• Dr. Timothy Smith

The Microbiome and Your Physical and Mental Health


Photo Source: Wikimedia Commons


Did you know that all along your digestive tract and over your skin lives an invisible world of microorganisms collectively called the microbiome? The cells in our microbiome outnumber the 30 trillion cells in your body by another 9 trillion cells. (sciencefocus.com) All these microorganisms do not simply hang out. Over the past 20 years, incredible research has emerged demonstrating that our microbiome directly connects to our physical and mental health. Advances in artificial intelligence spurred on the ability of scientists to understand the complex world of the microbiome and offers clues to new ways to improve our health.


The microbiome refers to the world of microorganisms that live in and on our bodies. The microbiome contains hundreds of different microscopic organisms, from various bacteria to fungi and archaea to protozoa. Good bacteria such as lactobacillus help humans break down food, absorb nutrients, and battle harmful bacteria. Bad bacteria for people include salmonella and Vibrio cholerae, which causes the dangerous disease cholera. Microscopic fungi found in the microbiome include different types of yeast. Archaea represent another member of the microbiome. First discovered in extreme conditions such as hot springs and salt lakes, Archaea play an essential role in the health of human skin by making the skin more acidic, which protects it from infection. The other prominent member of the microbiome is called protozoa. Protozoa refer to single-cell organisms that have similarities to both bacteria and plants. Some familiar protozoa include Giardia, which causes the intestinal disease giardiasis in dogs and humans, or Plasmodium, which causes malaria.


Research shows that the microbiome has an essential role in human physical health. In a paper published in Nature Reviews Microbiology titled, “Gut Microbiota in Human Health and Disease,” the authors nicely summarize the ways that the microbiome interacts with its host. “The gut microbiome has important roles in the training of the host immunity, digesting food, regulating gut endocrine function and neurological signaling, modifying drug action and metabolism, eliminating toxins and producing numerous compounds that influence the host.” (nature.com) A good, well-functioning microbiome supports overall health and, more specifically, good metabolic health. Such a notion does not only reside in scientific research papers. One only has to watch TV or go to the grocery store to see all the advertisements promoting probiotic products such as yogurt and dietary supplements to improve digestive health. However, the microbiome can become imbalanced through poor diet, prolonged antibiotic use, or a compromised immune system. A poorly functioning microbiome directly influences metabolic diseases such as type 2 diabetes, obesity, non-alcoholic liver disease, and cancer. Doctors are now using microbiome transplants to treat diseases. For example, a healthy microbiome transplant is the most successful treatment today for a recurring intestinal infection caused by a microorganism called C. difficile. (blog.scientificamerican.com)


Based on new research, the gut microbiome also plays vital roles in mental health. In humans and other animals, the brain and the gut talk to each other through a group of nerves that act as a hotline sharing information about feeling full or hungry or feeling sick. This hotline can also get stimulated by substances produced by the microbiome. Research shows that microbiome health has a relationship to mental health, such as autism spectrum disorder and depression. Autism spectrum disorder refers to a group of developmental disorders that result in behavioral challenges, including difficulty in social interaction, repeated body movements, and over or under reaction to different senses. Autism spectrum disorder affects 1 in 59 children, according to the Brain & Behavior Research Foundation. (bbrfoundation.org) Research published in the journal Cell detailed an experiment that showed a connection between different microbiomes and autism spectrum disorder. The paper titled “Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice” described an experiment where the scientists took the gut microbiome from either typically developing human children or children with autism and transplanted them in laboratory mice. They found an astonishing result. The mice given normally developing children’s microbiome grew and developed normally, while those mice given the microbiome from autistic children displayed autistic characteristics such as impaired social communication/interactions and repetitive behaviors. (CellPress) A scientific review paper titled “Gut Microbiome and Depression: How Microbes Affect the Way We Think” looked across many research papers and found a growing body of research that connects the microbiome with depression and anxiety. (nih.gov) The research is preliminary, but the relationship between the gut microbiome, the immune system, and depression looks compelling.


Part of the surge in microbiome research owes itself to advances in artificial intelligence. Microbiome researchers face unique hurdles trying to make sense of the complex mixture of different microorganisms and its relationship to human health. To put these research challenges in perspective, we are looking at trillions of microorganisms. With all the various organisms in the human microbiome, scientists need to collect vast amounts of data such as genetic sequences and metabolites from thousands of different organisms. To manage such extensive data, scientists have turned to artificial intelligence and machine learning. Using genetic data, metabolite production, and measuring various elements of health, artificial intelligence can comb through the data hundreds of times faster than a human to find patterns that link microbiome composition to human health.


The microbiome represents a vast microscopic world of organisms that, for the most part, live in a mutually beneficial relationship with humans. The research connecting the composition of different microbiomes with physical and mental health has opened up a new branch of study. Evidence indicates that our well-being and its connection to the billions of microorganisms we live with can directly impact our physical health, from obesity to type 2 diabetes to mental health such as autism spectrum disorder to depression. The powerful tools of artificial intelligence combined with more information will continue to drive discoveries leading to new insights and therapeutics for physical and mental health based on the microbiome.




Dr. Smith’s career in scientific and information research spans the areas of bioinformatics, artificial intelligence, toxicology, and chemistry. He has published a number of peer-reviewed scientific papers. He has worked over the past seventeen years developing advanced analytics, machine learning, and knowledge management tools to enable research and support high level decision making. Tim completed his Ph.D. in Toxicology at Cornell University and a Bachelor of Science in chemistry from the University of Washington.



You can buy his book on Amazon in paperback and in kindle format here.