My Gut: One Year Later

It’s time to take a look at the progress I’ve made since I took what I believe were life-saving measures last year.

Quick synopsis, if you haven’t been following my blog:

I was given Cipro when my appendix ruptured. After Cipro, along with a bunch of other problems, I developed out-of-control IBS symptoms. It got to the point where I was starting to develop bowel incontinence, and the lab botched the c-diff test… not that I would have wanted to follow the currently accepted protocol for c-diff, which is MORE antibiotics. I went rogue, so-to-speak, and read as much as I could on fecal microbiota transplants. Knowing that I wouldn’t be able to get it done in a medical setting, I did it myself at home using a donation from a physically fit younger friend as well as milk from a healthy nursing mom with a healthy baby. I didn’t do the transplant in a vacuum, either. I read about fiber, and I increased my fiber up to about 4x the RDA from as large a variety of sources as I could. I’m not going to say it was pleasant. It wasn’t. However, my bowel no longer bothers me UNLESS I eat sugar. When I eat sugar, my gut blows up like a balloon… so, no sugar. Raw honey seems to be fine.

Now, onto the good stuff. Here are the results of the samples I took before and after the transplant. Keeping in mind that my before sample was frozen while I waited for the money to do the test, which I honestly think has no bearing on my results because the DNA, which is what was sequenced, would remain intact. The samples were taken several months apart.

2014 before and after HBM/FMT

As you can see, my Firmicutes started out ok, but in every other category, I was a mess. Even after, I was still a mess, but the Bacteroidetes at least exist now. Verrucomicrobia remain extremely high, which is something for me to research when I have more time, but I’d like to send in another sample this winter to see what kind of equilibrium my gut has managed before making any more major changes to my diet.

Note: the “rare taxa” notes are not necessarily new species, but ones in quantaties large enough to be detected. I know I was a mycoplasma carrier prior to this experiment.

Also of note: there is apparently one Akkermansia strain that is hardy against broad-spectrum antibiotics, and Cipro may explain why my profiles are dominated by Akkermansia. It survives where other microbes perish. It’s the microbe that exists in thin people, but at 5-6%, not anywhere near my proportion, and it can’t be the only factor in thinness, because my weight has been swinging between 115-150 lbs. without any good reason (I have tiny bones and I’m only 5’3″, so ideally I’d weigh about 125 lbs.).

After I get test results back for the next round, I’ll try to do a more detailed report of what’s living in my gut and how the past year has influenced it.

Day 59: Microbiome Update

To date, I’ve used donated fecal matter from one donor and human breast milk from one donor to give myself retention enemas. The results have been astounding. One of the most significant things I’ve noticed (aside from being cured of IBS) is that my cognitive processes have improved. Things that I thought were forever lost to me are starting to come back… like the ability to read a book and keep track of the story, or to fix things that are broken, or to focus long enough to pay my bills.

Today I ran across this article on the importance of maternal microbiota in forming the protective blood-brain barrier in utero. I found it very interesting that fecal microbiota transplant is cited as healing the BBB in adult mice and I wonder if that has anything to do with my sudden and profound improvements in mental clarity.

I decided not to use my second donor’s milk as an enema after learning that she suffered from several late-term miscarriages. I didn’t learn about the miscarriages until after I’d purchased the milk and read an article implicating microbiota imbalance in late-term miscarriage. I seriously doubt that her milk would harm me, but I decided not to risk bottom-up delivery and have been using it in smoothies and to make kefir instead. I also put a bit of her milk in my neti pot along with more L. Sakei the other day because of one persistent stuffy spot in my right sinus, and it seems to have finally “taken”. I’d had a couple of minor episodes of eyelash crusting so treated my eyeslashes with her milk twice and have had no further crusting.

In addition to drinking the human milk plain and fermented, I’m drinking raw camel milk from camels fed on a GMO-free diet, brewing ginger beer, and making homemade saurkraut. I also eat miso soup made from raw miso paste about once a week, half-cooked organic eggs, and am continuing with a high fiber diet. I’ve continued to see improvement in my gut function. I occasionally experience bloating, but from what, I’m not sure. I’ve had absolutely no more instances of soft stool and no bowel urgency. I’ve had a couple of pimples, but overall my skin is quite clear. It’s been extremely difficult lately to stick to an organic diet, or to get my supplements, because of a financial set-back that almost resulted in my utilities getting shut off, and I’m developing a deep fear of ingesting anything treated with glyphosate because of its antimicrobial nature, so I hope the new year treats me more kindly in money matters.

When it’s possible, I plan to purchase more milk from my first milk donor, and to approach the person who I’d like to be my 2nd fecal microbiota donor. When it’s kidding season, I’ll be able to puchase raw goat milk locally… it’s almost as beneficial to the gut as camel milk but much less expensive.

Day 28: Farting vs. Burping

The number of changes in my body over the past 4 weeks is, frankly, stunning. I still suffer from intense pain in my extremities, my back still burns, I deal daily with heart palpitations and random overheating, and my eyes still feel like they’re floating in acid, but here’s what has improved, and when I say improved, I mean holy shit things are so much better!

I now fart, but I rarely burp. That means the microbes in my small intestine, that were causing horrible bloating, burping and tummy pain are no longer there, and I have successfully recolonated my large intestine with microbes that process my intestinal slurry into poops of the right consistency so as to not cause me distress. I no longer have bowel spasms, bowel urgency and soft stools. At the end of the day, my tummy is not hard and bloated and it doesn’t hurt to bend over… and truthfully, I don’t think I’m actually farting as much as I was.

One very odd, and very unexpected side effect of the changes in my microbiome is the alteration to my circadian rhythm. I have twice been diagnosed with Delayed Sleep Phase Syndrome. I am awake until 3 am. Nothing has been able to change that in all the decades that I’ve tried… not bright lights, not any amount of sleep hygiene, nothing. Yet suddenly, I find myself asleep by 1 am every night, consistently, for the past week. It’s a nice change.

Next month I’ll be adding more microbes via milk from a second mama, and I’m looking at getting some raw camel’s milk as soon as possible after that. I think I’m developing a passion for diversifying my microbe collection! If I encounter good fecal matter donor candidates in the future, I will gladly give myself another fecal matter transplant, if they are willing to donate.


Day 17: Fecal Matter Transplant

This morning my friend rushed her fresh fecal matter over to me, after texting me that she hadn’t been this excited about her poo since potty training.

I had everything ready to go, having decided to use an old french press to remove larger bits that might clog the enema tube. The odor of her fecal matter reminded me of the smell of an herbiverous grazer, not unpleasant at all. What I ended up with was more liquid than what I would have liked, as I read it’s recommended that the transplant be more pastey to make retention easier… and it was difficult to retain much of it for long, but I made it about 15 minutes before my body insisted I void. I still attempted to retain as much as possible, and soaked in a warm epsom salt bath for an hour to relax my tummy.

My skin is still clear of acne after the human breast milk enema, and my digestion is good, so the fecal matter transplant will diversify my microbiota even more.

I even got away with gorging myself on no-bake oatmeal cookies the other day, without bloating… it was risky, I know, but I wanted to test my reaction with my upgraded microbiome and high fiber diet.

Day 11: Human Breast Milk Progress

This morning I consumed about 10 ounces of human breast milk, followed by filtered water. It didn’t taste as weird as the first day I drank it. I have enough left for another couple of treatments, so I’m going to save it to use concurrently with the fecal matter transplant.

I also ingested some liquid magnesium, to test how I tolerate it. I want to be able to start ingesting magnesium to repair the magnesium depletion in the cells lining my gut. So far so good.

My tummy was less bloated than usual. After dinner it did swell up a little, but for a very short time compared to usual… perhaps 15 minutes instead of multiple hours.

I soaked in an epsom salt bath for two hours, rinced in an raw apple cider vinegar bath, towel dried and applied about a half ounce of human breast milk to my skin, especially my head hair roots, including my eyelash roots, which look less puffy. I’m starting to suspect that my tear ducts are missing microbiota, which led to the Blepharitis. I’m going to look into that… although the idea of getting a healthy tear donor to cry into my face seems terribly odd and funny and got me thinking of how it would go…

Me: ok, so… I’m just going to lay down here, and you just prop yourself up over me so your eyes are right above mine.

Donor: um. ok, like this?

Me: yeah… ok, now I’m going to have to make you cry… (berating insults ensue, with some pinching and slapping thrown in)

Nah, I don’t think so. I’ll have to brainstorm this one a bit more.

One last thing: one of the benefits of fecal matter transplants I read all the time is acne clearing up within days. I wasn’t expecting to see it so profoundly from the human breast milk, and I don’t know if it was the topical or the internal treatment that did it, but there you go. My acne cleared up.

Day 1: Setting the Stage

As I’ve been researching and reading over the past month and finally settling on my plan to rebuild my microbiome using human breast milk and a fecal matter transplant, I’ve learned some interesting things about our microbe friends and what an alarming situation most of us are in. I don’t know how many species I lost, but I feel like it must be a significant number, and I would like to maintain whatever I can recapture. There’s a lot of work going on that is helping demystify what supports a healthy microbiome, and luckily I’m already doing most of it, like eating organic, eating fermented foods, no processed food, no GMO, low-carb, but I upped my game a bit over the past month by adding raw apple cider vinegar to my daily diet, and by increasing my fiber intake with chia seeds and coconut flour in my smoothies. I also lowered my dairy intake a bit… I love cheese, but I’m cutting myself back to a few servings a week, and maybe a cup of raw yogurt a week. My real weakness is adding a bit of half-and-half to my morning mocha, but it’s just a couple of tablespoons to a half-cup or so of hazelnut or hemp milk and I’m just not ready to give that up… yet.

The biggest change is probably switching my coffee out for a blend of dandelion root, burdock root and chickory root, boiled and strained. It does not taste like coffee, but does impart a nice flavor to my mochas, and most importantly gives me a daily dose of inulin to support microbiota in my lower gut. I find that I don’t actually miss coffee at all, but I’ll allow myself a cup if I go out for a gluten-free pastry.

A friend gave me the link to, and I located a mama today who is lifestyle compatible: eats organic, gluten-free, antibiotic-free, and paleo, who agreed to ship her milk to me frozen, so I’ve purchased 30 ounces. That will get my started and I can assess if I need more after I get into this process for a few weeks.

As of today, a few things have already improved. The horrible fungus on my left foot, that got 100x worse after I was floxed, seems to have started to clear up. My gut is functioning a little bit better than it was when I hit a crisis point 2 weeks ago that left me feeling like I’ll never have a normal life again. I’ll take these tiny signs that I’m on the right track and keep going.