The-New-Perception-of-Your-Microbiome

We live in a culture where most of the answers to our problems are a click, call or swipe away. Yet we have not created a simple technology solution to address the rise of complex diseases like autoimmunity, mental health disorders and obesity. From a healthcare perspective, what good is an algorithm for an individual suffering from Crohn's disease? Is an app really going to help a patient lose excess weight that is impeding their health? And isn’t mental health supposed to be left to the social workers and psychologists? Technology is just a tool for industry, and healthcare is no exception.

Take the microbiome, for instance. For those that don’t know, the human gut microbiome is a vast array of microorganisms collected throughout one's life, an estimated 100 trillion.¹ We are all born into the world clean and the first of our collection is given to us from our mothers through childbirth and breastfeeding. These bacteria are vital to the development of brain function, human behavior, the innate immune system², protection against pathogens, production of short-chain fatty acids for host energy metabolism, synthesis of vitamins among other compounds essential for metabolism and fat storage.¹ They can affect how human genes are expressed. Trying to live without these little guys is like trying to live without water. The microbiome is essential for the human body to properly function. Many factors play into the development of the system including the host’s genetics, environment, culture, gender and diet. What’s more is their ratios can change with age¹. Even the ways that the microbes interact with one another can influence the types and ratios of each bacterial species that are found in the human gut.

(infographic by Seres Therapeutics)

The microbiome is a wonderful symphony of symbiosis until it’s not. When there is a dysbiosis, it may cause all kinds of harmful conditions including but not limited to obesity, autoimmune disease, depression, anxiety, cardiovascular disease, diabetes, metabolic disorder, intestinal permeability, bacterial translocation, chronic and systemic inflammation, and bacterial infections just to name a few. Per example: Irritable Bowel Disease (IBD) patients have presented altered colonization patterns compared to healthy individuals of a few key species: Bacteroidetes, Proteobacteria, and Firmicutes.³ They have also shown to have fewer species in their microbiome overall. A study of a Crohn’s-affected patient categorized the microbes of their ileum before and after a medical nutrition therapy intervention. Not only did the levels of those three species normalize, the bacterial diversity in the patient’s ileum expanded and overall inflammation of the intestinal tract was reduced.³ This study outlines the importance of nutrition on gut health, disease intervention and a temporal understanding of the microbiota. See the chart below for results of the patient:

Fig2.²https://www.sciencedirect.com/science/article/pii/S0009898115000170

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When all external and internal factors affecting the composition of the microbiome are considered, there are an exponential number of reasons as to why and how an individual may become ill. It is no wonder that research on the microbiome takes time to make its way into mainstream medicine. This is where Systems Imagination’s hypergraph, codename “TKR”, come into play.

Simply put, a hypergraph is a collection of nodes and edges where the edges aren’t just between sets of two nodes, but can combine any number of nodes and edges. This gives TKR the ability to represent large complex data more accurately than a graph alone. From there, SII has made an efficient solution to representing nodes and hyperedges in this hypergraph over time. The combination of hypergraph technology with temporal knowledge representation could be groundbreaking for microbiome research. This would expedite medical research, boost job creation, outline future business possibilities, all the while focusing on better care for patients.

There is an abundance of data in existence already thanks to several international organizations working to categorize and characterize our intestinal microbes. The Metagenomics of the Human Intestinal Tract (MetaHIT) has gathered data on 600 European individuals that are healthy, overweight/obese and IBD patients.⁴ The project has collected 3.3 million non-redundant microbial genes that play active roles in human function. More than 99% of those genes are bacterial. The other 0.1% are eukaryotic and viral in origin. They have found over 1000 different bacterial species, with each member of the cohort hosting an average of 160 separate species within their gut. Of those 160 species, 40% are shared with at least half of the cohort.⁴ What this means is that there is a basic core of bacterial species found in the majority of an adult population of the same culture. Culture-dependent studies have shown that this core microbiota can be altered over time.

By processing this data through technology built at Systems Imagination, a ‘healthy’ microbiome becomes a possibility in the near future. Eventually, the data would be used for more than an understanding of the current state of a patient’s microbiome, but to predict where that patient's health is heading. This enables healthcare practitioners to transition from a model of treating sick individuals to a preventative care model, saving people years of discomfort, financial strains and freeing up resources within the healthcare industry. Health-minded technology such as TKR offers a new solution to solve complex problems, and bring forth innovative opportunities.

References:
  1. Amon P, Sanderson I. What is the microbiome? Archives of Disease in Childhood - Education and Practice 2017; 102: 257-260.
  2. Rizzetto L, Fava F, Tuohy KM, Selmi C. Connecting the immune system, systemic chronic inflammation and the gut microbiome: The role of sex. J Autoimmune 2018; 18: 30190-2.
  3. D’Argenio V, Salvatore S. The role of the gut microbiome in healthy gut status. Clinica Chimica Acta 2015; 451: 97-102.
  4. Dore J, Simren M, Buttle L, Guarner F. Hot topics in gut microbiota. United European Gastroenterol Journal 2013;1; 5: 311-318.
  5. Why is Microbiome research so important in Medicine? Some Figures from an Infographic by Seres (Source: Seres Therapeutics)

erin washbon
Erin working on a problem at ASU.

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