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 34: Reduced Calorie Fasting

I saw my doc today and we discussed my research on fasting because I need to know I’m on the right track with my thoughts on forcing my damaged cells to self-destruct.

Everyone has been suggesting to me that I take in nothing but water when I fast, and it just doesn’t feel right when I think about how we evolved and how our bodies work. Zero calorie fastng sounds like something a healthy person can do for a quick reboot, but not a good idea for someone whose cells can’t even produce enough energy to make it through a day. I explained to her what I’ve been researching, and she agreed with me that zero calories is not a good idea for someone as sick as me. We talked about a couple of interesting studies, and based on them she wants me to do reduced calorie fasting at 600 calories a day, as long as I want, but I have to calorie-load a couple of days a week. So, I can fast 5 days and then eat as much as I want for 2 days, and take ALL my supplements because a lack of cell-building nutrients won’t be good while I’m trying to heal my cells.

I then presented to her my hypothesis that the reason I got so sick around 18 months after being given the Cipro is because too many of my cells were damaged, because fluoroquinolones cleave to human DNA and are phototoxic, so the damage continued until my body decided to shut down and try to repair itself, which is why I lost my appetite… it’s like my body wanted to heal and forced me into cell regeration mode… but I was not detoxing at the time because I had no idea I’d been poisoned, so while my body was killing off a lot of cells, I could not clear the waste and got really sick. My liver, spleen and lymph nodes all swelled up and I only started to get better when I started nutrient loading and detoxing, as well as treating viral infections that had been in remission and all became active post-flox. She listened to my presentation, punctuated with my references to medical studies, and told me that in the absence of any other explanation (and there is none, that she is aware of), my hypothesis makes perfect sense!

So, I will now proceed with trying out a fasting cycle that is 3-5 days a week at 600 calories a day. I’m going to have to use a calorie tracker while I get the hang of it. I’m also going to make a concerted effort to keep on the detox regimen until I feel that my body has replaced most of my broken cells.

Then, hopefully, I will be able to get adipose stem cell therapy to repair my tendons.

Day 27: Fasting to Provoke DNA Repair

In my support group, several articles came through the newsfeed on the DNA repair cycle that reduced caloric intake provokes in humans.

I think my body naturally tried to do this last winter about 18 months post-flox. I lost my appetite and then I got really sick, I think because I was completely ignorant of what was happening, so I was not supporting my body when it was trying really hard to repair my cells. Because flouroquinolones cause a lot of DNA damage, I think I was losing a lot of cells. I became weak and my I had tremors. My liver and spleen swelled up and all the lymph nodes on my right side and I ended up in the ER twice with what I now think was toxicity from cell die off that my body could not clear out. Even though my labs were off my liver swollen, they sent me home with “anxiety” once and “fibromyalgia” the other.

I want to try that again, but more gently. I’m trying to figure out how much of a caloric reduction is necessary, so that I can provoke cell repair but not in a way that will overwhelm my ability to clear the toxic by-products. It’s also difficult to go completely without nourishment when you’re weak. I’m not convinced we have to reduce calories to zero, but most people who’ve responded to my questions believe I must reduce my caloric intake to zero. While I wait for an opportunity to talk to my primary care doc, I will proceed much as I did this past week.

The fast I just finished wasn’t as successful as I wanted. I needed a couple of days of rest and thought I’d have it when my kid went to a campout, but they got rained out and it ended up being more stressful than I wanted, but I managed 48 hours with 400 calories each 24 hour period. I would have made it to 60 hours if it wasn’t for that bowl of oatmeal.

Next time I want to do a coffee enema as I start the fast, maybe one when I end it, and depending on what I find out from my doctor, somewhere between zero and 400 calories each 24 hours… I’d at least like to drink my turmeric, cinnamon, modified citrus pectin tea with a splash of half and half a couple of times a day. Maybe I’ll make it past 2 days next time, but I think gentle is the way to go for a few months. I was in a great deal of pain last night, but for two days in a row I’ve now woken up without quite as much pain in my extremities.

I also need to figure out what supplements should be cut out during a fast. I don’t want to skip the ones needed for DNA repair, or the ones my tendons need, since they’re expremely delicate.

I have a feeling it will be a slow process.

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.

Day 11: Black Garlic

In my heavy research phase into antioxidants to combat the damage done by Cipro, I read about black garlic. I immediately got out my rice cooker and dumped every bulb of garlic I’d harvested from my garden, plus the bulbs I’d purchased at my co-op.

I have now sampled 2 out of the 3 varieties I stuck in my rice cooker, and I can tell you that the purple varieties are WAY TASTIER than the porcelain varieties. I don’t like to cook with the purples because the bulbs are smaller and harder for my damaged hands to peel, but they are perfect for black garlic and peel more easily after being in the rice cooker than the porcelain bulbs do… and now I’m eating the little cloves like candy.

I haven’t sampled the elephant garlic yet… it’s technically not a garlic, it’s a leek, but it’s also high in allicin so it should work.

Why make black garlic?

Physicochemical and Antioxidant Properties of Black Garlic

The Analysis of Saccharide in Black Garlic and its Antioxidant Activity

Day 10: L. Sakei to The Sinus, etc.

The sausage probiotic arrived today, and the package was much larger than I thought it would be. I think there’s enough starter in their to colonate at least a dozen people. My teen child consented to give it a try, because she was just resigning herself to a lifetime of sinus issues and is now hoping she won’t have to, so I mixed us each up a Neti pot-ful with water I boiled earlier and let cool. It stung a bit more than the usual Neti-pot experience.

I also started my morning with 5 ounces of human breast milk and filtered water, and a bit later a high-fiber smoothie. My tummy feels fine today. I haven’t experienced any of the painful bloating I usually do toward the end of the day. In fact I just ate and my tummy is rumbling, which is a sound I haven’t heard for a while!

My hair smells and feels better than it did a couple of days ago, in spite of just rinsing it well with no shampoo. I’m skipping the soak tonight and just applied a little HBM to the back of my neck, chest, feet and hands.

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.