Distinct gut microbiota and metabolite profiles induced by delivery mode in healthy Chinese infants

CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data

MOTIVATION

Numerous microbiome studies have revealed significant associations between the microbiome and human health and disease. These findings have motivated researchers to explore the causal role of the microbiome in human complex traits and diseases. However, the complexities of microbiome data pose challenges for statistical analysis and interpretation of causal effects.

RESULTS

We introduced a novel statistical framework, CRAmed, for inferring the mediating role of the microbiome between treatment and outcome. CRAmed improved the interpretability of the mediation analysis by decomposing the natural indirect effect into two parts, corresponding to the presence-absence and abundance of a microbe, respectively. Comprehensive simulations demonstrated the superior performance of CRAmed in Recall, precision, and F1 score, with a notable level of robustness, compared to existing mediation analysis methods. Furthermore, two real data applications illustrated the effectiveness and interpretability of CRAmed. Our research revealed that CRAmed holds promise for uncovering the mediating role of the microbiome and understanding of the factors influencing host health.

AVAILABILITY AND IMPLEMENTATION

The R package CRAmed implementing the proposed methods is available online at https://github.com/liudoubletian/CRAmed.

Fecal Microbiome and Metabolomic Profiles of Mixed-Fed Infants Are More Similar to Formula-Fed than Breastfed Infants

Many infants consume both human milk and infant formula (mixed-fed); however, few studies have investigated how mixed feeding affects the gut microbiome composition and metabolic profiles compared to exclusive breastfeeding or formula feeding. Herein, how delivery mode and early nutrition affect the microbiome and metabolome of 6-week-old infants in the STRONG Kids2 cohort was investigated. Fecal samples were collected from exclusively breastfed (BF; n = 25), formula-fed (FF; n = 25) or mixed-fed (MF; n = 25) participants. Within each feeding group, infants were either delivered vaginally (VD; n = 13) or by Cesarean section (CS; n = 12). Feeding mode affects the fecal microbiome diversity, composition, and functional potential, as well as metabolomic profiles regardless of delivery mode. Alpha and beta diversity of MF differed from that of BF (p < 0.05) but were comparable to FF infants. Functional analyses have shown 117 potential metabolic pathways differed between BF and FF, 112 between BF and MF, and 8 between MF and FF infants (p < 0.05, q < 0.10). Fecal metabolomic profiles of MF and FF clustered together and separated from BF infants. In total, 543 metabolites differed between BF and FF, 517 between BF and MF, and 3 between MF and FF (p < 0.05, q < 0.10). Delivery mode affected overall microbial composition (p = 0.022) at the genus level and 24 potential functional pathways, with 16 pathways being higher in VD than CS infants (p < 0.05, q < 0.10). Metabolomic analysis identified 47 differential metabolites between CS and VD, with 39 being lower in CS than VD (p < 0.05, q < 0.10). In summary, fecal microbiota composition and function and metabolite profiles of 6-week-old MF infants are closer to FF than BF infants.

Impact of complementary feeding on infant gut microbiome, metabolites and early development

Introducing complementary foods is critical for promoting infant health and development. During the weaning period, the dietary patterns provide essential nutrients and facilitate the development of a diverse gut microbiome, which plays significant roles in the regulation of immune, metabolic, and neurological functions. This study enrolled 200 families to assess the impact of complementary feeding on infant growth and health outcomes. Data included detailed records of feeding practices, infant growth measurements, health assessments, and fecal samples and breast milk collected between weeks 12 and 32 postpartum. The gut microbiome was analyzed using 16S rRNA sequencing, while metabolites such as human milk oligosaccharides (HMOs), monosaccharides, and short-chain fatty acids (SCFAs) were measured using chromatography-mass spectrometry. Results revealed a high prevalence of breastfeeding, with complementary food introduced at around 16 weeks. Significant alterations in the infant gut microbiome were observed, particularly in the genera Lactobacillus, Akkermansia, and Staphylococcus. Additionally, the levels of HMOs, monosaccharides, and SCFAs were found to be influenced by the introduction of complementary foods. Significant correlations emerged between complementary feeding practices, gut microbiome diversity, specific bacterial genera (e.g., Streptococcus, Lactobacillus, Bifidobacterium, and Clostridioides), and key metabolites (such as lacto-N-tetraose, lacto-N-neotetraose, mannose, and butyric acid). This study offers valuable insights into the complex interactions between complementary feeding, gut microbiome development, and metabolite profiles during early infant growth. Future research with larger cohorts and targeted dietary interventions is recommended to further elucidate the underlying mechanisms.

Effect of different delivery modes on intestinal microbiota and immune function of neonates

Different delivery methods can cause variations in the composition and structure of intestinal microbiota in neonates. However, the impact of the microecological environment on host immune function requires further investigation. In this study, 75 healthy neonates were divided into two groups: vaginal delivery group (n = 36) and cesarean section group (n = 39). Fecal and peripheral blood samples were collected from the 7th to the 10th day. 16S rRNA sequencing technique was performed to investigate the gut microbiota on fecal samples. Levels of immunoglobulins and Th1 and Th2 cells in the peripheral blood of neonates were measured. The abundance of Escherichia, Bifidobacterium, and Bacteroides in neonates in the cesarean section group was significantly lower than that in the vaginal delivery group. Metabolic pathway analysis showed three significantly up-regulated metabolic pathways in the intestinal microbiota of neonates in the cesarean section group. The levels of serum IgG and IL-12p70 in the cesarean section group were lower than those in the vaginal delivery group, and the proportion of IFN-γ/IL-4 was significantly lower in the cesarean section group compared to the vaginal delivery group. The mode of delivery has potential impact on the intestinal microbiota and immune functions of neonates, potentially leading to an imbalance of Th1/Th2 cells in neonates delivered by cesarean section.

Dynamic impact of delivery modes on gut microbiota in preterm infants hospitalized during the initial 4 weeks of life

Preterm infants face a high risk of various complications, and their gut microbiota plays a pivotal role in health. Delivery modes have been reported to affect the development of gut microbiota in term infants, but its impact on preterm infants remains unclear. Here, we collected fecal samples from 30 preterm infants at five-time points within the first four weeks of life. Employing 16 S rRNA sequencing, principal coordinates analysis, the analysis of similarities, and the Wilcoxon rank-sum test, we examined the top dominant phyla and genera, the temporal changes in specific taxa abundance, and their relationship with delivery modes, such as Escherichia-Shigella and Enterococcus based on vaginal delivery and Pluralibacter related to cesarean section. Moreover, we identified particular bacteria, such as Taonella, Patulibacter, and others, whose proportions fluctuated among preterm infants born via different delivery modes at varying time points, as well as the microbiota types and functions. These results indicated the influence of delivery mode on the composition and function of the preterm infant gut microbiota. Importantly, these effects are time-dependent during the early stages of life. These insights shed light on the pivotal role of delivery mode in shaping the gut microbiota of preterm infants and have significant clinical implications for their care and management.

Bifidobacterium longum K5 Prevents Enterohaemorrhagic Escherichia coli O157:H7 Infection in Mice through the Modulation of the Gut Microbiota

Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is a commonly encountered foodborne pathogen that can cause hemorrhagic enteritis and lead to hemolytic uremic syndrome (HUS) in severe cases. Bifidobacterium is a beneficial bacterium that naturally exists in the human gut and plays a vital role in maintaining a healthy balance in the gut microbiota. This study investigated the protective effects of B. longum K5 in a mouse model of EHEC O157:H7 infection. The results indicated that pretreatment with B. longum K5 mitigated the clinical symptoms of EHEC O157:H7 infection and attenuated the increase in myeloperoxidase (MPO) activity in the colon of the mice. In comparison to the model group, elevated serum D-lactic acid concentrations and diamine oxidase (DAO) levels were prevented in the K5-EHEC group of mice. The reduced mRNA expression of tight junction proteins (ZO-1, Occludin, and Claudin-1) and mucin MUC2, as well as the elevated expression of virulence factors Stx1A and Stx2A, was alleviated in the colon of both the K5-PBS and K5-EHEC groups. Additionally, the increase in the inflammatory cytokine levels of TNF-α and IL-1β was inhibited and the production of IL-4 and IL-10 was promoted in the K5-EHEC group compared with the model group. B. longum K5 significantly prevented the reduction in the abundance and diversity of mouse gut microorganisms induced by EHEC O157:H7 infection, including blocking the decrease in the relative abundance of Roseburia, Lactobacillus, and Oscillibacter. Meanwhile, the intervention with B. longum K5 promoted the production of acetic acid and butyric acid in the gut. This study provides insights into the use of B. longum K5 for developing probiotic formulations to prevent intestinal diseases caused by pathogenic bacterial infections.

Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China

Introduction

Children have regional dynamics in the gut microbiota development trajectory. Hitherto, the features and influencing factors of the gut microbiota and fecal and plasma metabolites in children from Northwest China remain unclear.

Methods

Shotgun metagenomic sequencing and untargeted metabolomics were performed on 100 healthy volunteers aged 2-12 years.

Results

Age, body mass index (BMI), regular physical exercise (RPE), and delivery mode (DM) significantly affect gut microbiota and metabolites. Lactobacillus, Butyricimonas, Prevotella, Alistipes, and predicted pathway propanoate production were significantly increased with age while Bifidobacterium breve, B. animalis, B. pseudocatenulatum, Streptococcus infantis, and carbohydrate degradation were decreased. Fecal metabolome revealed that the metabolism of caffeine, amino acids, and lipid significantly increased with age while galactose metabolism decreased. Noticeably, BMI was positively associated with pathogens including Erysipelatoclostridium ramosum, Parabacteroides distasonis, Ruminococcus gnavus, and amino acid metabolism but negatively associated with beneficial Akkermansia muciniphila, Alistipes finegoldii, Eubacterium ramulus, and caffeine metabolism. RPE has increased probiotic Faecalibacterium prausnitzii and Anaerostipes hadrus, acetate and lactate production, and major nutrient metabolism in gut and plasma, but decreased pathobiont Bilophila wadsworthia, taurine degradation, and pentose phosphate pathway. Interestingly, DM affects the gut microbiota and metabolites throughout the whole childhood. Bifidobacterium animalis, Lactobacillus mucosae, L. ruminis, primary bile acid, and neomycin biosynthesis were enriched in eutocia, while anti-inflammatory Anaerofustis stercorihominis, Agathobaculum butyriciproducens, Collinsella intestinalis, and pathogenic Streptococcus salivarius, Catabacter hongkongensis, and amino acid metabolism were enriched in Cesarean section children.

Discussion

Our results provided theoretical and data foundation for the gut microbiota and metabolites in preadolescent children's growth and development in Northwest China.

Human milk oligosaccharides combine with Bifidobacterium longum to form the "golden shield" of the infant intestine: metabolic strategies, health effects, and mechanisms of action

Human milk oligosaccharides (HMOs) are the third most important nutrient in human milk and are the gold standard for infant nutrition. Due to the lack of an enzyme system capable of utilizing HMOs in the infant intestine, HMOs cannot be directly utilized. Instead, they function as natural prebiotics, participating in the establishment of the intestinal microbiota as a "bifidus factor." A crucial colonizer of the early intestine is Bifidobacterium longum (B. longum), particularly its subspecies B. longum subsp. infantis, which is the most active consumer of HMOs. However, due to the structural diversity of HMOs and the specificity of B. longum strains, studies on their synergy are limited. An in-depth investigation into the mechanisms of HMO utilization by B. longum is essential for applying both as synbiotics to promote early intestinal development in infants. This review describes the colonization advantages of B. longum in the infant intestinal tract and its metabolic strategies for HMOs. It also summarizes recent studies on the effect and mechanism of B. longum and HMOs in infant intestinal development directly or indirectly through the action of metabolites. In conclusion, further structural analysis of HMOs and a deeper understanding of the interactions between B. longum and HMOs, as well as clinical trials, are necessary to lay the foundation for future practical applications as synbiotics.

The potential role of early life feeding patterns in shaping the infant fecal metabolome: implications for neurodevelopmental outcomes

Infant fecal metabolomics can provide valuable insights into the associations of nutrition, dietary patterns, and health outcomes in early life. Breastmilk is typically classified as the best source of nutrition for nearly all infants. However, exclusive breastfeeding may not always be possible for all infants. This study aimed to characterize associations between levels of mixed breastfeeding and formula feeding, along with solid food consumption and the infant fecal metabolome at 1- and 6-months of age. As a secondary aim, we examined how feeding-associated metabolites may be associated with early life neurodevelopmental outcomes. Fecal samples were collected at 1- and 6-months, and metabolic features were assessed via untargeted liquid chromatography/high-resolution mass spectrometry. Feeding groups were defined at 1-month as 1) exclusively breastfed, 2) breastfed >50% of feedings, or 3) formula fed ≥50% of feedings. Six-month groups were defined as majority breastmilk (>50%) or majority formula fed (≥50%) complemented by solid foods. Neurodevelopmental outcomes were assessed using the Bayley Scales of Infant Development at 2 years. Changes in the infant fecal metabolome were associated with feeding patterns at 1- and 6-months. Feeding patterns were associated with the intensities of a total of 57 fecal metabolites at 1-month and 25 metabolites at 6-months, which were either associated with increased breastmilk or increased formula feeding. Most breastmilk-associated metabolites, which are involved in lipid metabolism and cellular processes like cell signaling, were associated with higher neurodevelopmental scores, while formula-associated metabolites were associated with lower neurodevelopmental scores. These findings offer preliminary evidence that feeding patterns are associated with altered infant fecal metabolomes, which may be associated with cognitive development later in life.

Assessing multiple factors affecting the gut microbiome structure of very preterm infants

The composition and diversity of the gut microbiota are essential for the health and development of the immune system of infants. However, there is limited information on factors that influence the gut microbiota of very preterm infants. In this study, we analyzed factors that affect the gut microbiota of very preterm infants. The stool samples from 64 very preterm infants with a gestational age less than 32 weeks were collected for 16S rRNA gene sequencing. The infants were divided according to the delivery mode, antibiotic use during pregnancy, and feeding methods. The abundance of Proteobacteria was high in both cesarean (92.7%) and spontaneous (55.5%) delivery groups and then shifted to Firmicutes after the first week of birth. In addition, Proteobacteria was also the dominant phylum of infant gut microbiome for mothers with antibiotic use, with more than 50% after the first week of birth. In comparison, the dominant phylum for mothers without antibiotic use was Firmicutes. Proteobacteria level was also high in breastfeeding and mixed-feeding groups, consisting of more than 90% of the community. By contrast, Proteobacteria was the dominant phylum at the first week of birth but then shifted to Firmicutes for the formula-fed group. The alterations of gut microbiota in infants can affect their health condition during growth. This study confirmed that the different feeding types, delivery modes, and use of antibiotics during pregnancy can significantly affect the composition of the gut microbiota of very preterm infants.

Effect of Probiotic Supplementation on the Gut Microbiota Composition of Infants Delivered by Cesarean Section: An Exploratory, Randomized, Open-label, Parallel-controlled Trial

BACKGROUND

Infants born via cesarean section (CS) are at an increased risk of immune-related diseases later in life, potentially due to altered gut microbiota. Recent research has focused on the administration of probiotics in the prevention of gut microbiota dysbiosis in neonates delivered by CS. This study was performed to investigate the effects of probiotic supplementation on the gut microbiota of CS-delivered infants.

METHODS

Thirty full-term neonates delivered by CS were randomized into the intervention (supplemented orally with a probiotic containing Bifidobacterium longum, Lactobacillus acidophilus, and Enterococcus faecalis for 2 weeks) and control groups. Stool samples were collected at birth and 2 weeks and 42 days after birth. The composition of the gut microbiota was analyzed using 16S rRNA sequencing technology.

RESULTS

The applied bacterial strains were abundant in the CS-delivered infants supplemented with probiotics. Probiotics increased the abundance of some beneficial bacteria, such as Bacteroides, Acinetobacter, Veillonella, and Faecalibacterium. Low colonization of Klebsiella, a potentially pathogenic bacterium, was observed in the intervention group.

CONCLUSIONS

Our results showed that probiotics supplemented immediately after CS enriched the gut microbiota composition and altered the pattern of early gut colonization.

TRIAL REGISTRATION

registration number NCT05086458.

Identification of Novel Biomarkers in Late Preterm Neonates with Respiratory Distress Syndrome (RDS) Using Urinary Metabolomic Analysis

Urine metabolomics is gaining traction as a means of identifying metabolic signatures associated with health and disease states. Thirty-one (31) late preterm (LP) neonates admitted to the neonatal intensive care unit (NICU) and 23 age-matched healthy LPs admitted to the maternity ward of a tertiary hospital were included in the study. Proton nuclear magnetic resonance (¹H NMR) spectroscopy was employed for urine metabolomic analysis on the 1st and 3rd days of life of the neonates. The data were analyzed using univariate and multivariate statistical analysis. A unique metabolic pattern of enhanced metabolites was identified in the NICU-admitted LPs from the 1st day of life. Metabolic profiles were distinct in LPs presenting with respiratory distress syndrome (RDS). The discrepancies likely reflect differences in the gut microbiota, either due to variations in nutrient intake or as a result of medical interventions, such as the administration of antibiotics and other medications. Altered metabolites could potentially serve as biomarkers for identifying critically ill LP neonates or those at high risk for adverse outcomes later in life, including metabolic risks. The discovery of novel biomarkers may uncover potential targets for drug discovery and optimal periods for effective intervention, offering a personalized approach.

Longitudinal profiles of the fecal metabolome during the first 2 years of life

During the first 2 years of life, the infant gut microbiome is rapidly developing, and gut bacteria may impact host health through the production of metabolites that can have systemic effects. Thus, the fecal metabolome represents a functional readout of gut bacteria. Despite the important role that fecal metabolites may play in infant health, the development of the infant fecal metabolome has not yet been thoroughly characterized using frequent, repeated sampling during the first 2 years of life. Here, we described the development of the fecal metabolome in a cohort of 101 Latino infants with data collected at 1-, 6-, 12-, 18-, and 24-months of age. We showed that the fecal metabolome is highly conserved across time and highly personalized, with metabolic profiles being largely driven by intra-individual variability. Finally, we also identified several novel metabolites and metabolic pathways that changed significantly with infant age, such as valerobetaine and amino acid metabolism, among others.

Maturation of the gut metabolome during the first year of life in humans

The gut microbiota is involved in the production of numerous metabolites that maintain host wellbeing. The assembly of the gut microbiome is highly dynamic, and influenced by many postnatal factors, moreover, little is known about the development of the gut metabolome. We showed that geography has an important influence on the microbiome dynamics in the first year of life based on two independent cohorts from China and Sweden. Major compositional differences since birth were the high relative abundance of Bacteroides in the Swedish cohort and Streptococcus in the Chinese cohort. We analyzed the development of the fecal metabolome in the first year of life in the Chinese cohort. Lipid metabolism, especially acylcarnitines and bile acids, was the most abundant metabolic pathway in the newborn gut. Delivery mode and feeding induced particular differences in the gut metabolome since birth. In contrast to C-section newborns, medium- and long-chain acylcarnitines were abundant at newborn age only in vaginally delivered infants, associated by the presence of bacteria such as Bacteroides vulgatus and Parabacteroides merdae. Our data provide a basis for understanding the maturation of the fecal metabolome and the metabolic role of gut microbiota in 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.

Infant formula supplemented with 1,3-olein-2-palmitin regulated the immunity, gut microbiota, and metabolites of mice colonized by feces from healthy infants

Infant formula is currently an important food to cope with insufficient breastfeeding. Although 1,3-olein-2-palmitin (OPO) has been used in infant formula, its effects on the immune system, gut microbiota, and metabolites for infants remain unclear. This study constructed a mouse model of colonizing healthy infant feces using antibiotic treatment and fecal microbial transplantation. Thus, the gap between the infant formula supplemented with OPO and human milk in mouse serum biochemistry, immune system, intestinal microbiota, short-chain fatty acid production, and metabolites was evaluated. Our results showed that regarding IL-9, IL-10 levels, fecal secretory IgA, and endotoxin, formula supplemented with OPO and human milk types had comparable levels. Additionally, OPO slightly increased the content of short-chain fatty acids. The 16S rRNA gene sequence analysis and metabonomics analysis demonstrated that feeding different foods affects the gut microbiota of mice; in particular, supplementing formula feeding with OPO enriched the abundance of bifidobacteria. Furthermore, feeding different foods leads to unique intestinal content of metabolites, and the gut microbiota regulates the metabolites' differences. Our results reveal a brand new perspective of OPO regarding gut microbiota and metabolites.

Gut Microbiota in Psoriasis

Psoriasis is a chronic inflammatory skin disease with autoimmune pathogenic characteristics and is caused by chronic inflammation, which results in uncontrolled keratinocyte growth and defective differentiation. The link between the gut microbiota and immune system regulation opened a novel angle to understand the pathogenesis of many chronic multifactorial diseases, including psoriasis. Current evidence suggests that modulation of the gut microbiota, both through dietary approaches and through supplementation with probiotics and prebiotics, could represent a novel therapeutic approach. The present work aims to highlight the latest scientific evidence regarding the microbiome alterations of psoriatic patients, as well as state of the art insights in terms of microbiome-targeted therapies as promising preventive and therapeutic tools for psoriasis.

Metagenomics Approaches to Investigate the Neonatal Gut Microbiome

Early infancy is critical for the development of an infant's gut flora. Many factors can influence microbiota development during the pre- and postnatal periods, including maternal factors, antibiotic exposure, mode of delivery, dietary patterns, and feeding type. Therefore, investigating the connection between these variables and host and microbiome interactions in neonatal development would be of great interest. As the "unculturable" era of microbiome research gives way to an intrinsically multidisciplinary field, microbiome research has reaped the advantages of technological advancements in next-generation sequencing, particularly 16S rRNA gene amplicon and shotgun sequencing, which have considerably expanded our knowledge about gut microbiota development during early life. Using omics approaches to explore the neonatal microbiome may help to better understand the link between the microbiome and newborn diseases. Herein, we summarized the metagenomics methods and tools used to advance knowledge on the neonatal microbiome origin and evolution and how the microbiome shapes early and late individuals' lives for health and disease. The way to overcome limitations in neonatal microbiome studies will be discussed.

Effects of an Amino Acid-Based Formula Supplemented with Two Human Milk Oligosaccharides on Growth, Tolerability, Safety, and Gut Microbiome in Infants with Cow's Milk Protein Allergy

This open-label, non-randomized, multicenter trial (Registration: NCT03661736) aimed to assess if an amino acid-based formula (AAF) supplemented with two human milk oligosaccharides (HMO) supports normal growth and is well tolerated in infants with a cow's milk protein allergy (CMPA). Term infants aged 1-8 months with moderate-to-severe CMPA were enrolled. The study formula was an AAF supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT). Infants were fed the study formula for 4 months and were offered to remain on the formula until 12 months of age. Tolerance and safety were assessed throughout the trial. Out of 32 infants (mean age 18.6 weeks; 20 (62.5%) male), 29 completed the trial. During the 4-month principal study period, the mean weight-for-age Z score (WAZ) increased from -0.31 at the baseline to +0.28 at the 4-months' follow-up. Linear and head growth also progressed along the WHO child growth reference, with a similar small upward trend. The formula was well tolerated and had an excellent safety profile. When comparing the microbiome at the baseline to the subsequent visits, there was a significant on-treatment enrichment in HMO-utilizing bifidobacteria, which was associated with a significant increase in fecal short-chain fatty acids. In addition, we observed a significant reduction in the abundance of fecal Proteobacteria, suggesting that the HMO-supplemented study formula partially corrected the gut microbial dysbiosis in infants with CMPA.

First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment

The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.

Association of Cesarean Delivery and Formula Supplementation with the Stool Metabolome of 6-Week-Old Infants

Cesarean delivery and formula feeding have both been implicated as important factors associated with perturbations to the infant gut microbiome. To investigate the functional metabolic response of the infant gut microbial milieu to these factors, we profiled the stool metabolomes of 121 infants from a US pregnancy cohort study at approximately 6 weeks of life and evaluated associations with delivery mode and feeding method. Multivariate analysis of six-week stool metabolomic profiles indicated discrimination by both delivery mode and diet. For diet, exclusively breast-fed infants exhibited metabolomic profiles that were distinct from both exclusively formula-fed and combination-fed infants, which were relatively more similar to each other in metabolomic profile. We also identified individual metabolites that were important for differentiating delivery mode groups and feeding groups and metabolic pathways related to delivery mode and feeding type. We conclude based on previous work and this current study that the microbial communities colonizing the gastrointestinal tracts of infants are not only taxonomically, but also functionally distinct when compared according to delivery mode and feeding groups. Further, different sets of metabolites and metabolic pathways define delivery mode and diet metabotypes.