There are many bugs in the microbiome that cannot be cultivated, and thus are incredibly difficult to study using normal culturing techniques. We only know about these bugs through DNA sequencing, and it often difficult to draw any substantial conclusions from this information. One such group of bugs that is highly abundant in the microbiome is the bacterial phylum TM7. TM7 has been associated with numerous inflammatory diseases, like vaginosis, inflammatory bowel diseases and periodontitis, and DNA analysis shows that this bug has the ability to create many toxins. Studying this bug could lead to breakthroughs in microbiome diseases, but until now it was unculturable. Recently though, a team of scientists from around the United States were able to cultivate these bacteria and in doing so learned what makes this bacteria so unique, and possibly so pathogenic. The results were published in PNAS.
The team aimed their investigation at the oral microbiome, because TM7 is abundant in the mouth and highly associated with periodontitis. They took samples of spit and realized that TM7 only could grow when another bacteria, Actinomyces odontolyticus, was present. When they cultured these bacteria together in a saliva-like media they realized that the TM7 was physically attached to the surface of A. odontolyticus. Through further experimentation they learned that TM7 could never grow on its own, and needed A. odontolyticus to replicate. Furthermore, TM7 is parasitic, and kills A. odontolyticus when they are starved.
The researchers then investigated the pathogenicity of TM7. They learned that TM7 can evade detection by the immune system for itself and A. odontolyticus. They also discovered that the particular strain of TM7 they were studying was antibiotic resistant. Furthermore, sequencing of the TM7 showed the strain had amongst the smallest genomes ever discovered, and relies on the A. odontolyticus for production of many essential molecules, like amino acids. However, TM7’s small genome is very dense in the production of virulent molecules and toxins, perhaps necessary for its parasitic nature, which could also affect its human host.
This study raises many interesting points about pathogens in the microbiome. DNA sequencing is a great start to defining the microbiome, but often times culture, or in this case co-culture is necessary to drill down into the true virulence of bacteria. For instance, prior to this study A. odontolyticus was considered to be associated with many inflammatory diseases, but these researchers showed that it is likely TM7, not A. odontolyticus that is the true culprit. Alas, the complexity of the microbiome often times reveals many more questions than answers.