DOI: 10.5061/dryad.15dv41p7p
title: Data for: Gut microbial composition and diversity vary by CREBRF genotype among Samoan infants

description: Over 40% of Samoans have at least one copy of the minor A allele at
 rs373863828 in CREB3 regulatory factor (CREBRF), which is associated with
 increased BMI but decreased odds of type 2 diabetes mellitus. The
 mechanisms underlying this paradoxical effect remain unknown. We
 hypothesized that gut microbiota may play a role and examined associations
 between CREBRF genotype and gut microbial diversity and composition among
 Samoan infants. Fecal samples were collected from Samoan infants
 aged 0 (n=23), 4 (n=20), and 21 (n=27) months. Microbiota community
 structure was analyzed using 16S rRNA bacterial gene
 sequencing. Both cross-sectional and longitudinal analyses
 revealed no associations between CREBRF genotype and overall microbiome
 composition or diversity at 0 or 4 months. Cross-sectional analysis at 21
 months revealed a significant association between genotype and unweighted
 UniFrac distances (F1,24=1.855, R2=0.072, p=0.015). Longitudinal
 differential abundance analysis also revealed several differentially
 abundant taxa at 21 months. Notably, the AG genotype was associated with
 lower relative abundance of Escherichia Shigella (β=-6.741, SE=2.243,
 p=.004, q=.042). Significant genotype differences in gut microbiome
 composition and diversity at 21 months suggest that gut microbiota may be
 involved in relationships between CREBRF genotype and metabolic health. No
 genotype differences were observed at 0 or 4 months, suggesting that
 environmental and/or maternal variables have a greater influence on the
 gut microbiome in early infancy, and genotype effects emerge later.
 Further research should examine whether genotype differences in gut
 microbiota are associated with functional differences in metabolic or
 immune signaling pathways or energy extraction.
description: # Data for: Gut microbial composition and diversity vary by CREBRF
 genotype among Samoan infants Dataset DOI:
 [10.5061/dryad.15dv41p7p](10.5061/dryad.15dv41p7p) ## Description of the
 data Fecal samples were collected from Samoan infants aged 0
 (n=23), 4 (n=20), and 21 (n=27) months. Microbiota community structure was
 analyzed using 16S rRNA bacterial gene sequencing. ### Supplementary
 Figures #### Supplementary Figure 1 ##### File:
 Supplementary\_Figure\_1.pdf **Description:** **Associations between
 covariates and alpha diversity metrics at age 0, 4, and 21 months.**
 Student’s t-test results are shown for categorical variables. Pearson’s
 correlation coefficients are shown for continuous variables. a. Mode of
 birth i. Shannon’s entropy ii. Faith’s phylogenetic diversity b.
 Breastfeeding status (substituted with breastfeeding status at age 6
 months for the 21-month timepoint) i. Shannon’s entropy ii. Faith’s
 phylogenetic diversity c. Maternal BMI i. Shannon’s entropy ii. Faith’s
 phylogenetic diversity d. Antibiotic use within 2 weeks prior to sample
 collection i. Shannon’s entropy ii. Faith’s phylogenetic diversity ####
 Supplementary Figure 2 ##### File: Supplementary\_Figure\_2.pdf
 **Description:** **Associations between covariates and nonmetric
 multidimensional scaling ordination of variation in bacterial community
 structure at age 0, 4, and 21 months.** a. Mode of birth i. Unweighted
 UniFrac distances ii. Weighted UniFrac distances b. Breastfeeding status
 (substituted with breastfeeding status at age 6 months for the 21-month
 timepoint) i. Unweighted UniFrac distances ii. Weighted UniFrac distances
 c. Maternal BMI i. Unweighted UniFrac distances ii. Weighted UniFrac
 distances d. Antibiotic use within 2 weeks prior to sample collection i.
 Unweighted UniFrac distances ii. Weighted UniFrac distances ####
 Supplementary Figure 3 ##### File: Supplementary\_Figure\_3.pdf
 **Description:** **Comparison of relative abundance of bacterial taxa at
 0, 4, and 21 months by CREBRF genotype.** For clarity, only taxa with the
 relative abundance of &gt;1% are included in each figure. a. 0 months i.
 Phylum level ii. Family level iii. Genus level b. 4 months i. Phylum level
 ii. Family level iii. Genus level c. 21 months i. Phylum level ii. Family
 level iii. Genus level ### Supplementary Tables #### Supplementary Table 1
 ##### File: Supplementary\_Table\_1a.csv ##### File:
 Supplementary\_Table\_1b.csv ##### File: Supplementary\_Table\_1c.csv
 ##### File: Supplementary\_Table\_1.pdf **Description:** **Results of
 age-stratified differential abundance analysis by infant age conducted in
 ANCOMBC2.** Analyses were conducted on unrarefied data from samples with
 more than 3000 reads. Differences in relative abundance of bacterial taxa
 between (a) 0 vs 4 months, (b) 0 vs 21 months, and (c) 4 vs 21 months were
 investigated. Features with q-value &lt; 0.25 that passed the sensitivity
 analysis in ANCOMBC2 are shown. LFC = log-fold change. SD = standard
 deviation. SE = standard error. #### Supplementary Table 2 ##### File:
 Supplementary\_Table\_2a.csv ##### File: Supplementary\_Table\_2b.csv
 ##### File: Supplementary\_Table\_2c.csv ##### File:
 Supplementary\_Table\_2.pdf **Description:** **Results of age-stratified
 differential abundance analysis by infant age conducted in MaAslin2.**
 Analyses were conducted on data rarefied to 3000 reads. Differences in
 relative abundance of bacterial taxa between (a) 0 vs 4 months, (b) 0 vs
 21 months, and (c) 4 vs 21 months were investigated. Features with q-value
 &lt; 0.25 in MaAslin2 are shown. SD = standard deviation. SE = standard
 error. #### Supplementary Table 3 ##### File: Supplementary\_Table\_3a.csv
 ##### File: Supplementary\_Table\_3b.csv ##### File:
 Supplementary\_Table\_3c.csv ##### File: Supplementary\_Table\_3.pdf
 **Description:** **Results of longitudinal differential abundance analysis
 by infant age conducted in MaAslin2.** Analyses were conducted on data
 rarefied to 3000 reads. Differences in relative abundance of bacterial
 taxa between (a) 0 vs 4 months, (b) 0 vs 21 months, and (c) 4 vs 21 months
 are shown. Features with q-value &lt; 0.25 are shown. SD = standard
 deviation. SE = standard error. #### Supplementary Table 4 ##### File:
 Supplementary\_Table\_4a.csv ##### File: Supplementary\_Table\_4b.csv
 ##### File: Supplementary\_Table\_4c.csv ##### File:
 Supplementary\_Table\_4d.csv ##### File: Supplementary\_Table\_4.pdf
 **Description:** **Results of age-stratified differential abundance
 analysis by covariates conducted in ANCOMBC2.** Analyses were conducted on
 unrarefied data from samples with more than 3000 reads. Differences in
 relative abundance of bacterial taxa by (a) antibiotic use within the 2
 weeks prior to sample collection, (b) mode of delivery, (c) exclusive
 breastfeeding status, and (d) maternal BMI were investigated. Features
 with q-value &lt; .25 that passed the sensitivity analysis for
 pseudo-count addition in ANCOMBC2 are shown. LFC = log-fold change. SD =
 standard deviation. SE = standard error. #### Supplementary Table 5 #####
 File: Supplementary\_Table\_5a.csv ##### File:
 Supplementary\_Table\_5b.csv ##### File: Supplementary\_Table\_5c.csv
 ##### File: Supplementary\_Table\_5d.csv ##### File:
 Supplementary\_Table\_5.pdf **Description:** **Results of age-stratified
 differential abundance analysis by covariates conducted in MaAslin2.**
 Analyses were conducted on data rarefied to 3000 reads. Associations in
 relative abundance of bacterial taxa and (a) antibiotic use within the 2
 weeks prior to sample collection, (b) mode of delivery, (c) exclusive
 breastfeeding status, and (d) maternal BMI were investigated. Features
 with q-value &lt; 0.25 in MaAslin2 are shown. SD = standard deviation. SE
 = standard error. #### Supplementary Table 6 ##### File:
 Supplementary\_Table\_6a.csv ##### File: Supplementary\_Table\_6b.csv
 ##### File: Supplementary\_Table\_6c.csv ##### File:
 Supplementary\_Table\_6d.csv ##### File: Supplementary\_Table\_6.pdf
 **Description:** **Results of longitudinal differential abundance analysis
 by covariates conducted using linear mixed-effects models in Maaslin2.**
 Analyses were conducted on data rarefied to 3000 reads. Differences in
 relative abundance of bacterial taxa by (a) antibiotic use within the 2
 weeks prior to sample collection, (b) mode of delivery, (c) feeding mode,
 and (d) maternal BMI were investigated. All models included the covariate
 of interest, age (factor variable), and their interaction as fixed effects
 and a random intercept for each infant. When the covariate alone was
 significant, age is listed as 0mo and relative abundances at 0 months are
 listed. When the interaction term was significant, the age of interaction
 and relative abundances at that age are listed. Features with q-value &lt;
 0.25 are shown. SD = standard deviation. SE = standard error. ####
 Supplementary Table 7 ##### File: Supplementary\_Table\_7.csv ##### File:
 Supplementary\_Table\_7.pdf **Description:** **Alpha-diversity
 multivariable regression results.** Model 1 includes CREBRF genotype (ref
 = GG genotype) and all covariates. At 0 months, the covariates were mode
 of birth (Cesarean versus vaginal [ref]), breastfeeding status
 (exclusively breastfed versus mixed- for formula-fed [ref]), and maternal
 BMI (continuous). At 4 months, the covariates were mode of birth (Cesarean
 versus vaginal [ref], breastfeeding status (exclusively breastfed versus
 mixed- for formula-fed [ref]), and maternal BMI (continuous), and
 antibiotic use within the 2 weeks prior to sample collection (yes versus
 no [ref]). At 21 months, the covariates were mode of birth (Cesarean
 versus vaginal [ref]), exclusive breastfeeding status at age 6 months
 (exclusively breastfed versus mixed- for formula-fed [ref]), maternal BMI
 (continuous), and antibiotic use within the 2 weeks prior to sample
 collection (yes versus no [ref]). Model 2 only includes the CREBRF
 genotype. Model 3 only includes covariates. β (beta) coefficient, standard
 error (SE), and p-values are provided for each predictor variable. ####
 Supplementary Table 8 ##### File: Supplementary\_Table\_8.csv ##### File:
 Supplementary\_Table\_8.pdf **Description:** **Beta-diversity PERMANOVA
 test results.** Model 1 includes CREBRF genotype (ref = GG genotype) and
 all covariates. At 0 months, the covariates were mode of birth (Cesarean
 versus vaginal [ref]), breastfeeding status (exclusively breastfed versus
 mixed- for formula-fed [ref]), and maternal BMI (continuous). At 4 months,
 the covariates were mode of birth (Cesarean versus vaginal [ref],
 breastfeeding status (exclusively breastfed versus mixed- for formula-fed
 [ref]), and maternal BMI (continuous), and antibiotic use within the 2
 weeks prior to sample collection (yes versus no [ref]). At 21 months, the
 covariates were mode of birth (Cesarean versus vaginal [ref]), exclusive
 breastfeeding status at age 6 months (exclusively breastfed versus mixed-
 for formula-fed [ref]), maternal BMI (continuous), and antibiotic use
 within the 2 weeks prior to sample collection (yes versus no [ref]). Model
 2 only includes *CREBRF* genotype. Model 3 only includes covariates. The
 sum of squares, R2, and p-values are provided for each predictor variable.
 #### Supplementary Table 9 ##### File: Supplementary\_Table\_9.csv #####
 File: Supplementary\_Table\_9.pdf **Description:** **Results of
 age-stratified differential abundance analysis by CREBRF genotype
 conducted using ANCOMBC2.** Analyses were conducted on unrarefied data
 from samples with more than 3000 reads. Features with q-value &lt; 0.25
 that passed the sensitivity analysis for pseudo-count addition in ANCOMBC2
 are shown. SD = standard deviation. LFC = log-fold change. SE = standard
 error. #### Supplementary Table 10 ##### File:
 Supplementary\_Table\_10.csv ##### File: Supplementary\_Table\_10.pdf
 **Description:** **Results of longitudinal differential abundance analysis
 by CREBRF genotype conducted in Maaslin2.** Analyses were conducted on
 data rarefied to 3000 reads. All models included genotype, age (factor
 variable), and their interaction as fixed effects and a random intercept
 for each infant. When genotype alone was significant, age is listed as 0mo
 and relative abundances at 0 months are listed. When the interaction term
 was significant, the age of interaction and relative abundances at that
 age are listed. Features with q-value &lt; 0.25 are shown. SD = standard
 deviation. SE = standard error. #### Supplementary Table 11 ##### File:
 Supplementary\_Table\_11.csv ##### File: Supplementary\_Table\_11.pdf
 **Description:** **Significant associations between relative abundance of
 bacterial taxa identified and body size indices identified by ANCOMBC2 on
 unrarefied data.** Associations between relative abundance of bacterial
 taxa and (a) height-for-age z-score, (b) weight-for-length z-score
 [substituted with weight-for-height z-score at 21 months], and
 total-body-less-head% body fat were investigated. Features with q-value
 &lt;0.25 that passed the sensitivity analysis for pseudo-count addition in
 ANCOMBC2 are shown. There were no features associated with
 total-body-less-head% body fat with q-value &lt;0.25. LFC =
 log-fold-change. SE = standard error. #### Supplementary Table 12 #####
 File: Supplementary\_Table\_12.csv ##### File:
 Supplementary\_Table\_12.pdf **Description:** **Significant associations
 between relative abundance of bacterial taxa identified and body size
 indices identified by age-stratified analyses in MaAslin on data rarefied
 to 3000 reads.** Associations between relative abundance of bacterial taxa
 and (a) height-for-age z-score, weight-for-length z-score [substituted
 with weight-for-height z-score at 21 months], and (b)
 total-body-less-head% body fat were investigated. Features with q-value
 &lt;0.25 are shown. There were no features associated with
 weight-for-length z-score with q-value &lt;0.25. SE = standard error. ####
 Supplementary Table 13 ##### File: Supplementary\_Table\_13.csv #####
 File: Supplementary\_Table\_13.pdf **Description:** **Significant
 associations between relative abundance of bacterial taxa and body size
 indices identified by longitudinal analyses in MaAslin2.** Associations
 between relative abundance of bacterial taxa and (a) height-for-age
 z-score and (b) weight-for-length z-score [substituted with
 weight-for-height z-score at 21 months], and total-body-less-head% body
 fat were investigated. Features with q-value &lt;0.25 are shown. There
 were no features associated with total-body-less-head% body fat with
 q-value &lt;0.25. SE = standard error.