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.

Probiotics for MS

A friend asked me how to help her compromised gut without going as far as using fecal matter or breast milk to replace species that have been found to be compromised in people with MS, and because MS is an inflammatory disease, I decided it would be useful to have a list of probiotics that can be purchased that might decrease the severity of inflammatory diseases, if not prevent them. Working off the published study, I went looking for products that contain the compromised species, or a strain that plays a similar role. Where I could find them, I’ve linked the products with my Amazon associate number, because if you buy from Amazon, you help me get the supplements I need, too. Get them where it’s convenient for you, though. This was just my disclosure that buying through some of  the links will benefit me 🙂

When taking probiotics, take them with a high-fiber diet, and rotate through them. Eat naturally fermented foods. You don’t need to take every probiotic every day. If you tailor your diet to provide plenty of soluble (prebiotics and resistant starch) and insoluble fiber, you’ll be able to build a sustainable and healthy gut profile over time. If you want to get really sciencey about fiber, read this.

I’ll also note if my FMT/human breast milk treatments introduced a species, although my microbial analysis does not provide the specific strain in every case… and I promise to post my thoughts on my “before” and “after” microbiota profiles as soon as I’m done analyzing them, as there were some changes. I also want to note that many of the species listed here are anaerobic, which means that “miracle cures” like Mineral Miracle Supplement, which introduce oxygen to the gut, will kill beneficial species.

The article my friend asked me to look at was this one: Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters

The study found “… a depletion of 19 species was striking in MS samples, and fourteen of them belonged to Clostridia clusters XIVa and IV” and “also found a reduction in the proportion of several Bacteroides” (which are also reduced in the guts of people with IBD).

Here they are, with any useful information I could dredge up.

Faecalibacterium prausnitzii: no replacement available, although this study found that consumption of Bacillus coagulans GBI-30 increased the f. prausnitzii population. Bacillus coagulans GBI-30 is patented and can be found in Life Extension Florassist Oral Hygiene Lozenges and Schiff Digestive Advantage.

Anaerostipes hadrus: not available in supplement form. I did pick up an Anaerostipes strain from either FMT or HBM.

Eubacterium rectale ATCC 33656: not available in supplement form.

Clostridium sp.: we’re talking Clostridium species in general… there are a handful that will make you horribly sick if they crowd out beneficial microbes, but the genus is largely beneficial. You can get a beneficial strain in Advanced Orthomolecular Research AOR, Advanced Series, Probiotic-3.

Specifically mentioned in the study – Clostridium sp. RT8, Clostridium sp. ID5: Not available in supplement form. However, of note : Phytonutrient diet supplementation promotes beneficial Clostridia species and intestinal mucus secretion resulting in protection against enteric infection.

butyrate-producing bacterium SL7/1, butyrate-producing bacterium A2-175: Not available in supplement form, but I found one clinically-studied butyrate-producing bacteria (Lactobacillus rhamnosus GG) product on the market, Culturelle Health & Wellness Probiotic in addition to Advanced Orthomolecular Research AOR, Advanced Series, Probiotic-3.

Bacteroides stercoris, Bacteroides coprocola, Bacteroides coprophilus: Bacteroides are so sensitive to exposure to air that they cannot at this time be put in supplements. However, a study found that echinacea will naturally increase your Bacteroide population. Not all Bacteroides are beneficial, so proceed with caution. I had approximately 5x more Bacteroides after FMT/HBM.

Lactobacillus rogosae: Not available in supplement form. However, The Scientific Basis for Probiotic Strains of Lactobacillus examines other strains of benefit. Culturelle Health & Wellness Probiotic contains Lactobacillus rhamnosus GG. Jarrow Formulas FemDophilus contains Lactobacillus rhamnosus GR-1. Garden of Life Once Daily Ultra contains Lactobacillus acidophilus NCFM. BioGaia ProTectis drops D3  and Pedia-Lax Probiotic Yums contain L. reuteri MM53, which is now known as L. reuteri protectis. Asian markets carry a product called Yakult which contains L. casei Shirota.

Lachnospira pectinoschiza: patented in 2012 but not yet available in supplement form.

Roseburia sp.1120: Not available in supplement form.

Clostridiaceae bacterium SH032: Not available in supplement form.

Sutterella wadsworthensis 2_1_59BFAA: Not available in supplement form.

Desulfotomaculum sp. CYP1: Not available in supplement form.

Prevotella copri DSM 18205: Not available in supplement form… and nor does it seem that P. copri is beneficial as it’s been linked to RA… so the result of this study is interesting indeed and hopefully more research will be done. Incidentally, I had no detectable Prevotella strains prior to FMT/HBM, but picked up a small amount in the process.

Megamonas funiformis YIT 11815: Not available in supplement form.

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 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 15: Human Breast Milk Update

I seem to be holding steady. My tummy regularly makes rumbling noises, and I fart more than I burp now. Soft stools have not reappeared since I gave myself an enema of human breast milk.

I even ate cookies yesterday and didn’t bloat up.

I’m continuing to eat a very high fiber diet. Eating in the morning has never been easy for me, but now I’m eating oatmeal first thing and doing very well with it.

I’m also taking magnesium orally every day, and it’s no longer giving me diarrhea. My bloodwork shows my magnesium on the low side of normal, so the topical magnesium oil has been absorbing… but it’s time to up my game and take more magnesium to reverse the magnesium depletion that occurs with floxing.