Why was 16s sequencing chosen over shallow shotgun, deep shotgun and metatranscriptomics?

16s rRNA sequencing was chosen as it allows us to tap into thousands of gut microbiome research publications. While we do build our own analytical models to gain insights from our customers' data, we also rely heavily on the research conducted over the last 20 years. 16s rRNA continues to be the leading technology used by researchers today. It is one of the best techniques for high-throughput analysis of thousands of samples. The 16S gene is present in every bacterium. Because many labs all over the world are using this approach, 16S sequence databases are unparalleled in size.

We evaluated shallow shotgun sequencing (such as those used by DayTwo) but found that the relative abundances using this technique did not correlate enough to 16s sequencing methods and would therefore not allow us to leverage others' research findings. This sequencing method, however, do make sense for DayTwo as they specialize in Type 2 diabetes and can therefore build up and refer to their own dataset in their research. The service that Biomesight provides is much more general. In terms of price, some laboratories now offer shallow sequencing for close to the same price as 16s sequencing so our decision is entirely driven by the ability to leverage the scientific literature.

Deep shotgun sequencing (normally upwards of 5 million base pair reads) is also a consideration for us. This powerful technology allows for identification down to strain level as well as the sequencing of other organisms, e.g. viruses. It does have the same drawback as shallow shotgun sequencing, in that we cannot leverage existing research findings. We do however see this as a viable technique to utilize occasionally alongside regular 16s sequencing tests as knowing the exact strains of bacteria can be very meaningful. If there is enough interest from our customers, we would consider this test alongside our current 16s based test.

Metatranscriptomics do not aim to establish the taxonomy (e.g. DNA profiling) of organisms. Instead the focus is on functional gene expression. In other words, an organism can be present but not necessarily expressing the genes we'd expect. This technique is used by Viome. While this is indeed a viable technique, it is newer than DNA profiling and as such do not yet have much in terms of supporting research literature.

We strongly recommend reading the below medium article written by the researchers at uBiome discussing the differences and merits of Viome's technique compared to 16s rRNA sequencing.


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