Probiotics for C Diff – Probiotics to Take With or After Treatment With Antibiotics

probiotics for c diff

Clostridium difficile (C. diff) infections can follow antibiotic treatment or may be acquired following an innocent hospital stay. Many people wonder if there are probiotics for C. diff that you should take during or after infection.

C. diff causes diarrhea and colitis of varying severity and can become life-threatening if the infection moves to the blood. The infection can recur and develop antibiotic resistance, adding to its potential for harm.

Rates of C. diff have been generally increasing and up to 453,000 individuals are diagnosed with C. diff infection per year. The severity of infection has also increased, and it often comes back as much as 20% of the time following treatment. Treatment costs our healthcare system >$5,000,000,000 per year.

It accounts for as many as 30,000 deaths per year! (reference)

How can antibiotic treatment lead to an infection?

When you take antibiotics, healthy bugs are killed too. These bugs normally keep a healthy intestinal pH, maintain immune balance, and crowd out bad guys with a diverse ecosystem.

When that diversity is gone, pathogenic organisms like C. diff overgrow and can become infectious.

Probiotics and c diff what probiotics should be taken with or after treatment with antibiotics

Current Medical Approach to C. diff Infection

Medicine will turn to standard antibiotics to treat a C. diff infection. But as antibiotics can be an initial trigger of C. diff overgrowth in the first place, this approach is sometimes necessary, but not without its limitations.

C. diff is also a natural inhabitant of the gut. It becomes opportunistic and dangerous when all of the other microbes are thrown off (or lacking diversity).

If you keep turning to antibiotics, fail to address long-term dietary changes, or struggle to maintain healthy probiotics, sooner or later, antibiotic resistance will develop and the future risks can start to compound – especially as you age.

The use of fecal transplants is a new “cutting edge” option for ridding C. diff.  

Yes, the procedure transplants poop from a healthy donor to an infected person. The feces from a healthy donor will contain a diverse balance of healthy microbes. When the feces are transplanted to the infected person, microbe diversity & balance is restored. Research has shown the transplant can restore healthy flora and crowd out opportunistic pathogens like C. diff.

It’s increasingly covered by the media and due to the profit potential of a fecal transplant – you’re seeing a lot of motivated parties to sing its praises.

Transplants are discussed not only for gut infections – but for weight loss, diabetes, and other conditions that can relate to the gut and microbiome.

I don’t like it. I don’t like the false sense of security it creates in our minds.

Why bother changing one’s lifestyle when you can just borrow poop from someone who has a healthy lifestyle?

And, making it more enticing…the procedure will likely be covered by insurance.

For now, its use is not widespread, and the FDA has limited approval only to those with antibiotic-resistant C. diff infections.

A fecal transplant procedure can be expensive and invasive compared to alternatives.

As great as the technology is, I don’t love the direction it takes us. Even if it is covered by insurance, the co-pays and fees are still likely to be higher than taking on a supplement and lifestyle approach. And, as soon as you go back to eating the same foods and living the same lifestyle – sooner or later, you’ll be back where you started.

And, as you might guess, the “yuck factor” of fecal transplants is not favorably viewed by candidates either (1).

You know mainstream media is not going to cover the restorative potential of natural products. Talking about transplanting poop person-to-person is sure to make for click-worthy headlines!

So what proactive options does that leave us with, aside from conventional antibiotics?


Let’s consider which probiotics to take during and after antibiotic treatment with C. diff.

Probiotics Taken During or After Antibiotics

Probiotics can help reduce C. diff growth by these mechanisms:

  • Competition with pathogens for growth
  • Direct interference with C. diff metabolism
  • Immune stimulation and modulation
  • General maintenance of intestinal health (1; 2).

Saccharomyces boulardii, Lactobacillus acidophilus, Lactobacillus rhamnosus, and Bacillus probiotics (Bacillus coagulans and Bacillus subtilis) can be taken during or after antibiotic treatment to help maintain gut flora, reduce the potential severity of infection, and actively keep C. diff levels at bay.

Spore probiotics, specifically in the formulation Megasporebiotic, have also been studied in a mouse model to help support leaky gut,  inflammation, and the immune response to recurrent C diff infection (reference).

See C diff study details.

The use of the probiotic yeast, Saccharomyces boulardii, has been well-regarded in the literature (3; 4). Clinical trials demonstrate S. boulardii may prevent C. diff recurrence, but its use may be limited to a first-time infection (5; 6).

When using S. boulardii, I use RestorFlora as my preferred source as it combines the probiotic yeast with spore probiotics. I use S. boulardii when supplementing the strain individually.

Lactobacillus acidophilus and Lactobacillus rhamnosus reduce inflammation and the severity of C. diff-related diarrhea (7; 8).

Lactobacilli probiotics may also have difficulty making it past the acidic stomach intact. Their health benefits may result from immune activation and modulation by dead Lactobacilli cells and not via a true colonization of the intestinal tract. A high-quality and high-dose Lactobacilli product may help overcome this disadvantage.

I often use Bacillus probiotics foremost to ensure entry past the gut. Lactobacilli probiotics are also sometimes overgrown in Small Intestinal Bowel Overgrowth (SIBO)- and have the potential too aggravate gut rebalancing early on. Your decision to add them is case-by-case – as they can also be “cleansing” to the small intestine – crowding out the unwanted strains with the preferred strains.

TruFlora by Master Supplements is a good source of Lactobacilli combined with a small amount of spore probiotic to support the health of the small intestine as well as cycled for periodic intestinal cleansing.

While spore probiotics are not affected by stomach acid, Lactobacilli strains are killed by the acidic pH. Master Supplements has a special capsule ingredient that forms a shell around the probiotics in an acidic environment of the stomach, and then naturally thins in the higher pH environment of the intestines – safely delivering past the stomach acid while also promoting the growth of the strains.

Alternatively, levels of Lactobacilli (and other healthy flora) can be promoted indirectly by consuming prebiotics.

Prebiotics are fibers and starches that feed and maintain gut flora. Prebiotics can come from eating diverse vegetables and leafy greens, or they can be supplemented.

Again, prebiotics are a case-by-case decision with SIBO clients – adding them too early can aggravate SIBO. Start with more targeted and precise prebiotics that preferentially support preferred strains of intestinal flora – then move to more complex prebiotics.

A good targeted prebiotic to start is MegaPrebiotic. Sunfiber (PHGG) is also a good choice. I slowly progress to FloraSpectrum Prebiotic Powder

It’s been recognized more recently that polyphenols have prebiotic properties as good bacteria work on them and turn them into useful compounds for the body. I use PhytoFlora Microbiome Support as a non-bloating means to support a number of prebiotic and general gut benefits. Prebiotics are bundled together in my Prebiotic Diversity Trio.

Long-term, my goal is to add complexity and rotate prebiotics as much as I can to keep my gut microbiome diverse and happy.

You can now test the diversity of your microbiome with high accuracy using a fantastic new home stool test known as BiomeFx.

Focus first on crowding out the bad bacteria and adding healthy diversity. Look to sustain that diversity later on.

When you eat, you are eating for two – you, and your flora!

With any treatment choice, once you heal the gut, you must maintain it by eating as many different types of vegetables as you can muster. If you go back to an inflammatory, high-carbohydrate diet rich in bad oils like canola, soy, corn, safflower, and others that caused an imbalance in the first place – you’re asking for future trouble no matter how comprehensive your care plan.

Balance out bad oils and curb inflammation with omega 3 fats.

I like MegaOmega by Microbiome Labs as it combines a full spectrum of omega 3 fats along with PRMs/SPMs (specialized pro-resolving mediators) that promote a healthy gut barrier, and help to resolve or “turn off” inflammation.

In addition to leaky gut, low levels of omega 3 fats are another key contributor to whole-body inflammation inside and outside of the gut. For higher levels of fish oil for whole-body needs, use Omega Complete – EPA, DHA, and DPA Support.

Monolaurin, Soil-Based Probiotics, and Saccharomyces boulardii 

Support Microbial Balance:

When it comes to C. diff infections, generally I will assume that someone is taking antibiotics, but is concerned about making sure it stays away once addressed.  In other cases, someone may have had a problem in the past and is just concerned about a repeat infection.

For natural antimicrobial support, I used to use Ultimate Monolaurin. First, it’s safe to take alongside conventional antibiotics, and it hasn’t been shown to cause microbial resistance.

Monolaurin decreases the growth of gram-positive organisms such as C. diff, while also helping to reduce its release of microbial toxins (exotoxins) into the blood.

Monolaurin is unique because it also leaves alone gram-negative bacteria. So you essentially clear out bad guys, while leaving the good.

Monolaurin was discovered in breast milk – and helps to maintain gut health in the breastfeeding infant while also protecting from certain bacteria, viruses and yeast.

Your intake of Ultimate Monolaurin is easy to personalize, as it comes in small, bead-like pellets that are swallowed like pills. You can start with just a few pellets and work your way up to the scoop in the jar – taking it three times per day.

  • Another popular immune support I’m using more often now is Biocidin in liquid or capsules. I prefer the liquid because it is pleasant tasting, and I can swish with it prior to swallowing to support oral microbiome health too.
  • Berberine Complex by Integrative Therapeutics is a mix of berberine-containing herbs that are used to support microbial balance in the gut. I use Berberine as a lifestyle strategy to support metabolic efficiency when it comes to blood sugar and insulin support when levels are normal. It also helps to maintain microbial balance in the gut. I use Berberine Reset by Doctor Alex Supplements as it adds alpha lipoic acid and grapeseed extract to amplify the properties of Berberine.
  • Microbial-balancing herbs and extracts like Biocidin, and Berberine complex can be integrated over periods of 1-3 months, sometimes up to 6 months for complex cases. If taking more than 3 months, seek guidance from a natural health professional as eventually, you want to focus on adding and maintaining healthy flora. Some herbs can discourage the growth of healthy bacteria in addition to crowding out the unwanted flora when taken at a high dose or for longer periods of time. Start low and work your way up slowly with probiotics and microbe-balancing herbs.
  • When you start to crowd out unwanted bacteria, toxins and debris can be released from cell death – you can help bind up some of this debris with formulas like GI Detox, Activated Charcoal, or IgG-Boost 2500 /MegaIgG2000.
    • Immunoglobulins have been shown to bind to C diff toxins and improve outcomes in IBS and inflammatory bowel disease.

Probiotics for C Diff Taken During and After Gut Infection:

The use of soil probiotics such as Bacillus coagulans is widespread in Europe, but their use is still catching on in the US. Bacillus coagulans is unique in that it has been shown to not only improve outcomes during C. diff treatment but also prevent recurrence (9; 10).

Mice treated with vancomycin often experience a recurrence of C. diff symptoms following treatment.  One study demonstrated that mice treated concurrently with Bacillus coagulans survived longer and had better bowel consistency and metabolic markers following vancomycin treatment (9; 10).

While there are a number of ways to approach C. diff infections naturally and medically, I personally use Biocidin, Megasporebiotic, RestorFlora, and HU58  in my gut protocol usually with IgG-Boost 2500, and MegaMucosa to support lining health and binding and neutralization of wastes, debris, and toxins. This combination gives direct antimicrobial support and takes advantage of high-dose Bacillus probiotics (found in Megaspore and SporeBoost IG) and S. boulardii (found in RestorFlora).

While taking all can be preferred due to the potential seriousness of C. diff, someone can mix and match according to their need or budget. These are not substitutes for medical care, but may be useful adjuncts – or to help support protection against recurrence.

I like adding Theralac by Master Supplements as it is a well-rounded probiotic containing both Lactobacillus acidophilus and Lactobacillus rhamnosus – which were mentioned above to help support inflammation and bowel regularity in C. diff clients.

If SIBO or high inflammation is a concern early on, I may start with TrubifidoPRO as it focuses on probiotics predominant in the large bowel – and then, I will transition to TheralacPRO as tolerated.

I’ll later use supplementary and dietary prebiotics as tolerated to sustain Lactobacilli and Bifidobacteria.

Remember, most Lactobacilli/Bifidobacteria probiotics are killed in the stomach acid. This is why I emphasize spores foremost.

Master Supplements owns a patented, “acid-proof” delivery technique that protects Lactobacilli and Bifidobacteria probiotics from stomach acid.

As these are potent formulations – if you start killing too much at once – it can create a backup in your ability to detoxify the wastes.

As a general rule, start low and work your way up, especially when combining! 

I may also have to open up the capsules of Megaspore and sprinkle it in food or liquid when first starting. The capsule contents are heat-stable and have no taste.

Other practitioners seem to be getting the best results when also adding HU58 to the mix – which is a high dose of a microbial-balancing strain of Bacillus subtilis. 

HU58 is intended to take alongside Megaspore in support of more difficult (and potentially more serious) gastrointestinal imbalances – such as C. diff.

So if you don’t want to mess around, consider adding HU58 alongside Megasporebiotic and RestorFlora. You can also add Theralac if it’s also tolerated.

In many cases, you will be taking an antibiotic concurrently with the supplements, so be sure to run the support options with your doctor.

Here’s what a support protocol might look like during or after antibiotic treatment for C diff:c diff protocol

This list represents a sample of educational guidelines & not a substitute for professional advice.

  • Biocidin / Berberine Reset / or Berberine Complex (can be used alone or in combination; check with your health professional if prescribed prescription antibiotics or not sure how much support may be needed)
  • Megasporebiotic
  • Theralac
    • Note: TrubifidoPRO may be used instead of Theralac if you suspect SIBO, or if your gut tends to be on the more sensitive side with probiotics (sensitivity is usually due to stimulation from Lactobacilli). One isn’t “better” than the other – the reasoning is that the bifidobacteria in Trubifido target large intestine bacteria, while Theralac targets probiotics of the small & large intestines. The small intestinal bacteria (Lactobacilli) tend to be more immune-stimulating in nature. Some research suggests that taking Lactobacilli too early in a protocol can delay recovery.

      If unsure, a general rule of thumb is to start with TrubifidoPRO for a month or more prior to switching to Theralac.
  • RestorFlora
  • Add HU58 for more potent support if you have elevated concerns, diarrhea, or more moderate symptoms.

When it comes to a probiotic protocol, here is what a sample day may look like:

  1. After Breakfast: 2 capsules Megasporebiotic
  2. After Lunch: 2 capsules RestorFlora + 1 capsule Theralac (or TrubifidoPRO* see above)
  3. After Dinner: 2 capsules Hu58

If taking Biocidin, or Berberine, follow health professional or manufacturer’s guidelines

The length of supplemental support can last 1-6 months.

For long-term probiotic guidelines and how to transition to a “wellness schedule”, I recommend checking out: Dr. Rinehart’s Probiotic Blueprint

If I had to choose ONE formula to skip the complexity while getting great baseline support – I’d choose Megasporebiotic.

Start Low and Work Your Way Up

If we had to put an order of introduction as you approach the sample schedule above…

1. Biocidin, and/or Berberine Complex as recommended
2. Megasporebiotic + TrubifidoPRO or TheralacPRO
3. RestorFlora
4. HU58

TrubifidoPRO and Theralac are the only products that are best to store in your refrigerator – the others are optional.

It can be best practice to make sure you fully tolerate one formula before moving on to the next. Too much support too early can be an unnecessary stress on your body even if that stress is a “healthy” response to rebalancing flora in a supportive way.

  • Megaspore, Restorflora, and HU58 capsules can be opened up and sprinkled directly in food or water.
  • Trubifido or Theralac should be taken via capsule for best results as the capsule is designed to protect the probiotics as they pass through the acidic stomach.
  • Support can be personalized to you, your level of concern, and your budget. Not all support is necessary but the greater the concern, the greater the supportive mechanisms you can choose to leverage.

This sample outline is not a substitute for standard medical care. Other formulas may contain the same strains and work fine for your protocol.

Physician opinion differs as to taking probiotics and immune support supplements during and after antibiotic therapy.

Seek professional opinion and testing from your physician as is warranted.


  • IgG Boost 2500 Powder or Mega IgG2000 may help mop up wastes, toxins, & debris released during both an infection and the healing process without potential long-term concerns of activated charcoal. Activated charcoal can still be turned to over the short term.
  • Candidase PRO (formerly Candida Control) by Enzyme Science is a proteolytic enzyme blend high in protease & cellulase. Cellulase specifically helps digest the debris from Candida or yeast cell membranes. The protease content helps to digest Candida toxins released from yeast metabolism & cell death. For general cleanup, consider their Enzyme Defense Pro formulation that is less specific to Candida.
  • MegaMycoBalance by Microbiome Labs contains undecylenic acid from castor beans and bee propolis. Undecylenic acid has been shown to help dis-embed fungal roots (called “hyphae”) in the GI tract. This is a unique anti-fungal mechanism and makes it a fantastic adjunct to other supplements when Candida or other fungal infections are of concern. Bee propolis is how bees keep their hives sterile from outside pathogens – and we can leverage its unique antimicrobial properties supplementally using the combination formula of MegaMyco.
  • MegaOmega by Microbiome Labs – is a fish oil with added pro-resolving mediators and a ratio of omega 3’s specifically formulated to support inflammation and flora balance in the gut. For a more traditional Omega 3, I use Omega Complete – EPA, DHA, and DPA Support.

Of course, you do not need to wait until you have C. diff overgrowth to be motivated to fix your gut microbes. Most of us could benefit from some gut reconditioning using these same strategies.

Megasporebiotic has been demonstrated to heal markers of leaky gut in a recently published clinical trial (11). A leaky gut is usually present with any flora imbalance and allows inflammatory proteins and bacterial toxins to easily migrate into the bloodstream.

I love spore probiotics as much as anyone – but don’t forget about Bifidobacteria & Lactobacilli!

That’s why I love using Megaspore in combination with products like Theralac or TrubifidoPRO.  Together they provide more complete probiotic diversity without being killed by stomach acid.

What happens after I’m finished with an antibiotic?

Long-term – it’s about healing the gut lining and re-establishing microbial diversity in the gut to protect you for the long haul. When the gut is leaky and damaged – you absorb wastes & toxins into the blood that create inflammation throughout the entire body.

If you want to keep poop out of your bloodstream…heal leaky gut! I’ve collected the 7 Core Strategies to Heal the Gut Lining and Manage Leaky Gut

Using the products above in combination can make a strong difference in outcomes. All have good support behind them for yeast overgrowth too. If you have gut imbalance – it’s a strong guess that yeast (such as Candida) is involved as well at least two-thirds of the time.

Prebiotics are important to maintain gut health long-term once you’ve cleared pathogens and have slowly added back probiotic diversity. I use MegaPrebiotic by Microbiome Labs, PhytoFlora Microbiome Support, Sunfiber, and FloraSpectrum Prebiotic Powder, I usually integrate them in that order and then rotate them long-term.

I generally work in the blends in that order as tolerated as each will target a different set of flora. The goal is diversity – so I rotate these on monthly basis & mix it up during the month too.

Start low and work up with prebiotic fibers.

If bloating or constipation occurs with prebiotics, you may be introducing them too early (or too much). If you have this reaction, it shows you need the support – just work with your body’s tolerance, and maybe get a little more aggressive with your previous probiotic/antimicrobial strategy.

When treating bacterial overgrowth, you may want to limit prebiotics in food (Low-FODMAP diet) and gradually reintroduce them via supplementation or food sources. This process can take as little as 3-month but can last 6-12 months as you personalize your own strategy.  There are plenty of resources available online to help you with these strategies.

Eventually, you’ll transition to a plant-rich, Paleo-style diet. I like the general rule of 75% diverse veggies, and 25% of my plate protein/fat/starch. You can increase the percentage of starch & fruit with higher activity level. Try new vegetables every chance you get to promote & sustain diversity long-term.

I take Megaspore and in addition to Megaspore, I will rotate between bottles of SporeBoost IG, TrubifidoPRO, TheralacPRO, RestorFlora, & TruFlora. I keep Biocidin on hand for seasonal support & periodic conditioning of my immune system against biofilm and other stealth infections. I use a more metabolic-targeted version of Berberine Reset for support of blood sugar control prior to meals (as well as microbial balance).

The Berberine Complex is geared slightly better to actively cleanse the GI system.

Check out Dr. Rinehart’s Probiotic Blueprint on how to introduce and evolve your probiotic protocol independent of concerns with antibiotics and C. diff.

Six to twelve months may sound excessive, yet as tricky as gut restoration can be, the health of your gut is critical to wellness as you age. You may take a step forward and back a few times until you find a strategy that works.

The tips above will give you intensive support when you need it – while keeping the strategies affordable for long-term wellness support as you rotate probiotics & prebiotics long-term.

When it comes to the gut and Clostridium difficile, the long path is often the shortest path to reduce the incidence, improve outcomes, and most importantly, prevent a recurrence.

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