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Having spent time in the past studying probiotics and the gut microbiome, as well as being a student in the dietetics program, I certainly do choose pro/prebiotic foods as opposed to other, less microbially healthy choices. I have tried my best to incorporate probiotics into my regular diet. For example, instead of using milk in a smoothie, I will choose kefir because it has benefits as a probiotic (it does help that I vastly prefer the taste of kefir to milk; the tartness of fermented foods tastes very good to me). Additionally, whenever I want to include probiotics in a meal, I am careful not to kill them by cooking or adding food products that may negatively impact the microbes.

One concerning unintentional alteration to my microbiome is the microbiomes of the people that I live with. During the Coronavirus pandemic, I moved to live with my parents, and recently will be going back to Corvallis and living with a group of roommates. It is somewhat gross to think about, but the changes that they make to their microbiomes will have an impact on my microbiome.

You know how they say that there’s a thin layer of fecal matter on pretty much everything in your house? That fecal matter has microbes that were previously living in someone, and so it only stands to reason that as you live in a house with people, your microbiomes begin to converge. On the flip side, I could look at it from the opposite direction. Instead of them making my microbiome less healthy, maybe I am making their microbiomes healthier!

I think that there are very few intentional decisions that you could make in terms of food and nutrition. It basically boils down to whether you decide to purchase and eat them or not. I do think that more people should be educated on the topic of probiotics so that they can make a more informed decision when faced with one, but past that, there is not much else to do.

Rhetorical Precis:

Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S. 2017. Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology 152.

Stephan J Ott and his colleagues, in this research article published in the journal Gastroenterology, entitled “Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients with Clostridium difficile Infection” (2017), asserts that sterilized fecal filtrates are equally effective to traditional fecal transplant therapies while also being safer. They show this by conducting a study of patients with C. diff infections, and their results demonstrated that using a sterilized fecal filtrate was effective at eliminating the infection just like a common fecal transplant, with the added benefit of eliminating risk for adverse effects. Ott, et al, conducted this research to find better therapies that can eventually replace the traditional fecal transplant therapy, which has inherent risks associated with the introduction of a large number of unknown bacteria. The intended audience for this piece is likely doctors and health practitioners that work with the gut microbiome, as well as those who hold interest in fecal transplantation as therapy for other diseases.

General lifestyle changes are the main mode of action that people have on their microbiome. From altering hygiene habits affecting the skin microbiome to usage of mouthwash affecting the oral microbiome, the microbiome in general is highly dynamic and variable. One more such body site microbial community that can be changed by lifestyle changes is the gut microbiome.

The most obvious change that can impact the gut microbial community is that of diet. This can affect change via two different mechanisms: prebiotics and probiotics.

Prebiotics refers to food that humans eat that microbes use as substrates to sustain growth and reproduction. Prebiotics usually encompasses most fibers, especially soluble fibers, because these components are not digestible by the human body so microbes have free reign to digest these fibers. The presence of these fibers in the diet preferentially selects for microbes that can digest the same fibers. That doesn’t mean that prebiotic fibers are the only thing that microbes will consume. There have been recorded differences in gut microbial communities in people with and without high fiber intakes (vegans and high proportion meat eaters), which suggests that diet outside of specifically named prebiotics also has an effect on the microbial community of the gut

Probiotics are a different story altogether. These are foods that contain bacteria in them already, and these bacteria are the same ones that like to colonize the gut. When people eat these probiotic foods, they introduce these microbes to the general gut microbial community. With sustained, repeated exposure to probiotic foods, the probiotic bacteria will colonize and begin to grow in the gut, effectively changing the microbial community.

With the two prior changes, there is not necessarily a precedent as to whether or not the change will result in a healthier microbial community, because everything is variable between human microbiomes, and what may be invaluably healthful to one person may be entirely harmful to another.

One possible change that could be universally healthy is a decrease in stress. The gut and the brain are linked by the Vagus nerve, and what one does has an impact on the other: the gut microbiome can be affected by the brain and vice versa. This overall reduction in stress can come from meditation, mental health therapies, or exercise. Each of these lifestyle changes have been associated with change in the microbiome, which suggests that stress has an impact on the gut microbiome. It has been further theorized that the microbiome has an impact on stress, so there is the potential for a positive feedback loop that can work for or against stress. General stress may lead to negative changes in the microbiome which may in turn have a negative effect on stress which can further negatively impact the microbiome, and so on. Therefor, reduction in stress could overall positively affect the microbiome.

According to the reading, it seems like a vaccine that includes multiple HPV strains should include HPVs 16, 18, 31, and 45 at minimum. This would stem the root of a reported 80% of cervical cancer associated HPV infections. This is the ideal likely gives the best cost/benefit analysis, but it does leave the window open for other carcinogenic HPV strains to take hold and increase the proportion of cancers that they cause.

If we wanted to most effectively eliminate cervical cancers associated with HPV, we would include all of the other associated carcinogenic HPV strains (HPVs 33, 35, 39, 51 52, 56, 58, and 59). This would, however, be extraordinarily expensive to develop, produce, and (due to the nature of healthcare in America) administer. Likely so expensive that nobody would willingly sink the costs to produce a vaccine with every carcinogenic HPV strain, and very few people would go about getting it.

One possibility is that the most carcinogenic HPV strains could remain separated as different vaccines as opposed to mixed into one. This might make it more cost effective and more people might be inclined to get at least one of the shots. One potential issue with this set up would be needle phobias impacting rates of vaccinations.

The best time to administer these vaccines is before sexual contact, where HPV runs the risk of spreading. this can occur at any point, but likely before puberty would be a good starting point for vaccine doses.

Interestingly, after further research, it looks like a broad spectrum HPV vaccine is already being produced. Gardasil-9, a vaccine that protects against 7 of the most common carcinogenic HPV strains and 2 strains associated with genital warts, is already approved by the FDA and is being administered starting from the age of 9. This approval came mere weeks ago, after an accelerated FDA approval process that went through on June 12th, 2020.

Prompt: List as many human non-infectious diseases that you can think of that are influenced by microorganisms.

I know that many different microbes have influence on a myriad different non-infectious diseases, and that a lot of these diseases have to do with the human microbiome. The microbiome has been implicated in many different metabolic diseases including diabetes and obesity. This makes sense, due to the direct interface that the microbiome has with the gut, one of the main body sites for metabolism. Additionally, certain cancers can be influenced by the microbiome. There are certain bacteria and viruses that can both promote certain cancers, including a correlation between the Human Papilloma Virus (HPV) and cervical cancer. On the other hand, in the presence of soluble fiber in the large intestine, microbes have been shown to metabolize butyrate, a short chain fatty acid that cancerous colon cells are unable to metabolize, leading to their eventual lysis. In this way the bacteria are preventing colon cancers. 

Perhaps most interestingly of all is the association with the gut microbiome and the presence of neural and mental health conditions. The gut and the brain are directly connected by the Vagus nerve in what is called the “Gut-Brain Axis”. Microbes have the ability to produce metabolites like neurotransmitters that can directly interact with the Vagus nerve, and the nerve itself can release metabolites that alter the microbial composition of the gut. Studies have shown a relationship between the microbiome and diseases like Alzheimer’s or Parkinson’s disease, as well as mental health conditions like depression, anxiety, and schizophrenia. It’s important to keep in mind that just because these health states are associated with microbes doesn’t necessarily mean that they are caused by microbes, just that there is a relationship between said microbes that hasn’t been well studied. 

Outside of the gut, the microbiome of the mouth has been associated with dental caries, gingivitis and have been implicated in the development of canker sores. The microbiome of the skin has been associated with dandruff, body odor, and eczema. The microbiome of the vagina is associated with a healthy pH and an appropriate flora, but when the microbiome isn’t made up of microbes that it is meant to be (certain species of Lactobacillus), it can lead to bacterial vaginosis. Microbes have also been associated with systemic infections introduced either orally or via leaky gut, which can itself be caused by microbes. 

Some ‘diseases’ behave differently. One example of a disease state related to microorganisms that is a little bit odd is the association between parasitic infections and the development of the aforementioned eczema. Parasitic infections are unique, requiring different white blood cells than a bacterial infection, and often teaching the immune system about different antibodies. These unique infections actually end up teaching the immune system. In one study, pregnant women from non-industrialized countries were given an anti-worming agent, and those mothers gave birth to babies that had three times the rate of eczema as those born to mothers who received a placebo. This has opened up the idea that the development of the immune system when exposed to parasites can influence other future diseases states, but of course, more research needs to be done.

When it comes to disease states, aside from things like accidents or natural disasters, microbes have their role to play in essentially every possible disease state imaginable.