Ethnic diversity in infant gut microbiota is apparent before the introduction of complementary diets

Jia Xu, Blair Lawley, Gerard Wong, Anna Otal, Li Chen, Toh Jia Ying, Xinyi Lin, Wei Wei Pang, Fabian Yap, Yap-Seng Chong, Peter D Gluckman, Yung Seng Lee, Mary Foong-Fong Chong, Gerald W Tannock, Neerja Karnani, Jia Xu, Blair Lawley, Gerard Wong, Anna Otal, Li Chen, Toh Jia Ying, Xinyi Lin, Wei Wei Pang, Fabian Yap, Yap-Seng Chong, Peter D Gluckman, Yung Seng Lee, Mary Foong-Fong Chong, Gerald W Tannock, Neerja Karnani

Abstract

The human gut microbiota develops soon after birth and can acquire inter-individual variation upon exposure to intrinsic and environmental cues. However, inter-individual variation has not been comprehensively assessed in a multi-ethnic study. We studied a longitudinal birth cohort of 106 infants of three Asian ethnicities (Chinese, Malay, and Indian) that resided in the same geographical location (Singapore). Specific and temporal influences of ethnicity, mode of delivery, breastfeeding status, gestational age, birthweight, gender, and maternal education on the development of the gut microbiota in the first 2 years of life were studied. Mode of delivery, breastfeeding status, and ethnicity were identified as the main factors influencing the compositional development of the gut microbiota. Effects of delivery mode and breastfeeding status lasted until 6M and 3M, respectively, with the primary impact on the diversity and temporal colonization of the genera Bacteroides and Bifidobacterium. The effect of ethnicity was apparent at 3M post-birth, even before the introduction of weaning (complementary) foods, and remained significant after adjusting for delivery mode and breastfeeding status. Ethnic influences remained significant until 12M in the Indian and Chinese infants. The microbiota of Indian infants was characterized by higher abundances of Bifidobacterium and Lactobacillus, while Chinese infants had higher abundances of Bacteroides and Akkermansia. These findings provide a detailed insight into the specific and temporal influences of early life factors and ethnicity in the development of the human gut microbiota. Trial Registration: Clinicaltrials.gov registration no. NCT01174875.

Keywords: Early gut microbiota; birth cohort; breastfeeding; delivery mode; ethnicity.

Figures

Figure 1.
Figure 1.
Developmental trajectory of infant gut microbiota from 3 to 24M. A. Change in α-diversity of gut microbiota over time as indicated by the Shannon diversity index. Data are shown as mean ± 95% confidence interval. B. Principal coordinate analysis (PCoA) of gut microbiota based on the Bray-Curtis dissimilarity distance over time. C. Clustering of gut microbiota based on distances between different time points using MANOVA test with Bray-Curtis distance-based PCoA scores (accounting for 80% of total variations).
Figure 2.
Figure 2.
Effects of ethnicity, delivery mode, breastfeeding status and maternal education on the infant gut microbiota over time. A. Canonical correspondence analysis (CCA) ordination biplots illustrating the individual effects of ethnicity, delivery mode, breastfeeding status and maternal education on the variation of infant gut microbiota at four time points (3M, 6M, 12M, and 24M) without adjustment for covariates. B-E. Partial CCA ordination biplots illustrating the independent effects of ethnicity (b), delivery mode (c), breastfeeding status (d) and maternal education (e) on infant gut microbiota after adjusting for the covariates. B-E: At 3M, ethnicity, delivery mode, and breastfeeding status were all used as covariates and adjusted mutually; From 6 M to 24 M, only ethnicity and delivery mode were regarded as covariates and adjusted mutually. The significance of the effects of the environmental variable was tested using the Monte-Carlo Permutation Procedure (MCPP) on each environmental variable.
Figure 3.
Figure 3.
Comparison of changes in the abundances of key OTUs associated with LSCS and vaginally delivered infants over time identified by partial CCA. Only OTUs with mean relative abundance higher than 0.1% in any group and at any time point were shown in the plot. LSCS, lower segment cesarean section. OTUs with higher abundance in the gut of vagina-delivered infants were plotted in the upper panel, and lower abundance in the lower panel.
Figure 4.
Figure 4.
Comparison in the abundances of key OTUs associated with different breastfeeding status identified by partial CCA. Only OTUs with mean relative abundance higher than 0.1% in any group are shown in the plot. B – breastfed only; B + F – breastfed with formula milk; F – formula milk only.
Figure 5.
Figure 5.
Key bacteria differentiating Indians from Chinese and Malay identified by partial CCA. Only OTUs with mean relative abundance higher than 0.1% in any ethnicity and at any time point are shown in the plot. OTUs with higher abundance in the microbiota of Indian infants were plotted in the upper panel, and lower abundance in the lower panel.

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