Information to Insights

November 24, 2021

“Simplicity is the ultimate sophistication” – Leonardo Da Vinci

What happens after our lab receives your sample? And how does your sample translate into a colourful report with straightforward findings and easy to follow recommendations?

This is what happens in the AMILI lab. Your stool sample is assessed physically, processed, and then the genetic material is extracted using AMILI proprietary methods – this is a crucial step as the extraction process is ‘operator dependant’, which means it needs a high degree of skill to be done right, otherwise the next steps cannot be done. It is then sequenced, where all the building blocks of the DNA are individually pieced together – much like a 1000-piece puzzle, but millions of puzzle pieces in this case. Each stool DNA sample is sequenced to a depth of 100,000 to 160,000 paired end raw reads, achieving at least 99% sequencing coverage. This very comprehensive identification of the microbes in one’s microbiome is important and enables the richness of subsequent analysis.

Fig 1. Example of Krona plot from AMILI BIO & ME user (de-identified)

The resulting raw reads are then checked for quality again, filtered, and processed using AMILI’s pipeline to an average depth of 89625 +- 18813.37 reads.

Fig 2. Example of sequence coverage disguised from AMILI BIO & ME user

Once we have characterised the taxonomy of the microbes in the sample, we need to map the individual microbial profiles and how they interact with each other as shown in the figure below.

Fig 3. The complex network of microbes in our gut – disguised example from AMILI’s data

With this completed, the functions of the microbes can be worked out in the form of functional pathways which result in digestion as well as synthesis / production of metabolites, vitamins etc. Approximately 500 pathways can be detected per sample, but we specifically extract a set of functional pathways most relevant to health in the BIO & ME report. It encompasses functions such as secondary metabolite biosynthesis, neurotransmitter biosynthesis, vitamin biosynthesis, carbohydrate biosynthesis (and degradation), fatty acid and lipid biosynthesis (and degradation) etc. We further compare the abundance of the bacterial taxa and pathways with the AMILI BIO & ME database.

It is worth highlighting here that the AMILI BIO & ME database is a big part of what makes BIO & ME so special and unique to Asia. The database is built up from AMILI’s research collaborations with over 20 academic institutions and hospitals, and integrates public datasets relevant to Asia. Hence, BIO & ME users get the best of both worlds – the latest the world of science has to offer and AMILI’s multi-ethnic datasets which greatly enhance the relevance of the findings to those of us living in Asia. Note that we are talking about people living in Asia and not people of Asian ethnicities as the microbiome is primarily driven by diet, lifestyle, and the environment and hence people living in the same region would have more similar microbiome profiles than even their relatives who reside in distant lands. AMILI possesses one of the world’s largest Asia-centric, multi-ethnic databases consisting of more than 82 million sequence reads, covering more than 150,000 sequence variants.

Finally, we deliberately remove all the complexity. Users just want science-based, actionable insights that they can use as they go about their lives. Forget the 8-10 syllable microbial names or the unpronounceable pathways named after long-gone scientists – what matters is simple, easy to use knowledge and recommendations to live the best lives we can.

Fig 4.1 Illustration of report sample pages showing Think Well scores

Fig 4.2 Illustration of report sample pages showing specific food recommendations for ‘Think Well’

About the author

Dr Saishreyas Sundarajoo is Head of Clinical Affairs at AMILI.