Effect of Environmental Exposures on the Gut Microbiota from Early Infancy to Two Years of Age

Postnatal nighttime light exposure and infant temperament at age 12 months: mediating role of genus Akkermansia

The gut microbiome has been reported to be associated with nighttime light (NTL) exposure and temperament. However, the specific role of infant gut microbiome plays in NTL exposure and temperament is unclear. This study investigated the potential mediating role of infants' gut microbiome in correlations between NTL exposure and temperament. Demographic information, stool samples, and temperament scores were collected from 40 infants. Temperament was evaluated using the Infants Behavior Questionnaire-Revised (IBQ-R). The gut microbiota was analyzed using 16S rRNA sequencing. Cumulative and lagged effects of NTL exposure were calculated based on residential address (NTLpoint) and a concentric 1 km radius buffer zone around the address (NTL1000m), respectively. Mediation models were utilized for assessing the mediating effects of the gut microbiome. The gut microbiome of infants with higher fear scores was characterized by a higher abundance of Akkermansia and Clostridium_sensu_stricto_1 and a lower abundance of Bacteroides. Mediation models indicated Akkermansia played a full mediating role in associations between NTLpoint, NTL1000m and fear in specific time periods. Genus Akkermansia explained 24.46% and 33.50% of associations between fear and cumulative exposure to NTLpoint and NTL1000m, respectively. This study provides evidence for the mediating role of Akkermansia between NTL exposure and fear. However, further experimental is required to elucidate the mechanisms through which the gut microbiome mediates between NTL exposure and temperament in infants.

Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema

Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk component, human milk oligosaccharides (HMOs), plays an important role as a prebiotic in establishing the infant gut microbiome and has immunomodulatory effects on the infant immune system. The purpose of this review is to summarize the available information about bacterial members of the intestinal microbiota capable of metabolizing HMOs, the bacterial genes or metabolic products present in the intestinal tract during early life, and the relationship of these genes and metabolic products to the development of AD/eczema in infants. We find that specific HMO metabolism gene sets and the metabolites produced by HMO metabolizing bacteria may enable the protective role of human milk against the development of atopy because of interactions with the immune system. We also identify areas for additional research to further elucidate the relationship between the human milk metabolizing bacteria and atopy. Detailed metagenomic studies of the infant gut microbiota and its associated metabolomes are essential for characterizing the potential impact of human milk-feeding on the development of atopic dermatitis.

Oral Prevalence of Akkermansia muciniphila Differs among Pediatric and Adult Orthodontic and Non-Orthodontic Patients

Akkermansia muciniphila (AM) is one of many highly abundant intestinal microbes that influences homeostasis and metabolic disorders and may also play a role in oral disorders. However, there is little evidence regarding the oral prevalence of this organism. Based upon this lack of evidence, the primary goal of this project is to survey an existing saliva repository to determine the overall prevalence of this organism and any associations with demographic or patient characteristics (age, sex, body mass index, race/ethnicity, orthodontic therapy). Using an approved protocol,, a total n = 141 pediatric samples from an existing saliva repository were screened using qPCR revealing 29.8% harbored AM with nearly equal distribution among males and females, p = 0.8347. Significantly higher percentages of pediatric, non-orthodontic patients were positive for AM (42.3%) compared with age-matched orthodontic patients (14.3%)-which were equally distributed among non-orthodontic males (42.1%) and non-orthodontic females (42.5%). In addition, analysis of the adult samples revealed that nearly equal percentages of males (18.2%) and females (16.7%) harbored detectable levels of salivary AM, p = 0.2035. However, a higher proportion of non-orthodontic adult samples harbored AM (21.3%) compared to orthodontic samples (12.8%, p = 0.0001), which was equally distributed among males and females. These results suggest that both age and the presence of orthodontic brackets may influence microbial composition and, more specifically, are associated with reduction in AM among both pediatric and adult populations from their baseline levels.

Associations between maternal obesity and offspring gut microbiome in the first year of life

BACKGROUND

Maternal obesity is an important determinant of offspring obesity risk, which may be mediated via changes in the infant microbiome.

OBJECTIVES

We examined infant faecal microbiome, short-chain fatty acids (SCFA), and maternal human milk oligosaccharides (HMO) in mothers with overweight/obese body mass index (BMI) (OW) compared with normal weight (NW) (Clinicaltrials.gov NCT01131117).

METHODS

Infant stool samples at 1, 6, and 12 months were analysed by 16S rRNA sequencing. Maternal (BODPOD) and infant (quantitative nuclear magnetic resonance [QMR]) adiposity were measured. HMOs at 2 months postpartum and faecal SCFAs at 1 month were also assessed. Statistical analyses included multivariable and mixed linear models for assessment of microbiome diversity, composition, and associations of taxonomic abundance with metabolic and anthropometric variables.

RESULTS

At 1 month, offspring of women with obesity had lower abundance of SCFA-producing bacteria (including Ruminococcus and Turicibacter) and lower faecal butyric acid levels. Lachnospiraceae abundance was lower in OW group at 6 months, and infant fat mass was negatively associated with the levels of Sutterella. Gradient boosting machine models indicated that higher α-diversity and specific microbial taxa at 1 month predicted elevated adiposity at 12 months with overall accuracy of 76.5%. Associations between maternal HMO concentrations and infant bacterial taxa differed between NW and OW groups.

CONCLUSIONS

Elevated maternal BMI is associated with relative depletion of butyrate-producing microbes and faecal butyrate in the early infant faecal microbiome. Overall microbial richness may aid in prediction of elevated adiposity in later infancy.

Development of the gut microbiota in healthy twins during the first 2 years of life and associations with body mass index z-score: Results from the Wuhan twin birth cohort study

The gut microbiota undergoes rapid and vital changes to microbial community structure and the microbial-immune crosstalk during the first 3 years of life, which is thought to be involved in the pathobiology of later-life disease. Compared to single-born children, little is known about the gut microbiota of twins in early childhood. Based on the Wuhan Twin Birth Cohort study, 344 stool samples from 204 twin families were analyzed to investigate the difference in gut microbiota composition at 6, 12, and 24 months of age. Furthermore, this study evaluated the association between gut microbiota development curves and body mass index z-score (BMI_Z) curves at 6, 12, and 24 months of age. The predominant microbiota phyla identified in twins were Proteobacteria, Actinobacteriota, Firmicutes, Bacteroidota, and Verrucomicrobiota. The richness and diversity of gut microbiota increased from 6 to 24 months old (alpha diversity with p < 0.05). Beta diversity revealed 61 gut microbiota genera that were significantly different in relative abundance among the three age groups. Among the 61 gut microbiota genera, 30 distinct trajectory curves (DTCs) were generated by group-based trajectory models after log2 transformation of their relative abundance. Subsequently, Spearman correlation analysis revealed that only five gut microbiota DTC were correlated with the BMI_Z DTC. Therefore, we further examined the association between the five gut microbiota genera DTC and BMI_Z DTC using generalized estimation equation models. The results revealed a significant association between the DTC groups of Parabacteroides and that of BMI_Z (coefficient = 0.75, p = 0.04). The results of this study validated the hypothesis that the richness and diversity of gut microbiota developed with age in twins. Moreover, participants with a higher DTC of log2-transformed Parabacteroides had a higher BMI_Z DTC during the first 2 years of life. Further studies are needed to confirm the association between Parabacteroides and BMI_Z in other populations.

Epidemiological Studies of Children's Gut Microbiota: Validation of Sample Collection and Storage Methods and Microbiota Analysis of Toddlers' Feces Collected from Diapers

The composition of human gut microbiota influences human health and disease over the long term. Since the flora in specimens can easily change at ambient temperature outside the body, epidemiological studies need feasible methods of stool specimen collection and storage to be established. We aimed to validate two methods: feces frozen-stored in tubes containing guanidine thiocyanate solution for two months after collection (Method B), and feces excreted in diapers and frozen-stored (Method C). Validation was by comparison with a gold standard Method A. Bacterial flora of five adults were sampled and stored by all three methods. Bacterial composition was examined by amplicon sequencing analysis. Bland-Altman analyses showed that Methods B and C might change relative abundances of certain bacterial flora. Thereafter, we analyzed the bacterial flora of 76 toddlers (two age groups) in stools sampled and processed by Method C. The diversity indices of toddlers' flora were less than those of adults. The relative abundance of some bacteria differed significantly between children aged 1.5 and 3 years. The specimen collection and storage methods validated in this study are worth adopting in large-scale epidemiological studies, especially for small children, provided the limited accuracy for some specific bacteria is understood.

Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time

Microbial time-series analysis, typically, examines the abundances of individual taxa over time and attempts to assign etiology to observed patterns. This approach assumes homogeneous groups in terms of profiles and response to external effectors. These assumptions are not always fulfilled, especially in complex natural systems, like the microbiome of the human gut. It is actually established that humans with otherwise the same demographic or dietary backgrounds can have distinct microbial profiles. We suggest an alternative approach to the analysis of microbial time-series, based on the following premises: 1) microbial communities are organized in distinct clusters of similar composition at any time point, 2) these intrinsic subsets of communities could have different responses to the same external effects, and 3) the fate of the communities is largely deterministic given the same external conditions. Therefore, tracking the transition of communities, rather than individual taxa, across these states, can enhance our understanding of the ecological processes and allow the prediction of future states, by incorporating applied effects. We implement these ideas into Cronos, an analytical pipeline written in R. Cronos’ inputs are a microbial composition table (e.g., OTU table), their phylogenetic relations as a tree, and the associated metadata. Cronos detects the intrinsic microbial profile clusters on all time points, describes them in terms of composition, and records the transitions between them. Cluster assignments, combined with the provided metadata, are used to model the transitions and predict samples’ fate under various effects. We applied Cronos to available data from growing infants’ gut microbiomes, and we observe two distinct trajectories corresponding to breastfed and formula-fed infants that eventually converge to profiles resembling those of mature individuals. Cronos is freely available at https://github.com/Lagkouvardos/Cronos.

Identifying single-strain growth patterns of human gut microbes in response to preterm human milk and formula

The intestinal microbiota of the preterm neonate has become a major research focus, with evidence emerging that the microbiota influences both short and long-term health outcomes, in the neonatal intensive care unit and beyond. Similar to the term microbiome, the preterm gut microbiome is highly influenced by diet, specifically formula and human milk use. This study aims to analyze next-generation products including preterm formula, human milk-oligosaccharide term formula, and preterm breastmilk. We used a culture-based model to differentially compare the growth patterns of individual bacterial strains found in the human intestine. This model probed 24 strains of commensal bacteria and 8 pathobiont species which have previously been found to cause sepsis in preterm neonates. Remarkable differences between strain growth and culture pH were noted after comparing models of formulas and between human milk and formula. Both formula and human milk supported the growth of commensal bacteria; however, the formula products, but not human milk, supported the growth of several specific pathogenic strains. Computational analysis revealed potential connections between long-chain fatty acid and iron uptake from formula in pathobiont organisms. These findings indicate that there is a unique profile of growth in response to human milk and formula and shed light into how the infant gut microbiota could be influenced.

Gut microbiome development and childhood undernutrition

Forty-five percent of deaths among children under 5 years of age are associated with undernutrition. Globally, almost 200 million children exhibit the two major forms of undernutrition-wasting (low weight-for-height) or stunting (low height-for-age), with many affected by both. Undernutrition is not due to food insecurity alone. Growing evidence indicates that perturbed postnatal gut microbiome development contributes to its pathogenesis. This perspective focuses on defining and repairing these defects in gut microbiome development. We describe an approach that involves the analysis of well-phenotyped human cohorts, followed by preclinical studies using gnotobiotic animals colonized with microbiota from these cohorts. Additionally, these models can be used to identify therapeutic targets and candidates that can then be tested clinically. Furthermore, introducing pretreatment microbiota from trial participants into gnotobiotic animals and re-enacting trial conditions allow mechanisms to be dissected. We highlight these recent advances as well as gaps in existing knowledge that present opportunities for future research.

The Developing Microbiome From Birth to 3 Years: The Gut-Brain Axis and Neurodevelopmental Outcomes

The volume and breadth of research on the role of the microbiome in neurodevelopmental and neuropsychiatric disorders has expanded greatly over the last decade, opening doors to new models of mechanisms of the gut-brain axis and therapeutic interventions to reduce the burden of these outcomes. Studies have highlighted the window of birth to 3 years as an especially sensitive window when interventions may be the most effective. Harnessing the powerful gut-brain axis during this critical developmental window clarifies important investigations into the microbe-human connection and the developing brain, affording opportunities to prevent rather than treat neurodevelopmental disorders and neuropsychiatric illness. In this review, we present an overview of the developing intestinal microbiome in the critical window of birth to age 3; and its prospective relationship with neurodevelopment, with particular emphasis on immunological mechanisms. Next, the role of the microbiome in neurobehavioral outcomes (such as autism, anxiety, and attention-deficit hyperactivity disorder) as well as cognitive development are described. In these sections, we highlight the importance of pairing mechanistic studies in murine models with large scale epidemiological studies that aim to clarify the typical health promoting microbiome in early life across varied populations in comparison to dysbiosis. The microbiome is an important focus in human studies because it is so readily alterable with simple interventions, and we briefly outline what is known about microbiome targeted interventions in neurodevelopmental outcomes. More novel examinations of known environmental chemicals that adversely impact neurodevelopmental outcomes and the potential role of the microbiome as a mediator or modifier are discussed. Finally, we look to the future and emphasize the need for additional research to identify populations that are sensitive to alterations in their gut microbiome and clarify how interventions might correct and optimize neurodevelopmental outcomes.