has revolutionised the study of the microbiome in all its environments, with its ability to discern and discriminate what microbial populations exist, in size and in structure in all environments, ranging from the desert floor to the deep ocean bed
However, with a myriad of processes attributed, beneficial or otherwise, to the presence of certain groups of bacteria contained within any given environment, deciphering that data requires committed and costly analysis to determine the range of processes potentially contained within that sample. Combine this with the initial expense of processing samples for NGS, the final cost per sample can reach a high level.
SCFAs and Carbersol prebiotic fiber consumption
At Carbiotix, our mission statement revolves around the application of a range of smart prebiotic fibers designed to stimulate and promote the growth of a range of bacteria proven to have gut health benefits through the production of Short Chain Fatty Acids (SCFAs), and secondary metabolites produced by bacteria alone and unable to be directly synthesised by human physiological processes.
SCFAs are vital to the correct functioning of a range of human physiological processes, ranging from serving as an energy source for the immune system, ensuring normal cell replication, to maintaining gut cell integrity amongst the many, many roles they have been directly implicated in.
Instead of having to deal with regular costly NGS runs to hypothetically determine the ratio of bacteria present that can produce SCFAs, our strategy is to directly measure the presence of those genes directly implicated in the production of these essential secondary metabolites when related to the overall population in any given sample.
PCR based approach
With a PCR based approach, targeting pathways that contribute towards SCFA production allow us to ‘cut to the chase’ and allow us to monitor, cost effectively and longitudinally, what responses are occurring within the host in response to whatever intervention is administered without having to critically analyse and decipher reams of time-consuming data. Underlying longer term trends not related nor observed in relation to the PCR based principal investigation would be highlighted over a longer period with intermittent NGS, if required.
One failing in this approach is that we cannot directly identify the individual bacterial species contributing to this affect, however, the important thing to remember is that the beneficial metabolite of concern is being produced and it is being measured, thereby highlighting the efficacy of any intervention taken. Succinctly, with a PCR approach we don’t know what is producing SCFAs at a species level, we only know that they are being produced, and that is all that matters in the context of good gut health.
At Carbiotix, to determine the efficacy of our smart prebiotic Carbersol, long term observation is the guiding principle to prove to you and/or your customers that real term positive effects are happening in the gut in response to the administering of Carbersol. In that way, you will not only feel better, but have genuine, palpable results to back up that feeling.
Ultimately, the mission is to ensure that this already low-cost testing becomes a value driving accessory to our range of smart prebiotic fibers which do exactly what diagnostics are supposed to do; to unequivocally prove to you that it works at no cost, for your peace of mind.