The aim of the study was to compare the compositions of the fecal microbiotas of infants fed goat milk formula to those of infants fed cow milk formula or breast milk as the gold standard. Pyrosequencing of 16S rRNA gene sequences was used in the analysis of the microbiotas in stool samples collected from 90 Australian babies (30 in each group) at 2 months of age. Beta-diversity analysis of total microbiota sequences and Lachnospiraceae sequences revealed that they were more similar in breast milk/goat milk comparisons than in breast milk/cow milk comparisons. The Lachnospiraceae were mostly restricted to a single species (Ruminococcus gnavus) in breast milk-fed and goat milk-fed babies compared to a more diverse collection in cow milkfed babies. Bifidobacteriaceae were abundant in the microbiotas of infants in all three groups. Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium bifidum were the most commonly detected bifidobacterial species. A semiquantitative PCR method was devised to differentiate between B. longum subsp. longum and B. longum subsp. infantis and was used to test stool samples. B. longum subsp. infantis was seldom present in stools, even of breast milk-fed babies. The presence of B. bifidum in the stools of breast milk-fed infants at abundances greater than 10% of the total microbiota was associated with the highest total abundances of Bifidobacteriaceae. When Bifidobacteriaceae abundance was low, Lachnospiraceae abundances were greater. New information about the composition of the fecal microbiota when goat milk formula is used in infant nutrition was thus obtained.
Natural microbial communities such as those that inhabit the human bowel carry out diverse and complex biochemical processes (1, 2). Investigations of factors involved in community structure and function require an understanding of the trophic requirements of the microbial members. Optimally, this requires laboratory experiments with cultured bacteria. However, the first step in ecological research is to determine the phylogenetic composition of the microbial community of interest.Most infant formulas are manufactured using cow milk as a base. Goat milk provides an alternative basis for the production of infant formula. Like cow milk, goat milk needs to be fortified to provide optimal nutrition for infants (3). The amount of lactose in cow and goat milk is about the same, but there are other compositional differences (4). Alpha-s1 casein is present in ruminant milk but not in breast milk. Compared to cow milk, goat milk contains much lower concentrations of alpha-s1 casein and higher concentrations of nucleotides and polyamines as well as some of the essential amino acids. Breast milk differs from ruminant milks in that sialylated and fucosylated oligosaccharides (human milk oligosaccharides [HMO]) are the third largest component (5). The HMO are utilized for growth by bifidobacteria, and their presence in breast milk is the likely explanation as to why there is generally a greater abundance of these bacteria in th...