For some probiotics, specifically, all 0f the E.Coli probiotics, we have studies of them persisting for weeks and months:

• “In a randomized double-blind clinical trial, healthy newborns were given the bacteria during their first 5 days of life [46]. The stools were (Mutaflor – E.Coli Nissle 1917) EcN-positive in >90% of infants for as long as 6 months.”[2016]
• “for the control group (not receiving mesalazine), within 2 weeks after secession of EcN administration, the strain could be detected in the stools of only 40% of individuals, dropping to 20% after 9 weeks [35]” [2016]
• Colinfant (another E.Coli Probiotic) “reported that the strain could still be detected in stools 25 weeks after dosage [13].” [2016]
• “a human volunteer study was performed to investigate the colonization potential of Symbioflor 2, which resulted in long-term colonization in all five volunteers, for a period of at least 20 weeks;”[2016]

On the other hand, the commonly taken ones — stay just hours,

• “Seven days after the VSL-3 treatment suspension, no patients and subjects harbored B. infantis Y 1 and B. breve Y 8, indicating a transient presence of these exogenous strains.” [2000]
• “Streptococcal population was detected after 3 days of administration and persisted for 6 days after the treatment suspension.” [2003]
• “The probiotic bacterium [Lactobacillus acidophilus] was detected in feces via ribotyping and RNA gene sequencing during the probiotic administration phase but not 2 weeks after cessation of administration.” [2004]
• ” Dead vegetative cells were detected 9 hr after administration, and C. butyricum cells were not detected in the intestine after 3 days.” [1997]
• “After 24 h, [Bacillus] spores constituted only 12% of the total counts in the stomach, caecum, and mid-colon. Less spores and more vegetative cells were detected after 24 h…The two Bacillus strains can temporarily remain in the GI system, but will be unable to permanently colonize the GI tract.” [2008]

“After oral consumption of probiotics, E. coli and enterococci could be detected in stool samples (57% and 67%, respectively) [after one week of stopping]. In contrast, with only one exception, ingested lactobacilli and bifidobacteria could not be detected in human feces.” [2007]

Bottom Line: E.Coli probiotics taken for a few days every month or two months, will keep the E.Coli in your system constantly. Enterococcus probiotics appear to have similar staying power.  For almost everything else, the benefit will last only for 1-2 days after you stop taking them.  E.Coli may be more expensive, but is likely a wiser buy.