Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome

Abstract

The development of the infant intestinal microbiome in response to dietary and other exposures may shape long-term metabolic and immune function. We examined differences in the community structure and function of the intestinal microbiome between four feeding groups, exclusively breastfed infants before introduction of solid foods (EBF), non-exclusively breastfed infants before introduction of solid foods (non-EBF), EBF infants after introduction of solid foods (EBF+S), and non-EBF infants after introduction of solid foods (non-EBF+S), and tested whether out-of-home daycare attendance was associated with differences in relative abundance of gut bacteria. Bacterial 16S rRNA amplicon sequencing was performed on 49 stool samples collected longitudinally from a cohort of 9 infants (5 male, 4 female). PICRUSt metabolic inference analysis was used to identify metabolic impacts of feeding practices on the infant gut microbiome. Sequencing data identified significant differences across groups defined by feeding and daycare attendance. Non-EBF and daycare-attending infants had higher diversity and species richness than EBF and non-daycare attending infants. The gut microbiome of EBF infants showed increased proportions of Bifidobacterium and lower abundance of Bacteroidetes and Clostridiales than non-EBF infants. PICRUSt analysis indicated that introduction of solid foods had a marginal impact on the microbiome of EBF infants (24 enzymes overrepresented in EBF+S infants). In contrast, over 200 bacterial gene categories were overrepresented in non-EBF+S compared to non-EBF infants including several bacterial methyl-accepting chemotaxis proteins (MCP) involved in signal transduction. The identified differences between EBF and non-EBF infants suggest that breast milk may provide the gut microbiome with a greater plasticity (despite having a lower phylogenetic diversity) that eases the transition into solid foods.

The role of early life nutrition in the establishment of gastrointestinal microbial composition and function

“…Many studies have reported that BF infants are colonized with higher proportions of microbes from the phylum Actinobacteria and less Firmicutes than FF infants. 23,25,26,28,33 Other studies report that BF infants have similar levels of Actinobacteria and Firmicutes 28,30 but lower proportions of Bacteroidetes 31,36 and Proteobacteria 26,28 compared to FF infants.…”

“…Several studies found bifidobacteria to be significantly greater in BF infants 18,23,26,28,33,36,37,39,47,51 ; Fan and colleagues 26 reported roughly double the relative abundance of bifidobacteria in BF than FF infants. Bifidobacteria have been shown to account for 70% of the sequences of exclusively breastfed (EBF) infants 40 and appear earlier in the feces of EBF than in FF infants 38 In addition, infants who were exclusively breastfed in early life maintained greater colonization with bifidobacteria later in infancy.…”

“…Within the phyla Bacteroidetes and Firmicutes, BF infants contain lower levels of Bacteroides, 33,50-53 Atopobium, 51,53 Clostridiales, Lachnospiraceae, and Faecalibacterium than FF. 33 Fan and colleagues 26 found that Bifidobacterium, Streptococcus, and Lactobacillus were dominant members in both feeding groups sampled between 3 and 6 mos; other dominant genera included Clostridium in BF infants and Klebsiella and Enterococcus in FF infants. Bergstrom and coworkers 45 reported a positive association between breastfeeding duration and levels of Lactobacillus spp.…”

“…26,49 The fecal microbiota of BF infants is more stable over time, 26,39 and characterized by a lower alpha-diversity compared to FF infants. 15,23,31,33 Exclusive breastfeeding is inversely related to alphadiversity in 3 mo-old infants. 23 Conversely, exclusive breastfeeding and breastfeeding duration, 23 as well as predominant breastfeeding for the first 3 mos, 25 are positively related to alpha-diversity at 12 mos.…”

“…24,45 Additional findings demonstrate that pre-weaning feeding mode remains associated with the post-weaning microbial communities. 18,33,55 For example, continued breastfeeding during the introduction of solid foods seems to support consistent levels of Lactobacillus spp. and Bifidobacterium spp.…”