This is an update of a post that I did back in 2018 [Original Post]. A reader had messaged me about the safety of soil based organisms probiotics. For hundreds of thousands of years, soil based organism was a part of our diet because of the absence of safe water, soil was often on the food consumed. I recall reading that the human gut bacteria has strong similarity to that seen around root vegetables. This is not surprising, pulling roots out of the ground (without washing!!!) was likely common for most of these thousands of years…
“But I read about someone getting sick from SBO!”
- There are two types of sick to consider: bacteremia or endocarditis (BAD), and herxheimer reaction (usually a good sign — I was really sick when I first started Mutaflor, it ebbed and I was much better afterwards)
This recent event caused me to revisit this item: “FDA investigating baby’s death linked to probiotic given by hospital” with FDA Letter pointing out that it was not legal to sell it with the claims it made.
Some Counts of Adverse Probiotic Infections
- 149 reports for Lactobacillus bacteremia probiotic
- 183 reports for Lactobacillus endocarditis
- 14 for Bifidobacteria bacteremia probiotic
- 17 for Enterococcus bacteremia probiotic
- 13 for Bacillus bacteremia probiotic
The most dangerous probiotic (using report counts) are Lactobacillus.
There are similar risk from eating “safe” lactobacillus probiotics, cheese, yogurt, etc. Even deaths have been reported: “Lactobacillus-Cause of Death ” 
” Lactobacillus has been used as a probiotic bacteria to treat diarrhea and is also present in dairy foods. It is hence commonly used. Lactobacillus endocarditis, an exceedingly unusual disorder, is accompanied by high mortality and poor response to treatment. ” – OUCH!
- “In recent years, infections caused by Lactobacillus and Bifidobacterium made up 0.05% to 0.4% of cases of endocarditis and bacteremia. In most cases, the infections were caused by endogenous microflora of the host or bacterial strains colonizing the host’s oral cavity. According to a review of cases of infections caused by bacteria of the genus Lactobacillus from 2005 (collected by J.P. Cannot’a), 1.7% of infections have been linked directly with intensive dairy probiotic consumption by patients. ” [Lactic acid bacteria and health: are probiotics safe for human?]. 
Some more citations…’ bacteremia is a bad bacteria infection, endocarditis is a bacteria infection of the heart. It has been only in the last few years
- Lactobacillus gasseri endocarditis on the aortic valve bioprosthesis – a case report.
- Recurrent Lactobacillus Bacteremia in a Patient With Leukemia. 
- Persistent bacteremia secondary to delayed identification of <i>Lactobacillus</i> in the setting of mitral valve endocarditis. 
- Lactobacillus rhamnosus Endocarditis After Upper Endoscopy. 
- Endocarditis due to Lactobacillus rhamnosus in a patient with bicuspid aortic valve: Potential role for the consumption of probiotics? 
- Lactobacillus coryniformis Causing Pulmonary Infection in a Patient with Metastatic Small Cell Carcinoma: Case Report and Review of Literature on Lactobacillus Pleuro-Pulmonary Infections. 
- Infective endocarditis due to Lactobacillus rhamnosus: Risks of probiotic consumption in a patient with structural heart disease. 
- Lactobacillus rhamnosus endocarditis: An unusual culprit in a patient with Barlow’s disease. 
- Lactobacillus paracasei endocarditis in a consumer of probiotics with advanced and severe bicuspid aortic valve stenosis complicated with diffuse left ventricular mid-layer fibrosis. 
- Bacterial Endocarditis Caused by Lactobacillus acidophilus Leading to Rupture of Sinus of Valsalva Aneurysm. 
- Importance of Molecular Methods to Determine Whether a Probiotic is the Source of LactobacillusBacteremia. 
- Endocarditis of the native aortic valve caused by Lactobacillus jensenii. 
- Isolated Lactobacillus chronic prosthetic knee infection. 
- Lactobacillus paracasei endocarditis in a consumer of probiotics. 
- Infectious endocarditis caused by Lactobacillus acidophilus in a patient with mistreated dental caries. 
Probiotics are generally safe. No probiotic is 100% safe. To me, soil based bacteria are likely more beneficial then lactobacillus because they went along with our ancestor’s diet long before we started domestication of milk producing animals. There may be considerable basis to the hygiene hypothesis which would result from our modern pathological obsession with sterilization of food in the belief that all bacteria are bad.
The general belief is that issues arise with a weak immune system, after surgeries, and with a “leaky gut”.