Polly: You will have to go by how you react to the probiotics. Start slow. Nothing is ever perfectly correct. Here are a few considerations.
1) You want your immune system in the intestines to react to the probiotics, but you don’t want a full out war. So if large doses make you sick, cut back on the dose.
2) Dr. Leo Galland warns that probiotics could increase the growth of protozoal parasites. Therefore use the probiotics only after these parasites have been eradicated. 
3) When you take probiotics orally, this puts an unusually high number of microorganisms in the small bowel. (A healthy small intestine will have very few of these microorganisms. Most of the bacteria should reside in the colon.) If you have very poor buffering capability, you should be wary of adding in so many acid forming bacteria into the small bowel. When acid forming bacteria come in contact with the large amount of sugar there, too much acid may be formed. In the book Cleanse and Purify Thyself, Richard Anderson, ND, NMD claims that people have gotten sick with acidosis by ingesting too many acid forming bacteria. (Dr. Anderson’s website can be found at http://www.ariseandshine.com ) Note: There are some probiotics on the market that do not produce D-lactic acid. These are better tolerated by some people.
4) If you have small bowel bacterial overgrowth, then adding in more bacteria could help or harm. If the bacteria you are replacing are particularly harmful, then you will feel better. If all you are doing is adding in more bacteria to the small intestine, then you might even feel a little worse.
5) For infants and toddlers, you cannot use the same bacteria that you use for adults. The amount used is less too. Get a product made especially for them.
6) If a person’s immune system is greatly compromised, they may have trouble removing bacteria that make it from the intestines into the bloodstream. These people should be particularly careful with using soil-based probiotic bacteria. These bacteria are sometimes resistant to antibiotics. So if you get sick from them, your doctor can’t help you with an antibiotic.
Mary W: Hi, just curious if anyone has experienced this? I’ve just done 7 weeks of antifungals/antibiotics treatment and am finding all probiotics except one, are now making me violently ill, with Custom Probitotics and the SCD (Specific Carbohydrate Diet) yogurt (trillions of cfus) being the absolute worst. This mirrors my experience of 3 years ago where I was treated with lots of antibiotics for an acute parasitic infection and couldn’t tolerate any probiotics afterwards. I eventually found my way to Natrens Healthy Trinity and I was able to tolerate that and found it somewhat helpful, but by then it was too little too late. So I’m back on the Healthy Trinity but I’m only tolerating 1 capsule per day. The yogurt is a complete disaster, no matter how little or strained. It seems as if my body is rejecting all these probiotic strains as foreign organisms. Perhaps Healthy Trinity is closer to a human strain? Perhaps mostly Bifidus is preferable right now, but why? (Before the drugs, I could tolerate up to 80 billion cfus of any probiotic strains or 3 cups of the yogurt once a week).
Any theories or suggestions appreciated. I’m considering probiotic implants again as an alternative but am a little worried given the violence of the reaction.
(Note, this experience was several months after Mary had tried the soil-based probiotics, and only after she had taken a combined antibiotic and antifungal treatment.)
Avandish: Nutrients to feed the production of mucous lining cells of the GI tract come from the growth of Bifido. As these nutrients are gradually delivered, the production of mucous gradually builds. This affords protection to the wall of the intestine from the acids produced by other bacteria and prevents direct attachment of the bacteria to the GI tract wall. Most likely the drugs you have been using have reduced your good bacteria populations in the large intestine, causing a reduction in mucous production throughout the entire GI tract. Most likely the acids produced by the organisms you are using, including the long fermentation period yogurt (Specific Carbohydrate Diet) are too acidic for the unprotected wall of the small intestine. This lack of mucous also allows direct attachment of bacteria to the villi in this area (something you don’t want).
Try taking just Bifido, as these are milder strains. They produce more of the essential nutrients and less of the irritating acids. Even these may be a little strong for you right now. Taking a little long chain inulin without free sugar at the end of a meal will help deliver some of the needed food to the large intestine. Taking inulin with food slows the bacteria growth in the small intestine, but stimulates growth in the large intestine. Don’t take inulin or FOS on an empty stomach or with your probiotics as this will stimulate fast growth in the stomach and small intestine, creating much irritation, especially for people with long-standing dysbiosis. Also, if you have significant GI inflammation, unrefined wheat germ oil taken after a meal can be helpful. I only use refrigerated wheat germ oil. I use Spectrum brand in the black bottle, liquid, stored in the fridge. I take a tablespoon at the end of breakfast when inflammation is a problem. Do not heat this oil, as it is mostly polyunsaturated. Spectrum is a large veggie oil producer in the health food store. Good Luck Sport.
Mary W: AHA. Finally, an intelligent explanation. Thank you!
MM: Mary, as I was reading Avandish’s response to you, one thought dawned on me. The people who follow the Specific Carbohydrate Diet (SCD) who have ulcerative colitis and Crohns disease get fish oil capsules that are protected from digestion in the stomach. A large number of studies have shown that these protected fish oil capsules help to minimize inflammation in the gut. See pubmed, etc. for abstracts. You can also ask the Healing Crow and SCD list members about how the protected fish oil capsules have worked for them.
Mary W: According to all those studies, those people were taking tons of fish oil capsules a day, 8-10. That amount is hard on the liver. In the first year of my illness, I took one a day and they did nothing. Funny how the SCD people are totally against Bifidus. They say some ulcerative colitis people have had flares with them.
Polly: Seems like in this situation, you have to treat the intestinal lining like that of a newborn, with special care. There certainly is a lot more that needs to be learned about using probiotics to our best advantage.
later — Polly: Mary, you were taking soil-based probiotics about a year ago. Why did you stop the soil-based probiotics?
Mary W: I stopped Primal Defense last March specifically because I found (along with Mary in Pennsylvania) that as we got to higher doses our dysbiosis actually increased. We posited (along with your help) that since the plant sterols/sterolins they had added in the last 2 years were ALL derived from estrogenic sources, they were boosting our hormone levels. Then I tried Nature’s Biotics, which supposedly had the same two soil-based microorganisms (bacillus subtilis and bacillus lichenformis) without the sterolins but with phytoplanktons. That just gave me more and more gastric distress. Then I tried a custom version (no maltodextrim) of a different soil-based microorganism called Bacillus laterosporus BOD, which has been shown in labs to be effective against candida albicans specifically. I had a little improvement from it but it didn’t last.
Based on my dramatic improvement initially, I still personally believe that bacillus lichenformis and bacillus subtilis can be very effective for gut infections. The problem may be that these products are now packaged with all kinds of substances (plant sterols, maltodextrin, FOS, reishi mushrooms, etc.) These trials of Nature’s Biotics and the laterosporus BOD were during the months of March to June. Then I went on a round of using EVERY natural antibiotic and antifungal for about 4 to 5 months, including colloidal silver and tons of propolis. (My selection of propolis was based on a case history in the Townsend letter.) Since I become allergic to herbs/foods very quickly, I was rotating through all this stuff except the propolis. (I did not become allergic to the propolis.)
In December I went to a new doctor who found seven pathogens including Blastocystis hominis (parasites), Candida krusei, Klebsiella, etc. He put me on a massive 6-week tiered drug therapy of antifungals and antibiotics. I tolerated this amazingly well, but now here I am with a stripped mucus layer. The same thing happened to me three years ago after taking lots of antibiotics to treat an acute parasitic infection. I had terrible gut inflammation afterwards and NO tolerance for probiotics. I just didn’t know what was causing it, nor did my hopeless doctors. This went on for months. But this time, I’m getting some control much faster, thanks to Avandish identifying the problem. Once he identified the stripped mucosa, I took a supplement called Colixen to help restore the mucosa. This allowed me to start tolerating a mostly Bifidus probiotic about a week later.
I think any antifungal or antibiotic, natural or drug, has the potential to harm the mucosa. If the treatment results in dehydration, I think this is a warning that damage is being done. According to my research, dehydration is not a common side effect with Diflucan. Yet for me, the Diflucan was INCREDIBLY dehydrating. The same dehydration happened three years ago, when I took all those antibiotics and also got the stripped mucosa.
Note from Polly: Primal Defense has changed their formulation a few times. As of September 2003 they state that each pill contains “80 mg PhytoSterol/Sterolin Blend from sprouts in their natural whole food form.”
The main plant sterol called beta-sitosterol shifts the immune sytem from Th2 towards Th1, which is often helpful. However, just like the controversy over the phytoestrogens in soy, there is reason to have some concern about beta-sitosterol. Beta-sitosterol is considered a phytoestrogen / hormone disrupter.