Background The human body is the home to thousands of microbes, bacteria, Archae, and fungi. These organisms are what make up the human microbiome. There are actually known to be more cells in the microbiome than in our actual body. The human microbiome is located in several parts of the body but the most abundant region of these organisms is the human gut. More than one thousand species can call the gut of the human body their home and have created a highly diverse and variable community within the human body. Without these microorganisms, our health would cease to exist as it is today. The sheer variation and quantity of organisms found in the human gut has sparked the interest of many researchers. Their interest has mainly been focused on seeing how each of these microorganisms may relate to not only each other, but to our human body as well. According to Liu’s research, a little over three hundred of these microbes have been fully sequenced and annotated. These sequences are vital in studying anything and everything there is to know about the human gut microbiome. One of the major characteristics that researchers have been looking at in regards to the microbiome is their ability to exchange genes with one another through a process called horizontal gene transfer. Horizontal gene transfer is a transfer of genes between organisms in ways other than traditional reproduction. Horizontal gene transfer is vital for things such as bacterial antibiotic resistance and is used in processes like transformation, transduction, and bacterial conjugation.Horizontally transferred genes “may have characters in the gene sequence composition that differ from the host genome such as GC content, codon usage, etc.” This is exactly why they are so interesting to study because there is so many different methods that can be used to cross-reference and confirm results of potential gene transfer. Generally, when trying to identify horizontally transferred genes within a microbiome there are two categories of experimental tests that can be run to find this out. The first of the two is composition-based tests. These involve looking at different elements within a gene to find abnormalities from recently acquired genes that may have been adapted from horizontal gene transfer. This method is not full proof however, so usually scientists will look at many different elements and see where their results may overlap when coming to a final conclusion if they believe a gene may have contributed towards horizontal gene transfer. The second category of detection for horizontal gene transfer candidates is the phylogenetic methods. This method involves looking at family trees, and finding incongruences between gene trees and species trees. These methods truly rely on orthologous genes. These methods are very reliable because they are so accurate with all the recently acquired genomic information. However, these types of methods also take a lot more time and effort to conduct. In general most scientists try to use several types and categories of data analysis so that their conclusions are complete and as accurate as possible.Studying horizontal gene transfer in regions like the human gut microbiome is essential. It has been suggested that the horizontal gene transfer events that may have taken place have essential effects on evolution and adaptation to the environment for the microorganism. A scientist looks for the best and most often identified genes to be associated with horizontal gene transfer. They then take these genes and look at their functions, what other genes they may be similar to and which organisms they come from so that they may come even closer to mapping out the horizontal gene transfer events that make the human gut microbiome as diverse as it is today. These types of studies have occurred numerous times over the years on different parts of the human microbiome. However, what seems to be the most diverse and the most abundant with possible genes contributing to horizontal gene transfer is that of the human gut.The human gut microbiome is the most diverse and the most abundant microbe community that exists in the human body. What also makes it such a great source for scientific research on microbiome research on horizontal gene transfer is that their genomes are sequenced and those sequences have been made a public domain/resource. This makes it easier for researchers to be able to go in and run tests such as GC content, or codon usage to then analyze for possible genes involved in horizontal gene transfer. These genomes can also be used to run through other programs to look at the phylogenetic contribution to horizontal gene transfer within the microbiome.In our project we focused on three types of analysis to identify genes within the human gut microbiome. The first of which was GC content analysis of the genomes. GC content is relatively normal across most species, so when there is a difference in GC content of a gene or genome, there is a very high chance that gene has contributed to horizontal gene transfer, or is a gene that has been horizontally transferred to that organism or species. The second type of analysis we will be looking at is that of codon usage. Again, like the GC content, this is relatively normalized across a distribution of species within the human gut microbiome, so when differences or standard deviations from the mean are noticed, these genes are likely to be involved in the horizontal gene transfer as well. Lastly, we are using a small portion phylogenetic analysis by running the genomes or genes through programs such as dark horse or blast to find evidence of horizontal gene transfer. Once all three of the data analyses have taken place, we can compile all the data and see where the overlaps lie in the genes hypothesized to be a part of a horizontal gene transfer event. By cross-referencing all three analyses’ we are easily able to come to accurate conclusions about certain genes contributing to horizontal gene transfer and then research can be done more on the specific genes that contribute, why they contribute, and how they contribute.It’s an interesting topic not only in the genetic and biological world but also in the medical world. The human microbiome is what keeps us alive and healthy so running studies like this on it is vital to keeping that health we all know and love today. Hopefully, a study like ours can one day go towards curing a disease or preventing someone from suffering anything relating to poor health.