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Certain milk factors may promote the growth of a host-friendly gastrointestinal microbiota, for example, one that is predominated by bifidobacteria, a perceived health-promoting genus. This may explain why breast-fed infants experience fewer intestinal infections than their formula-fed counterparts who are believed to have a more diverse microbiota, which is similar to that of adults. The effects of formulas supplemented with 2 such ingredients from bovine milk, α-lactalbumin (α-lac) and casein glycomacropeptide (GMP), on gut flora were investigated in this study.Six-week-old (4–8 wk), healthy term infants were randomised to a standard infant formula or 1 of 2 test formulae enriched in α-lac with higher or lower GMP until 6 months. Faecal bacteriology was determined by the culture-independent procedure fluorescence in situ hybridisation.There was a large fluctuation of bacterial counts within groups with no statistically significant differences between groups. Although all groups showed a predominance of bifidobacteria, breast-fed infants had a small temporary increase in counts. Other bacterial levels varied in formula-fed groups, which overall showed an adult-like faecal microflora.It can be speculated that a prebiotic effect for α-lac and GMP is achieved only with low starting populations of beneficial microbiota (eg, infants not initially breast-fed.