Probiotics: Is There a Role for Routine Stool Cultures?

The human gastrointestinal tract contains a large, complex, mostly unknown microbial population. Over 90% of the microorganisms known to be present by 16S rRNA sequencing cannot be cultured. Fecal cultures primarily reflect cultivable microbes predominantly in the descending colon and rectum. They do not accurately reflect the microbial populations in the cecum and distal small bowel. The normal intestinal microflora consists almost entirely of obligate anaerobes. Accurate stool culture assessment of normal fecal flora requires meticulous anaerobic techniques and rapid processing. Fecal culture is a poor guide for evaluating the need for probiotic supplementation. Stool cultures are inadequate for the assessment of probiotic bowel colonization and therefore have little or no role in the selection and assessment of probiotics for supplementation.