Our Microbiome

As we learned in my Microbiology class, the human microbiome consists of ecological communities of commensal, symbiotic, and pathogenic organisms in a 1:1 human to bacterial cell proportion. According to Microbiome of Soil, Plants, and Animals a book edited by Rachael Antwis, Xavier Harrison, and Michael Cox, microbiota can fundamentally include algae, bacteria, archaea, fungi, protists, and viruses. As a result of these organisms living in close communities, co-evolution has occurred over millions of years which contributes to commensal relationships we have with them. Co-evolution has also played a critical role in producing great diversity of these organisms which can be important in host cell health. In fact, the human microbiota has over 10,000 microbial strains and around 8 million unique protein encoding genes (Antwis et al).

There are many questions coming out of this emerging field of microbiome research. One of the main questions is how many different kinds of microbiota do humans have, and how do we identify them? One common way to identify many microbiota is to identify their 16S ribosimal sequence, a construct we learned about in class. The 16S sequence is unique to different organisms and can classify them based on their strain type. In an article by the NIH titled, “Defining the Human Microbiome,” researchers using the 16S technique showed that community microbiome structures differ depending on the host’s diet.

According to the article, “Microbiota Research: From History of Advances,” since the beginning of the Human Microbiome Project, an international project to identify the types and roles of the human microbiome, there has been special emphasis on the microbiota residing in the human intestines. For example, dietary changes can lead to significant changes in bacterial metabolism of fatty acids and amino acids. Not only that, but these gut bacteria are important in allowing mammals to digest compounds via metabolic pathways that are not explicitly coded for in the mammalian genome. This allows us to extract even more nutrients and energy from the food we eat. Not surprisingly, antibiotics can deplenish your natural gut micrbiota, leading to decreased taxonomic richness, diversity, evenness which can cause more susceptibility to disease. In fact, after a course of antibiotics, it can take up to 3 or 4 years to reestablish your microbiota (Ursell et all). A rich and diversified microbiota can enhance digestion and overall health though metabolic pathways, as I mentioned previously, that the host cell can use to flourish and grow.