Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota

Transcription

1 Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota Authors: Jasmine C. C. Davis 1,2, Zachery T. Lewis 2,3, Sridevi Krishnan 4, Robin M. Bernstein 6,7, Sophie E. Moore 8,9, Andrew M. Prentice 9, David A. Mills 2,3,5, Carlito B. Lebrilla 1,2, and Angela M. Zivkovic 2,4 * Affiliations: 1 Department of Chemistry, 2 Foods for Health Institute, 3 Department of Food Science and Technology, 4 Department of Nutrition, and 5 Department of Viticulture and Enology, University of California, Davis, CA 95616, United States 6 Department of Anthropology, 7 Health and Society Program, Institute of Behavioral Science, University of Colorado, Boulder, CO 80309, United States 8 Medical Research Council (MRC) Human Nutrition Research, Cambridge, UK 9 MRC Unit, The Gambia and MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, UK *To whom correspondence should be addressed: Angela M. Zivkovic, amzivkovic@ucdavis.edu 1

2 Supplementary Figure Legends Supplementary Figure S1. Differences in individual human milk oligosaccharides (HMOs) between infants who were sick and those who were not sick. Plots are divided by sick ( ) vs. not sick ( ) infants, displaying average and standard error bars for relative abundances of (A) F- LNO (fucosyllacto-n-octaose) at week 4, (B) MFpLNH IV (fucosyl-para-lacto-n-hexaose) at week 16, and (C) IFLNH III (isomer III fucosyl-paralacto-n-hexaose) at week 16. P-value based on Mann-Whitney U tests. HMO structures pictured with monosaccharides Glc ( ), Gal ( ), GlcNAc ( ), and Fuc ( ). Supplementary Figure S2. Relative abundance plots showing the differences in the gut microbiota between infants who were sick and those who were not. The plots show the classwise distribution of the enriched taxa at the lowest taxonomic level at which they are enriched. Supplementary Figure S3. Box plots displaying change in infant fecal calprotectin levels (mg/kg) at 4, 16, and 20 weeks postpartum. Median is given as a line, 25th and 75th percentiles are the top and bottom of the box, whiskers are data within 1.5*(75th 25th percentile) of the median, outliers displayed as dots above the box. N at each week given above plot with P-value based on linear mixed effects model. Supplementary Figure S4. Relative abundance plots showing the differences in the gut microbiota between infants categorized into having normal, borderline, or abnormal calprotectin levels. The plots show the class-wise distribution of the enriched taxa at the lowest taxonomic level at which they are enriched. Supplementary Figure S5. Cladogram plots of microbiota enriched in infants categorized by (A) WAZ and (B) HAZ scores. Infants with WAZ scores <-2 were assigned as underweight, 2

3 infants with scores >-2 were desired weight, infants with HAZ scores <-2 were assigned as stunted, and infants with scores >-2 were not stunted. Plots indicate microbes that were enriched in infants who were at desired weight ( ) or underweight ( ), and not stunted ( ) or stunted ( ) based on LefSe analysis. Supplementary Figure S6. Cladogram plot of microbiota enriched in infants born in either the dry ( ) or wet ( ) season. Supplementary Figure S7. Changes in the predicted functional profile of the infant fecal microbiome over time from week 4 ( ) to week 16 ( ) to week 20 ( ). The median of the data is shown as a line, the mean of the data as a star, the 25th and 75th percentiles of the data as the top and bottom of the box, and the most extreme data point within 1.5*(75th 25th percentile) of the median as whiskers. Data points outside of the whiskers are shown as crosses. Supplementary Figure S8. Associations between growth, morbidity, and a decrease in bifidobacteria abundance for infant 25. From week 16 to week 20, the relative abundance of bifidobacteria ( ) severely dropped and infant calprotectin ( ) severely increased. Infant 25 also had 12 morbidity instances ( ), unlike weeks 4 and 16 in which she experienced zero. Her WAZ score ( ) also dropped during these time points. 3

4 Supplementary Table 1. Major microbial contributors of metabolic functions found to change over the first 20 weeks of life. Gene Order Family Genus Proportional contribution in all samples Hexokinase Bacteroidales Bacteroidaceae Bacteroides Hexokinase Clostridiales Veillonellaceae Megasphaera Hexokinase Bacteroidales Porphyromonadaceae Parabacteroides Butyrateacetoacetate CoA-transferase Butyrateacetoacetate CoA-transferase Butyrateacetoacetate CoA-transferase Glutaconyl- CoA decarboxylase Glutaconyl- CoA decarboxylase Glutaconyl- CoA decarboxylase Clostridiales Veillonellaceae Megasphaera Fusobacteriales Fusobacteriaceae Fusobacterium Clostridiales Lachnospiraceae All Clostridiales Veillonellaceae All Clostridiales Lachnospiraceae All Clostridiales Clostridiaceae All

5 Supplementary Table 2. Morbidity instances used to assign infants to sick or not sick categories. Sample Number of Morbidity Instances Sick or Not Sick Week 4 Week 16 Week 20 Week 4 Week 16 Week Not Sick Sick Not Sick Sick Sick Not Sick Sick Sick Not Sick Sick Not Sick Not Sick Not Sick Not Sick Sick Sick Not Sick Not Sick Sick Sick Sick Not Sick Sick Not Sick Not Sick Sick Sick Sick Not Sick Not Sick Not Sick Not Sick Not Sick Not Sick Sick Sick Not Sick Sick Not Sick Not Sick Not Sick Not Sick Sick Not Sick Sick Sick Not Sick Sick Sick Sick Sick Sick Sick Sick Not Sick Not Sick Not Sick Sick Not Sick Sick Not Sick Not Sick Not Sick Not Sick Sick Sick Not Sick Sick Sick Not Sick Sick Not Sick Not Sick Not Sick Sick Not Sick Not Sick Sick Sick Not Sick Not Sick Not Sick Not Sick Sick Not Sick Sick Not Sick Not Sick Sick Sick Not Sick Sick Not Sick Not Sick Not Sick Not Sick Not Sick Not Sick Not Sick 5

6 Supplementary Table 3. Weight-for-age (WAZ) and height-for-age (HAZ) Z scores calculated for each infant against a Gambian reference. Sample WAZ score HAZ score Week 4 Week 16 Week 20 Week 4 Week 16 Week

7 Supplementary Table 4. Maternal age and weight, and infant sex, weight, and height. Sample Maternal Age (years) Maternal Weight (kg) Infant Sex Infant Weight (kg) Infant Height (cm) Week 1 Week Week Week Week Week Week M F M F M F M M F F F M M F M M F F M F F F M M F M F F F M M M M

8 Supplementary Figure S1. Differences in individual human milk oligosaccharide (HMO) structures between sick and not sick infants. 8

9 Supplementary Figure S2. Relative abundance plots of enriched taxa of infants who were classified as sick or not sick. 9

10 Supplementary Figure S3. Infant fecal calprotectin levels by week. 10

11 Supplementary Figure S4. Relative abundance plots of enriched taxa of infants with normal, borderline, and abnormal calprotectin levels. 11

12 Supplementary Figure S5. Cladograms of microbiota enriched in infants separated by growth outcomes. 12

13 Supplementary Figure S6. Cladograms of microbiota enriched in infants based on birth season. 13

14 Supplementary Figure S7. Changes in predicted functional profiles of microbiota over time. 14

15 Supplementary Figure S8. Associations between growth faltering and increased morbidity with a decrease in abundance of bifidobacteria. 15