Microbiome Data Science
Do I have your attention? Good! This blog talks of how Data Scientists, Microbiologists, and other amateur researchers (like me) can bring about change in treating and eradicating acute and chronic diseases. Do Read on, you can also contribute to the long-term welfare of everyone!!!
The pandemic (Covid-19) has been one of the worst things that Humanity has faced in quite a long time. In comparison, the other pandemic like situations; Black Death, Spanish Flu, Cholera outbreak among others seem trivial (which may not be the case). I won’t be going into the details of why Covid-19 has had a massive impact on today's society. Although in my perspective, Covid-19 has caused so much trouble because the world is far more connected than ever before. A connected world (global village) is undoubtedly a good thing, but coming together in times like these to battle a global pandemic is more important. The reach of Covid-19 is colossal and hence it is more deadly.
For researches (change-bringers) like me and you, who wish to contribute to society, understanding the inner workings of the human body is a great place to start. The endless collaboration of microbiology and computer science (i.e technology) have and will give rise to a multitude of discoveries in the treatment of diseases and infections.
How?
To understand the inner workings of the human body (or other “Multi-cellular organisms”) one must look at something called Microbiome or Microbiota. So, Microbiome is a collection (community) of viruses, fungi, algae, bacteria (major-contender) and other microorganisms. Microbiomes are present all over the human body. Research has been conducted mainly on the microbiota of gut, mouth, skin, and faeces, and the Gut Microbiome constitutes to being the largest.
Microorganisms have lived approximately for 3.5 billion years and, now I really think its time we start seriously researching on this subject. To understand the magnitude of the number of microorganisms present in/on a human, there are 3 times as more non-human cells compared to the human cells, the ratio of 3:1. To put things more into perspective there are around 100 trillion microbes present on a human body.
Research in this domain has yielded results varying from the identification of early symptoms for cancer, and the drug invention for diseases to the creation of targeted diets for each individual based on the Gut Microbiota.
Therefore, understanding the workings of these microorganisms is of the utmost importance. Today the technology is ready, it is just the willingness of people to dive into research and help everyone (Animal or Human).
Why Microbiomes?
To be honest, understanding Microbiomes is tedious and at times you will want to give up. But, keep at it, I assure you the results will be fascinating.
To begin with, you can go through this paper [4] and [1]. This paper gently introduces the reader to a vast spectrum of the applications of Microbiomes without going into much technical detail.
Until a few years ago, traditional techniques were used to analyze the microbial community. These traditional techniques involved observing the microbes under the microscope with the culturing techniques to study the biological characteristics of the microorganisms. Culturing is the process of exploring the complex interactions between microorganisms and their environment. Observing microorganisms under the microscope, and culturing requires a good deal of expertise and therefore is very time-intensive and costly.
But, with the advent of High-Throughput Sequencing technologies, the tedious task of observing and collecting data from the microbiomes were eliminated. In a nut-shell, High-throughput sequencing parallelizes the sequencing process, producing thousands and millions of sequences simultaneously. These are cost-effective and work on multiple microorganisms at once.
Therefore, a massive amount of data has been and is being generated that is publicly available. This provides everyone with an opportunity to do their own research and contribute.
Application of Machine Learning:
This is where we come in. Enough data enables analysis and prediction. This can be achieved using Machine Learning. Mainly there are 2 ways Machine Learning is applied to Microbiomes:
The first one is Classification and Prediction, and this can be further divided into 3 sections:
i. Prediction of Microbial species
ii. Prediction and Classification of Environmental and Host Phenotypes (Phenotypes are like characteristics)
iii. Prediction of Diseases
And, the second one is the Interaction and association of Microorganisms.
Developing an understanding of how microbes interact with their environment is crucial. How a foreign microbe (virus, harmful bacteria) influences a microbiota differs from person to person and, therefore creates more complexity. Innovating an easy technique that identifies these interactions will reduce the risk for that individual.
Hope you enjoyed reading the blog, I will be posting a more detailed blog on how to apply Machine Learning to Microbiomes; it will be out soon!
References:
- Qu K, Guo F, Liu X, Lin Y and Zou Q (2019) Application of Machine Learning in Microbiology. Front. Microbiol. 10:827. doi: 10.3389/fmicb.2019.00827
- Turnbaugh, P., Ley, R., Hamady, M. et al. The Human Microbiome Project. Nature 449, 804–810 (2007). https://doi.org/10.1038/nature06244
- https://www.medicalnewstoday.com/articles/comparing-covid-19-with-previous-pandemics#The-many-returns-of-cholera
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831009/
