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. 2019 Dec 11;10:2866. doi: 10.3389/fimmu.2019.02866

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Copyright © 2019 Drall, Tun, Morales-Lizcano, Konya, Guttman, Field, Mandal, Wishart, Becker, Azad, Lefebvre, Mandhane, Moraes, Sears, Turvey, Subbarao, Scott and Kozyrskyj.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Frequency of C. difficile colonization in our study population and infant microbial alpha-diversity according feeding mode (n = 1,554). Colonization rates differ within feeding groups (A) 22.63% of exclusively breastfed infants (N = 193/853), 35.96% of partially breastfed infants (N = 155/431) and 49.63% of formula fed infants were colonized (N = 134/270) (Fishers' exact p < 0.001). Scatter box-plots of the median (middle line), Q3 and Q1 quartiles (box limits), IQR (whiskers) and outlying values (dots). Data were normally distributed (Supplementary Figure 3) and thus two-sided p-values were calculated with students t-test within infant feeding groups, comparing colonized and non-colonized infants at a significance threshold of α = 0.05. Higher α-diversity was observed for infants colonized with C. difficile (CD+) and breastfed (either exclusively or partially) than non-carriers (CD–) on the same diet. This was the case for both the Shannon diversity index (B) and Chao1 species richness index (C). Purple represents EBF, green for PBF and gray for EFF.