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Hanaway explains that evaluating the effectiveness of probiotics in normalizing the gut flora may not be as simple as measuring the change in bacterial counts in stool culture at the species level, although these are the best clinical tools that we have right now.
Microbial analysis of stool samples provides clinical insight into the flora population of the distal colon. The predominant beneficial bacteria in the large intestine are Bifidobacteria, strict anaerobes that constitute as much as 25% of the overall colonic flora in healthy adults.
In the colon, obligate anaerobes such as Bifidobacteria predominate over facultative anaerobes such as Lactobacilli by 1,000:1.
Recovery of these organisms in stool culture should therefore ideally be in the 3+ or 4+ ranges.