Genetic technologies have advanced in many ways in recent decades, and have opened up entirely new fields of study. The human microbiome is one of those fields; scientists have been able to sequence the genetic material contained in fecal samples and in this way, have gained insight into the vast community of microbes that lives in our gastrointestinal tract - the gut microbiome and how it impacts our health and well-being. Learn more from the recent video by the Microbiology Society.
Many connections have been made between microbes in the gut microbiome and human disease. In some studies, specific microbial strains have been associated with an illness, while in others, more general characteristics have been revealed; low levels of diversity in the microbiome has been linked to disease, for example. But we still don’t know a lot about exactly how the microorganisms are exerting their effects. Scientists at Oregon State University (OSU) have now learned more not only about the microbiota but also about how they function. Their work has been reported in mSystems.
An assessment of various metagenomics analysis, which sequences the DNA in some environmental sample - in this case, fecal matter, was performed by the researchers. Led by microbiology and statistics researcher Thomas Sharpton of OSU, the scientists analyzed eight studies, including seven diseases in their meta-analysis, which contained around 2,000 samples from patients with various diseases including type 2 diabetes, rheumatoid arthritis, and ulcerative colitis.
The microbiota in the gut carries many genes and corresponding proteins of their own. There are roughly 1,000 bacteria that may be a part of any one gut microbiome, and the microbes have to communicate with one another as wells the host using peptides or signaling molecules.
"In our study, we looked at how gut microbiome protein family richness, composition, and dispersion relate to disease," Sharpton said. "Our analysis of protein family richness showed that patients with Crohn's disease, obesity, type 2 diabetes or ulcerative colitis feature a smaller number of protein families compared to their respective control populations. On the other hand, people with colorectal cancer had a larger number of microbiome protein families than their controls."
In an analysis of the microbiome, ‘beta-dispersion’ can be used to measure how the composition of the microbe varies.
"Prior work linked disease to an increase in taxonomic beta-dispersion," Sharpton said. "We looked at whether gut microbiome functional beta-dispersion is different between healthy and diseased populations and saw an increase in functional beta-dispersion in patients with colorectal cancer, Crohn's disease, and liver cirrhosis. Individuals with obesity displayed reduced beta-dispersion relative to their controls."
The researchers were struck by the amount of overlap of bacterial functions linked to disease. The researchers acknowledged that there is still a lot more to learn. Ultimately, they want clinicians to be able to rapidly and accurately use metagenomic data to diagnose disease.
"Our work points to information coded in the metagenome that could be used for that, but that requires more data to make those diagnoses more robust," he said. "We're trying to disentangle cause and effect, to resolve these needles in haystacks and find the links between the microbiome and health. Future research can leverage this new knowledge to test microbiome functions against the presence and severity of various diseases."