Associations between stool micro-transcriptome, gut microbiota, and infant growth

Abstract

Rapid infant growth increases the risk for adult obesity. The gut microbiome is associated with early weight status; however, no study has examined how interactions between microbial and host ribonucleic acid (RNA) expression influence infant growth. We hypothesized that dynamics in infant stool micro-ribonucleic acids (miRNAs) would be associated with both microbial activity and infant growth via putative metabolic targets. Stool was collected twice from 30 full-term infants, at 1 month and again between 6 and 12 months. Stool RNA were measured with high-throughput sequencing and aligned to human and microbial databases. Infant growth was measured by weight-for-length z-score at birth and 12 months. Increased RNA transcriptional activity of Clostridia (R = 0.55; Adj p = 3.7E-2) and Burkholderia (R = −0.820, Adj p = 2.62E-3) were associated with infant growth. Of the 25 human RNAs associated with growth, 16 were miRNAs. The miRNAs demonstrated significant target enrichment (Adj p < 0.05) for four metabolic pathways. There were four associations between growth-related miRNAs and growth-related phyla. We have shown that longitudinal trends in gut microbiota activity and human miRNA levels are associated with infant growth and the metabolic targets of miRNAs suggest these molecules may regulate the biosynthetic landscape of the gut and influence microbial activity.

Maternal-Child Microbiome and Impact on Growth and Neurodevelopment in Infants and Children: A Scoping Review

“…Stunting was correlated negatively and positively with Bifidobacterium longum by Dinh et al (2016) and Mirzaei et al (2020), respectively. Carney et al (2021) found an association between rapid growth in infants and abundance of Clostridium spp., Alistipes spp. and Actinomyces spp.…”

“…In a study comparing healthy infants who were fed breast milk or formula, an earlier maturity of gut microbiome and increased weight gain was reported in the breast milk fed infants compared to formula fed (Lei et al, 2021). Two studies (Aldrete et al, 2021; Carney et al, 2021) examined the trajectory of growth and incidence of obesity (rapid infant growth) and the microbiome of the gut. Alderete et al reported higher alpha diversity and differences in relative abundances of bacterial taxa in rapidly growing infants compared to typical growing infants.…”

Critical Steps for Human Gut Exfoliome RNA Profiling Analysis Using Non-Invasive Stool Samples

“…In addition, by this methodology, it was described that children’s gastrointestinal tract functionality is influenced by different factors that may affect the gut transcriptome, as could the nutrition by the kind of milk or their origin, by the modulation of the intestinal microbiota [10] or the mucosal immune system [13] and also by the induction of maturation of gene-specific methylation, thereby permanently altering the expression of developmental genes in the intestine [4, 6]. Recently, the relationship between infant growth, microbial, and host RNA expression has been studied from infant stool samples by RNA sequencing; that study identified several human RNAs and microbes associated with accelerated growth, and the principal pathways involved were related to biosynthesis/metabolism or degradation/digestion [27]. Therefore, microarrays analysis was suitable for evaluating and detecting differences of the gut transcriptome, but larger studies should be carried out to confirm these associations.…”

Polysaccharide Extracts Derived from Defloration Waste of Fruit Pitaya Regulates Gut Microbiota in a Mice Model

“…The miRNAs regulate the gut microbes and human transcriptome, and miRNAs in the gut mainly affect cell metabolism, not immune function [36]. Gut microbiota is highly correlated with host metabolism.…”