Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

Birth mode has been implicated as a major factor influencing neonatal gut microbiome development, and it has been assumed that lack of exposure to the maternal vaginal microbiome is responsible for gut dysbiosis among caesarean-delivered infants. Consequently, practices to correct dysbiotic gut microbiomes, such as vaginal seeding, have arisen while the effect of the maternal vaginal microbiome on that of the infant gut remains unknown. We conducted a longitudinal, prospective cohort study of 621 Canadian pregnant women and their newborn infants and collected pre-delivery maternal vaginal swabs and infant stool samples at 10-days and 3-months of life. Using cpn60-based amplicon sequencing, we defined vaginal and stool microbiome profiles and evaluated the effect of maternal vaginal microbiome composition and various clinical variables on the development of the infant stool microbiome. Infant stool microbiomes showed significant differences in composition by delivery mode at 10-days postpartum; however, this effect could not be explained by maternal vaginal microbiome composition and was vastly reduced by 3 months. Vaginal microbiome clusters were distributed across infant stool clusters in proportion to their frequency in the overall maternal population, indicating independence of the two communities. Intrapartum antibiotic administration was identified as a confounder of infant stool microbiome differences and was associated with lower abundances of Escherichia coli, Bacteroides vulgatus, Bifidobacterium longum and Parabacteroides distasonis. Our findings demonstrate that maternal vaginal microbiome composition at delivery does not affect infant stool microbiome composition and development, suggesting that practices to amend infant stool microbiome composition focus factors other than maternal vaginal microbes.

Changes in the Global Epidemiology of Type 1 Diabetes in an Evolving Landscape of Environmental Factors: Causes, Challenges, and Opportunities

The worldwide incidence of type 1 diabetes mellitus (T1DM) has increased in recent decades. The reasons behind this phenomenon are not yet fully understood. Early life infections, prenatal and perinatal factors, and diet composition have been associated with the triggering of autoimmunity and the risk of presentation of T1DM. However, the rapid increase in new cases of the disease raises the hypothesis that lifestyle factors, which have traditionally been associated with type 2 diabetes, such as obesity and unhealthy eating patterns could also play a role in the genesis of autoimmune diabetes. This article aims to highlight the changing epidemiology of T1DM and the importance of properly recognizing the environmental factors behind it, as well as the connections with the pathogenesis of the disorder and the need to prevent or delay T1DM and its long-term complications.

Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome?

Dysregulated immune system with a failure to recognize self from non-self-antigens is one of the common pathogeneses seen in autoimmune diseases. The complex interplay of genetic and environmental factors is important for the occurrence and development of the disease. Among the environmental factors, disturbed gut microbiota (gut dysbiosis) has recently attracted particular attention, especially with advancement in human microbiome research. Although the alterations in microbiota have been seen in various autoimmune diseases, including those of nervous system, there is paucity of information on neuromuscular system diseases. Myasthenia gravis (MG) is one such rare autoimmune disease of neuromuscular junction, and is caused by generation of pathogenic autoantibodies to components of the postsynaptic muscle endplate. In the recent years, accumulating evidences have endorsed the key role of host microbiota, particularly those of gut, in the pathogenesis of MG. Differential microbiota composition, characterized by increased abundance of Fusobacteria, Bacteroidetes, and Proteobacteria, and decreased abundance of Actinobacteria and Firmicutes, has been seen in MG patients in comparison to healthy subjects. Disturbance of microbiota composition, particularly reduced ratio of Firmicutes/Bacteroidetes, alter the gut permeability, subsequently triggering the immunological response. Resultant reduction in levels of short chain fatty acids (SCFAs) is another factor contributing to the immunological response in MG patients. Modulation of gut microbiota via intervention of probiotics, prebiotics, synbiotics, postbiotics (metabiotics), and fecal microbiota transplantation (FMT) is considered to be the futuristic approach for the management of MG. This review summarizes the role of gut microbiota and their metabolites (postbiotics) in the progression of MG. Also, various bacteriotherapeutic approaches involving gut microbiota are discussed for the prevention of MG progression.

Nutritional implications in the mechanistic link between the intestinal microbiome, renin-angiotensin system, and the development of obesity and metabolic syndrome

Obesity and metabolic disorders represent a significant global health problem and the gut microbiota plays an important role in modulating systemic homeostasis. Recent evidence shows that microbiota and its signaling pathways may affect the whole metabolism and the Renin-Angiotensin System (RAS), which in turn seems to modify microbiota. The present review aimed to investigate nutritional implications in the mechanistic link between the intestinal microbiome, renin-angiotensin system, and the development of obesity and metabolic syndrome components. A description of metabolic changes was obtained based on relevant scientific literature. The molecular and physiological mechanisms that impact the human microbiome were addressed, including the gut microbiota associated with obesity, diabetes, and hepatic steatosis. The RAS interaction signaling and modulation were analyzed. Strategies including the use of prebiotics, symbiotics, probiotics, and biotechnology may affect the gut microbiota and its impact on human health.

Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months

BACKGROUND

Preterm infants suffer higher morbidity and mortality rates compared to full-term infants, but little is known about how changes to oral and respiratory tract microbiota may impact disease development.

METHODS

Here, very preterm neonates (n = 50) were selected to study oral and respiratory microbiota development during the first few months post-birth, where 26 individuals were diagnosed with BPD and/or sepsis. These infants were compared to 14 healthy full-term infants and 16 adults. Microbiota diversity, composition, and species abundances were calculated from 16S ribosomal RNA gene sequences in buccal swabs and tracheal aspirates at two time points (within a week and 1-3 months post-birth).

RESULTS

Collection time point was the biggest factor to significantly influence the preterm oral microbial diversity and composition. In addition, BPD and sepsis were linked to distinct preterm oral microbiota diversity and composition, and opportunistic pathogens previously associated with these diseases were identified in the initial sample for both healthy preterm neonates and those with the disease. Compared to the full-term infant and adult dataset, preterm infant diversity and composition was initially significantly different, but resembled full-term infant diversity and composition over time.

CONCLUSION

Overall, consequences of microbiota development need further examination in preterm infant infections and later development.

IMPACT

Non-gut microbiota research on preterm infants is limited. At one week post-birth, preterm infants harbor distinct oral microbiota that are not shared with full-term children or adults, eventually becoming similar to full-term infants at 36 weeks postmenstrual age. DNA from potential opportunistic pathogens was observed in the mouth and lungs of preterm infants within a week of birth, and microbes associated with BPD were identified in the lungs. Oral microbiota in preterm infants over the first 2-3 months is unique and may be connected to short- and long-term health outcomes in these children.

Breastfeeding might partially contribute to gut microbiota construction and stabilization of propionate metabolism in cesarean-section infants

PURPOSE

This study was aimed to determine how delivery mode and feeding pattern influence the infant's gut microbiota construction and the variation of fecal microbial metabolites from a birth cohort.

METHODS

Fecal samples collected from 61 full-term born Chinese infants at four time points: day 0, day 7, month 1, and month 3. Based on delivery mode (vaginal delivery [V] or cesarean section [C]) and feeding pattern (breastfeeding [B] or mixed feeding [M]), infants were divided into four groups, namely VB, CB, VM, and CM groups. The gut microbiota composition and bacterial diversity were assessed using 16S rRNA sequencing. Short-chain fatty acid (SCFA) concentrations were determined via gas chromatography-mass spectrometry (GC-MS).

RESULTS

The CM group had a significantly higher relative abundance of Firmicutes (day 0 and month 1), Enterococcaceae (month 3), and Enterococcus (month 3) than the VB group and a significantly higher abundance of Firmicutes (month 1) and Blautia (month 3) than the CB group. The VB and CB groups exhibited a stable SCFA variation and a significantly lower level of propionate compared with the VM and CM groups. All groups showed an intense transition of enterotypes within 1 month and became stable at 3 months. The correlation between SCFA and enterotypes showed a significant positive correlation between Bifidobacteriaceae and acetate in the CB group (day 7 and month 3) and a significant positive correlation between Clostridiaceae and butyrate in the CB and VB groups (day 7 and month 3), respectively.

CONCLUSION

These results indicated that C-section was associated with higher abundance of the phylum Firmicutes and family Enterococcaceae, and intense fluctuation of SCFA, at least propionate. And breastfeeding might partially contribute to gut microbiota construction and stabilization propionate metabolism in cesarean-section infants.

Breast Milk Exposure is Associated With Cortical Maturation in Preterm Infants

OBJECTIVE

Breast milk exposure is associated with improved neurocognitive outcomes following preterm birth but the neural substrates linking breast milk with outcome are uncertain. We tested the hypothesis that high versus low breast milk exposure in preterm infants results in cortical morphology that more closely resembles that of term-born infants.

METHODS

We studied 135 preterm (<32 weeks' gestation) and 77 term infants. Feeding data were collected from birth until hospital discharge and brain magnetic resonance imaging (MRI) was performed at term-equivalent age. Cortical indices (volume, thickness, surface area, gyrification index, sulcal depth, and curvature) and diffusion parameters (fractional anisotropy [FA], mean diffusivity [MD], radial diffusivity [RD], axial diffusivity [AD], neurite density index [NDI], and orientation dispersion index [ODI]) were compared between preterm infants who received exclusive breast milk for <75% of inpatient days, preterm infants who received exclusive breast milk for ≥75% of inpatient days and term-born controls. To investigate a dose response effect, we performed linear regression using breast milk exposure quartile weighted by propensity scores.

RESULTS

In preterm infants, high breast milk exposure was associated with reduced cortical gray matter volume (d = 0.47, 95% confidence interval [CI] = 0.14 to 0.94, p = 0.014), thickness (d = 0.42, 95% CI = 0.08 to 0.84, p = 0.039), and RD (d = 0.38, 95% CI = 0.002 to 0.77, p = 0.039), and increased FA (d = -0.38, 95% CI = -0.74 to -0.01, p = 0.037) after adjustment for age at MRI, which was similar to the cortical phenotype observed in term-born controls. Breast milk exposure quartile was associated with cortical volume (ß = -0.192, 95% CI = -0.342 to -0.042, p = 0.017), FA (ß = 0.223, 95% CI = 0.075 to 0.372, p = 0.007), and RD (ß = -0.225, 95% CI = -0.373 to -0.076, p = 0.007) following adjustment for age at birth, age at MRI, and weighted by propensity scores, suggesting a dose effect.

INTERPRETATION

High breast milk exposure following preterm birth is associated with a cortical imaging phenotype that more closely resembles the brain morphology of term-born infants and effects appear to be dose-dependent. ANN NEUROL 2023;93:591-603.

Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu, Philippines

OBJECTIVES

The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members.

MATERIALS AND METHODS

As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition.

RESULTS

Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables.

CONCLUSIONS

Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.

Infant Fecal Fermentations with Galacto-Oligosaccharides and 2′-Fucosyllactose Show Differential Bifidobacterium longum Stimulation at Subspecies Level

The objective of the current study was to evaluate the potential of 2′-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12–18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2′-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME® model. For young toddlers, significant increases in the genera Bifidobacterium, Veillonella, and Streptococcus, and decreases in Enterobacteriaceae, Clostridium XIVa, and Roseburia were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2′-FL, increased Collinsella and decreased Salmonella, whereas 2′-FL, and combined GOS and 2′-FL, decreased Dorea. Alpha diversity increased significantly in infants with GOS and/or 2′-FL, as well as the relative abundances of the genera Veillonella and Akkermansia with 2′-FL, and Lactobacillus with GOS. Combinations of GOS and 2′-FL significantly stimulated Veillonella, Lactobacillus, Bifidobacterium, and Streptococcus. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2′-FL. When zooming in on the different (sub)species of Bifidobacterium, GOS and 2’-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of Bifidobacterium longum in a dose-dependent manner: GOS stimulated Bifidobacterium longum subsp. longum, whereas 2′-FL supported outgrowth of Bifidobacterium longum subsp. infantis.

Epicutaneous Sensitization and Food Allergy: Preventive Strategies Targeting Skin Barrier Repair-Facts and Challenges

Food allergy represents a growing public health and socio-economic problem with an increasing prevalence over the last two decades. Despite its substantial impact on the quality of life, current treatment options for food allergy are limited to strict allergen avoidance and emergency management, creating an urgent need for effective preventive strategies. Advances in the understanding of the food allergy pathogenesis allow to develop more precise approaches targeting specific pathophysiological pathways. Recently, the skin has become an important target for food allergy prevention strategies, as it has been hypothesized that allergen exposure through the impaired skin barrier might induce an immune response resulting in subsequent development of food allergy. This review aims to discuss current evidence supporting this complex interplay between the skin barrier dysfunction and food allergy by highlighting the crucial role of epicutaneous sensitization in the causality pathway leading to food allergen sensitization and progression to clinical food allergy. We also summarize recently studied prophylactic and therapeutic interventions targeting the skin barrier repair as an emerging food allergy prevention strategy and discuss current evidence controversies and future challenges. Further studies are needed before these promising strategies can be routinely implemented as prevention advice for the general population.

Breastfeeding enrichment of B. longum subsp. infantis mitigates the effect of antibiotics on the microbiota and childhood asthma risk

BACKGROUND

Early antibiotic exposure is linked to persistent disruption of the infant gut microbiome and subsequent elevated pediatric asthma risk. Breastfeeding acts as a primary modulator of the gut microbiome during early life, but its effect on asthma development has remained unclear.

METHODS

We harnessed the CHILD cohort to interrogate the influence of breastfeeding on antibiotic-associated asthma risk in a subset of children (n = 2,521). We then profiled the infant microbiomes in a subset of these children (n = 1,338) using shotgun metagenomic sequencing and compared human milk oligosaccharide and fatty acid composition from paired maternal human milk samples for 561 of these infants.

FINDINGS

Children who took antibiotics without breastfeeding had 3-fold higher asthma odds, whereas there was no such association in children who received antibiotics while breastfeeding. This benefit was associated with widespread "re-balancing" of taxonomic and functional components of the infant microbiome. Functional changes associated with asthma protection were linked to enriched Bifidobacterium longum subsp. infantis colonization. Network analysis identified a selection of fucosylated human milk oligosaccharides in paired maternal samples that were positively associated with B. infantis and these broader functional changes.

CONCLUSIONS

Our data suggest that breastfeeding and antibiotics have opposing effects on the infant microbiome and that breastfeeding enrichment of B. infantis is associated with reduced antibiotic-associated asthma risk.

FUNDING

This work was supported in part by the Canadian Institutes of Health Research; the Allergy, Genes and Environment Network of Centres of Excellence; Genome Canada; and Genome British Columbia.

Effects of a Novel Infant Formula on the Fecal Microbiota in the First Six Months of Life: The INNOVA 2020 Study

Exclusive breastfeeding is highly recommended for infants for at least the first six months of life. However, for some mothers, it may be difficult or even impossible to do so. This can lead to disturbances in the gut microbiota, which in turn may be related to a higher incidence of acute infectious diseases. Here, we aimed to evaluate whether a novel starting formula versus a standard formula provides a gut microbiota composition more similar to that of breastfed infants in the first 6 months of life. Two hundred and ten infants (70/group) were enrolled in the study and completed the intervention until 12 months of age. For the intervention period, infants were divided into three groups: Group 1 received formula 1 (INN) with a lower amount of protein, a proportion of casein to whey protein ratio of about 70/30 by increasing the content of α-lactalbumin, and with double the amount of docosahexaenoic acid/arachidonic acid than the standard formula; INN also contained a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis). Group 2 received the standard formula (STD) and the third group was exclusively breastfed (BF) for exploratory analysis. During the study, visits were made at 21 days, 2, 4, and 6 months of age, with ±3 days for the visit at 21 days of age, ±1 week for the visit at 2 months, and ±2 weeks for the others. Here, we reveal how consuming the INN formula promotes a similar gut microbiota composition to those infants that were breastfed in terms of richness and diversity, genera, such as Bacteroides, Bifidobacterium, Clostridium, and Lactobacillus, and calprotectin and short-chain fatty acid levels at 21 days, 2 and 6 months. Furthermore, we observed that the major bacteria metabolic pathways were more alike between the INN formula and BF groups compared to the STD formula group. Therefore, we assume that consumption of the novel INN formula might improve gut microbiota composition, promoting a healthier intestinal microbiota more similar to that of an infant who receives exclusively human milk.

Analysis of Fecal Short-Chain Fatty Acids (SCFAs) in Healthy Children during the First Two Years of Life: An Observational Prospective Cohort Study

Short-chain fatty acids (SCFAs) are important metabolites of the gut microbiota. The aim is to analyze the influence of perinatal factors, which can affect the gut microbiota, on the concentrations of fecal SCFAs over the first two years of life. Gas chromatography was used to analyze SCFA in a total of 456 fecal samples from 86 children. Total SCFA concentrations increased until 12 months and stabilized after that. Antibiotic treatment during pregnancy was associated with an increase in acetic acid, propionic acid and total SCFA in meconium and a decrease in the same SCFAs at 6 months. Butyric acid was increased after Caesarean delivery until 1 month. In formula-fed children, propionic acid (at 1 month) and butyric acid and total SCFA (at 12 months) were increased. Acetic and linear butyric acids and total SCFAs were also increased at 12 months in children born vaginally that were also formula-fed. Higher butyric acid was observed in children of mothers with normal pre-pregnancy weight and adequate weight gain during pregnancy. Butyric acid was also elevated in 6-month-old infants with a higher body weight (≥85th percentile). Acetic acid concentrations were significantly higher in 2-year-old females vs. males. We conclude that perinatal factors are linked to changes in fecal SCFAs and further long-term epidemiological studies are warranted.

Altered intestinal microbiota composition with epilepsy and concomitant diarrhea and potential indicator biomarkers in infants

Introduction

The diversity and dysregulation of intestinal microbiota is related to the pathology of epilepsy. Gut microbiota plays an important role in epilepsy, and regulating intestinal microbiota through exogenous intervention can alleviate symptoms. However, there are no studies about the effects of epilepsy-related diarrhea on gut microbiota.

Methods

The diversity and dysregulation of intestinal microbiota is related to the pathology of epilepsy. Gut microbiota plays an important role in epilepsy, and regulating intestinal microbiota through exogenous intervention can alleviate symptoms. However, there are no studies about the effects of epilepsy-related diarrhea on gut microbiota. To evaluate changes in gut microbiota structure and composition in patients with epilepsy and associated diarrhea, the structure and composition of the fecal microbiota among patients with epilepsy (EP, 13 cases), epilepsy with diarrhea (ED, 13 cases), and probiotic treatments (PT, 13 cases), and healthy controls (CK, seven cases) were investigated and validated by utilizing high-throughput 16S rRNA sequencing.

Results

The results showed that the α-diversity indexes indicated that richness and phylogenetic diversity had no significant differences among groups. However, the variation of β-diversity indicated that the structure and composition of intestinal microbiota were significantly different among the CK, EP, ED, and PT groups (permutational multivariate analysis of variance, p-value = 0.001). Normalized stochasticity ratio and β-nearest taxon index indicated that stochastic mechanisms exerted increasing influence on community differences with epilepsy and associated diarrhea. ED microbiome alterations include increased Proteobacteria and decreased Actinobacteria and Firmicutes at the phylum level. Bifidobacterium was the core microbe in CK, EP, and PT, whereas it decreased significantly in ED. In contrast, Escherichia/Shigella was the core microbe in CK and ED, whereas it increased significantly in ED (Tukey's multiple comparisons test, adjusted p-value <0.05). The association network in CK has higher complexity and aggregation than in the other groups. The EP network indicated high connectivity density within each community and high sparsity among communities. The bacterial community network of the ED had a more compact local interconnection, which was in contrast to that of PT. The top 7 microbial amplicon sequence variant-based markers that were selected by machine learning to distinguish the groups of epilepsy, probiotic treatments, and healthy infants had stronger discrimination ability. In addition, ASVs_1 (Escherichia/Shigella) and ASVs_3 (Bifidobacterium) had the most importance in the recognition.

Discussion

Our research finally showed that infants with epilepsy, epilepsy with diarrhea, and probiotic treatments exhibit substantial alterations of intestinal microbiota structure and composition, and specific intestinal strains are altered according to different clinical phenotypes and can therefore be used as potential biomarkers for disease diagnosis.

Breastfeeding and the major fermentation metabolite lactate determine occurrence of Peptostreptococcaceae in infant feces

Previous studies indicated an intrinsic relationship between infant diet, intestinal microbiota composition and fermentation activity with a strong focus on the role of breastfeeding on microbiota composition. Yet, microbially formed short-chain fatty acids acetate, propionate and butyrate and other fermentation metabolites such as lactate not only act as substrate for bacterial cross-feeding and as mediators in microbe-host interactions but also confer antimicrobial activity, which has received considerably less attention in the past research. It was the aim of this study to investigate the nutritional-microbial interactions that contribute to the development of infant gut microbiota with a focus on human milk oligosaccharide (HMO) fermentation. Infant fecal microbiota composition, fermentation metabolites and milk composition were analyzed from 69 mother-infant pairs of the Swiss birth cohort Childhood AlleRgy nutrition and Environment (CARE) at three time points depending on breastfeeding status defined at the age of 4 months, using quantitative microbiota profiling, HPLC-RI and 1H-NMR. We conducted in vitro fermentations in the presence of HMO fermentation metabolites and determined the antimicrobial activity of lactate and acetate against major Clostridiaceae and Peptostreptococcaceae representatives. Our data show that fucosyllactose represented 90% of the HMOs present in breast milk at 1- and 3-months post-partum with fecal accumulation of fucose, 1,2-propanediol and lactate indicating fermentation of HMOs that is likely driven by Bifidobacterium. Concurrently, there was a significantly lower absolute abundance of Peptostreptococcaceae in feces of exclusively breastfed infants at 3 months. In vitro, lactate inhibited strains of Peptostreptococcaceae. Taken together, this study not only identified breastfeeding dependent fecal microbiota and metabolite profiles but suggests that HMO-derived fermentation metabolites might exert an inhibitory effect against selected gut microbes.

Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health

BACKGROUND

The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.

METHODS

Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.

RESULTS

Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.

CONCLUSIONS

We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.

Health Effects of Infant Formula Supplemented with Probiotics or Synbiotics in Infants and Toddlers: Systematic Review with Network Meta-Analysis

Supplementation of infant and follow-up formula with probiotics or synbiotics has become a common practice. In 2011 and 2017, the evidence regarding the impact of these interventions was analysed systematically. Recently new evidence was published. To evaluate through a systematic review with network meta-analysis the evidence on the impact of infant formula supplemented with probiotics or synbiotics for healthy infants and 36-month-old toddlers. RCTs published between 1999-2019 for infant formulas supplemented with probiotics alone or synbiotics in healthy infants and toddlers were identified. Data analysis included clinical (gastrointestinal symptoms, risk reduction of infectious diseases, use of antibiotics, weight/height gain and frequency of adverse events) and non-clinical outcomes (changes in faecal microbiota and immune parameters). A random effect model was used. Hedges' standard mean difference (SMD) and risk ratio (RR) were calculated. Rank analysis was performed to evaluate the superiority of each intervention. Twenty-six randomised controlled trials with 35 direct comparisons involving 1957 children receiving probiotic-supplemented formula and 1898 receiving control formula were reviewed. The mean duration of intervention was 5.6 ± 2.84 months. Certain strains demonstrated a reduction in episodes of colic, number of days with fever and use of antibiotics; however, there was considerable heterogeneity which reduced the level of certainty of effect. No significant effects were observed on weight, height or changes in faecal proportions of Bifidobacteria, Lactobacillus, Bacteroides or Clostridia. Although there is some evidence that may support a potential benefit of probiotic or synbiotic supplementation of infant formulas, variation in the quality of existing trials and the heterogeneity of the data preclude the establishment of robust recommendations.

Human Milk Microbiome and Microbiome-Related Products: Potential Modulators of Infant Growth

Infant growth trajectory may influence later-life obesity. Human milk provides a wide range of nutritional and bioactive components that are vital for infant growth. Compared to formula-fed infants, breastfed infants are less likely to develop later-onset obesity, highlighting the potential role of bioactive components present in human milk. Components of particular interest are the human milk microbiota, human milk oligosaccharides (HMOs), short-chain fatty acids (SCFAs), and antimicrobial proteins, each of which influence the infant gut microbiome, which in turn has been associated with infant body composition. SCFAs and antimicrobial proteins from human milk may also systemically influence infant metabolism. Although inconsistent, multiple studies have reported associations between HMOs and infant growth, while studies on other bioactive components in relation to infant growth are sparse. Moreover, these microbiome-related components may interact with each other within the mammary gland. Here, we review the evidence around the impact of human milk microbes, HMOs, SCFAs, and antimicrobial proteins on infant growth. Breastfeeding is a unique window of opportunity to promote optimal infant growth, with aberrant growth trajectories potentially creating short- and long-term public health burdens. Therefore, it is important to understand how bioactive components of human milk influence infant growth.

Gut-dependent inflammation and alterations of the intestinal microbiota in individuals with perinatal HIV exposure and different HIV serostatus

OBJECTIVE

HIV-exposed infected (HEI) and uninfected (HEU) children represent the two possible outcomes of maternal HIV infection. Modifications of the intestinal microbiome have been linked to clinical vulnerability in both settings, yet whether HEI and HEU differ in terms of gut impairment and peripheral inflammation/activation is unknown.

DESIGN

We performed a cross-sectional, pilot study on fecal and plasma microbiome as well as plasma markers of gut damage, microbial translocation, inflammation and immune activation in HIV-infected and uninfected children born from an HIV-infected mother.

METHODS

Fecal and plasma microbiome were determined by means of 16S rDNA amplification with subsequent qPCR quantification. Plasma markers were quantified via ELISA.

RESULTS

Forty-seven HEI and 33 HEU children were consecutively enrolled. The two groups displayed differences in fecal beta-diversity and relative abundance, yet similar microbiome profiles in plasma as well as comparable gut damage and microbial translocation. In contrast, monocyte activation (sCD14) and systemic inflammation (IL-6) were significantly higher in HEI than HEU.

CONCLUSION

In the setting of perinatal HIV infection, enduring immune activation and inflammation do not appear to be linked to alterations within the gut. Given that markers of activation and inflammation are independent predictors of HIV disease progression, future studies are needed to understand the underlying mechanisms of such processes and elaborate adjuvant therapies to reduce the clinical risk in individuals with perinatal HIV infection.

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases

Background

Dozens of studies have demonstrated gut dysbiosis in COVID-19 patients during the acute and recovery phases. However, a consensus on the specific COVID-19 associated bacteria is missing. In this study, we performed a meta-analysis to explore whether robust and reproducible alterations in the gut microbiota of COVID-19 patients exist across different populations.

Methods

A systematic review was conducted for studies published prior to May 2022 in electronic databases. After review, we included 16 studies that comparing the gut microbiota in COVID-19 patients to those of controls. The 16S rRNA sequence data of these studies were then re-analyzed using a standardized workflow and synthesized by meta-analysis.

Results

We found that gut bacterial diversity of COVID-19 patients in both the acute and recovery phases was consistently lower than non-COVID-19 individuals. Microbial differential abundance analysis showed depletion of anti-inflammatory butyrate-producing bacteria and enrichment of taxa with pro-inflammatory properties in COVID-19 patients during the acute phase compared to non-COVID-19 individuals. Analysis of microbial communities showed that the gut microbiota of COVID-19 recovered patients were still in unhealthy ecostates.

Conclusions

Our results provided a comprehensive synthesis to better understand gut microbial perturbations associated with COVID-19 and identified underlying biomarkers for microbiome-based diagnostics and therapeutics.

The development of human gut microbiota fermentation capacity during the first year of life

Fermentation capacity of microbial ecosystems intrinsically depends on substrate supply and the ability of a microbial community to deliver monomers for fermentation. In established microbial ecosystems, the microbial community is adapted to efficiently degrade and ferment available biopolymers which is often concurrently reflected in the richness of the microbial community and its functional potential. During the first year of life, the human gut microbial environment is a rather dynamic system that is characterized by a change in physiological conditions (e.g. from aerobic to anaerobic conditions, physical growth of the gastrointestinal tract, development of the intestinal immune system) but also by a change in nutrient supply from a compositionally limited liquid to a diverse solid diet, which demands major compositional and functional changes of the intestinal microbiota. How these transitions link to intestinal microbial fermentation capacity has gained comparatively little interest so far. This mini-review aims to collect evidence that already after birth, there is seeding of a hidden population of various fermentation organisms which remain present at low abundance until the cessation of breastfeeding removes nutritional restrictions of a liquid milk-based diet. The introduction of solid food containing plant and animal material is accompanied by an altering microbiota. The concurrent increases in the abundance of degraders and fermenters lead to higher intestinal fermentation capacity indicated by increased faecal levels of the final fermentation metabolites propionate and butyrate. Recent reports indicate that the development of fermentation capacity is an important step during gut microbiota development, as chronic disorders such as allergy and atopic dermatitis have been linked to lower degradation and fermentation capacity indicated by reduced levels of final fermentation metabolites at 1 year of age.

The road not taken: host genetics in shaping intergenerational microbiomes

The early-life gut microbiome is linked to human phenotypes as an imbalanced microbiome of this period is implicated in diseases throughout life. Several determinants of early-life gut microbiome are explored, however, mechanisms of acquisition, colonization, and stability of early-life gut microbiome and their interindividual variability remain elusive. Host genetics play a vital role to shape the gut microbiome and interact with it to modulate individual phenotypes in human studies and animal models. Given the microbial linkage between host generations, we discuss the current state of roles of host genetics in forming intergenerational microbiomes associated with mothers, offspring, and those vertically transmitted, providing a basis for taking into account host genetics in future early-life microbiome research. We further expand our discussion to the bidirectional interactions between host gene expression and microbiome in human health.

Infant nutrition affects the microbiota-gut-brain axis: Comparison of human milk vs. infant formula feeding in the piglet model

Early nutrition plays a dominant role in infant development and health. It is now understood that the infant diet impacts the gut microbiota and its relationship with gut function and brain development. However, its impact on the microbiota-gut-brain axis has not been studied in an integrative way. The objective here was to evaluate the effects of human milk (HM) or cow’s milk based infant formula (IF) on the relationships between gut microbiota and the collective host intestinal-brain axis. Eighteen 10-day-old Yucatan mini-piglets were fed with HM or IF. Intestinal and fecal microbiota composition, intestinal phenotypic parameters, and the expression of genes involved in several gut and brain functions were determined. Unidimensional analyses were performed, followed by multifactorial analyses to evaluate the relationships among all the variables across the microbiota-gut-brain axis. Compared to IF, HM decreased the α-diversity of colonic and fecal microbiota and modified their composition. Piglets fed HM had a significantly higher ileal and colonic paracellular permeability assessed by ex vivo analysis, a lower expression of genes encoding tight junction proteins, and a higher expression of genes encoding pro-inflammatory and anti-inflammatory immune activity. In addition, the expression of genes involved in endocrine function, tryptophan metabolism and nutrient transport was modified mostly in the colon. These diet-induced intestinal modifications were associated with changes in the brain tissue expression of genes encoding the blood-brain barrier, endocrine function and short chain fatty acid receptors, mostly in hypothalamic and striatal areas. The integrative approach underlined specific groups of bacteria (Veillonellaceae, Enterobacteriaceae, Lachnospiraceae, Rikenellaceae, and Prevotellaceae) associated with changes in the gut-brain axis. There is a clear influence of the infant diet, even over a short dietary intervention period, on establishment of the microbiota-gut-brain axis.

Review of the Current State of Freely Accessible Web Tools for the Analysis of 16S rRNA Sequencing of the Gut Microbiome

Owing to the emergence and improvement of high-throughput technology and the associated reduction in costs, next-generation sequencing (NGS) technology has made large-scale sampling and sequencing possible. With the large volume of data produced, the processing and downstream analysis of data are important for ensuring meaningful results and interpretation. Problems in data analysis may be encountered if researchers have little experience in using programming languages, especially if they are clinicians and beginners in the field. A strategy for solving this problem involves ensuring easy access to commercial software and tools. Here, we observed the current status of free web-based tools for microbiome analysis that can help users analyze and handle microbiome data effortlessly. We limited our search to freely available web-based tools and identified MicrobiomeAnalyst, Mian, gcMeta, VAMPS, and Microbiome Toolbox. We also highlighted the various analyses that each web tool offers, how users can analyze their data using each web tool, and noted some of their limitations. From the abovementioned list, gcMeta, VAMPS, and Microbiome Toolbox had several issues that made the analysis more difficult. Over time, as more data are generated and accessed, more users will analyze microbiome data. Thus, the availability of free and easily accessible web tools can enable the easy use and analysis of microbiome data, especially for those users with less experience in using command-line interfaces.

Human milk microbiome is shaped by breastfeeding practices

There is evidence that breastfeeding practices may impact the milk microbiota diversity and differential abundance at the genera level; however, the possibility that distinct feeding practices, such as exclusive (EBF) and non-exclusive breastfeeding (non-EBF), might alter the milk microbiome at the species level has not been explored. This cross-sectional study analyzed the milk microbiome of 64 Mam-Mayan indigenous mothers from San Juan Ostuncalco in Guatemala. Two breastfeeding practices [exclusive (EBF) vs non-exclusive (non-EBF)] were analyzed at two stages of lactation [early (5–46 days post-partum) vs late (109–184 days post-partum)]. EBF was defined as offering only human milk and non-EBF was defined as feeding the infant herbal teas (agüitas) and/or complementary foods while continuing to breastfeed. Results identified four clusters with distinct microbial communities that segregated bacterial species by both breastfeeding practices and stage of lactation. Comparison among these clusters identified several notable patterns. First, during EBF, the microbiome differed by stage of lactation where there was a shift in differential abundance from Actinobacteria and Firmicutes in early to Bacteroidetes and Proteobacteria species in late lactation. Second, a similar comparison between non-EBF mothers by stage of lactation also identified a higher differential abundance of Actinobacteria and Firmicutes species in early lactation, but only Proteobacteria and not Bacteroidetes in late lactation, indicating a further shift in the milk microbial ecosystem with fewer oral bacteria present in late lactation. Third, comparisons between EBF and non-EBF mothers at both early and late lactation showed that mothers who exclusively breastfed had more differentially abundant species in early (11 vs 1) and late (13 vs 2) lactation. Fourth, EBF at early and late lactation had more commensal and lactic acid bacteria, including Lactobacillus gasseri, Granulicatella elegans, Streptococcus mitis, and Streptococcus parasanguinis, compared to those who did not exclusively breastfeed. Collectively, these results show that EBF has more differentially abundant bacteria, including commensal and lactic acid bacteria, and that the addition of agüitas (herbal teas) and/or complementary foods modify the milk microbiome composition by reducing the oral bacteria and introducing more environmentally sourced bacteria to the ecosystem.

Comparative Proteomic Analysis of Proteins in Breast Milk during Different Lactation Periods

Breast milk is an unparalleled food for infants, as it can meet almost all of their nutritional needs. Breast milk in the first month is an important source of acquired immunity. However, breast milk protein may vary with the stage of lactation. Therefore, the aim of this study was to use a data-independent acquisition approach to determine the differences in the proteins of breast milk during different lactation periods. The study samples were colostrum (3-6 days), transitional milk (7-14 days), and mature milk (15-29 days). The results identified a total of 2085 different proteins, and colostrum contained the most characteristic proteins. Protein expression was affected by the lactation stage. The proteins expressed in breast milk changed greatly between day 3 and day 14 and gradually stabilized after 14 days. The expression levels of lactoferrin, immunoglobulin, and clusterin were the highest in colostrum. CTP synthase 1, C-type lectin domain family 19 member A, secretoglobin family 3A member 2, trefoil factor 3 (TFF3), and tenascin were also the highest in colostrum. This study provides further insights into the protein composition of breast milk and the necessary support for the design and production of infant formula.

Exclusive breast-feeding, the early-life microbiome and immune response, and common childhood respiratory illnesses

BACKGROUND

The impact of breast-feeding on certain childhood respiratory illnesses remains controversial.

OBJECTIVE

We sought to examine the effect of exclusive breast-feeding on the early-life upper respiratory tract (URT) and gut microbiome, the URT immune response in infancy, and the risk of common pediatric respiratory diseases.

METHODS

We analyzed data from a birth cohort of healthy infants with prospective ascertainment of breast-feeding patterns and common pediatric pulmonary and atopic outcomes. In a subset of infants, we also characterized the URT and gut microbiome using 16S ribosomal RNA sequencing and measured 9 URT cytokines using magnetic bead-based assays.

RESULTS

Of the 1949 infants enrolled, 1495 (76.71%) had 4-year data. In adjusted analyses, exclusive breast-feeding (1) had an inverse dose-response on the ⍺-diversity of the early-life URT and gut microbiome, (2) was positively associated with the URT levels of IFN-α, IFN-γ, and IL-17A in infancy, and (3) had a protective dose-response on the development of a lower respiratory tract infection in infancy, 4-year current asthma, and 4-year ever allergic rhinitis (odds ratio [95% CI] for each 4 weeks of exclusive breast-feeding, 0.95 [0.91-0.99], 0.95 [0.90-0.99], and 0.95 [0.92-0.99], respectively). In exploratory analyses, we also found that the protective association of exclusive breast-feeding on 4-year current asthma was mediated through its impact on the gut microbiome (P = .03).

CONCLUSIONS

Our results support a protective causal role of exclusive breast-feeding in the risk of developing a lower respiratory tract infection in infancy and asthma and allergic rhinitis in childhood. They also shed light on potential mechanisms of these associations, including the effect of exclusive breast-feeding on the gut microbiome.

Gut microbiome and breast-feeding: Implications for early immune development

Establishment of the gut microbiome during early life is a complex process with lasting implications for an individual's health. Several factors influence microbial assembly; however, breast-feeding is recognized as one of the most influential drivers of gut microbiome composition during infancy, with potential implications for function. Differences in gut microbial communities between breast-fed and formula-fed infants have been consistently observed and are hypothesized to partially mediate the relationships between breast-feeding and decreased risk for numerous communicable and noncommunicable diseases in early life. Despite decades of research on the gut microbiome of breast-fed infants, there are large scientific gaps in understanding how human milk has evolved to support microbial and immune development. This review will summarize the evidence on how breast-feeding broadly affects the composition and function of the early-life gut microbiome and discuss mechanisms by which specific human milk components shape intestinal bacterial colonization, succession, and function.

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data

It is well-known that human gut microbiota form an ecosystem where microbes interact with each other. Due to complex underlying interactions, some microbes may correlate nonlinearly. There are no measures in the microbiome literature we know of that quantify these nonlinear relationships. Here, we develop a methodology called Sparse Estimation of Correlations among Microbiomes (SECOM) for estimating linear and nonlinear relationships among microbes while maintaining the sparsity. SECOM accounts for both sample and taxon-specific biases in its model. Its statistical properties are evaluated analytically and by comprehensive simulation studies. We test SECOM in two real data sets, namely, forehead and palm microbiome data from college-age adults, and Norwegian infant gut microbiome data. Given that forehead and palm are related to skin, as desired, SECOM discovers each genus to be highly correlated between the two sites, but that is not the case with any of the competing methods. It is well-known that infant gut evolves as the child grows. Using SECOM, for the first time in the literature, we characterize temporal changes in correlations among bacterial families during a baby's first year after birth.

Effect of a reduced fat and sugar maternal dietary intervention during lactation on the infant gut microbiome

Objective

A growing body of literature has shown that maternal diet during pregnancy is associated with infant gut bacterial composition. However, whether maternal diet during lactation affects the exclusively breastfed infant gut microbiome remains understudied. This study sets out to determine whether a two-week of a reduced fat and sugar maternal dietary intervention during lactation is associated with changes in the infant gut microbiome composition and function.

Design

Stool samples were collected from four female and six male (n = 10) infants immediately before and after the intervention. Maternal baseline diet from healthy mothers aged 22–37 was assessed using 24-h dietary recall. During the 2-week dietary intervention, mothers were provided with meals and their dietary intake was calculated using FoodWorks 10 Software. Shotgun metagenomic sequencing was used to characterize the infant gut microbiome composition and function.

Results

In all but one participant, maternal fat and sugar intake during the intervention were significantly lower than at baseline. The functional capacity of the infant gut microbiome was significantly altered by the intervention, with increased levels of genes associated with 28 bacterial metabolic pathways involved in biosynthesis of vitamins (p = 0.003), amino acids (p = 0.005), carbohydrates (p = 0.01), and fatty acids and lipids (p = 0.01). Although the dietary intervention did not affect the bacterial composition of the infant gut microbiome, relative difference in maternal fiber intake was positively associated with increased abundance of genes involved in biosynthesis of storage compounds (p = 0.016), such as cyanophycin. Relative difference in maternal protein intake was negatively associated with Veillonella parvula (p = 0.006), while positively associated with Klebsiella michiganensis (p = 0.047). Relative difference in maternal sugar intake was positively associated with Lactobacillus paracasei (p = 0.022). Relative difference in maternal fat intake was positively associated with genes involved in the biosynthesis of storage compounds (p = 0.015), fatty acid and lipid (p = 0.039), and metabolic regulator (p = 0.038) metabolic pathways.

Conclusion

This pilot study demonstrates that a short-term maternal dietary intervention during lactation can significantly alter the functional potential, but not bacterial taxonomy, of the breastfed infant gut microbiome. While the overall diet itself was not able to change the composition of the infant gut microbiome, changes in intakes of maternal protein and sugar during lactation were correlated with changes in the relative abundances of certain bacterial species.

Clinical trial registration: Australian New Zealand Clinical Trials Registry (ACTRN12619000606189).

Neonatal Diet and Gut Microbiome Development After C-Section During the First Three Months After Birth: A Systematic Review

Background

Cesarean section (C-section) delivery imprints fundamentally on the gut microbiota composition with potential health consequences. With the increasing incidence of C-sections worldwide, there is a need for precise characterization of neonatal gut microbiota to understand how to restore microbial imbalance after C-section. After birth, gut microbiota development is shaped by various factors, especially the infant’s diet and antibiotic exposure. Concerning diet, current research has proposed that breastfeeding can restore the characteristic gut microbiome after C-section.

Objectives

In this systematic review, we provide a comprehensive summary of the current literature on the effect of breastfeeding on gut microbiota development after C-section delivery in the first 3 months of life.

Methods

The retrieved data from PubMed, Scopus, and Web of Science were evaluated according to the PICO/PECO strategy. Quality assessment was conducted by the Newcastle–Ottawa Scale.

Results

After critical selection, we identified 14 out of 4,628 studies for the evaluation of the impact of the diet after C-section delivery. The results demonstrate consistent evidence that C-section and affiliated intrapartum antibiotic exposure affect Bacteroidetes abundance and the incapacity of breastfeeding to reverse their reduction. Furthermore, exclusive breastfeeding shows a positive effect on Actinobacteria and Bifidobacteria restoration over the 3 months after birth. None of the included studies detected any significant changes in Lactobacillus abundance in breastfed infants after C-section.

Conclusion

C-section and intrapartum antibiotic exposure influence an infant’s gut microbiota by depletion of Bacteroides, regardless of the infant’s diet in the first 3 months of life. Even though breastfeeding increases the presence of Bifidobacteria, further research with proper feeding classification is needed to prove the restoration effect on some taxa in infants after C-section.

Systematic Review Registration:

[www.crd.york.ac.uk/prospero/], identifier [CRD42021287672].

Human milk nutrient fortifiers alter the developing gastrointestinal microbiota of very-low-birth-weight infants

Nutrient fortifiers are added to human milk to support the development of very-low-birth-weight infants. Currently, bovine-milk-based fortifiers (BMBFs) are predominantly administered, with increasing interest in adopting human-milk-based fortifiers (HMBFs). Although beneficial for growth, their effects on the gastrointestinal microbiota are unclear. This triple-blind, randomized clinical trial (NCT02137473) tested how nutrient-enriching human milk with HMBF versus BMBF affects the gastrointestinal microbiota of infants born < 1,250 g during hospitalization. HMBF-fed infants (n = 63, n = 269 stools) showed lower microbial diversity, altered microbial community structure, and changes in predicted microbial functions compared with BMBF-fed infants (n = 56, n = 239 stools). HMBF-fed infants had higher relative and normalized abundances of unclassified Enterobacteriaceae and lower abundances of Clostridium sensu stricto. Post hoc analyses identified dose-dependent relationships between individual feed components (volumes of mother's milk, donor milk, and fortifiers) and the microbiota. These results highlight how nutrient fortifiers impact the microbiota of very-low-birth-weight infants during a critical developmental window.

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.

Maternal Diet Is Associated with Human Milk Oligosaccharide Profile

SCOPE

Human milk oligosaccharides (HMOs) are complex glycans that are abundant in human milk. The potential impact of a maternal diet on individual HMOs and the association with secretor status is unknown. Thus, this study is aimed to examine the association between maternal diet and HMO profiles.

METHODS AND RESULTS

This is a cross-sectional study of the MAMI cohort with 101 human milk samples from healthy mothers. HMO profiling is assessed by quantitative HPLC. Maternal dietary information is recorded through an FFQ, and perinatal factors including the mode of delivery, antibiotic exposure, and breastfeeding practices, are collected. A more significant effect of diet on HMO profiles is observed in secretor mothers than in non-secretor mothers. (Poly)phenols and fibers, both soluble and insoluble, and several insoluble polysaccharides, pectin, and MUFA are associated with the secretor HMO profiles.

CONCLUSIONS

Maternal diet is associated with the composition and diversity of HMO in a secretor status-dependent manner. The relationship between maternal diet and bioactive compounds, including HMOs, which are present in human milk, needs further research due its potential impact on infant development and health outcomes.

Increasing early exposure to mother's own milk in premature newborns

OBJECTIVE

Increase the proportion of ≤33 weeks newborns exposed to mother's own milk (MOM) oral care by 12 h of age by 20% over 2 years to support a healthier microbiome.

STUDY DESIGN

We implemented interventions to support early expression of colostrum and reliable delivery of resultant MOM to premature newborns. Statistical process control charts were used to track progress and provide feedback to staff. Proportions of newborns exposed to MOM by 12 h were compared relative to baseline.

RESULTS

There were 46, 66, and 46 newborns in the baseline, implementation, and sustainability periods, respectively. The primary outcome improved from 48% to 61% in the implementation period (relative change 1.27, 95% CI 0.89, 1.81, p = 0.2), to 69% in sustainability period (relative to baseline 1.45, 95% CI 1.02, 2.08, p = 0.03).

CONCLUSION

An interdisciplinary team-based, multicycle, quality improvement intervention resulted in increased rates of early exposure to MOM.

Breastfeeding and Allergy Effect Modified by Genetic, Environmental, Dietary, and Immunological Factors

Breastfeeding (BF) is the most natural mode of nutrition. Its beneficial effect has been revealed in terms of both the neonatal period and those of lifelong effects. However, as for protection against allergy, there is not enough data. In the current narrative review, the literature within the last five years from clinical trials and population-based studies on breastfeeding and allergy from different aspects was explored. The aim of this review was to explain how different factors could contribute to the overall effect of BF. Special consideration was given to accompanying exposure to cow milk, supplement use, the introduction of solid foods, microbiota changes, and the epigenetic function of BF. Those factors seem to be modifying the impact of BF. We also identified studies regarding BF in atopic mothers, with SCFA as a main player explaining differences according to this status. Conclusion: Based on the population-based studies, breastfeeding could be protective against some allergic phenotypes, but the results differ within different study groups. According to the new research in that matter, the effect of BF could be modified by different genetic (HMO composition), environmental (cesarean section, allergen exposure), dietary (SCFA, introduction of solid food), and immunologic factors (IgG, IgE), thus partially explaining the variance.

Adaptation of the infant gut microbiome during the complementary feeding transition

The infant gut microbiome progresses in composition and function during the introduction of solid foods throughout the first year of life. The purpose of this study was to characterize changes in healthy infant gut microbiome composition, metagenomic functional capacity, and associated metabolites over the course of the complementary feeding period. Fecal samples were obtained at three ‘snapshot’ timepoints from infants participating in the ‘Nourish to Flourish’ pilot study: before the introduction of solid foods at approximately 4 months of age, after introducing solid foods at 9 months of age, and after continued diet diversification at 12 months of age. KEGG and taxonomy assignments were correlated with LC-MS metabolomic profiles to identify patterns of co-abundance. The composition of the microbiome diversified during the first year of life, while the functional capacity present in the gut microbiome remained stable. The introduction of solid foods between 4 and 9 months of age corresponded to a larger magnitude of change in relative abundance of sequences assigned to KEGG pathways and taxonomic assignments, as well as to stronger correlations with metabolites, compared to the magnitude of changes and number of correlations seen during continued diet diversification between 9 and 12 months of age. Changes in aqueous fecal metabolites were more strongly correlated with KEGG pathway assignments, while changes in lipid metabolites associated with taxonomic assignments, particularly between 9 and 12 months of age. This study establishes trends in microbiome composition and functional capacity occurring during the complementary feeding period and identifies potential metabolite targets for future investigations.

Pathways of atopic disease and neurodevelopmental impairment: assessing the evidence for infant antibiotics

INTRODUCTION

Epidemiologic studies are starting to report associations between antibiotic use in early life and neurodevelopmental disorders. Through mechanisms within the gut microbiota-brain axis, indeed, it is plausible that infant antibiotic treatment plays a role in the development of atopic disease and neurodevelopmental disorders.

AREAS COVERED

This narrative review summarizes and interprets published evidence on infant antibiotic use in future outcomes of atopic disease, and neurodevelopmental delay and disorders, including attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). To this end, we critically assess study bias from 2 main confounding factors, maternal/infant infection and infant feeding status. We also discuss common mechanisms that link atopy and neurodevelopment, and propose hypotheses related to immune activation and the gut microbiome.

EXPERT OPINION

Atopic disease and neurodevelopmental disorders share many risk factors and biological pathways. Infant antibiotic use has been linked to both disorders and is likely a marker for prenatal or infant infection. The mediating role of breastfeeding can also not be discounted. The exploration of causal pathways along the gut-brain axis leading towards neurodevelopmental impairment is evolving and of future interest.

Breastfeeding Affects Concentration of Faecal Short Chain Fatty Acids During the First Year of Life: Results of the Systematic Review and Meta-Analysis

Short chain fatty acids (SCFAs) are important metabolites of the gut microbiota. It has been shown that the microbiota and its metabolic activity in children are highly influenced by the type of diet and age. Our aim was to analyse the concentration of fecal SCFAs over two years of life and to evaluate the influence of feeding method on the content of these compounds in feces. We searched PubMed/MEDLINE/Embase/Ebsco/Cinahl/Web of Science from the database inception to 02/23/2021 without language restriction for observational studies that included an analysis of the concentration of fecal SCFAs in healthy children up to 3 years of age. The primary outcome measures-mean concentrations-were calculated. We performed a random-effects meta-analysis of outcomes for which ≥2 studies provided data. A subgroup analysis was related to the type of feeding (breast milk vs. formula vs. mixed feeding) and the time of analysis (time after birth). The initial search yielded 536 hits. We reviewed 79 full-text articles and finally included 41 studies (n = 2,457 SCFA analyses) in the meta-analysis. We found that concentrations of propionate and butyrate differed significantly in breastfed infants with respect to time after birth. In infants artificially fed up to 1 month of age, the concentration of propionic acid, butyric acid, and all other SCFAs is higher, and acetic acid is lower. At 1–3 months of age, a higher concentration of only propionic acid was observed. At the age of 3–6 months, artificial feeding leads to a higher concentration of butyric acid and the sum of SCFAs. We concluded that the type of feeding influences the content of SCFAs in feces in the first months of life. However, there is a need for long-term evaluation of the impact of the observed differences on health later in life and for standardization of analytical methods and procedures for the study of SCFAs in young children. These data will be of great help to other researchers in analyzing the relationships between fecal SCFAs and various physiologic and pathologic conditions in early life and possibly their impact on health in adulthood.

Technical Report: Breastfeeding and the Use of Human Milk

Breastfeeding and human milk are the normative standards for infant feeding and nutrition. The short- and long-term medical and neurodevelopmental advantages of breastfeeding make breastfeeding or the provision of human milk a public health imperative. The American Academy of Pediatrics (AAP) recommends exclusive breastfeeding for approximately 6 months after birth. Furthermore, the AAP supports continued breastfeeding, along with appropriate complementary foods introduced at about 6 months, as long as mutually desired by mother and child for 2 years or beyond. These recommendations are consistent with those of the World Health Organization (WHO). Medical contraindications to breastfeeding are rare. The AAP recommends that birth hospitals or centers implement maternity care practices shown to improve breastfeeding initiation, duration, and exclusivity. The Centers for Disease Control and Prevention and The Joint Commission monitor breastfeeding practices in United States hospitals. Pediatricians play a critical role in hospitals, their practices, and communities as advocates of breastfeeding and, thus, need to be trained about the benefits of breastfeeding for mothers and children and in managing breastfeeding. Efforts to improve breastfeeding rates must acknowledge existing disparities and the impact of racism in promoting equity in breastfeeding education, support, and services.

The effect of electronic job aid assisted one‐to‐one counselling to support exclusive breastfeeding among 0–5‐month‐old infants in rural Bangladesh

Exclusive breastfeeding (EBF) for the first 6 months has established benefits, yet had slow improvements globally. Little is known about electronic job aid‐assisted counselling to support EBF. As a secondary outcome of a cluster randomized controlled trial in Bangladesh, we assessed the effect of electronic job aid‐supported nutrition counselling and practical demonstration on EBF. We randomized pregnant women to one of five study arms in the trial and followed mother–child dyads until 2 years of age. Community health workers (CHWs) provided breastfeeding counselling with or without prenatal and complementary nutrient supplements in all four intervention arms. The comparison arm continued with the usual practice where mothers could receive nutrition counselling at routine antenatal and postnatal care, and during careseeking for childhood illnesses. We assessed breastfeeding indicators at birth and monthly until the child was 6 months old, in both intervention and comparison arms. To evaluate the effect of nutrition counselling on breastfeeding, we combined all four intervention arms and compared them with the comparison arm. Intervention newborns had half the risk (relative risk [RR]: 0.54, 95% confidence interval [CI]: 0.39, 0.76) of receiving prelacteal feeds than those in the comparison arm. EBF declined steeply in the comparison arm after 3 months of age. EBF was 16% higher in the intervention than the comparison arm at 4 months (RR: 1.16, 95% CI: 1.08, 1.23) and 22% higher at 5 months of age (RR: 1.22, 95% CI: 1.12, 1.33). Maternal background and household characteristics did not modify the intervention effect, and we observed no difference in EBF among caesarean versus vaginal births. Breastfeeding counselling and practical demonstration using an electronic job aid by CHWs are promising interventions to improve EBF and are scalable into existing community‐based programmes.

Using an electronic job aid, repeated, one‐to‐one counselling and practical demonstration to mothers by locally recruited CHWs reduced prelacteal feeding and improved EBF practice by delaying the early introduction of complementary food.

The positive effect of counselling on EBF remains similar with or without nutrient supplementation.

Electronic job aid supported counselling to promote breastfeeding should be integrated into existing community‐based maternal and child health programmes.

Gut Microbiota Dysbiosis in Childhood Vasculitis: A Perspective Comparative Pilot Study

Kawasaki disease (KD) and Henoch–Schönlein purpura (HSP) are the most frequent vasculitis in childhood. For both, a multifactorial mechanism has been hypothesised, with an abnormal immune response in genetically predisposed children. Gut microbiota (GM) alterations might trigger the hyperimmune reaction. Our aim was to explore the GM in KD and compare it with the GM of HSP and febrile children. Children diagnosed with KD, HSP and non-KD febrile illness (F) were enrolled. GM was profiled by 16S rRNA gene sequencing and compared with the profiles of healthy children from previous studies. We enrolled 13 KD, 10 HSP and 12 F children. Their GM significantly differed from controls, with an overall reduction in the relative abundance of beneficial taxa belonging to the Ruminococcaceae and Lachnospiraceae families. Potential KD and HSP signatures were identified, including smaller amounts of Dialister in the former, and Clostridium and Akkermansia in the latter. Notably, the GM structures of KD, HSP and F patients stratified by abdominal involvement, with more severe dysbiosis in those suffering from intestinal symptoms. This is the first study analysing GM in a mostly Caucasian cohort of KD and HSP children. Our data could open up new opportunities for childhood vasculitis treatment.

Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum

Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is influenced by breastfeeding exclusivity, and its role in infant gut microbiota assembly are not clear. To interrogate these questions, we examined the relationships among fecal, oral, breast skin, and human milk microbiota of 33 exclusively breastfeeding (EBF) and mixed-feeding (MF; human milk + infant formula) mother–infant pairs at 6 weeks postpartum. Here, we show that MF infants have a significantly more diverse oral microbiome comprised of lower relative abundances of Streptococcus and Gemella and higher abundances of Veillonella. Using both SourceTracker2 and FEAST, we demonstrate breast skin and infant saliva as the principal contributing sources to the human milk microbiota. Of the sampled sites, human milk and maternal stool were predicted to contribute the largest fraction to the infant fecal microbiome, but the majority of the community was estimated to arise from unknown sources. Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites. These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life.

Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life

Background

Current evidence suggests that the composition of infant formula (IF) affects the gut microbiome, intestinal function, and immune responses during infancy. However, the impact of IF on circulating lipid profiles in infants is still poorly understood. The objectives of this study were to (1) investigate how extensively hydrolyzed IF impacts serum lipidome compared to conventional formula and (2) to associate changes in circulatory lipids with gastrointestinal biomarkers including intestinal permeability.

Methods

In a randomized, double-blind controlled nutritional intervention study (n = 73), we applied mass spectrometry-based lipidomics to analyze serum lipids in infants who were fed extensively hydrolyzed formula (HF) or conventional, regular formula (RF). Serum samples were collected at 3, 9, and 12 months of age. Child’s growth (weight and length) and intestinal functional markers, including lactulose mannitol (LM) ratio, fecal calprotectin, and fecal beta-defensin, were also measured at given time points. At 3 months of age, stool samples were analyzed by shotgun metagenomics.

Results

Concentrations of sphingomyelins were higher in the HF group as compared to the RF group. Triacylglycerols (TGs) containing saturated and monounsaturated fatty acyl chains were found in higher levels in the HF group at 3 months, but downregulated at 9 and 12 months of age. LM ratio was lower in the HF group at 9 months of age. In the RF group, the LM ratio was positively associated with ether-linked lipids. Such an association was, however, not observed in the HF group.

Conclusion

Our study suggests that HF intervention changes the circulating lipidome, including those lipids previously found to be associated with progression to islet autoimmunity or overt T1D.

Clinical Trial Registration

[Clinicaltrials.gov], identifier [NCT01735123].

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.

Fecal Bacterial Communities Differ by Lactation Status in Postpartum Women and Their Infants

BACKGROUND

Previous research examined effects of human milk on the infant gut microbiota, but little attention has been given to the microbiota of lactating women.

RESEARCH AIM

To determine associations between exclusive human milk feeding and gut microbiota characteristics in mothers and infants at 6-weeks postpartum.

METHODS

A sample of mother-infant dyads (N = 24) provided fecal samples and questionnaire responses at 6-weeks postpartum as part of the Pregnancy, EAting & POstpartum Diapers study. Deoxyribonucleic acid was extracted from stool samples, followed by (V4) 16S ribosomal ribonucleic acid gene amplicon sequencing. Alpha and beta diversity, in addition to taxa differences, were compared by human milk exposure status, exclusive versus non-exclusive. A subset of dyads (those exclusively fed human milk; n = 14) was analyzed for shared bifidobacterial species using polymerase chain reaction.

RESULTS

Alpha diversity was significantly lower in exclusively human milk-fed infants. Maternal lactation status (exclusive vs. partial) and Shannon diversity were associated in univariate analysis but were no longer associated in multivariable regression including body mass index category in the model. Beta diversity (Sorensen dissimilarity) of fecal samples from women and infants was significantly associated with human milk feeding. Of six infants with Bifidobacterium longum subspecies longum in their fecal samples, all their mothers shared the same species.

CONCLUSION

Maternal gut microbiotas differ by lactation status, a relationship potentially confounded by body mass index category. Further research is needed to identify whether lactation directly influences the maternal gut microbiota, which may be another mechanism by which lactation influences health.