A digital twin of the infant microbiome to predict neurodevelopmental deficits.

Despite the recognized gut-brain axis link, natural variations in microbial profiles between patients hinder definition of normal abundance ranges, confounding the impact of dysbiosis on infant neurodevelopment. We infer a digital twin of the infant microbiome, forecasting ecosystem trajectories from a few initial observations. Using 16S ribosomal RNA profiles from 88 preterm infants (398 fecal samples and 32,942 abundance estimates for 91 microbial classes), the model (Q-net) predicts abundance dynamics with R2 = 0.69. Contrasting the fit to Q-nets of typical versus suboptimal development, we can reliably estimate individual deficit risk (Mδ) and identify infants achieving poor future head circumference growth with ≈76% area under the receiver operator characteristic curve, 95% ± 1.8% positive predictive value at 98% specificity at 30 weeks postmenstrual age. We find that early transplantation might mitigate risk for ≈45.2% of the cohort, with potentially negative effects from incorrect supplementation. Q-nets are generative artificial intelligence models for ecosystem dynamics, with broad potential applications.

Microbiome function and neurodevelopment in Black infants: vitamin B12 emerges as a key factor.

The early life gut microbiome affects the developing brain, and therefore may serve as a target to support neurodevelopment of children living in stressful and under-resourced environments, such as Black youth living on the South Side of Chicago, for whom we observe racial disparities in health. Microbiome compositions/functions key to multiple neurodevelopmental facets have not been studied in Black children, a vulnerable population due to racial disparities in health; thus, a subsample of Black infants living in urban, low-income neighborhoods whose mothers participated in a prenatal nutrition study were recruited for testing associations between composition and function of the gut microbiome (16S rRNA gene sequencing, shotgun metagenomics, and targeted metabolomics of fecal samples) and neurodevelopment (developmental testing, maternal report of temperament, and observed stress regulation). Two microbiome community types, defined by high Lachnospiraceae or Enterobacteriaceae abundance, were discovered in this cohort from 16S rRNA gene sequencing analysis; the Enterobacteriaceae-dominant community type was significantly negatively associated with cognition and language scores, specifically in male children. Vitamin B12 biosynthesis emerged as a key microbiome function from shotgun metagenomics sequencing analysis, showing positive associations with all measured developmental skills (i.e., cognition, language, motor, surgency, effortful control, and observed stress regulation). Blautia spp. also were identified as substantial contributors of important microbiome functions, including vitamin B12 biosynthesis and related vitamin B12-dependent microbiome functions, anti-inflammatory microbial surface antigens, competitive mechanisms against pathobionts, and production of antioxidants. The results are promising with respect to the potential for exploring therapeutic candidates, such as vitamin B12 nutritional or Blautia spp. probiotic supplementation, to support the neurodevelopment of infants at risk for experiencing racial disparities in health.

Microbiota from Preterm Infants Who Develop Necrotizing Enterocolitis Drives the Neurodevelopment Impairment in a Humanized Mouse Model.

Necrotizing enterocolitis (NEC) is the leading basis for gastrointestinal morbidity and poses a significant risk for neurodevelopmental impairment (NDI) in preterm infants. Aberrant bacterial colonization preceding NEC contributes to the pathogenesis of NEC, and we have demonstrated that immature microbiota in preterm infants negatively impacts neurodevelopment and neurological outcomes. In this study, we tested the hypothesis that microbial communities before the onset of NEC drive NDI. Using our humanized gnotobiotic model in which human infant microbial samples were gavaged to pregnant germ-free C57BL/6J dams, we compared the effects of the microbiota from preterm infants who went on to develop NEC (MNEC) to the microbiota from healthy term infants (MTERM) on brain development and neurological outcomes in offspring mice. Immunohistochemical studies demonstrated that MNEC mice had significantly decreased occludin and ZO-1 expression compared to MTERM mice and increased ileal inflammation marked by the increased nuclear phospho-p65 of NFκB expression, revealing that microbial communities from patients who developed NEC had a negative effect on ileal barrier development and homeostasis. In open field and elevated plus maze tests, MNEC mice had worse mobility and were more anxious than MTERM mice. In cued fear conditioning tests, MNEC mice had worse contextual memory than MTERM mice. MRI revealed that MNEC mice had decreased myelination in major white and grey matter structures and lower fractional anisotropy values in white matter areas, demonstrating delayed brain maturation and organization. MNEC also altered the metabolic profiles, especially carnitine, phosphocholine, and bile acid analogs in the brain. Our data demonstrated numerous significant differences in gut maturity, brain metabolic profiles, brain maturation and organization, and behaviors between MTERM and MNEC mice. Our study suggests that the microbiome before the onset of NEC has negative impacts on brain development and neurological outcomes and can be a prospective target to improve long-term developmental outcomes.

The Impact of Maternal Probiotics on Intestinal Vitamin D Receptor Expression in Early Life.

Vitamin D signaling via the Vitamin D Receptor (VDR) has been shown to protect against intestinal inflammation. Previous studies have also reported the mutual interactions of intestinal VDR and the microbiome, indicating a potential role of probiotics in modulating VDR expression. In preterm infants, although probiotics have been shown to reduce the incidence of necrotizing enterocolitis (NEC), they are not currently recommended by the FDA due to potential risks in this population. No previous studies have delved into the effect of maternally administered probiotics on intestinal VDR expression in early life. Using an infancy mouse model, we found that young mice exposed to maternally administered probiotics (SPF/LB) maintained higher colonic VDR expression than our unexposed mice (SPF) in the face of a systemic inflammatory stimulus. These findings indicate a potential role for microbiome-modulating therapies in preventing diseases such as NEC through the enhancement of VDR signaling.

Gut Microbiome-Brain Axis as an Explanation for the Risk of Poor Neurodevelopment Outcome in Preterm Infants with Necrotizing Enterocolitis.

Necrotizing Enterocolitis (NEC) is characterized by an inflammation of intestinal tissue that primarily affects premature infants. It is the most common and devastating gastrointestinal morbidity of prematurity, but beyond intestinal morbidity, this condition has also been associated with an increased risk of neurodevelopmental delays that persist beyond infancy. Prematurity, enteral feeding, bacterial colonization, and prolonged exposure to antibiotics are all risk factors that predispose preterm infants to NEC. Interestingly, these factors are all also associated with the gut microbiome. However, whether or not there is a connection between the microbiome and the risk of neurodevelopmental delays in infants after NEC is still an emerging area of research. Furthermore, how microbes in the gut could impact a distant organ such as the brain is also poorly understood. In this review, we discuss the current understanding of NEC and the role of the gut microbiome-brain axis in neurodevelopmental outcomes after NEC. Understanding the potential role of the microbiome in neurodevelopmental outcomes is important as the microbiome is modifiable and thus offers the hope of improved therapeutic options. We highlight the progress and limitations in this field. Insights into the gut microbiome-brain axis may offer potential therapeutic approaches to improve the long-term outcomes of premature infants.

Limosilactobacillus reuteri normalizes blood-brain barrier dysfunction and neurodevelopment deficits associated with prenatal exposure to lipopolysaccharide.

Maternal immune activation (MIA) derived from late gestational infection such as seen in chorioamnionitis poses a significantly increased risk for neurodevelopmental deficits in the offspring. Manipulating early microbiota through maternal probiotic supplementation has been shown to be an effective means to improve outcomes; however, the mechanisms remain unclear. In this study, we demonstrated that MIA modeled by exposing pregnant dams to lipopolysaccharide (LPS) induced an underdevelopment of the blood vessels, an increase in permeability and astrogliosis of the blood-brain barrier (BBB) at prewean age. The BBB developmental and functional deficits early in life impaired spatial learning later in life. Maternal Limosilactobacillus reuteri (L. reuteri) supplementation starting at birth rescued the BBB underdevelopment and dysfunction-associated cognitive function. Maternal L. reuteri-mediated alterations in ß-diversity of the microbial community and metabolic responses in the offspring provide mechanisms and potential targets for promoting BBB integrity and long-term neurodevelopmental outcomes.

A randomized controlled trial of oropharyngeal therapy with mother's own milk for premature infants.

OBJECTIVE: To determine if oropharyngeal therapy with mother's own milk (OPT-MOM) reduces late-onset sepsis (L-OS; primary outcome), NEC, death, length of stay, time to full enteral nutrition (FEN) and full oral feeds in preterm infants (BW < 1250 g). DESIGN: Infants (N = 220) were randomized to Group A (milk) or B (placebo) and received 0.2 mL every 2 h for 48 h, then every 3 h until 32 weeks CGA. RESULTS: There were no significant differences in L-OS, NEC or death. Group A trended towards an 8-day reduction in stay, 8-day reduction in time to FEN and a 6-day reduction in time to full oral feeds, compared to B. While clinically relevant, due to large variability in outcomes and lack of power, p values were > 0.05. CONCLUSION: OPT-MOM did not reduce L-OS, NEC or death. Group A trended towards a reduced stay and better nutritional outcomes, but results were not statistically significant. CLINICALTRIALS: GOV: NCT02116699.

Neurodevelopmental outcome of infants who develop necrotizing enterocolitis: The gut-brain axis.

Necrotizing enterocolitis (NEC) poses a significant risk for neurodevelopmental impairment in extremely preterm infants. The gut microbiota shapes the development of the gut, immune system, and the brain; and dysbiosis drive neonatal morbidities including NEC. In this chapter, we delineate a gut-brain axis linking gut microbiota to the adverse neurological outcomes in NEC patients. We propose that in NEC, immaturity of the microbiome along with aberrant gut microbiota-driven immaturity of the gut barrier and immune system can lead to effects including systemic inflammation and circulating microbial mediators. This nexus of gut microbiota-driven systemic effects further interacts with a likewise underdeveloped blood-brain barrier to regulate neuroinflammation and neurodevelopment. Targeting deviant gut-brain axis signaling presents an opportunity to improve the neurodevelopmental outcomes of NEC patients.

Early preterm infant microbiome impacts adult learning.

Interventions to mitigate long-term neurodevelopmental deficits such as memory and learning impairment in preterm infants are warranted. Manipulation of the gut microbiome affects host behaviors. In this study we determined whether early maturation of the infant microbiome is associated with neurodevelopment outcomes. Germ free mice colonized at birth with human preterm infant microbiomes from infants of advancing post menstrual age (PMA) demonstrated an increase in bacterial diversity and a shift in dominance of taxa mimicking the human preterm microbiome development pattern. These characteristics along with changes in a number of metabolites as the microbiome matured influenced associative learning and memory but not locomotor ability, anxiety-like behaviors, or social interaction in adult mice. As a regulator of learning and memory, brain glial cell-derived neurotrophic factor increased with advancing PMA and was also associated with better performance in associative learning and memory in adult mice. We conclude that maturation of the microbiome in early life of preterm infants primes adult associative memory and learning ability. Our findings suggest a critical window of early intervention to affect maturation of the preterm infant microbiome and ultimately improve neurodevelopmental outcomes.

The Role of Childhood Asthma in Obesity Development: A Nationwide US Multicohort Study.

RATIONALE: Asthma and obesity often co-occur. It has been hypothesized that asthma may contribute to childhood obesity onset. OBJECTIVES: To determine if childhood asthma is associated with incident obesity and examine the role of asthma medication in this association. METHODS: We studied 8,716 children between ages 6 and 18.5 years who were nonobese at study entry participating in 18 US cohorts of the Environmental influences on Child Health Outcomes program (among 7,299 children with complete covariate data mean [SD] study entry age = 7.2 [1.6] years and follow up = 5.3 [3.1] years). MEASUREMENTS AND MAIN RESULTS: We defined asthma based on caregiver report of provider diagnosis. Incident obesity was defined as the first documented body mass index ≥95th percentile for age and sex following asthma status ascertainment. Over the study period, 26% of children had an asthma diagnosis and 11% developed obesity. Cox proportional hazards models with sex-specific baseline hazards were fitted to assess the association of asthma diagnosis with obesity incidence. Children with asthma had a 23% (95% confidence intervals [CI] = 4, 44) higher risk for subsequently developing obesity compared with those without asthma. A novel mediation analysis was also conducted to decompose the total asthma effect on obesity into pathways mediated and not mediated by asthma medication use. Use of asthma medication attenuated the total estimated effect of asthma on obesity by 64% (excess hazard ratios = 0.64; 95% CI = -1.05, -0.23). CONCLUSIONS: This nationwide study supports the hypothesis that childhood asthma is associated with later risk of obesity. Asthma medication may reduce this association and merits further investigation as a potential strategy for obesity prevention among children with asthma.

Bacteroidota and Lachnospiraceae integration into the gut microbiome at key time points in early life are linked to infant neurodevelopment.

The early life microbiome plays critical roles in host development, shaping long-term outcomes including brain functioning. It is not known which initial infant colonizers elicit optimal neurodevelopment; thus, this study investigated the association between gut microbiome succession from the first week of life and head circumference growth (HCG), the earliest validated marker for neurodevelopment. Fecal samples were collected weekly from a preterm infant cohort during their neonatal intensive care unit stay and subjected to 16S rRNA gene sequencing for evaluating gut microbiome composition, in conjunction with clinical data and head circumference measurements. Preterm infants with suboptimal HCG trajectories had a depletion in the abundance/prevalence of Bacteroidota and Lachnospiraceae, independent of morbidity and caloric restriction. The severity of gut microbiome depletion matched the timing of significant HCG pattern separation between study groups at 30-week postmenstrual age demonstrating a potential mediating relationship resultant from clinical practices. Consideration of the clinical variables indicated that optimal infant microbiome succession is primarily driven by dispersal limitation (i.e., delivery mode) and secondarily by habitat filtering (i.e., antibiotics and enteral feeding). Bacteroidota and Lachnospiraceae are known core taxa of the adult microbiome, with roles in dietary glycan foraging, beneficial metabolite production and immunity, and our work provides evidence that their integration into the gut microbiome needs to occur early for optimal neurodevelopment.

The microbiome, guard or threat to infant health.

Despite improvements in survival for very low birthweight (VLBW) premature infants, there continues to be significant morbidity for these infants at remarkable cost to the healthcare system. Concurrent development of the preterm infant intestine alongside the gut microbiome in the clinical setting rather than in the protected in utero environment where it would usually occur creates significant vulnerabilities for the infant's immature intestine and immune system, resulting in devastating illness and neurological injury. However, the microbiome also has the capacity to promote healthy development. Studies of parallel gut microbiome and preterm infant development have given key insight into the impact of the microbiome on intestinal as well as neural development and may provide potential therapeutic targets to prevent preterm infant morbidities.

Epigenome - A mediator for host-microbiome crosstalk.

The interaction between the gut and its eventual trillions of microbe inhabitants during microbial colonization, represents a critical time period for establishing the overall health and wellbeing of an individual. The gut microbiome represents a diverse community of microbes that are critical for many physiological roles of the host including host metabolism. These processes are controlled by a fine-tuned chemical cross talk between the host and microbiota. Although the exact mechanisms behind this cross talk remains elusive, microbiota induced epigenetic mechanisms like DNA methylation and histone modifications may be key. This review presents our perspective on the epigenome as a mediator for host-microbiota cross talk, as well as methodology to study epigenetics, the role of dysbiosis in disease, and how the gut microbiome-host axis may be used in personal medicine.

The human gut microbiome and health inequities.

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host-gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

Necrotizing enterocolitis intestinal barrier function protection by antenatal dexamethasone and surfactant-D in a rat model.

BACKGROUND: Necrotizing enterocolitis (NEC) is the most common gastrointestinal disorder in premature neonates. Possible therapeutic approaches are centered on promoting maturation of the gastrointestinal mucosal barrier. Studies have demonstrated that antenatal administration of corticosteroids can decrease NEC incidence and mortality. METHODS: Pregnant rat dams were administered dexamethasone 48 h prior to delivery. The pups were subjected to an experimental NEC-like injury protocol. Ileal tissues and sera were collected and evaluated for inflammatory cytokines, gut permeability and expressions and localizations of tight junction proteins, and surfactant protein-D by immunohistochemistry/immunofluorescent staining. Intestinal epithelial cells (IEC-6) were pretreated with SP-D to examine the effect of SP-D on tight junction protein expressions when challenged with platelet-activating factor and lipopolysaccharide to model proinflammatory insults. RESULTS: Antenatal dexamethasone reduced systemic inflammation, preserved intestinal barrier integrity, and stimulated SP-D expression on the intestinal mucosal surface in pups exposed to NEC-like injury. Pretreatment of SP-D blocked platelet-activating factor/lipopolysaccharide-induced tight junction disruption in IEC-6 cells in vitro. CONCLUSIONS: Antenatal dexamethasone preserves the development of intestinal mucosal barrier integrity and reduces incidence and morbidity from an experimental NEC-like injury model. Dexamethasone upregulation of intestinal SP-D-protective effects on tight junction proteins. IMPACT: Antenatal administration of dexamethasone can function in concert with intestinal surfactant protein-D to decrease systemic inflammatory responses, and protect intestinal barrier integrity in a neonatal rat model of NEC. A novel role of intestinal SP-D in preserving tight junction protein structures under inflammatory conditions. We describe the intestinal SP-D-an overlooked role of antenatal dexamethasone in neonatal NEC?

Childhood Development and the Microbiome-The Intestinal Microbiota in Maintenance of Health and Development of Disease During Childhood Development.

The composition of the intestinal microbiome affects health from the prenatal period throughout childhood, and many diseases have been associated with dysbiosis. The gut microbiome is constantly changing, from birth throughout adulthood, and several variables affect its development and content. Features of the intestinal microbiota can affect development of the brain, immune system, and lungs, as well as body growth. We review the development of the gut microbiome, proponents of dysbiosis, and interactions of the microbiota with other organs. The gut microbiome should be thought of as an organ system that has important effects on childhood development. Dysbiosis has been associated with diseases in children and adults, including autism, attention deficit hyperactivity disorder, asthma, and allergies.

The early gut microbiome could protect against severe retinopathy of prematurity.

In this study, 6 infants with type 1 retinopathy of prematurity (ROP) were compared with 4 high-risk preterm neonates without any ROP but similar baseline neonatal comorbidities. The infants with type-1 ROP showed significant enrichment of Enterobacteriaceae at 28 weeks' postmenstrual age. Several metabolic pathways, including several amino acid metabolism pathways, were enriched in gut microbiota of infants without ROP. Based on these findings, we posit a possible association between early gut microbiome profile and ROP pathogenesis. Furthermore, it is possible that absence of Enterobacteriaceae overabundance, in addition to enrichment of amino acid biosynthesis pathways, may protect against severe ROP in high-risk preterm infants.