All posts for the month June, 2020

In late March, early April, of 2020 I updated my hypothesis paper (the one dedicated to describing the ideas coming out of my 2014 preliminary research for Project: Cancer-Fighting Gut Bacteria, the crowdfunded project this site is dedicated to) and last month I submitted it to the journal mBio. I also wrote a short proposal on how to leverage existing clinical trials to assist in finding cures or risk factors for COVID-19 symptoms (that I put into a podcast, which is referenced here), and in the written proposal I included some new, very small analyses which described potential interactions of products from my cancer-fighting gut bacterium, a strain of Lactobacillus johnsonii, and pathways involved in inflammation and cytokine storms, which are the reason why people get very ill with COVID-19. This gut bacterium has been characterized by people with more medical and immunology expertise than I have as anti-inflammatory, and the products I found it produces could provide at least a partial explanation as to why that is, and how we can use this mechanism to make new forms of medicines.

I submitted this to bioRxiv, and of course, because the second paper was a proposal, it was rejected. I also had submitted my original hypothesis paper which describes the experiments I did to find and characterize the products I looked at, and speculates on where the bacterial products come from, how they can be used, and how communities of bacteria in the gut or elsewhere can be affected by their environment to change the spectrum of such products provided. That was rejected as being too short. So not a real paper, I suppose. I am optimistic that the paper I submitted to mBio (exactly the same one as to the archive) will eventually be reviewed and I’ll get some kind of verdict, although this process is not occurring quickly at the moment. The other piece I may publish once the mBio submission, if it is accepted, gets published, in blog form. It may inspire someone, although I realize that the majority of scientists in the world will never see this blog.

It occurs to me that some of the ideas I’ve had regarding how to look at interactions over time between soil and plants and their microbiomes (and finding drivers, and indicators of ecosystem health, for these systems) might be applicable to the gut ecosystem. For example, I had used network analyses of soil bacterial and fungal communities characterized by next-generation sequencing of barcodes to come up with a means by which “healthy” soils and systems can be identified, on a relative scale where you rank networks from different sites or treatments that are comparable. It occurs to me that this could be applicable to groups of mice or patients who can be sorted into categories based on symptoms, and provide gut microbiome samples. I also note that if you took samples over a period of time, and monitored symptoms or other indicators of health or disease, it may be possible to look at relationships across time points (so link a phenotypic host trait at time 1 with a microbiome state at time 2, or the opposite temporal direction) and find whether the state of the host of the microbiome drives the gut microbiome composition, or whether the microbiome drives the state of the host (ie. which changes first). I suspect you’d need many time points, and that this interaction goes both ways; the strength of the interactions (which drives which, host or gut microbes) will probably vary with environmental factors that we already know affect microbiomes, such as exercise levels, sleep, stress, diet, in addition to factors including host genotype. I would find an experiment or project designed to test this fascinating.

I am too tired most days to jump onto public database sites or petition PIs for data so I can test these ideas myself, and I realize that I may not have the statistical “chops” to see these ideas tested thoroughly enough alone. The obvious solution is to get a laboratory of my own and I really wish I could say I could, but I’ve tried for 25 years or so and I’ve never been offered this opportunity, so the only way I can do real science is to interest someone else with more resources in what I have to say, write a grant, and do the work. I really wish I could find someone who took me seriously enough to listen to my soil health and productivity ideas, let alone seeing how the analytical concepts may apply to medicine and veterinary sciences. I will be happy if a single researcher finds this post and is interested enough in the concepts to contact me (, although I have limited my forwarding from this address so it is not a fast way) and ask me to elaborate, or send the preliminary thoughts I already have had.

It doesn’t help that I’m bipolar and struggle often with depression that makes me fatigued and interferes with my ability to get things done quickly, and it also does not help that when I come up with truly out-of-the box thinking or ideas, people that know I am bipolar tend to want to see those ideas put forward by someone else first so they know they are not “crazy”.

I’m heartened that someone at Cornell was kind enough to write to me to describe some work going on that might be publicly available in about a year or two, so I can test my soil health indicator ideas then, I would assume. I might ask who the PIs are that he references in this large multi-lab study so that I can ask them individually if they would be interested in either providing me with data, or taking the analysis I’ve thought of seriously enough to test it with me before the data goes public. That will have to wait for another day.

I hope you have a productive day and apologize if you came here looking for information you did not yet find. I plan on discussing both how clinical trials work and how gut bacteria might affect inflammatory pathways (which affects a surprising number of different disease states, including cytokine storms that are present in the more serious cases of COVID-19) in future episodes of my poor, neglected podcast- I keep putting it aside for more pressing things and it never seems to be continued. I will try to make more time for it in the near future.