I built OpenBiota because I was sick, I was struggling, and it was the only way forward.
Long COVID brought months upon endless months of debilitating fatigue and brain fog. Migraines could last for weeks. My body was covered in chronic hives, my face would swell, and my vision was becoming increasingly blurry. I desperately needed to feel like myself again. Instead, month after month, from doctor to doctor, I was still not improving. Still searching for answers.
I sought help from highly credentialed specialists, including a Harvard-educated immunologist and doctors at UCLA, my alma mater. Yet I was still left without a clear path forward. It was frightening to feel so unwell and find that even the experts I turned to for answers couldn’t give me the help I needed.
So I began poring over research. Working with Next Health and functional medicine doctors, gut testing from TinyHealth revealed major imbalances in my microbiome. Next Health and TinyHealth helped me make a connection I had been struggling to find: what was happening in my gut could be part of what was happening to the rest of me. Finally, I had something concrete to investigate. Addressing aspects of that dysbiosis with a combination of anti-microbial supplements, well-researched probiotics and a slate of fermented foods daily has truly helped improve my quality of life and reduce many of my symptoms, enough that I have the energy and strength to keep pushing forward and looking for a solution that would allow me to fully recover from this horrible condition.
Every clue kept pointing back to the gut.
Doing research daily, I kept finding papers describing microbiome patterns associated with long COVID, lupus, Parkinson’s, Crohn’s disease, ulcerative colitis, colorectal cancer, atherosclerotic cardiovascular disease, and Alzheimer’s. In the case of Long COVID it turns out the spike protien binds to the ace receptors in the gut and wreaks total havok on the gut microbiome, disturbing and destroying many key beneficial species. Curiously, many other diseases had very similar dysbiotic gut profiles. The research and evidence were scattered across disparate papers, genetic catalogs, and online databases — but one thing was absolutely clear: the gut microbiome was somehow a central factor in all of these conditions. I wanted to bring it together: compare my own microbial gut DNA with published disease signatures, understand what organisms are part of my gut biota, what my microbes could be producing, and track what changed over time.
There was another deeply personal reason. The results of multiple independent gut health tests all agreed with OpenBiota's results from my FASTQ metagenomic data: my gut was in an obviously unhealthy and dysbiotic diseased state. I consulted with multiple heads of gastroenterology and to my horror was told there was nothing they could do. The establishment medical providers — even with the best insurance, and even willing to pay out-of-pocket if necessary, in the most advanced country in the world — still left me helpless with no treatment options. The best that a couple of GI doctors could do was order an IBS breath test (which was negative), and prescribe an experimental antibiotic off-label (that did nothing and possibly left my microbiome even more depleted). Some just shrugged their shoulders, others recommended probiotics and fermented foods. Multiple probiotics, fermented foods, kombucha, sauerkraut, kimchi, natto and many more were all already a part of my journey and did help, but didn't solve the entire problem, the results did not last, and I was looking for lasting durable restoration. I learned the unfortunate secret that no probiotics company will tell you: almost all probiotics are temporary, transient and do not lead to permanent engraftment in the human gut microbiome. The fact is, you just poop them out. Depending on the strain and many other factors, they may or may not help, but no matter what, you have to keep taking them — they unfortunately do not stay in your gut in a way that is restorative. It became evident that these huge handfuls of probiotics I was forcing myself to take daily wasn't enough, and all of the many doctors I saw were all just reading from the same script, had no approved tools, incentives or motivation to fix the root cause of my issues, and there was no solution in sight to restore my gut to a healthy state.
I refused to give up. So I dug deeper.
As I dug deeper and added extensive pathogen DNA fragment detection to OpenBiota it confirmed something else: known fragments of C. difficile were detected in my gut. After over a year of recurrent gut problems that were having an incredibly negative impact on my quality of life, this unfortunate finding actually gave me hope. It made me a candidate for fecal microbiota transplantation, or FMT. FMT is actually being studied as an experimental treatment for longevity and weight loss by transplanting a younger healthier gut microbiome from younger healthier donors. It turns out that biological age can be roughly estimated by analyzing the microbiome. It also turns out that GLP-1 is produced in your gut, and we have all witnessed the massive therapeutic success of GLP-1 medications for weight loss. So as it turns out, aging and weight loss may both also be directly linked to the composition of your gut microbiome. Fascinating. As I explored this with my doctors, I wanted a more reliable way to screen the microbiome from the potential young healthy child donors. Based on everything I had discovered so far, I felt it was critical to look as closely as possible at the donor's metagenomic data alongside my own for screening and matching purposes.
Transferring a living microbiome ecosystem of trillions of organisms from another human being, even if that human is young, fit and healthy, meant confronting much bigger questions: which organisms might take hold, what they might produce, and how they may influence my health (both good and bad). I read reports of unexpected hair growth after FMT. Woah. If a new microbiome can regrow hair on a bald guy, what else can it do? Could the wrong organism in an otherwise healthy individual make me go bald? A recent study showed that the microbiome transferred from Long COVID patients to healthy subjects caused the donor's Long COVID symptoms to occur in the recipients! Colon cancer has one of the strongest microbiome gut signatures. Could colon cancer be transferred this same way? Some studies show it may. Your body weight and your actual mood appear to travel with a microbiome too — transfering a community of an obese twin from human twin pairs caused more fat to grow than did from the lean twin’s transplant, and the transfer of microbiomes from people with depression produced depression-like behavior in the recipients that received it! Can diseases or disorders be transmitted this way? These were suddenly all very powerful, real, deep and important questions that needed to be answered. It is not clear if the microbiome is definitively causal in all cases, but it is 100% certain that there is a very real biological effect there. The gut microbiome is so powerful, it can change how your genes express themselves; how might these epigenetic effects influence my health? So much remains unsolved. OpenBiota is an open project that can rapidly integrate the latest cutting-edge state-of-the-art published research from across silos at the speed of the internet, free from the slow adoption and obstinance of the mainstream medical establishment. I needed a tool to examine the donor samples for disease signatures, pathogens, functional metabolite potential, and to use that data to evaluate the presence of any disease-associated patterns. I needed a gut health report that I believed was a crucial layer of missing information for myself and for the clinical FMT donor screening process.
I couldn’t find the gut health report I needed.
By then, I had tried a long list of gut tests—from TinyHealth and Vitract to Genova’s GI Effects, and more. TinyHealth stood out: a great company, an excellent gut health report, and a phenomenal support team. But none of the reports gave me the depth of disease signatures, organism coverage, and functional detail I needed to understand my own microbiome, or to compare potential FMT donors with my doctor.
After completing a standard gut test with TinyHealth, I asked their support team for my raw FASTQ sequencing data. They happily provided download links. With data from my own test and the donor samples my doctor had tested, I had the material I needed to look deeper. If you’ve already tested, you can contact TinyHealth support to request your raw FASTQ files, too.
I knew there was more to uncover in those metagenomic DNA sequences. The underlying signals were there; I needed software to shine a light on them and connect them to the published research. I wanted that evidence brought together and explained.
So I built it.
I started building OpenBiota just for myself, on the side, trying to create the tool I needed to help with my own recovery. I’ve been building sophisticated software for well over 25 years, writing C++ code to build production machine learning models since the early 2000s. For OpenBiota, I combined my decades of engineering experience with the most capable state-of-the-art AI tools I could get my hands on. These tools let me turn decades of published research and scientific discoveries — motivated by a very personal need for answers — into an advanced bioinformatics software application at a pace I would have never previously believed possible.
The result is a 300+ page report measuring 1,600+ results that turns raw gene sequencing data into a detailed, highly personalized, readable investigation of your microbiome's ecosystem: its organisms, metabolic capacity, disease-pattern resemblance, and the research behind the findings.
A match to a disease signature is a clue for further investigation, not a diagnosis. And a sequencing report cannot establish that an FMT donor is safe. What it can do is help us ask better questions, see patterns we might otherwise miss, and have more informed conversations about this undiscovered ecosystem of trillions of organisms inside of us that appears to influence so many critical aspects of our health.
I’m still on this journey. OpenBiota is my way of turning the research I’ve spent so long piecing together into something anyone can use, freely. I’m sharing the code so others can add new discoveries and help carry it further. What began with my own search for answers is now a tool I’m giving to the world—with the hope that it can help millions more people understand the vital ecosystem inside them.
