The use of Probiotics is exploding for many ailments. Though considered generally harmless, probiotics can transmit Antibiotic-Resistant Genes (ARG), cause infection in immunocompromised hosts, and run the risk of unintended consequences by disrupting the dynamic equilibrium of the gut microbiome. So, evidence-based use of probiotics is recommended.

We reviewed the available evidence in probiotics and microbiome research, and present the probable conclusions for the clinician to decide on their use.

Conclusions: Structural defect in research: The biological effect of the microbiome is likely to be due to the microbiome in contact with the mucosa. It has been shown that this is different from the intraluminal (fecal) microbiome commonly analyzed in most studies. These studies also do not stratify according to genetic predisposition and native microbiome, both of which can affect colonization of the gut by probiotics.

Study Design: There is a lack of case control design, adequate sample size, and selection of specific probiotic species.

Diarrhea: LGG and Saccharomyces Boulardi were recommended in acute diarrhea based on low-quality evidence. Studies done in the US and Canada did not support their use. For prevention of antibiotic-associated diarrhea, LGG and Saccharomyces Boulardi were useful, but only S Boulardi reduced C Diff diarrhea.

Constipation: No consistent beneficial effect of probiotics reported. Infantile Colic: L. reuteri DSM 17938 reduced colic duration only in breastfed babies.

Regurgitation: There is insufficient data to recommend L. reuteri DSM 17938.

Functional Abdominal Pain/IBS: The studies' limitations, especially the inadequate sample size, prevent an evidence-based recommendation of probiotics.

Necrotizing Enterocolitis: Though Lactobacillus subsp. and Bifidobacterium subsp administration has shown better prevention, the American Academy of Pediatrics didn’t support routine use in view of the chance of infection, especially in Very Low Birth Weight (VLBW) babies.

Pouchitis: Despite low quality of evidence, AGA has recommended an 8-strain proprietary probiotic mix to prevent and treat pouchitis.

Cow’s Milk Protein Allergy and Other Allergies: Though L. rhamnosus GG has shown some promise, high-quality studies are required for a firm recommendation.

Probiotics in Infant formula: No overwhelming consistent benefit has been shown. There is a chance of transmitting ARG through the indiscriminate use of probiotics in babies.