An Insider’s Guide to Gut Health Tracking with

Back in June of 2018, freshly stable from a newly adopted regime of long-term antibiotics for recurrent CDiff, I embarked on a journey to discover more about my daughter’s gut health. The idea initially was to wean off of vancomycin - her main oral antibiotic- the miracle worker that stopped all gut distress, returned stool to normal, and with that - the craziness of breathing issues, seizures, and near-constant hospitalizations for over a 16 months all stopped.

She gained weight, we went on vacation for the first time in two years. She came alive. But the weaning had to happen, no one can be on vancomycin forever, right? It causes its own issues, killing not only bad bacteria but good too. Lots of acid, yeast problems, nausea. But overall for the first few months, it was great. To prep for our wean attempts (I say attempts because we tried 5x unsuccessfully to come off), I wanted to diversify her microbiome and support the growth of healthy bacteria. We were making lots of changes with diet, going vegan for one, setting her up on new probiotics and actively introducing new foods with good bacteria she wouldn’t be exposed to normally (Korean pickled plums anyone?!).

Going off a recommendation from a friend, I was introduced to Ubiome. As their website states, Ubiome literally is ‘pioneering a new era of microbiome-based precision medicine’. What they do is make it easy to test and track your poo, or your kids, when you want, all while at home. You sign up, give insurance information, they send a kit one at a time to your home (we signed up for 10 total). It’s literally poo-testing done at home when you want. What you get back is data. And lots of it.

Initially, we discovered most of what we already knew. Her diversity was low, she had the combo of gut symptoms equating to IBD and IBS and the list goes on. But one thing I didn’t expect was that this home tool kit would grant us invaluable opportunities to test on and off her long term antibiotic- which we kept failing to wean off of.  Every time we tried, distress would come back in full force within 24-48hrs she would be turning blue (low blood oxygen levels) all day long. Put her back on, she stops turning blue. Simple. But not really.

Testing the gastrointestinal tract (GI) can be expensive- there are lots of variations of testing and tests that can be done. It is confusing. From my limited experience, if you are looking for bad bacteria the creme-de-la-creme test is a Biofire.

This is expensive, it is much more sensitive than a standard GI stool test looking for pathogens- which are little critters that can cause a lot of issues which is really bad in mommy terms. For a full scope medical definition of different pathogens, I would read more here.

Ordering the most accurate test available for GI tract doesn’t happen often. We had entire stays in Spring of 2018 where my kiddo was fasting for 5, 6, 7 days and the test still wasn’t ordered. Just another viral bug doctors would say. But we knew otherwise when the pain would reach heights where sleep didn’t happen, and a child is turning blue all day, and smelly, slimy stool reigns supreme - something is very wrong and resting the gut only provides temporary relief and the cycle continues. Alas, it is much easier to see the forest through the trees looking back.

It is frustrating from a parental/patient standpoint the way the GI world works. This is because accuracy kind of does matter in the world of GI. Especially when there is a suffering child who has triggered breathing issues involved. But the tests vary in accuracy and results can vary on or off certain meds. Knowing this, patients and parents can be informed and have the best chance of advocating for the right tests at the right times to fully gain a holistic perspective of what is going in a gut at any given time.

Fast-forward 5 tests into our Ubiome journey, I’m standing in an ICU with my laptop showcasing recent test results discussing Shigella with an attending physician. We tested for Shigella not once but 3x in private testing with Ubiome. Making the finding clinically significant (especially after discovering our dishwasher had no hot water connected). 

All those memes and graphics you see in social media about your gut and brain being connected, we live that reality - to an extreme. 

The life of the medically fragile is never simple. It is never easy to explain. But it DOES MAKE SENSE. Anyone who takes the time to see the patterns and realize the symptoms can see there are triggers, and those triggers are solvable. That approach is why Raegan is still alive today.  Why should our children be any different? The ones who cannot speak still feel. They feel loudly because they cannot speak - with their breath, arms, body - they communicate distress and pain and for ones like Raegan where the gut triggers breathing and seizures, it becomes a life-threatening issue. Some little gut issue becomes life or death.

One of the best parts of this journey using Ubiome was that even though a pathogen had slipped through, our last Ubiome test showed all our efforts with diet, all the work with prebiotics and probiotics - had shown some results. Her microbiome diversity for the first time showed as normal (see image below). This corresponds with a time where Raegan has been verbalizing more than ever before since she stopped talking. And I may not be a scientist or researcher. But I think this MEANS something. Don’t you? :)


Hi Jen! Sorry for the delay! Our saga has continued and all roads led to a fecal transplant. It just took place less than 10 days ago. We are currently off all antibtoics – Except one for motility. Breathing issues and seizures are stable. Her microbiome is undergoing a massive change but so far all signs are it’s going great. The biggest thing is keeping healthy and not requiring further anitbotics in the near future.

Janelle February 17, 2019

So did they treat the shigella, did it work and were you able to get off the antibiotic? If so, how?

Jen January 19, 2019

Thanks Richard for the comment! Actually, and we are updating the blog to make sure it calls this out, shegilla didn’t show up on a single test, it showed up 3 over the course of 2 months. combined with very bad symptoms. And a confirmed dishwasher that had a pipe issue and was not connected to hot water. So while understand your warning, and agree the usual use case for tests like these should not be to diagnose pathogens overall testing 10x over a period of time can collectively give a parent or individual a lot of data they can use to help gut conscious efforts to diversify gut bacteria. The tests should not be looked at in a single lense as you say, but in total over time can be extremely valuable. Depending on your situation. Thanks again for the comment and engaging!

Janelle January 11, 2019

Please, please don’t base medical decisions on a single uBiome test result, especially if it shows a happy result. Diversity levels fluctuate daily for all kinds of reasons. Test again!

Richard Sprague January 11, 2019

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