Pattern-Recognition Used to Determine the Function of Microbial Communities in the Body
Sun, April 18, 2021

Pattern-Recognition Used to Determine the Function of Microbial Communities in the Body

Millions of small organisms are living inside our body, which altogether is referred to as the human microbiota / Photo by: Kateryna Kon via Shutterstock

 

Millions of small organisms are living inside our body, which altogether is referred to as the human microbiota. The bacteria may either be found in the gut, mouth, nose, and skin. They co-exist with us all throughout our lives. In the past years, scientists have made progress to better understand the viruses and bacteria that live inside the human body and play a significant role, such as in metabolism, fighting diseases, and digestion. Yet, how the microbial communities function in the body is still a question.

Use of Computer Algorithm

This led a team of researchers from Drexel University in Pennsylvania to use a pattern-recognition ability to determine the microbial communities in the body. The algorithm they used was able to sift through data of genetic code. The team believes that their method can help speed up the development of treatments for ailments linked to microbiota, such as Crohn's disease.

Their study titled "Exploring thematic structure and predicted functionality of 16S rRNA amplicon data" states that making a clear explanation about the relations of microbiome data and disease state is usually difficult because microbiome data has high dimensionality, sparse, and is compositional. In the hope of answering the question, the team used a computer algorithm for genetic sequencing to analyze the Ribonucleic acid (RNA) codes that can potentially reveal how microbial communities are operating. 

RNA is different from DNA. RNA is a nucleic acid that is essential in the following biological roles: expression, regulation, decoding, and coding of genes.

RNA is different from DNA. RNA is a nucleic acid that is essential in the following biological roles: expression, regulation, decoding, and coding of genes / Photo by: nobeastsofierce via Shutterstock

 

Microbiome and Development of Treatments

Stephen Woloszynek from the Department of Electrical and Computer Engineering and colleagues believe that scientists need a broader understanding as to how the microbiome operates in the body to correct their imbalances. Drexel’s College of Engineering’s associate professor Gail Rosen, Ph.D. also said via science research platform Science Daily that they are just starting to “scrape the surface” of determining the health effects of the microbiome.

Rosen added that scientists in the past have jumped into the work without having a clear and full picture of what the microbiome looks like, how their internal configuration is having an effect on the immediate environment, and how prevalent the microbial communities are.

 
 

Deciphering Genetic Sequencing

The team used machine learning, which is an artificial intelligence application that provides the system with the ability to improve or learn from experience without being programmed, and algorithms to decipher the big dataset of genetic sequencing. Their work as well as of similar efforts have helped move genetic and microbiologic research from the experimental lab to the data center, paving the way for a computational approach in metagenomics or the study of genetic material recovered from the environmental samples.

For this kind of research approach, scans of genetic sample or RNA or DNA can be interpreted by the computer algorithm to reveal the organisms that are present in the material sample. For the team’s case, they called their work “themetagenomics” because they were specifically searching for the recurring microbiome themes that indicate co-occurring groups of microbial communities.

Using themetagenomics, the team was able to obtain a full map of the microbiome and this enabled them to observe how they were changing over time both in healthy individuals and those diagnosed with a disease. Moreover, by noticing the difference of the microbial communities, it can provide clues to how they function and will show the microbe species configuration.

Rosen shares that most methods of metagenomics available today simply tell which microbes in the body are abundant, hence they are important. Yet, these past methods don’t tell how each microbe species are supporting the other members of the community. With their method of using the algorithm’s pattern recognition ability, scientists can get a picture of the community’s configuration. For instance, it may have B. fragilis or E.coli bacteria and may indicate that the most abundant microbes are cross-feeding. If the microbes are in low numbers, it may indicate that they are feeding off whatever the other bacteria are creating.

Using themetagenomics, the team was able to obtain a full map of the microbiome and this enabled them to observe how they were changing over time both in healthy individuals and those diagnosed with a disease / Photo by: gopixa via Shutterstock

 

Analyzing the Human Microbiota

The team went on to say that one of their main goals for the study is to use the presence of microbe communities as a gauge to determine the diseases, such as Crohn’s, or cancer. 

The Human Microbiome: Facts

In a separate report by the University of Washington, it shared that more than 100 trillion microbes are found in our bodies. The majority of microbes live in the gut, specifically the large intestine. The number of genes found in the microbes is 200 times the number of genes found in the human genome. 

Since the microbiome is essential for human nutrition, development, and immunity, there is a need to better understand how they function. Worldwide research initiatives, such as that of the Drexel University team, help map the microbiome and give people the insight into these uncharted species.