We investigated the effect of consuming probiotic fermented milk (PFM) on the 
microbial community structure in the human intestinal tract by using 
high-throughput barcoded pyrosequencing. Six healthy adults ingested 2 servings 
of PFM daily for 3 wk, and their fecal microbiota were analyzed before and after 
3 wk of PFM ingestion period and for another 3 wk following the termination of 
PFM ingestion (the noningestion period). Fecal microbial communities were 
characterized by sequencing of the V1-V3 hypervariable regions of the 16S rRNA 
gene. All subjects showed a similar pattern of microbiota at the phylum level, 
where the relative abundance of Bacteriodetes species increased during the PFM 
ingestion period and decreased during the noningestion period. The increase in 
Bacteroidetes was found to be due to an increase in members of the families 
Bacteroidaceae or Prevotellaceae. In contrast to PFM-induced adaptation at the 
phylum level, the taxonomic composition at the genus level showed a considerable 
alteration in fecal microbiota induced by PFM ingestion. As revealed by analysis 
of operational taxonomic units (OTU), the numbers of shared OTU were low among 
the 3 different treatments (before, during, and after PFM ingestion), but the 
abundance of the shared OTU was relatively high, indicating that the majority 
(>77.8%) of total microbiota was maintained by shared OTU during PFM ingestion 
and after its termination. Our results suggest that PFM consumption could alter 
microbial community structure in the gastrointestinal tract of adult humans 
while maintaining the stability of microbiota.