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How to Cure C. Diff Part 1 of 2

24 February 2018

Disclaimer:  If you have C. Diff, don’t just DIY it based on reading this.  Please see your doctor.  This is a very serious infection.

C. Difficile (Clostridium Difficile) is a stubborn spore-forming bacteria that infects the large intestine. I never heard of it until my wife’s friend had it.  I didn’t get it from her, but I had it lurking inside me at the time.  How do I know?  Let’s walk through the 18 months from when I got it in October 2014 to when I found out what it was in February 2016.  It was not “full blown” the entire time, but I had symptoms all 18 months of poor digestion, reduced libido, more infections, bad moods, and less energy.

As I wrote in my article “Stress Revisited,” something had changed with my initial success of eating a Ray Peat based diet high in fruit sugar and dairy, and low in fibers.  At the time, I blamed it on excess liquids (store bought orange juice), excess skim milk (ultra pasteurized), and excessive use of supplements including niacinamide and aspirin. That said, maybe something I was doing like high liquid or low fiber, or the supplements may have made me more susceptible to a C. Diff infection.  But I suspect it was actually C. Diff mostly responsible for wreaking havoc on my health and not entirely the diet or supplements.

The origin.

On a Saturday in October 11, 2014, I fell extremely ill around noon which led to throwing up and diarrhea for about two straight days.  I just ate a pizza from a local pizza place, and on Friday evening ate a bunch of raw oysters.  I think the bacteria came from one of those two sources.  I think it able to “take hold” in my system because my gut was depleted from two years abstinence from fibers.  This is my speculation as many Ray Peat-ers typically think fiber is bothersome:  feeding bacteria, possibly increasing endotoxin (LPS) and possibly increasing serotonin.  I believed fiber, soluble or insoluble, caused all those things, and of course, maybe I misunderstood some of the recommendations and advice, or took it to extremes which are never good.

The rest of the day I continued to feel more and more screwed up – nausea and throwing up.  I planned to meet up with a girl I really liked that night.  Thank goodness I still did as she is now my wife.  Even though I was very excited, I still went home early because of how I was feeling.  The next day I didn’t feel any better – diarrhea and vomiting.  I couldn’t keep a thing down or in.  Being a single person in this state is no fun.  I felt helpless and my usual cures – charcoal, carrots, apple sauce, water – did nothing.

Finally on Monday morning after no reprieve, I walked to the ER near me.  The doctor and nurses ran some tests.  Before getting the lab results back, they asked me “do you have any history of alcohol or drug abuse?”  “No” was my response.  My liver enzymes were extremely high: AST of 713 on a UL of 39, and ALT of 1136 on UL of 65.  This shows how bad for your body this infection is at a systemic level, and how gut issues can affect everything.

The doctor put me on some anti-nausea medicine, told me to eat lightly, and to return in five days or sooner if the symptoms don’t get better.

I returned in five days for further lab testing.  PS – NEVER go back to an ER if you don’t have emergency symptoms even if the ER doctor told you to come back.  Your insurance won’t cover it.  The liver enzymes had returned to mostly normal.  I was getting slightly better.

The next few months it was one thing after another – respiratory sickness, flu, cysts along my neck/hairline, low testosterone – first old man type erectile dysfunction failure in my life.  Yes, C Diff can affect all of this.  I went to my primary care physician.  He gave me some sulfur based antibiotics, and was ready to prescribe me some testosterone because it was extremely low – 180.  He didn’t know what was going on either.  The antibiotics took care of the respiratory issue and the cysts, but I didn’t want to take the testosterone shots as it was something I didn’t want to rely on in the future.  I started to accept this as the new normal, and moved on with my life.

I tried going back to my ultra pasteurized (this has something to do with it) skim milk and store bought pasteurized orange juice diet.  The milk gave me diarrhea – every time no matter what.  Same for store bought orange juice.  Fresh home pressed orange juice didn’t.  Yogurt didn’t.  Honey didn’t.  Kefir didn’t.  What the hell is going on?  Iodine brought on miracles for me  – better digestion, better mood, better sex drive.  In hindsight, I guess it was blunting the activity of C. Diff in the gut through antibiotic like effects.  But I still wasn’t 100% back to normal, and I wouldn’t be for a while.  I managed everything through my diet by focusing on home made orange juice, ripe fruit, no milk whatsoever, and other specific-carbohydrate-diet type foods which focused on monosaccharides.  Honey and maple syrup also were a source of calories I could handle.

Gelatin and individual simple amino acids such as taurine or glycine made it worse.  This in the face of glycine supposedly being a miracle worker for the gut.  Charcoal made it worse.  All these things that were creating miracles for other people were terrible for me.  C. Diff is a spore forming bacteria.  When the spores aren’t germinating, the symptoms are somewhat suppressed if the gut has wide bacterial diversity.  Unfortunately, short chain amino acids like taurine and glycine germinate the spores causing toxins to be produced causing CDAD (C diff associated disease).

From Pubmed: 

“In a healthy individual, indigenous intestinal bacteria resist C. difficile colonization (). Immunocompromised patients, such as cancer patients with severe neutropenia () and patients in the postoperative period following organ transplantation (), are typically administered antibiotics prophylactically. Following aggressive antimicrobial treatments, the normal gut microflora is disrupted, allowing the germination of C. difficile spores. The resulting toxin-producing vegetative cells fill empty niches in the depleted microbial community, leading to the onset of CDAD ().”

“Clostridium difficile is a Gram-positive, rod-shaped, obligate anaerobic bacterium. As a survival mechanism, C. difficile forms metabolically inactive spores during nutrient deprivation (). Like those of Bacillus and ClostridiumC. difficile spores are highly resistant to many physical and chemical insults. Spores return to vegetative growth through a process called germination (). Germination is initiated as the spore encounters nutrient-rich environments, allowing the spores to revert to replicating cells ().

When C. difficile spores germinate in the human intestine, toxins are produced and host cells are damaged (). This disease is known as Clostridium difficile-associated disease (CDAD) and is responsible for approximately 25% of all antibiotic-associated diarrhea (). Contamination of hospital environments with C. difficile spores is a key factor associated with infection spread (). CDAD is primarily a nosocomial infection, and mortality and morbidity are estimated to cost the U.S. health care system over $3 billion per year ().” (1)

With that I basically learned what was good for me and what wasn’t in the context of whatever was happening in my gut.  I avoided irritants and ate whatever didn’t irritate it.  I learned to find foods that wouldn’t reach my gut undigested.  I came up with the theory that the milk lactose wasn’t being digested due to the skim milk not adequately stimulating digestion through lack of fat, and the high liquid / calcium combo de-acidifying stomach acid.  It’s a pretty good theory, and maybe is true.  But C. Diff also causes lactose intolerance and milk protein intolerance – see below from Pubmed:

“Clostridium difficile enterocolitis and lactose intolerance should be considered as differential diagnoses in neonatal foals with diarrhea, especially when the foal is bright and alert.” (2)

“We observed an association between cows milk protein intolerance and Cdifficile.” (3)

The Exacerbation.

This continued until late 2015 when I came down with a little respiratory infection.  My wife encouraged me to go to the Urgent Care.  There, I was prescribed the antibiotic Amoxicillin.  Diarrhea immediately started.  I didn’t think much of it as that is a common side effect of some antibiotics, and I had already lived with sporadic diarrhea for a year.  My gut sucked; I was used to it.

The trouble came when after 10 days of the antibiotic was up.  The diarrhea didn’t stop even with my managed diet.  The respiratory infection wasn’t gone.  This time I went to a different Urgent Care.  There, I was told I had a stomach virus and the flu.  I was given Tamiflu.  I woke up with uncontrollable diarrhea.  I ran to the bathroom, and didn’t make it.  My wife heard me scrubbing the floor in the middle of the night, and fussed at me.  I told her “You’re gonna be happy I’m doing this.”  She thought I was just bored so I was cleaning the tub.  I suppose weird thoughts happen when woken up.  Anyway, I was on the toilet the next ten hours.  I stopped the Tamiflu as diarrhea is a common symptom.   The diarrhea didn’t go away.  I went back to the same doctor, and told him I thought I had C. Diff.  My wife thought I had it because her friend had it, and she read some WebMD.  He didn’t think so but he begrudgingly gave me the test.  It came back positive.  He prescribed Flagyl for two weeks.

The Flagyl stopped the diarrhea.  I started feeling normal again.  I thought I was over the hump.  After the course was up, I began to introduce my old foods like milk and gelatin.  Immediately, I felt weird – chills, muscle weakness, and the diarrhea was back.  You see the Flagyl merely made C Diff spore up to protect itself and become asymptomatic.  It was still there – nothing had changed.  I began trying to manage it through food selection again.  The doctor gave me another test – which came back negative as I wasn’t testing diarrhea but a somewhat more normal bowel movement.  Actually false negatives only test for the toxin produced, and if symptoms aren’t there for the current bowel movement tested, chances are the test will turn up falsely negative.  C Diff toxin smells awful.  Normal diarrhea doesn’t – well not any worse than normal poop.

It continued, I went to another doctor.  I knew I still had it.  I took taurine and glycine and BAM, full blown diarrhea.  I took the sample and sure enough, tested positive once again.  She made me take Flagyl again – I told her I felt like shit while taking it.  The side effects of Flaygl are terrible (4) – I felt them all.  Mood changes, depressed, extremely cynical, and even hating my job – which is a pretty damn good job.  Notably, C Diff also causes many mental changes as do many Clostridium genus strains.  For example, it’s been linked heavily to autism.  And many people with it claim of depression like effects or anxiety.  They’ve also linked depression to C Diff infection.  But one must wonder if the C Diff was already there causing depression, and then the typically fluoride derived killed off competing species allowing a flourishing environment for C Diff.

“It has been demonstrated that a large amount of species under the Clostridium genus (10 times more) characterised the qualitative composition of fecal samples of autistic children[].” (5)

“Recent study by Rogers et al. (6) reveals that adults suffering from depression as well as those who take specific anti-depressants – mirtazapine and fluoxetine – are more likely to develop C difficile infection” (6)

At this time, I also started heavily researching homeopathic cures – iodine, MMS (chlorine dioxide), copper (metal), monolaurin, berberine, and more.  From reading on C Diff forums, I noticed most people had recurrent infections.  That made me think there must be more to this than just killing it.  I needed to permanently keep the vegetative state suppressed and remove the spores.  I needed gut diversity.  Part 2 will walk through my learning and problem solving process covering everything I tried and what ultimately worked.  I felt pretty desperate as this was the first time I wasn’t able to quickly remedy whatever was going on with my body.

It returned.  I called the doctor and told her about my experience with Flagyl.  She now prescribed Vancomycin which was made by a compounding pharmacist a local pharmacy.  The price was insane at around $500, and supposedly would’ve been higher had I went elsewhere.  This disease C. Diff was making me spend tons of money – I don’t know how poor people would handle it.  I took it for a month in the morning and evening.  My digestion returned to normal.  I was off the medicine for about a week then decided to try to go back to my hydrolyzed collagen again – isn’t Glycine supposed to be good for the gut?  I felt like I was on top of the world.  We went on a date to GW Finns which is a very prestigious restaurant we’d been meaning to try for at least a year.  We sat down.  Before we even started to eat, I had to go to the bathroom.  I started crying.  It was back. The Vancomycin merely killed the bacteria in the vegetative state, and caused it to spore up to “protect itself” to survive long term.  The collagen had germinated the spores.

I learned bacteria can protect itself in two ways – biofilm and sporulation.  Biofilm can prevent antibiotic penetration and uses something called quorum sensing communication for bacteria and yeast to protect themselves.  Spores are hardy – they can survive outside the body for months on door knobs, counter tops, and therefore, also in the gut.  Copper surfaces can actually kill the spores and vegetative bacteria (7).  Unfortunately there’s no easy way to administer metallic copper to the gut.  We began bleaching doorknobs and countertops regularly.  Chlorine does kill the spores and the vegetative form (8).  This is part of the reason something like MMS “Miracle Mineral Supplement” (chlorine dioxide) might work although I didn’t use it due to knowing chlorine’s detrimental effects on the thyroid.  I’ll admit I was close to trying it though.

I told the doctor it was back.  She made me do another stool test.  I made sure to take taurine and gelatin, and then yet again, tested positive for the toxin.  It was in there.  It smelled.  This time I was put on tapered Vancomycin which allows some form of surprise for the bacteria – to confuse it between being spores or vegetative.  This is now April 2016 – 18 months after initially getting it in October 2014, and five months of full-blown C. Diff.  This was also the beginning of the end as I decided I had to outsmart C. Diff to beat it.  All of the solutions will be included in part 2.

Thanks for stopping by.  There is hope.

Find part 2 here:  http://www.scottschlegel.net/how-to-cure-c-diff-part-2-of-2/

Disclaimer:  If you have C. Diff, don’t just DIY it based on reading this article.  Please see your doctor.  This is a very serious infection.

    1.  Mapping Interactions between Germinants and Clostridium difficile Spores https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019946/
    1. Association of Clostridium difficile with enterocolitis and lactose intolerance in a foal.  https://www.ncbi.nlm.nih.gov/pubmed/9926015
    1. Five Years Experience of Clostridium difficile Infection in Children at a UK Tertiary Hospital: Proposed Criteria for Diagnosis and Management https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530496/
    1. Flagyl side effects https://www.rxlist.com/flagyl-side-effects-drug-center.htm
    1. Gut microbiota in autism and mood disorders https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698498/
    1. Depression related to Clostridium difficile infection – is it a coincidence?https://medtube.net/tribune/depression-related-to-clostridium-difficile-infection-is-it-a-coincidence/
    1. Survival of Clostridium difficile on copper and steel: futuristic options for hospital hygiene https://www.ncbi.nlm.nih.gov/pubmed/18207284
  1. Efficacy of cleaning products for C difficile https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868609/


Share your opinion by posting or replying to others comments.


nadeem aslam – Reply

June 17, 2018 at 3:11 pm - 3 years ago

I am wondering if one of your solutions is a beneficial yeast
called saccharomyces boulardi. Useful for c.diff infections

    Scott SchlegelReply

    June 17, 2018 at 9:56 pm - 3 years ago

    Yes I used it but it wasn’t enough to beat it.


Joshua – Reply

July 4, 2018 at 5:17 pm - 3 years ago

Please write part 2, I experienced a similar illness little over a year ago and reading this has made me realize it was probably due to dangerous choices that altered my gut bacteria.

    Scott SchlegelReply

    July 10, 2018 at 8:25 pm - 3 years ago

    Hey bud, sorry it is quite unfair of me to tease with something so serious.

    Anyway, the short of the story is buy this product: EZ Protegrity

    Buy an enema bag, buy distilled water. Crumble up two or three tablets and dissolve in the water. Put into colon in accordance with normal enema safety – cleanliness, etc. Hold as long as possible. Move around. You should experience incredibly smelly gas – C. Diff smells terribly bad. You can also use orally with less effect as C Diff predominantly affects the large intestine. If that doesn’t work, try another round until symptoms abate. B. Subtilis PB6 is a spore forming bacteria proven to have anticlerical effects against C. Diff. Although called B. Subtilis PB6, DNA analysis has shown it to be a different strain. So normal B. Subtilis from other products will not work.

    I’m not a doctor so not able to give medical advice. This is what worked for me and for at least one other person I know. Please proceed with caution and see a doctor if you have C. Diff.


James Brossard – Reply

January 13, 2019 at 7:53 am - 2 years ago

Hi why do you say other b subtilis wouldnt work? Have you checked out c butyricum. Thx, fellow ray peater

    Scott SchlegelReply

    January 18, 2019 at 11:52 am - 2 years ago

    In the Russian literature I posted B. Subtilis itself was not effective at any concentration in killing C. Difficile.

    I tried Japanese C. Butyricum at the time and it made things worse – worse diarrhea and feeling overall. I think, in general, all Clostridia bacteria are best worth avoiding. Read some on pubmed about people with high amounts of Clostridia in their gut. There are other bacteria that can make the short chain fatty acids acetate, butyrate and propionate which have been linked to a healthy gut and healthy liver.


Gina Thomas – Reply

March 26, 2019 at 7:28 pm - 2 years ago

Scott, why would this only be approved for animals? How did you find it.

    Scott SchlegelReply

    April 2, 2019 at 8:47 am - 2 years ago

    Reading Russian patents I found it had effects against C. Difficile. Unsure why it would only be approved for animals. Likely for liability sake from the manufacturer. They’re a pet products company. To sell to humans would require increased liability.

    To me, it was either be sick with C. Diff and spend tons of money on Antibiotics. Or try this and potentially be cured while accepting the risk of the probiotic. Which is the higher risk? That’s up to the individual. I’m not a doctor.


Gthomas – Reply

March 27, 2019 at 5:50 pm - 2 years ago

How long before your retest did you take the taurine and the geletan to get cdiff into vegetative state.also there have been so many studies on animals showing effective of the product you took. Why do you think there’s been no human trials. Did you tell your physicians what you took? Lastly did you take the antibiotics again to get cdiff into spore form and then when finished abx took the spore killing vet product? Please help I may need to do this but scared. I just finished first 14 day of Vanco. Only been off 4 days. But I’ve been sick with presumed sibo for 4 years. On xifaxin many times. Recently flagyl and doxycycline. Then a colonoscopy and a week later cdiff. Wondering if this has been my problem all along but I’ve had many cdiff tests, but wonder if multiple courses of xifaxin kept tests from being positive

    Scott SchlegelReply

    April 2, 2019 at 8:41 am - 2 years ago

    Taurine, Gelatin – within a few hours I had effects.

    Not sure why there haven’t been human trials.

    I did not take antibiotics again. Literally, it was one and done with the probiotic. Email me, or call me if needed.



John Hauser – Reply

February 5, 2020 at 11:08 am - 12 months ago

Never eat ray oysters. Ever. Good luck everyone.

“You can get seriously ill and even die from eating raw oysters contaminated with Vibrio vulnificus – a bacterium commonly found in waters where oysters are cultivated such as the Gulf of Mexico. Vibrio vulnificus is found in higher concentrations during the summer months as water becomes warmer.”


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