Temporal development of the infant gut microbiome

Moore, Rebecca E.; Townsend, Steven D.

doi:10.1098/rsob.190128

Cited by 203 publications

(200 citation statements)

References 114 publications

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“…Conversely, in formula-fed infants, a greater abundance of Bacteroides and Clostridium spp. has been observed, this difference could have implications for the subsequent development of atopic diseases (57,58). The introduction of CF drives the gut microbiota composition favoring bacteria within the Bacteroidetes and Firmicutes phyla (58).…”

Section: Early Lifementioning

confidence: 99%

Current Insights on Early Life Nutrition and Prevention of Allergy

et al. 2020

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The incidence of allergic diseases in childhood appears to have significantly increased over the last decades. Since environmental factors, including diet, have been thought to play a significant role in the development of these diseases, there is great interest in identifying prevention strategies related to early nutritional interventions. Breastfeeding is critical for the immune development of newborns and infants through immune-modulating properties and it impacts the establishment of a healthy gut microbiota. However, the evidence for a protective role of breastfeeding against the development of food allergy in childhood is controversial, and there is little evidence to support the benefits of an antigen avoidance diet during lactation. Although it is not possible to draw a definitive conclusion about the protective role of breast milk against allergic diseases, exclusive breastfeeding is still recommended throughout the first 6 months of life due to associated health benefits. Furthermore, recommendations regarding complementary feeding in infancy have been significantly modified over the last few decades. Several studies have shown that delayed exposure to allergenic foods does not have a role in allergy prevention and recent guidelines recommend against delaying the introduction of complementary foods after 6 months of age, both in high-and low-risk infants. However, trials investigating this dietary approach have reported equivocal results so far. This review summarizes the available high-quality evidence regarding the efficacy of the principal dietary interventions proposed in early life to prevent allergic diseases in children.

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Section: Early Lifementioning

confidence: 99%

Current Insights on Early Life Nutrition and Prevention of Allergy

et al. 2020

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“…The gut is initially colonized by microaerophilic Proteobacteria and facultative anaerobic Actinobacteria, which consume oxygen and create a suitable niche for subsequent obligate anaerobes like Bacteroides, Clostridium, and Bifidobacterium spp. (3,4) Breast milk stimulates the growth of bifidabacteria, but weaning results in the emergence of Firmicutes and Bacteroidetes (5). These phyla proliferate with the introduction of solid foods and eventually come to dominate the gut microbiota (5).…”

Section: The Microbiomementioning

confidence: 99%

“…(3,4) Breast milk stimulates the growth of bifidabacteria, but weaning results in the emergence of Firmicutes and Bacteroidetes (5). These phyla proliferate with the introduction of solid foods and eventually come to dominate the gut microbiota (5). By 2.5 to 3 years of age, the infant gut microbiota structure stabilizes and resembles the adult gut microbiota, which is also dominated by Firmicutes and Bacteroidetes (3).…”

Section: The Microbiomementioning

confidence: 99%

Considering the Microbiome in Stress-Related and Neurodevelopmental Trajectories to Schizophrenia

et al. 2020

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Early life adversity and prenatal stress are consistently associated with an increased risk for schizophrenia, although the exact pathogenic mechanisms linking the exposures with the disease remain elusive. Our previous view of the HPA stress axis as an elegant but simple negative feedback loop, orchestrating adaptation to stressors among the hypothalamus, pituitary, and adrenal glands, needs to be updated. Research in the last two decades shows that important bidirectional signaling between the HPA axis and intestinal mucosa modulates brain function and neurochemistry, including effects on glucocorticoid hormones and brain-derived neurotrophic factor (BDNF). The intestinal microbiome in earliest life, which is seeded by the vaginal microbiome during delivery, programs the development of the HPA axis in a critical developmental window, determining stress sensitivity and HPA function as well as immune system development. The crosstalk between the HPA and the Microbiome Gut Brain Axis (MGBA) is particularly high in the hippocampus, the most consistently disrupted neural region in persons with schizophrenia. Animal models suggest that the MGBA remains influential on behavior and physiology across developmental stages, including the perinatal window, early childhood, adolescence, and young adulthood. Understanding the role of the microbiome on critical risk related stressors may enhance or transform of understanding of the origins of schizophrenia and offer new approaches to increase resilience against stress effects for preventing and treating schizophrenia.

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“…The majority of infants at weeks (62%) were exclusively breastfed, while that number is markedly less (35%) at 12 months, at which time infants are also consuming complimentary solid family foods. This transition in diet to solid foods have been shown to induce a change in the gut microbiome composition and diversity due to increased amounts of fiber and protein [54,55], which might favor certain microbes over others. Such changes in diet, particularly the cessation of breastmilk intake, also contributed towards the development of infant gut microbiomes towards a more "adult like" state [27,54].…”

Section: The Microbiome Is More Tightly Coupled With the Metabolome Imentioning

confidence: 99%

“…This transition in diet to solid foods have been shown to induce a change in the gut microbiome composition and diversity due to increased amounts of fiber and protein [54,55], which might favor certain microbes over others. Such changes in diet, particularly the cessation of breastmilk intake, also contributed towards the development of infant gut microbiomes towards a more "adult like" state [27,54]. We hypothesized that earlier in life when infants are only consuming a limited type of food (predominantly breast milk or formula), the microbiome participates more actively in host-microbiome co-metabolic activity as infants are more reliant on microbes to breakdown complex nutrients [56].…”

Section: The Microbiome Is More Tightly Coupled With the Metabolome Imentioning

confidence: 99%

Multi-omic Characterization of the Taxa-function Relationship in Infant Gut Microbiomes

Nguyen¹,

Madan²,

Dade³

et al. 2020

Preprint

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BackgroundThe infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationships within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life.ResultsStool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 168) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis of sample distances (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg. R2: -5.06% -- 6 weeks; -3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg. correlation: 0.344 – 6 weeks; 0.265 – 12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations. ConclusionsOur results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.

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Temporal development of the infant gut microbiome

Cited by 203 publications

References 114 publications

Current Insights on Early Life Nutrition and Prevention of Allergy

Current Insights on Early Life Nutrition and Prevention of Allergy

Considering the Microbiome in Stress-Related and Neurodevelopmental Trajectories to Schizophrenia

Multi-omic Characterization of the Taxa-function Relationship in Infant Gut Microbiomes

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