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The role of probiotics in preventing infections

When I prescribe antibiotics, I generally tell my patients that they should have a healthy diet, rich in natural probiotics.

The next question they ask is invariably is: why?, sometimes closely followed by: what are probiotics? and often followed by: what is the biome?

I have some suggestions based on what is known-

and here is an attempted summary:

Background: Hospitals have resistant bacteria-

Per Lax and colleagues- when a person is hospitalized their biome gets populated with hospital flora (See Ref 1)

The use of antibiotics is often a routine part of hospitalization-a significant portion of which is inappropriate. This often leads to clostridium difficile infection and sometimes these are recurrent. Why this happens is 'hits' to the patient’s healthy Biome- the protective intestinal microflora, which is damaged or decimated by antibiotic treatment; the initial antibiotic exposure thus leaves the host susceptible to colonization by hospital flora and subsequent infection by Clostridium difficile.

A so-called “second-hit” to the intestinal microflora occurs when the infected host is treated with flagyl or vancomycin for the C difficile infection, further destroying susceptible bacterial flora.

An approach to solving this compounded damage involves the introduction of competing, nonpathogenic (probiotic) organisms into the intestinal tract to restore microbial balance. The theoretical premise behind this approach is that the ‘Probiotic agents’ repopulate and give the diversity back to the gut providing competing healthy flora.

Probiotics such as Lactobacillus GG and Saccharomyces boulardii, have been studied for the treatment of Clostridium difficile. In general, most case series and case reports have shown favorable results with Lactobacillus rhamnosus GG or Saccharomyces boulardii. However, other reports have shown lack of benefit. Data analyzed from multiple studies (Meta-analysis) showed that these probiotics may be useful in treating or preventing recurrences of clostridial diarrhea. The heterogeneity of the studies makes definite conclusions difficult. Whatever the results of the studies, a fascination with this topic and its commercialization is inevitable. Pharmacy aisles seem to be chock full of pills with above organisms and many others with tall claims.

Based on smaller studies probiotics have some benefits in adults and children with post antibiotic diarrhea and infectious diarrhea. They may reduce symptoms and hasten recovery even in viral diarrheas like Rotavirus. But can probiotics prevent Clostridium difficile or its recurrence? The jury is still out –but it seems trying to treat the eradication of a complex gut biome with only one species of organism may be problematic. Hence the idea of an entire biome transfer: Stool transplantation.

As unpalatable as it may sound, it is possible to take stool from a healthy donor and transfer it by either a Naso-Gastric tube or by Colonoscopy into healthy gut. Thus “Re-Poopulation” of the gut! Other methods of transplant like pills and collection of spores (in smaller pills) are also being investigated-However there are unforeseen dangers of stool transplantation apart from the possibility of transmission of pathogenic flora.

So any alternatives to giving the protective biome a boost without transferring stool or taking pills?

Based on Dr Bakken’s limited study-It is possible

In Dr Bakken’s small study the idea was to eliminate organism and spores from the gut with a staggered oral regimen of vancomycin while giving kefir milk to provide as a source of a biome transplant to replace it. Daily administration of the probiotic kefir given in combination with a staggered and tapered antibiotic withdrawal regimen may resolve recurrent Clostridium difficile infection as effectively as fecal microbiota transplantation. (Ref 2)

So should you supplement your balanced diet with probiotics?

I would, that is, if I was taking antibiotics and that in suumary is what I tell my patients-

But what is a healthy diet rich in Probiotics? I feel these should be many different organisms from a variety of balanced natural sources-that is how the bacteria got there in the first place helped no doubt by our parents flora.

Here is a regimen with a healthy mix of dairy and fermented foods and things healthy gut bacteria like –Suggested by Dr

Basma Ali MD

Shortcut: Take lots of yogurt and kefir!

Fermented foods

Rich in gut bacteria. Please eat at least one per day but eat them on a rotation

  1. Kefir – 1/3 rd. cup

  2. Kimchi – 2 tbsp.

  3. Sauerkraut – 2 tbsp.

  4. Miso – 1 tbsp.

  5. Yogurt – 1/3 cup

  6. Kombucha – 1/3 cup

  7. Tempeh 2 oz.


Food for good gut bacteria - one per day

  1. Chicory – with coffee in morning otherwise bitter

  2. Dandelion with in salad or as tea

  3. Onions – raw and cooked.


1. Lax S, Sang wan N, Smith D, et al. Bacterial colonization and succession in a newly opened hospital. Science Translational Medicine 24 May 2017: Vol. 9, Issue 391, eaah6500) DOI: 10.1126/scitranslmed.aah6500.

2. Johan S. Bakken; Staggered and Tapered Antibiotic Withdrawal With Administration of Kefir for Recurrent Clostridium difficile Infection, Clinical Infectious Diseases, Volume 59, Issue 6, 15 September 2014,

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