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Randomized Controlled Trial
. 2013 May;79(9):3040-8.
doi: 10.1128/AEM.03910-12. Epub 2013 Mar 1.

Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk

Gerald W Tannock  1 , Blair Lawley, Karen Munro, Siva Gowri Pathmanathan, Shao J Zhou, Maria Makrides, Robert A Gibson, Thomas Sullivan, Colin G Prosser, Dianne Lowry, Alison J Hodgkinson
Affiliations
Randomized Controlled Trial

Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk

Gerald W Tannock et al. Appl Environ Microbiol. 2013 May.

Abstract

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 milk-fed 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.

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Figures

Fig 1
Fig 1
Scatter plots showing the proportions of Bifidobacteriaceae sequences with respect to total sequences obtained from pyrosequencing 16S rRNA genes associated with dietary groups (A), delivery method (B), and gender (C). Median values (horizontal lines) and significance values (P, Mann-Whitney) are shown. Thirty infants per goat, cow, and breast milk groups.
Fig 2
Fig 2
Comparisons of Bifidobacteriaceae abundances in stools from breast milk-fed infants where B. bifidum was less than (n = 20 infants) or greater than (n = 10 infants) 10% of the total bifidobacterial population. The greatest abundances of Bifidobacteriaceae occurred in stools with greater than 10% B. bifidum. Box plots showing horizontal line, median; box, 25 to 75% confidence limits; vertical bars, ranges.
Fig 3
Fig 3
Differentiation between B. longum subsp. longum and B. longum subsp. infantis using qPCR. Amplification curves (for clarity of reproduction, data generated by ABI software were used to prepare Prism graphs) for target 16S rRNA sequences. (A) DNA template from B. longum subsp. longum ATCC 15707T; (B) DNA template from B. longum subsp. infantis DSM 20088T; (C and D) templates from B. longum subsp. longum and infantis tested in the presence of stool DNA from an infant without bifidobacteria; (E) mixed templates (1:1 ratio); (F) the mixed templates in the presence of stool DNA. Note that the results in panels A and C, B and D, and E and F are highly similar, indicating that the presence of fecal DNA does not alter the amplification kinetics.
Fig 4
Fig 4
Similarity comparisons. (A) Alpha-diversity as measured by OTU accumulation with respect to sequence accumulation for the three dietary groups. Dashed lines indicate 95% confidence intervals. (B) Beta-diversity measures shown as unweighted UniFrac distances. Dietary groups were compared with themselves and with other diets. Mean values with SEM are shown. Significance values (P, Kruskal-Wallis) are also shown. Data from 30 infants per group were compared.
Fig 5
Fig 5
Biplot representation of principle coordinates of unweighted, pairwise UniFrac distances showing clustering of bacterial groups with stool samples. Stools from breast milk-fed infants, blue spheres; goat milk formula-fed infants, green spheres; cow milk formula-fed infants, red spheres. Taxon positions (gray spheres) are weighted (relative abundance) averages of the coordinates of all samples. Note association of Bacteroidaceae with breast milk-fed infant stool. Data from 30 infants per group were analyzed.
Fig 6
Fig 6
Similarity comparisons. Beta-diversity measures shown as unweighted, pairwise UniFrac distances applied to sequences originating in members of the family Lachnospiraceae, showing comparisons of dietary groups with themselves and with other groups. Mean values and SEM are shown. Significance values (P, Kruskal-Wallis) are also shown. Data from 30 infants per group were compared.
Fig 7
Fig 7
Relative abundances of nine bacterial families in infant stools where sequences representing Bifidobacteriaceae were less than 10% relative abundance (green bars) or greater than 10% relative abundance (red bars) in breast milk-fed (A), cow milk formula-fed (B), and goat milk formula-fed (C) infants. Means and SEM are shown. Data from 30 infants per group were compared.
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