What is it that bacteria, viruses and cakes all have in common? They live in my mouth.

Cake, anybody, no? Yes. Yes is the answer. It always has been and it always will. Cake is an institution. It is seemingly one of those rare things that all of humanity can agree on. The language we use to define cake reflects how it has over time ascended to godly status and come to represent the beauty found in nature. Examples: Angel cake, Butterfly cake, Caterpillar cake, the list goes on (it doesn't). Maybe you think I'm just cherry picking names of cakes to make an emotional plea for your support on this matter. Now that really would be the icing...

In slightly less sweet news, cake and virtually everything else you put in your gob can transfer microorganisms like bacteria and viruses. Most of these are harmless. They all cosy up together having a little party as morsels of food and other debris come their way. Unfortunately though, as with all things in nature, some of these are pathogenic, i.e., they gone mess you up. In most cases, your body is equipped to deal with the threat, but in a rare number of cases, some of these may slip past the immune system, set up shop in your mouth (or gut) and begin causing havoc. Scientists who study the relationship between these microorganisms and humans have begun to tease apart how certain species of bacteria and viruses can actually contribute to common diseases, in particular cancer.

Recently, I was tasked with identifying the microbial species associated with cases of head and neck cancer. Head and neck cancer occurs in the mouth, throat and neck and affects over half a million people each year globally, half of whom will die from the disease. Smoking and alcohol consumption has been strongly implicated, as have a number of bacterial and viral species including human papillomavirus or HPV for short. HPV has a precedent for this in other cancers and the links with cervical cancer are so strong that HPV vaccinations are routinely provided to women in the UK for free (until the age of 25).

Head and neck cancer that is caused by smoking and drinking is associated with certain mutations that cause cells to divide uncontrollably, and HPV cancers affect genes with similar functions, but which are slightly different. HPV cancers also affect immune cells differently, which means that you can stratify cancer patients by looking at gene expression and immune cell profiles. There are also bacteria present at higher levels in head and neck cancer like Fusobacterium.

Using publicly available data from a study by Cillo et al., I developed a pipeline (different computer tools applied in sequence) to find out which species of bacteria and viruses were more common in head and neck cancer. One thing to note was the results could be quite variable depending on which tools were used, so I chose tools that captured the most information and performed most consistently. 

The results confirmed what I found in the literature as Fusobacterium nucleatum, and Fusobacterium animalis were considerably more abundant in the tumours of head and neck cancer patients. I found Fusobacterium nucleatum was common in HPV cancers, as well as Clostridium botulinum and Mycoplasma wenyonii. Fusobacterium has well established links with cancer, but for a long time it was unclear whether it was driving the cancer or simply an opportunistic pathogen. However, recently scientists have begun to show how Fusobacterium causes cancer directly in animal models. It appears that Fusobacterium can negatively affect how the immune system functions, which may also affect other gastrointestinal diseases such as renal disease, ulcerative colitis, gastroesophageal reflex disease, alcoholism and inflammatory bowel disease.

Overall, it appears if doctors could identify the presence of HPV and Fusobacterium in your mouth, throat and neck (not cake), then this may indicate that you are at increased risk of developing cancer or other gastrointestinal diseases. I must stress that I'm not suggesting cake causes cancer, that would be unscientific and against everything I stand for as a human being. I'm just highlighting how seemingly innocuous microorganisms can get into our mouths from different sources and that over time they may increase our risk of disease.

Some limitations: there wasn't a huge number of samples used here (63 in total). This was also an association study so we can't infer causation. Additionally, samples from hospitals may become contaminated and skew our results. Finally, there's lots of information missing here that would have been informative, such as markers of immune system functioning. In the future, scientists should explore the relationship between microorganisms and the body in more detail using more sophisticated tools and to try and validate the results in larger groups of patients, which sounds easy, some would say a piece of cake, but unfortunately for me, it is anything but.