Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life

Abstract

HIV-exposed uninfected infants (HEU) have abnormal immunologic functions and increased infectious morbidity in the first 6 months of life, which gradually decreases thereafter. The mechanisms underlying HEU immune dysfunctions are unknown. We hypothesized that unique characteristics of the HEU gut microbiota associated with maternal HIV status may underlie the HEU immunologic dysfunctions. We characterized the infant gut, maternal gut, and breast milk microbiomes of mother-infant pairs, including 123 with HEU and 117 with HIV-uninfected infants (HUU), from South Africa. Pan-bacterial 16S rRNA gene sequencing was performed on (i) infant stool at 6, 28, and 62 weeks; (ii) maternal stool at delivery and 62 weeks; and (iii) breast milk at 6 weeks. Infant gut alpha and beta diversities were similar between groups. Microbial composition significantly differed, including 12 genera, 5 families and 1 phylum at 6 weeks; 12 genera and 2 families at 28 weeks; and 2 genera and 2 families at 62 weeks of life. Maternal gut microbiomes significantly differed in beta diversity and microbial composition, and breast milk microbiomes differed in microbial composition only. Infant gut microbiotas extensively overlapped with maternal gut and minimally with breast milk microbiotas. Nevertheless, exclusively breastfed HEU and HUU had less divergent microbiomes than nonexclusively breastfed infants. Feeding pattern and maternal gut microbiome imprint the HEU gut microbiome. Compared to HUU, the HEU gut microbiome prominently differs in early infancy, including increased abundance of taxa previously observed to be present in excess in adults with HIV. The HEU and HUU gut microbiome compositions converge over time, mirroring the kinetics of HEU infectious morbidity risk. IMPORTANCE HIV-exposed uninfected infants (HEU) are highly vulnerable to infections in the first 6 months of life, and this vulnerability decreases to the age of 24 months. Because the microbiome plays a critical role in the education of the infant immune system, which protects them against infections, we characterized the gut microbiomes of HEU and HIV-unexposed infants (HUU) in the first year of life. The HEU and HUU gut microbiomes showed prominent differences at 6 and 28 weeks of life but converged at 62 weeks of life, mirroring the time course of the HEU excess infectious morbidity and suggesting a potential association between the infant gut microbiome structure and susceptibility to infections. Infant gut microbiotas extensively overlapped with maternal gut and minimally with breast milk microbiotas. Moreover, exclusively breastfed HEU and HUU had less divergent microbiomes at 6 and 28 weeks than nonexclusively breastfed HEU and HUU. The factors that affect the HEU gut microbiome, maternal gut microbiome and exclusive breastfeeding, may be targeted by interventions.

Keywords: HIV; HIV-exposed uninfected infants; breast milk microbiome; gut microbiome; human immunodeficiency virus; pregnant women with HIV.

FIG 1

Consort diagram. “QC” indicates samples that were excluded because they did not pass sequence quality control (details are provided in Materials and Methods).

FIG 2

Infant gut microbiome. (A to C) Alpha diversity analysis of community richness (Chao1), evenness (Shannon H/Hmax), and diversity (Shannon H). There were no significant differences between HEU and HUU. (D) Genera with significantly different relative abundances between HEU and HUU at the indicated time points (FDR P < 0.05). (E) Genera with significantly different relative abundances between HEU and HUU exclusively (Excl.) breastfed at 28 weeks of life and not exclusively breastfed.

FIG 3

Maternal gut microbiome. (A to C) Alpha diversity analysis of community richness (Chao1), evenness (Shannon H/Hmax), and diversity (Shannon H). There were no significant differences between mothers with and without HIV. (D and E) Beta diversity showing significantly less similarity (higher diversity) among mothers with HIV than among mothers without HIV at delivery (FDR P = 0.03) but not postpartum (FDR P = 0.06). (F) Genera with significantly different relative abundances between mothers with and without HIV at the indicated time points (FDR P < 0.05).

FIG 4

Breast milk microbiome at 6 weeks postpartum. (A) Average relative abundance of bacterial breast milk taxa, stratified by HIV status. (B to D) Alpha diversity analysis of community richness (Chao1), evenness (Shannon H/Hmax), and diversity (Shannon H) showing no significant differences between mothers with and without HIV. (E) Beta diversity showing no differences between mothers with and without HIV. (F) Genera with significantly different abundances in mothers with and without HIV (FDR P < 0.05).

FIG 5

Similarities between breast milk and gut microbiomes, stratified by HIV status. Data were derived from paired analysis of Bray-Curtis similarity scores. The composition of infant gut and breast milk microbiomes at 6 weeks of life had equally little similarity in HEU and HUU mother-infant dyads, which was comparable to the compositions of maternal gut at delivery and breast milk at 6 weeks postpartum. There was equally high similarity between infant and maternal gut microbiomes at 6 weeks of life and delivery, respectively, in HEU and HUU mother-infant dyads.

FIG 6

Venn diagrams of core bacterial taxa in infant gut, maternal gut, and breast milk microbiomes. The numerals indicate the numbers of taxa in the shared compartments. (A) HEU gut and breast milk microbiomes at 6 weeks postpartum and maternal gut microbiome at delivery. (B) HEU infant and maternal gut microbiomes at 62 weeks postpartum. (C) HUU gut and breast milk microbiomes at 6 weeks postpartum and maternal gut microbiome at delivery. (D) HUU infant and maternal gut microbiomes at 62 weeks postpartum. (E) HEU and HUU gut microbiomes at 6 weeks of life and maternal gut microbiomes at delivery. (F) HEU, HUU, and maternal gut microbiomes at 62 weeks of life.