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

Association Between the Mode of Delivery and Infant Gut Microbiota Composition Up to 6 Months of Age: A Systematic Literature Review Considering the Role of Breastfeeding

CONTEXT

Cesarean section (CS), breastfeeding, and geographic location can influence the infant microbiota.

OBJECTIVE

In this systematic review, evidence of the association between mode of delivery and infant gut microbiota up to 6 months of age was evaluated, as was the role of breastfeeding in this association, according to PRISMA guidelines.

DATA SOURCE

The Pubmed, Web of Science, Scopus, Embase, Medical Database, and Open Grey databases were searched.

DATA EXTRACTION

A total of 31 observational studies with ≥2 infant stool collections up to the sixth month of age and a comparison of gut microbiota between CS and vaginal delivery (VD) were included.

DATA ANALYSIS

Infants born by CS had a lower abundance of Bifidobacterium and Bacteroides spp. at almost all points up to age 6 months. Populations of Lactobacillus, Bifidobacterium longum, Bifidobacterium catenulatum, and Escherichia coli were reduced in infants delivered by CS. Infants born by CS and exclusively breastfed had greater similarity with the microbiota of infants born by VD.

CONCLUSIONS

Species of Bifidobacterium and Bacteroides are potentially reduced in infants born by CS. Geographic location influenced bacterial colonization.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration no. 42017071285.

Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome

Complex dietary carbohydrate structures including β(1-4) galacto-oligosaccharides (GOS) are resistant to digestion in the upper gastrointestinal (GI) tract and arrive intact to the colon where they benefit the host by selectively stimulating microbial growth. Studies have reported the beneficial impact of GOS (alone or in combination with other prebiotics) by serving as metabolic substrates for modulating the assembly of the infant gut microbiome while reducing GI infections. N-Acetyl-D-lactosamine (LacNAc, Galβ1,4GlcNAc) is found in breast milk as a free disaccharide. This compound is also found as a component of human milk oligosaccharides (HMOs), which have repeating and variably branched lactose and/or LacNAc units, often attached to sialic acid and fucose monosaccharides. Human glycosyl-hydrolases do not degrade most HMOs, indicating that these structures have evolved as natural prebiotics to drive the proper assembly of the infant healthy gut microbiota. Here, we sought to develop a novel enzymatic method for generating LacNAc-enriched GOS, which we refer to as humanized GOS (hGOS). We showed that the membrane-bound β-hexosyl transferase (rBHT) from Hamamotoa (Sporobolomyces) singularis was able to generate GOS and hGOS from lactose and N-Acetyl-glucosamine (GlcNAc). The enzyme catalyzed the regio-selective, repeated addition of galactose from lactose to GlcNAc forming the β-galactosyl linkage at the 4-position of the GlcNAc and at the 1-position of D-galactose generating, in addition to GOS, LacNAc, and Galactosyl-LacNAc trisaccharides which were produced by two sequential transgalactosylations. Humanized GOS is chemically distinct from HMOs, and its effects in vivo have yet to be determined. Thus, we evaluated its safety and demonstrated the prebiotic's ability to modulate the gut microbiome in 6-week-old C57BL/6J mice. Longitudinal analysis of gut microbiome composition of stool samples collected from mice fed a diet containing hGOS for 5 weeks showed a transient reduction in alpha diversity. Differences in microbiome community composition mostly within the Firmicutes phylum were observed between hGOS and GOS, compared to control-fed animals. In sum, our study demonstrated the biological synthesis of hGOS, and signaled its safety and ability to modulate the gut microbiome in vivo, promoting the growth of beneficial microorganisms, including Bifidobacterium and Akkermansia.

The role of probiotics and postbiotics in modulating the gut microbiome-immune system axis in the pediatric age

The complex microbial community of the gut microbiome plays a fundamental role in driving development and function of the human immune system. This phenomenon is named the gut microbiome-immune system axis. When operating optimally, this axis influences both innate and adaptive immunity, which orchestrates the maintenance of crucial elements of host-microorganisms symbiosis, in a dialogue that modulates responses in the most beneficial way. Growing evidence reveals some environmental factors which can positively and negatively modulate the gut microbiome-immune system axis with consequences on the body health status. Several conditions which increasingly affect the pediatric age, such as allergies, autoimmune and inflammatory disorders, arise from a failure of the gut microbiome-immune system axis. Prenatal or postnatal modulation of this axis through some interventional strategies (including diet, probiotics and postbiotics), may lead to a positive gene-environment interaction with improvement of immune-modulatory effects and final positive effect on human health. In particular probiotics and postbiotics exerting pleiotropic regulatory actions on the gut-microbiome-immune system axis provide an innovative preventive and therapeutic strategy for many pediatric conditions.

Implication of Human Bacterial Gut Microbiota on Immune-Mediated and Autoimmune Dermatological Diseases and Their Comorbidities: A Narrative Review

During the last decade, the advent of modern sequencing methods (next generation techniques, NGS) has helped describe the composition of the human gut microbiome, enabling us to understand the main characteristics of a healthy gut microbiome and, conversely, the magnitude of its disease-related changes. This new knowledge has revealed that healthy gut microbiota allow the maintenance of several crucial physiological functions, such as the ability to regulate the innate and adaptive immune systems. Increasing evidence has pointed out a condition of dysbiosis in several autoimmune/immune mediated dermatological conditions and specific gut microbial signatures have also been reported to correlate with clinical and prognostic parameters of such diseases. Based on a literature search of relevant published articles, this review debates the current knowledge and the possible pathogenic implications of bacterial gut microbiota composition assessed through NGS techniques in systemic lupus erythematosus, atopic dermatitis, psoriasis, and alopecia areata. Evidence of a potential role of specific gut microbiota signatures in modulating the clinical course of such diseases and their main comorbidities has been also reviewed.

Microbiota and Metabolites as Factors Influencing Blood Pressure Regulation

The study of microbes has rapidly expanded in recent years due to a surge in our understanding that humans host a plethora of commensal microbes, which reside in their bodies and depending upon their composition, contribute to either normal physiology or pathophysiology. This article provides a general foundation for learning about host-commensal microbial interactions as an emerging area of research. The article is divided into two sections. The first section is dedicated to introducing commensal microbiota and its known effects on the host. The second section is on metabolites, which are biochemicals that the host and the microbes use for bi-directional communication with each other. Together, the sections review what is known about how microbes interact with the host to impact cardiovascular physiology, especially blood pressure regulation. © 2021 American Physiological Society. Compr Physiol 11:1731-1757, 2021.

Human Milk Microbiota in an Indigenous Population Is Associated with Maternal Factors, Stage of Lactation, and Breastfeeding Practices

BACKGROUND

Human milk contains a diverse community of bacteria that are modified by maternal factors, but whether these or other factors are similar in developing countries has not been explored. Our objective was to determine whether the milk microbiota was modified by maternal age, BMI, parity, lactation stage, subclinical mastitis (SCM), and breastfeeding practices in the first 6 mo of lactation in an indigenous population from Guatemala.

METHODS

For this cross-sectional study, Mam-Mayan indigenous mothers nursing infants aged <6 mo were recruited. Unilateral human milk samples were collected (n = 86) and processed for 16S rRNA sequencing at the genus level. Microbial diversity and relative abundance were compared with maternal factors [age, BMI, parity, stage of lactation, SCM, and 3 breastfeeding practices (exclusive, predominant, mixed)] obtained through questionnaires.

RESULTS

Streptococcus was the most abundant genus (33.8%), followed by Pseudomonas (18.7%) and Sphingobium (10.7%) but relative abundance was associated with maternal factors. First, Lactobacillus and Streptococcus were more abundant in early lactation whereas the common oral (Leptotrichia) and environmental (Comamonas) bacteria were more abundant in established lactation. Second, Streptococcus,Lactobacillus,Lactococcus,Leuconostoc, and Micrococcus had a higher abundance in multiparous mothers compared with primiparous mothers. Third, a more diverse microbiota characterized by a higher abundance of lactic acid bacteria (Lactobacillus,Leuconostoc, and Lactococcus), Leucobacter, and Micrococcus was found in mothers with a healthy BMI. Finally, distinct microbial communities differed by stage of lactation and by exclusive, predominant, or mixed breastfeeding practices.

CONCLUSION

Milk bacterial communities in an indigenous community were associated with maternal factors. Higher microbial diversity was supported by having a healthy BMI, the absence of SCM, and by breastfeeding. Interestingly, breastfeeding practices when assessed by lactation stage were associated with distinct microbiota profiles.

Impact of Maternal Nutritional Supplementation during Pregnancy and Lactation on the Infant Gut or Breastmilk Microbiota: A Systematic Review

Recent evidence indicates that maternal dietary intake, including dietary supplements, during pregnancy and lactation may alter the infant gut or breastmilk microbiota, with implications for health outcomes in both the mother and infant. To review the effects of maternal nutritional supplementation during pregnancy and lactation on the infant gut or breastmilk microbiota a systematic literature search was conducted. A total of 967 studies published until February 2020 were found, 31 were eligible and 29 randomized control trials were included in the qualitative synthesis. There were 23 studies that investigated the effects of probiotic supplementation, with the remaining studies investigating vitamin D, prebiotics or lipid-based nutrient supplements (LNS). The effects of maternal nutritional supplementation on the infant gut microbiota or breastmilk microbiota were examined in 21 and 12 studies, respectively. Maternal probiotic supplementation during pregnancy and lactation generally resulted in the probiotic colonization of the infant gut microbiota, and although most studies also reported alterations in the infant gut bacterial loads, there was limited evidence of effects on bacterial diversity. The data available show that maternal probiotic supplementation during pregnancy or lactation results in probiotic colonization of the breastmilk microbiota. There were no observed effects between probiotic supplementation and breastmilk bacterial counts of healthy women, however, administration of Lactobacillus probiotic to nursing women affected by mastitis was associated with significant reductions in breastmilk Staphylococcal loads. Maternal LNS supplementation during pregnancy and lactation increased bacterial diversity in the infant gut, whilst vitamin D and prebiotic supplementation did not alter either infant gut bacterial diversity or counts. Heterogeneity in study design precludes any firm conclusions on the effects of maternal nutritional supplementation during pregnancy and lactation on the infant gut or breastmilk microbiota, warranting further research.

Early Life Microbiota Colonization at Six Months of Age: A Transitional Time Point

Background

Early life gut microbiota is involved in several biological processes, particularly metabolism, immunity, and cognitive neurodevelopment. Perturbation in the infant’s gut microbiota increases the risk for diseases in early and later life, highlighting the importance of understanding the connections between perinatal factors with early life microbial composition. The present research paper is aimed at exploring the prenatal and postnatal factors influencing the infant gut microbiota composition at six months of age.

Methods

Gut microbiota of infants enrolled in the longitudinal, prospective, observational study “A.MA.MI” (Alimentazione MAmma e bambino nei primi MIlle giorni) was analyzed. We collected and analyzed 61 fecal samples at baseline (meconium, T0); at six months of age (T2), we collected and analyzed 53 fecal samples. Samples were grouped based on maternal and gestational weight factors, type of delivery, type of feeding, time of weaning, and presence/absence of older siblings. Alpha and beta diversities were evaluated to describe microbiota composition. Multivariate analyses were performed to understand the impact of the aforementioned factors on the infant’s microbiota composition at six months of age.

Results

Different clustering hypotheses have been tested to evaluate the impact of known metadata factors on the infant microbiota. Neither maternal body mass index nor gestational weight gain was able to determine significant differences in infant microbiota composition six months of age. Concerning the type of feeding, we observed a low alpha diversity in exclusive breastfed infants; conversely, non-exclusively breastfed infants reported an overgrowth of Ruminococcaceae and Flavonifractor. Furthermore, we did not find any statistically significant difference resulting from an early introduction of solid foods (before 4 months of age). Lastly, our sample showed a higher abundance of clostridial patterns in firstborn babies when compared to infants with older siblings in the family.

Conclusion

Our findings showed that, at this stage of life, there is not a single factor able to affect in a distinct way the infants’ gut microbiota development. Rather, there seems to be a complex multifactorial interaction between maternal and neonatal factors determining a unique microbial niche in the gastrointestinal tract.

The infant gut microbiota at 12 months of age is associated with human milk exposure but not with maternal pre-pregnancy body mass index or infant BMI-for-age z-scores

BACKGROUND

As obesity rates continue to rise, it is increasingly important to understand factors that can influence body weight and growth, especially from an early age. The infant gut microbiota has broad effects on a variety of bodily processes, but its relation to infant growth is not yet fully characterized. Since the infant gut microbiota is closely related to breastfeeding practices and maternal health, understanding the relationship between these factors and infant growth may provide insight into the origins of childhood obesity.

OBJECTIVES

Identify the relationship between human milk exposure, maternal pre-pregnancy body mass index (BMI), the infant gut microbiota, and 12-month-old BMI-for-age z-scores (12M BAZ) to identify key factors that shape infant growth.

METHODS

Two Michigan cohorts (ARCHGUT and BABYGUT) comprised of a total of 33 mother-infant dyads provided infant fecal samples at 12M. After DNA extraction, amplification, and sequencing of the V4 16S rRNA region using Illumina MiSeq v2 Chemistry, gut bacterial diversity metrics were analyzed in relation to human milk exposure, maternal pre-pregnancy BMI, and infant growth parameters.

RESULTS

Recent human milk exposure was inversely related to maternal pre-pregnancy BMI and most strongly associated with infant gut bacterial community membership and individual gut microbiota richness differences. Maternal pre-pregnancy BMI was not associated with the infant gut microbiota after adjusting for human milk exposure. However, maternal pre-pregnancy BMI was the only factor significantly associated with 12M BAZ.

CONCLUSIONS

Human milk exposure is one of the central influences on the infant gut microbiota at 12M of age. However, the lack of association between the infant gut microbiota and 12M-old infant BAZ suggests that genetic, physiological, dietary, and other environmental factors may play a more direct role than the gut microbiota in determining infant BAZ at 12M.

Breast Milk Virome and Bacterial Microbiome Resilience in Kenyan Women Living with HIV

Breast milk is nutritionally and immunologically beneficial in early life but is also a potential source of infection. Little is known about breast milk microbiota of women living with HIV (WLHIV), the impact of severe immunosuppression, and the contribution to mortality of HIV-exposed infants. Here, we performed metagenomic sequencing to characterize the bacterial microbiome and DNA virome of breast milk samples at 1 month postpartum from Kenyan WLHIV who were not receiving combination antiretroviral therapy (cART), 23 women with CD4 counts of <250 and 30 women with CD4 of >500; and additionally, 19 WLHIV with infants that lived and 26 WLHIV with infants that died during the first 2 years of life were included. We found that breast milk bacterial microbiomes in this study population were highly diverse but shared a core community composed of the Streptococcaceae, Staphylococcaceae, Moraxellaceae, and Eubacteriaceae families. The breast milk virome was dominated by human cytomegalovirus (CMV) and included the bacteriophage families Myoviridae, Siphoviridae, and Podoviridae. Bacterial microbiome and virome profiles and diversity were not significantly altered by HIV immunosuppression, as defined by a CD4 of <250. CMV viral load was not associated with maternal CD4 counts or infant mortality. In conclusion, we show that the core bacterial and viral communities are resilient in breast milk despite immunosuppression in WLHIV.

IMPORTANCE Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Although most studies focus on the diverse breast milk bacterial communities, little is known about the viral communities harbored in breast milk. We performed the first breast milk virome study of an HIV population. In this study cohort of Kenyan women living with HIV from the pre-antiretroviral therapy era, we found that breast milk harbors a core bacterial microbiome and a virome dominated by human cytomegalovirus. The virome and bacterial microbiome were not substantially altered by immunosuppression or associated with infant mortality. Together, these findings indicate resilience of the microbial community in breast milk compartmentalization. These findings advance out fundamental understanding of the breast milk core microbiome and virome interactions in the context of HIV disease.

A good start in life is important-perinatal factors dictate early microbiota development and longer term maturation

Maternal health status is vital for the development of the offspring of humans, including physiological health and psychological functions. The complex and diverse microbial ecosystem residing within humans contributes critically to these intergenerational impacts. Perinatal factors, including maternal nutrition, antibiotic use and maternal stress, alter the maternal gut microbiota during pregnancy, which can be transmitted to the offspring. In addition, gestational age at birth and mode of delivery are indicated frequently to modulate the acquisition and development of gut microbiota in early life. The early-life gut microbiota engages in a range of host biological processes, particularly immunity, cognitive neurodevelopment and metabolism. The perturbed early-life gut microbiota increases the risk for disease in early and later life, highlighting the importance of understanding relationships of perinatal factors with early-life microbial composition and functions. In this review, we present an overview of the crucial perinatal factors and summarise updated knowledge of early-life microbiota, as well as how the perinatal factors shape gut microbiota in short and long terms. We further discuss the clinical consequences of perturbations of early-life gut microbiota and potential therapeutic interventions with probiotics/live biotherapeutics.

Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial

The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health. In this study, we collected fecal samples at Day-10 (D10) and 4-months corrected-age (4M) from 227 moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management. A total of 320 samples underwent 16S amplicon sequencing, and shotgun metagenomic sequencing was performed on 94 samples from the 4M time point. The microbiome of babies whose families lived in lower socioeconomic status (SES) areas exhibited a significantly higher microbial alpha diversity at D10 (Wilcoxon test, p = 0.021), greater abundance of Bifidobacterium (linear model, q = 0.020) at D10 and Megasphaera (q = 0.031) at 4M. Hospital of birth explained 5.2% of the observed variance in 4M samples (PERMANOVA, p = 0.038), with Staphylococcus aureus more abundant in fecal samples from babies born in Middlemore hospital (linear model, q = 0.016). Maternal antibiotic (Wilcoxon test, p = 0.013) and probiotic (p = 0.04) usage within the four-week period before sample collection was associated with a reduction in the alpha diversity of D10 samples. Infant probiotic intake explained 2.1% (PERMANOVA, p = 0.021) of the variance in the D10 microbial profile with increased Lactobacillus (linear model, q = 1.1 × 10⁻¹⁰) levels. At 4M, the microbiome of infants who were breastmilk fed had reduced alpha diversity when compared to non-breastmilk fed infants (Wilcoxon test, p < 0.05). Although causality cannot be inferred within our study, we conclude that in MLPT babies, maternal socioeconomic factors, as well as the perinatal medical environment and nutrition impact on the development of the newborn microbiome.

The multifaceted roles of breast milk antibodies

Neonates are born with an immature immune system and rely on the transfer of immunity from their mothers. Maternal antibodies are transferred via the placenta and breast milk. Although the role of placentally transferred immunoglobulin G (IgG) is established, less is known about the selection of antibodies transferred via breast milk and the mechanisms by which they provide protection against neonatal disease. Evidence suggests that breast milk antibodies play multifaceted roles, preventing infection and supporting the selection of commensals and tolerizing immunity during infancy. Here, we discuss emerging data related to the importance of breast milk antibodies in neonatal immunity and development.

The crucial role of early-life gut microbiota in the development of type 1 diabetes

Early-life healthy gut microbiota has a profound implication on shaping the mucosal immune system as well as maintaining healthy status later in life, especially at the prenatal or neonatal stages, while intestinal dysbiosis in early life is associated with several autoimmune diseases, including type 1 diabetes (T1D). Since the gut microbiome is potentially modifiable, optimizing the intestinal bacterial composition in early life may be a novel option for T1D prevention. In this review, we will review current data depicting the crucial role of early-life intestinal microbiome in the development of T1D and discuss the possible mechanisms whereby early-life intestinal microbiome influences the T1D progression. We also summarize recent findings on environmental factors affecting gut microbiota colonization and interventions that may successfully alter microbial composition to discuss potential means of preventing T1D progression in at-risk children.

Transient Effect of Infant Formula Supplementation on the Intestinal Microbiota

Breastfeeding is the gold standard for feeding infants because of its long-term benefits to health and development, but most infants in the United States are not exclusively breastfed in the first six months. We enrolled 24 infants who were either exclusively breastfed or supplemented with formula by the age of one month. We collected diet information, stool samples for evaluation of microbiotas by 16S rRNA sequencing, and blood samples for assessment of immune development by flow cytometry from birth to 6 months of age. We further typed the Bifidobacterium strains in stool samples whose 16S rRNA sequencing showed the presence of Bifidobacteriaceae. Supplementation with formula during breastfeeding transiently changed the composition of the gut microbiome, but the impact dissipated by six months of age. For example, Bifidobacterium longum, a bacterial species highly correlated with human milk consumption, was found to be significantly different only at 1 month of age but not at later time points. No immunologic differences were found to be associated with supplementation, including the development of T-cell subsets, B cells, or monocytes. These data suggest that early formula supplementation, given in addition to breast milk, has minimal lasting impact on the gut microbiome or immunity.

The Triad Mother-Breast Milk-Infant as Predictor of Future Health: A Narrative Review

The benefits of human milk for both mother and infant are widely acknowledged. Human milk could represent a link between maternal and offspring health. The triad mother-breast milk-infant is an interconnected system in which maternal diet and lifestyle might have effects on infant's health outcome. This link could be in part explained by epigenetics, even if the underlining mechanisms have not been fully clarified yet. The aim of this paper is to update the association between maternal diet and human milk, pointing out how maternal diet and lifestyle could be associated with breast-milk composition, hence with offspring's health outcome.

How to promote exclusive breastfeeding in Ireland: a qualitative study on views of Chinese immigrant mothers

BACKGROUND

The exclusive breastfeeding rate in Ireland is very low with extremely slow annual growth. The population of immigrants in Ireland is increasing. Improving exclusive breastfeeding practice among immigrants may contribute to the overall improvement of exclusive breastfeeding rates in Ireland. This study was conducted to elicit suggestions on improving exclusive breastfeeding rate for the first 6 months among Chinese immigrants in Ireland.

METHODS

Fourteen semi-structured in-depth interviews were conducted with Chinese immigrant mothers residing in Ireland, who breastfed exclusively for 4 to 6 months. Interviews were recorded and transcribed in Chinese. Data were analyzed using a qualitative thematic analysis. Themes were developed through categorization of codes and via in-depth discussion between two researchers.

RESULTS

Themes generated from the thematic content analysis were: 1) suggestions for new mothers: being strong mentally and getting support from family and friends; 2) suggestions for employers: creating a supportive workplace by setting up private rooms and breastmilk storage facilities; 3) suggestions for healthcare professionals: advocating breastfeeding in the hospital and addressing cultural differences by recruiting multilingual staff; 4) suggestions for the government: promoting breastfeeding by initiating societal and policy changes.

CONCLUSIONS

The key findings emerging from this study may be considered in the development of breastfeeding promotion strategies in Ireland. Our findings could also have implications for other English-speaking countries with low rates of exclusive breastfeeding.

Implementation of microbiota analysis in clinical trials for cystic fibrosis lung infection: Experience from the OligoG phase 2b clinical trials

Culture-independent microbiota analysis is widely used in research and being increasingly used in translational studies. However, methods for standardisation and application of these analyses in clinical trials are limited. Here we report the microbiota analysis that accompanied two phase 2b clinical trials of the novel, non-antibiotic therapy OligoG CF-5/20 for cystic fibrosis (CF) lung infection. Standardised protocols (DNA extraction, PCR, qPCR and 16S rRNA gene sequencing analysis) were developed for application to the Pseudomonas aeruginosa (NCT02157922) and Burkholderia cepacia complex (NCT02453789) clinical trials involving 45 and 13 adult trial participants, respectively. Microbiota analysis identified that paired sputum samples from an individual participant, taken within 2 h of each other, had reproducible bacterial diversity profiles. Although culture microbiology had identified patients as either colonised by P. aeruginosa or B. cepacia complex species at recruitment, microbiota analysis revealed patient lung infection communities were not always dominated by these key CF pathogens. Microbiota profiles were patient-specific and remained stable over the course of both clinical trials (6 sampling points over the course of 140 days). Within the Burkholderia trial, participants were infected with B. cenocepacia (n = 4), B. multivorans (n = 6), or an undetermined species (n = 3). Colonisation with either B. cenocepacia or B. multivorans influenced the overall bacterial community structure in sputum. Overall, we have shown that sputum microbiota in adults with CF is stable over a 2 h time-frame, suggesting collection of a single sample on a collection day is sufficient to capture the microbiota diversity. Despite the uniform pathogen culture-positivity status at recruitment, trial participants were highly heterogeneous in their lung microbiota. Understanding the microbiota profiles of individuals with CF ahead of future clinical trials would be beneficial in the context of patient stratification and trial design.

Noncoding RNAs: Regulatory Molecules of Host-Microbiome Crosstalk

Recent emerging evidence has revealed that regulatory noncoding RNAs (microRNAs, circular RNAs) modulate host-microbe interactions and they have been proposed as potential biomarkers of the host's response to microbiome-linked pathologies such as cancers, obesity, and neurodegenerative diseases. Interactions between microRNAs and circular RNAs, however, increase the complexity of the mechanisms that modulate host-microbe interactions. Current knowledge on these noncoding RNAs (ncRNAs) is mainly generated from well controlled germ-free or knockout (small) animal models. Application of such knowledge to effective modulation outcomes in humans (and livestock) is challenging due to the complex nature of microbiome-linked pathologies in larger outbred animals that constantly interact with the changing environment. This review critically discusses the findings of regulatory noncoding RNAs and their roles in microbiome-linked pathologies in small and large animals and provides insights on their roles as potential therapeutic agents to improve human (and livestock) health.

Maternal exposures and the infant gut microbiome: a systematic review with meta-analysis

Early life, including the establishment of the intestinal microbiome, represents a critical window of growth and development. Postnatal factors affecting the microbiome, including mode of delivery, feeding type, and antibiotic exposure have been widely investigated, but questions remain regarding the influence of exposures in utero on infant gut microbiome assembly. This systematic review aimed to synthesize evidence on exposures before birth, which affect the early intestinal microbiome. Five databases were searched in August 2019 for studies exploring pre-pregnancy or pregnancy 'exposure' data in relation to the infant microbiome. Of 1,441 publications identified, 76 were included. Factors reported influencing microbiome composition and diversity included maternal antibiotic and probiotic uses, dietary intake, pre-pregnancy body mass index (BMI), gestational weight gain (GWG), diabetes, mood, and others. Eleven studies contributed to three meta-analyses quantifying associations between maternal intrapartum antibiotic exposure (IAP), BMI and GWG, and infant microbiome alpha diversity (Shannon Index). IAP, maternal overweight/obesity and excessive GWG were all associated with reduced diversity. Most studies were observational, few included early recruitment or longitudinal follow-up, and the timing, frequency, and methodologies related to stool sampling and analysis were variable. Standardization and collaboration are imperative to enhance understanding in this complex and rapidly evolving area.

Human Milk-Based or Bovine Milk-Based Fortifiers Differentially Impact the Development of the Gut Microbiota of Preterm Infants

Background: Preterm infants are exposed to different dietary inputs during their hospitalization in the neonatal intensive care unit (NICU). These include human milk (HM), with a human milk-based (HMF) or a bovine milk-based (BMF) fortifier, or formula. Milk consumption and the type of fortification will cause changes in the gut microbiota structure of preterm infants. This study aimed to characterize the gut microbiota of PT infant according to the type of feeding and the type of HM fortification and its possible association with infant's growth. Methods: Ninety-seven infants born ≤33 wks of gestation or <1,500 g were followed during the hospitalization period in the NICU after birth until discharge. Clinical and dietary information was collected, including mode of delivery, pregnancy complications, mechanical ventilation, use of antibiotics, weight, and type and amount of milk consumed. To characterize the gut microbiota composition, weekly stool samples were collected from study participants. The V3-V4 region of the 16S rRNA bacterial gene was Sequenced using Illumina MiSeq technology. Results: After birth, black maternal race, corrected gestational age (GA) and exposure to pregnancy complications, had a significant effect on gut microbial diversity and the abundance of Enterococcus, Veillonella, Bifidobacterium, Enterobacter, and Bacteroides. Over the course of hospitalization, corrected GA and exposure to chorioamnionitis remained to have an effect on gut microbial composition. Two different enterotypes were found in the gut microbiota of preterm infants. One enriched in Escherichia-Shigella, and another enriched in uncharacterized Enterobacteriaceae, Klebsiella and Clostridium sensu stricto 1. Overall, HM and fortification with HMF were the most common feeding strategies. When consuming BMF, PT infants had higher growth rates than those consuming HMF. Milk and type of fortification were significantly associated with the abundance of Clostridium sensu stricto 1, Bifidobacterium and Lactobacillus. Conclusions: This observational study shows the significant association between milk consumption and the exposure to HMF or BMF fortification in the fecal microbiota composition of preterm infants. Additionally, these results show the effect of other perinatal factors in the establishment and development of PT infant's gut microbiota.

The impact of Caesarean section on the infant gut microbiome

AIM

Description of the impact of caesarean section on the infant gut microbiome, infant health and solutions to restore the dysbiosis.

METHODS

We searched PubMed and Google Scholar for relevant articles. Only articles published in English were selected. Separate searches were performed for each topic. We selected 60 articles published between 1999 and 2019 by extracting subject headings and key words of interest for this topic.

RESULTS

Caesarean section is an obstetrical procedure that is increasing in prevalence worldwide. On top of the maternal and neonatal risks that this procedure carries, it also induces a dysbiosis of the infant intestinal microbiome possibly challenging the health outcome for the infant. Antibiotics administered during Caesarean deliveries contribute to the development of the gut microbiome. Nonetheless, breastfeeding and several interventions such as vaginal seeding and supplementation with probiotics, prebiotics and synbiotics may contribute to the restoration of the dysbiosis.

CONCLUSION

Caesarean section is associated with the development of an imbalance of the infant gut microbiome. Long-term consequences of this imbalance are debated. Besides breastfeeding, other strategies to restore this dysbiosis need further studies before they can be recommended.

Gut microbiota and aging

Aging is characterized by the functional decline of tissues and organs and increased risk of aging-associated disorders, which pose major societal challenges and are a public health priority. Despite extensive human genetics studies, limited progress has been made linking genetics with aging. There is a growing realization that the altered assembly, structure and dynamics of the gut microbiota actively participate in the aging process. Age-related microbial dysbiosis is involved in reshaping immune responses during aging, which manifest as immunosenescence (insufficiency) and inflammaging (over-reaction) that accompany many age-associated enteric and extraenteric diseases. The gut microbiota can be regulated, suggesting a potential target for aging interventions. This review summarizes recent findings on the physiological succession of gut microbiota across the life-cycle, the roles and mechanisms of gut microbiota in healthy aging, alterations of gut microbiota and aging-associated diseases, and the gut microbiota-targeted anti-aging strategies.

Clinical characteristics influence cultivable-bacteria composition in the meconium of Indonesian neonates

Background

Microbial colonization of a neonate's gastrointestinal tract has significant perinatal and lifetime health consequences. However, information regarding the profile of meconium microbiota in neonates and the influence of clinical parameters are lacking in the Indonesian population. This study aimed to preliminary investigate the profile of cultivable bacterial diversity of meconium isolated from neonates born at Cipto Mangunkusumo Hospital (CMH), Jakarta. The cultivable bacteria were isolated from meconium samples and were then processed for cultivation and molecular identification.

Results

Fourteen neonates were enrolled as described, i.e., seven hyperbilirubinemia (Hyp) and seven non-Hyp with ten neonates delivered by cesarean section (CS) and four others by vaginal route (VR), and with five exclusive breastfeeding (Ebf), four formula milk, and five combinations. Microbiological identification, molecular 16S rDNA PCR-Sanger sequencing, and PCA analysis of cultivable bacteria isolated from meconium showed Firmicutes' predominance (84.41%), with an abundant population of Staphylococcus, which consist of S. hominis, S. epidermidis, and S. haemolyticus. The influence of mode of delivery showed a lower diversity than the CS populates the VR, but their composition was similar. Concurrently, between feeding patterns, the genera profile did not show much difference; in the non-Ebf group, the total amount of Staphylococcus and Bacillus showed a higher amount but a less diverse. Interestingly, the non-Hyp group showed more abundant and diverse Staphylococcus than that of the Hyp group. In contrast, neonates diagnosed with NEC and proven sepsis showed the same pattern of Staphylococcus domination.

Conclusion

Staphylococcus predominated the composition of cultivable bacteria in neonates meconium. Due to the small sample size, only the hyperbilirubinemia parameter significantly influenced the profile, i.e., Staphylococcus's proportion (p = 0.037).

The Microbiota of the Human Mammary Ecosystem

Human milk contains a dynamic and complex site-specific microbiome, which is not assembled in an aleatory way, formed by organized microbial consortia and networks. Presence of some genera, such as Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium (formerly known as Propionibacterium), Lactobacillus, Lactococcus and Bifidobacterium, has been detected by both culture-dependent and culture-independent approaches. DNA from some gut-associated strict anaerobes has also been repeatedly found and some studies have revealed the presence of cells and/or nucleic acids from viruses, archaea, fungi and protozoa in human milk. Colostrum and milk microbes are transmitted to the infant and, therefore, they are among the first colonizers of the human gut. Still, the significance of human milk microbes in infant gut colonization remains an open question. Clinical studies trying to elucidate the question are confounded by the profound impact of non-microbial human milk components to intestinal microecology. Modifications in the microbiota of human milk may have biological consequences for infant colonization, metabolism, immune and neuroendocrine development, and for mammary health. However, the factors driving differences in the composition of the human milk microbiome remain poorly known. In addition to colostrum and milk, breast tissue in lactating and non-lactating women may also contain a microbiota, with implications in the pathogenesis of breast cancer and in some of the adverse outcomes associated with breast implants. This and other open issues, such as the origin of the human milk microbiome, and the current limitations and future prospects are addressed in this review.

The Gut Microbiota: A Promising Target in the Relation between Complementary Feeding and Child Undernutrition

Child undernutrition is a major public health challenge that is persistent and disproportionately prevalent in low- and middle-income countries. Undernourished children face adverse health, economic, and social consequences that can be intergenerational. The first 1000 days of life, from conception until the child's second birthday, constitute the period of greatest vulnerability to undernutrition. The transition process from milk-based diets to solid, semi-solid, and soft food and liquids other than milk, referred to as complementary feeding (CF), occurs between the age of 6 mo and 2 y. CF practices that do not meet the WHO's guiding principles and are lacking in both quality and quantity increase susceptibility to undernutrition, restrict growth, and jeopardize child development and survival. The gut microbiota develops toward an adult-like configuration within the first 2-3 y of life. Recent studies suggest that significant changes in the gut microbial composition and functional capacity occur during the CF period, but these studies were conducted in high-income countries. Research in low- and middle-income countries, on the other hand, has implicated a disrupted gut microbiota in child undernutrition, and animal experiments reveal the potential for a causal relation. Given the growing body of evidence for a plausible role of the gut microbiota in the link between CF and undernutrition, microbiota-targeted complementary food may be a promising treatment modality for undernutrition management. The aims of this paper are to review the evidence for the relation between CF and undernutrition and to highlight the potential of the gut microbiota to be a promising target in this relation. Our summary of the current state of the knowledge in this area provides a foundation for future research and helps inform the design of interventions targeting the gut microbiota to combat child undernutrition and promote healthy growth.

Vitamin D supplementation in pregnancy and early infancy in relation to gut microbiota composition and C. difficile colonization: implications for viral respiratory infections

In Canada and the US, the infant diet is supplemented with vitamin D via supplement drops or formula. Pregnant and nursing mothers often take vitamin D supplements. Since little is known about the impact of this supplementation on infant gut microbiota, we undertook a study to determine the association between maternal and infant vitamin D supplementation, infant gut microbiota composition and Clostridioides difficile colonization in 1,157 mother-infant pairs of the CHILD (Canadian Healthy Infant Longitudinal Development) Cohort Study over 2009-2012. Logistic and MaAsLin regression were employed to assess associations between vitamin D supplementation, and C. difficile colonization, or other gut microbiota, respectively. Sixty-five percent of infants received a vitamin D supplement. Among all infants, infant vitamin D supplementation was associated with a lower abundance of genus Megamonas (q = 0.01) in gut microbiota. Among those exclusively breastfed, maternal prenatal supplementation was associated with lower abundance of Bilophila (q = 0.01) and of Lachnospiraceae (q = 0.02) but higher abundance of Haemophilus (q = 0.02). There were no differences in microbiota composition with vitamin D supplementation among partially and not breastfed infants. Neither infant nor maternal vitamin D supplementation were associated with C. difficile colonization, after adjusting for breastfeeding status and other factors. However, maternal consumption of vitamin-D fortified milk reduced the likelihood of C. difficile colonization in infants (adjustedOR: 0.40, 95% CI: 0.19-0.82). The impact of this compositional difference on later childhood health, especially defense against viral respiratory infection, may go beyond the expected effects of vitamin D supplements and remains to be ascertained.

Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort

BACKGROUND

Obesity is an established risk factor for multiple cancer types. Lower microbial richness has been linked to obesity, but human studies are inconsistent, and associations of early-life body mass index (BMI) with the fecal microbiome and metabolome are unknown.

METHODS

We characterized the fecal microbiome (n = 563) and metabolome (n = 340) in the Northern Finland Birth Cohort 1966 using 16S rRNA gene sequencing and untargeted metabolomics. We estimated associations of adult BMI and BMI history with microbial features and metabolites using linear regression and Spearman correlations (rs ) and computed correlations between bacterial sequence variants and metabolites overall and by BMI category.

RESULTS

Microbial richness, including the number of sequence variants (rs = -0.21, P < 0.0001), decreased with increasing adult BMI but was not independently associated with BMI history. Adult BMI was associated with 56 metabolites but no bacterial genera. Significant correlations were observed between microbes in 5 bacterial phyla, including 18 bacterial genera, and metabolites in 49 of the 62 metabolic pathways evaluated. The genera with the strongest correlations with relative metabolite levels (positively and negatively) were Blautia, Oscillospira, and Ruminococcus in the Firmicutes phylum, but associations varied by adult BMI category.

CONCLUSIONS

BMI is strongly related to fecal metabolite levels, and numerous associations between fecal microbial features and metabolite levels underscore the dynamic role of the gut microbiota in metabolism.

IMPACT

Characterizing the associations between the fecal microbiome, the fecal metabolome, and BMI, both recent and early-life exposures, provides critical background information for future research on cancer prevention and etiology.

The Role of Human Milk in Decreasing Necrotizing Enterocolitis Through Modulation of the Infant Gut Microbiome: A Scoping Review

BACKGROUND

Necrotizing enterocolitis is associated with a high incidence of morbidity and mortality in premature infants. Human milk minimizes necrotizing enterocolitis risk, although the mechanism of protection is not thoroughly understood. Increasingly, dysbiosis of the infant gut microbiome, which is affected by infant diet, is hypothesized to play a role in necrotizing enterocolitis pathophysiology.

RESEARCH AIM

The aim of this scoping review was to summarize the state of the science regarding the hypothesis that the gut microbiome composition is a mediator of the relationship between human milk and decreased incidence of necrotizing enterocolitis within a sample of human infants.

METHODS

Electronic databases and reference lists were searched for peer-reviewed primary research articles addressing the link between human milk, gut microbiome composition, and subsequent incidence of necrotizing enterocolitis among human infants.

RESULTS

A total of four studies met criteria for inclusion in this review. Of these, evidence supporting the link between human milk, gut microbiome composition, and necrotizing enterocolitis was found in two (50%) studies.

CONCLUSION

Some evidence linking all three variables is provided in this review. Given the small number of available studies, and the limitations of those studies, more research is urgently needed to thoroughly understand the protection against necrotizing enterocolitis gained through the provision of human milk.

Mixed milk feeding: a systematic review and meta-analysis of its prevalence and drivers

CONTEXT

Extensive literature is available on exclusive breastfeeding and formula-feeding practices and health effects. In contrast, limited and unstructured literature exists on mixed milk feeding (MMF), here defined as the combination of breastfeeding and formula feeding during the same period in term infants > 72 hours old (inclusion criterion).

OBJECTIVE

A systematic review and meta-analysis were performed, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, on the global prevalence of MMF (primary outcome) and related drivers and practices (secondary outcomes).

DATA SOURCES

The search of MMF in generally healthy populations was conducted across 6 databases, restricted to publications from January 2000 to August 2018 in English, Spanish, French, and Mandarin.

DATA EXTRACTION

Two reviewers independently performed screenings and data extraction according to a priori inclusion and exclusion criteria.

DATA ANALYSIS

Of the 2931 abstracts identified, 151 full-text publications were included for data extraction and 96 of those were included for data synthesis (the majority of those were cross-sectional and cohort studies). The authors summarized data across 5 different categories (feeding intention prenatally, and 4 age intervals between > 72 hours and > 6-23 months) and 5 regional subgroups. The overall prevalence of MMF across different age intervals and regions varied between 23% and 32%; the highest rate was found for the age group 4-6 months (32%; 95% confidence interval, 27%-38%); regional comparisons indicated highest MMF rates in Asia (34%), North and South America (33%), and Middle East and Africa together (36%), using a random effects meta-analysis model for proportions. Some drivers and practices for MMF were identified.

CONCLUSION

MMF is a widespread feeding reality. A shared and aligned definition of MMF will help shed light on this feeding practice and evaluate its influence on the duration of total breastfeeding, as well as on infants' nutrition status, growth, development, and health status in the short and long terms. PROSPERO registration number CRD42018105337.

The influence of the gastrointestinal microbiome on infant colic

INTRODUCTION

Although infantile colic is relatively frequent, its pathophysiology is not yet understood. The aim of this paper is to provide a better understanding of the link between infantile colic and the gastrointestinal microbiome.

AREAS COVERED

The gastro-intestinal microbiome may already start to develop in the womb and grows exponentially immediately after birth. Factors influencing the microbiome can cause dysbiosis and precipitate symptoms of colic through several mechanisms such as increased gas production and low grade gut inflammation. Other possible factors are immaturity of the enterohepatic bile acid cycle and administration of antibiotics and other medications during the perinatal period. An effective treatment for all colicky infants has yet to be discovered, but the probiotic Lactobacillus reuteri DSM17938 was shown to be effective in breastfed infants with colic. The scientific databases 'Pubmed' and 'Google scholar' were searched from inception until 02/2020. Relevant articles were selected based on the abstract.

EXPERT OPINION

Recent literature confirmed that the composition of the gastrointestinal microbiome is associated with the development of infantile colic. It can be speculated that full sequencing and bioinformatics analysis to identify the microbiome down to the species level may provide answers to the etiology and management of infantile colic.

Dynamic Interplay Between Microbiota and Mucosal Immunity in Early Shaping of Asthma and its Implication for the COVID-19 Pandemic

The crosstalk between host immunity and the external environment in the mucous membranes of the gastrointestinal and respiratory tracts in bronchial asthma has recently been scrutinized. There is compelling evidence that the microbiota at these sites may play an important role in the pathogenesis of this chronic airway disease. The appearance of bacteria early in life in the gut before dissemination to the airways plays a pivotal role in shaping mucosal immunity. Loss of microbial diversity or dysbiosis can result in aberrant immune-mediated inflammation and mucosal barrier disruption, which coincides clinically with the successive development of the "allergic march" in asthma. Microbial manipulation may be effective in curbing asthma development by indirectly preserving homeostatic epithelial barrier functions. The protective effects and mechanisms of immunity-microbiome crosstalk at mucosal sites require further investigation to identify therapeutic and preventive measures in asthma. This topical review aims to highlight new evidence that compromised epithelial barrier function, which results in deregulated crosstalk between the microbiome and host mucosal immune system, is an important disease mechanism in asthma. In the light of current COVID-19 pandemic, the collective findings on the impact of mucosal microbiota on the suceptibility to SARS-CoV-2 infection and severity of COVID-19 is explored. The possible therapeutic implications to target these abnormalities are further discussed.

Human Respiratory and Gut Microbiomes-Do They Really Contribute to Respiratory Health?

Human gastrointestinal and respiratory tracts are colonized by diverse polymicrobial communities shortly after birth, which are continuously molded by environmental exposure. The development of the resident microbiota in early life is a critical factor in the maturation of a healthy immune system. Disturbances to the intricate relationship between environmental exposure and maturation of the infant microbiome have been increasingly identified as a potential contributor to a range of childhood diseases. This review details recent evidence that implicates the contribution of gut and airway microbiome to pediatric respiratory health.

Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status

Bacteria in human milk could directly seed the infant intestinal microbiota, while information about how milk microbiota develops during lactation and how geographic location, gestational hypertensive status, and maternal age influence this process is limited. Here, we collected human milk samples from mothers of term infants at the first day, 2 weeks, and 6 weeks postpartum from 117 longitudinally followed-up mothers (age: 28.7 ± 3.6 y) recruited from three cities in China. We found that milk microbial diversity and richness were the highest in colostrum but gradually decreased over lactation. Microbial composition changed across lactation and exhibited more discrete compositional patterns in 2-week and 6-week milk samples compared with colostrum samples. At phylum level, the abundance of Proteobacteria increased during lactation, while Firmicutes showed the opposite trend. At genus level, Staphylococcus, Streptococcus, Acinetobacter, Pseudomonas, and Lactobacillus were predominant in colostrum samples and showed distinct variations across lactation. Maternal geographic location was significantly associated with the milk microbiota development and the abundance of predominant genus. In addition, milk from mothers with gestational prehypertension had a different and less diverse microbial community at genus level in early lactation times, and contained less Lactobacillus in the 2-week milk samples than those from normotensive mothers. Findings of our study outlined the human milk microbial diversity and community development over lactation, and underscored the importance of maternal geographic locations and gestational hypertensive status on milk microbiota, which might have important implications in the establishment of the infant intestinal microbiota via breastfeeding.

Maternal and infant factors that shape neonatal gut colonization by bacteria

INTRODUCTION

Early life is a critical developmental window coinciding with the establishment of a community of neonatal gut microbes which are vitally important for immune development. The composition of this microbial community is affected by multiple factors.

AREAS COVERED

The effect of pre-pregnancy and pregnancy maternal health, maternal nutrition, pregnancy disorders such as gestational diabetes, maternal antibiotic usage, delivery mode, infant feeding, and infant antibiotic usage on gut microbial composition are outlined along with the potential impact of associated microbiota differences on infant health.

EXPERT OPINION

Recent developments in understanding what shapes our microbiota indicates that the greatest impact on infant gut microbiota composition during the first year of life is seen with the mode of delivery, infant diet, and infant antibiotic usage. Current data is insufficient to fully establish the role of apparently less important factors such as maternal health on microbiota development although their impact is likely smaller. Technological advances will allow for improved understanding of underlying mechanisms by which specific microbes impact on infant health, which in time will enable full appreciation of the role of the gut microbiota in early life development.

Engineering the Gut Microbiome for Treatment of Obesity: A Review of Current Understanding and Progress

Obesity is a complex, multifactorial disease that is increasing in prevalence despite extensive research and efforts to curb it. Over the last decade, gut microbiome has emerged as an important contributor to the pathogenesis of obesity. Microbiome profile is altered in obese phenotype and the causative role of microbiome in obesity is demonstrated in fecal microbiota transplantation studies. Herein, recent evidences supporting the role of gut microbiome in obesity and the current therapies designed to engineer gut microbiome for treatment of obesity will be reviewed. The microbial enterotypes associated with obesity is outlined, and the gut microbiota-driven metabolism and low-grade inflammation linking gut microbiome and obesity is examined. How the different intrinsic and extrinsic factors such as host genetics, mode of childbirth delivery, diet, lifestyle habits and use of antibiotics influence the composition of the gut microbiome in the development of obesity is evaluated. Also, the efficacy of current microbiome-based therapies in the forms of prebiotics, probiotics and engineered microbes that are used to manipulate gut microbiome in treating obesity is discussed.

Concentrated Preterm Formula as a Liquid Human Milk Fortifier at Initiation Stage in Extremely Low Birth Weight Preterm Infants: Short Term and 2-year Follow-up Outcomes

Human milk (HM) must be accurately fortified for extremely low birth weight (ELBW) preterm infants with human milk fortifiers (HMFs). Powdered HMF has some limitations in terms of sterilization and accuracy. A concentrated preterm formula (CPF) may serve as a safe liquid HMF to facilitate growth. Hence, we launched a quality improvement project for fortification accuracy of minute volume HM. A CPF, Similac Special Care 30 (SSC30), was newly introduced as an HMF when daily feeding reached 100 cm³/kg. CPF + HM (1:2 volume ratio), CPF + HM (1:1 volume ratio), and powdered HMF + HM (1 packet in 25 cm³) represented three fortification stages. Fortification shifted to powdered HMF while tolerable feeding reached 25 cm³/meal. The outcome was compared before (Period-I, January 2015 to June 2016, n = 37) and after the new implement (Period-II, July 2016 to December 2017, n = 36). Compared with the Period-I group, the Period-II group had significantly higher daily enteral milk intake in the first 4 weeks of life, and higher percentages of fortification in the HM-fed infants in the first 8 weeks after birth. The Period-II group also significantly increased in body weight growth in terms of z-score at term equivalent age (p = 0.04) and had better language and motor performance at 24 months old (p = 0.048 and p = 0.032, respectively). Using the liquid CPF as a strategical alternative fortification of HM might be beneficial for extremely preterm infants in terms of growth as well as neurodevelopment.

Nutri-Epigenetics and Gut Microbiota: How Birth Care, Bonding and Breastfeeding Can Influence and Be Influenced?

Maternal lifestyle is an important factor in the programming of an infant's epigenome, in particular when considered alongside the mode of birth and choice of feeding method (i.e., breastfeeding or formula feeding). Beginning in utero, and during the first two years of an infant's life, cells acquire an epigenetic memory of the neonatal exposome which can be influential across the entire lifespan. Parental lifestyle (e.g., malnutrition, alcohol intake, smoke, stress, exposure to xenobiotics and/or drugs) can modify both the maternal and paternal epigenome, leading to epigenetic inheritance in their offspring. This review aims to outline the origin of early life modulation of the epigenome, and to share this fundamental concept with all the health care professionals involved in the development and provision of care during childbirth in order to inform future parents and clinicians of the importance of the this process and the key role it plays in the programming of a child's health.

The influence of the gut microbiome on obesity

Obesity is a disease with multiple environmental and genetic factors, which when combined contribute to the maintenance of an elevated body weight, thereby reducing long-term success of weight loss. The human gut microbiome is becoming a new potential contributor to obesity. Specifically, gut bacteria and their metabolites are known to affect dysbiosis, metabolism, endotoxemia, and inflammation. Many environmental and lifestyle factors can alter the gut microbiota affecting obesity. Potential therapies to alter the gut microbiota include supplementation with probiotic organisms and the use of fecal microbiota transplantation. This review will examine the growing evidence supporting the mechanisms with which the human gut microbiota may influence obesity, various influences on the microbiota, and potential therapies.

Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers' Milk and the Infant Gut: the CHILD Cohort Study

Gut microbiota play a critical role in infant health. It is now accepted that breastmilk contains live bacteria from endogenous and exogenous sources, but it remains unclear whether these bacteria transfer to the infant gut and whether this process is influenced by breastmilk feeding practices. Here, we show that certain bacteria, including Streptococcus spp. and Veillonella dispar, co-occur in mothers' milk and their infants' stool, and co-occurrence is reduced when infants receive pumped breastmilk. The relative abundances of commonly shared species are positively correlated between breastmilk and stool. Overall, gut microbiota composition is strongly associated with breastfeeding exclusivity and duration but not breastmilk feeding mode (nursing versus pumping). Moreover, breastmilk bacteria contributed to overall gut microbiota variation to a similar extent as other modifiers of the infant microbiome, such as birth mode. These results provide evidence that breastmilk may transfer bacteria to the infant gut and influence microbiota development.

Like mother, like microbe: human milk oligosaccharide mediated microbiome symbiosis

Starting shortly after parturition, and continuing throughout our lifetime, the gut microbiota coevolves with our metabolic and neurological programming. This symbiosis is regulated by a complex interplay between the host and environmental factors, including diet and lifestyle. Not surprisingly, the development of this microbial community is of critical importance to health and wellness. In this targeted review, we examine the gut microbiome from birth to 2 years of age to characterize the role human milk oligosaccharides play in early formation of microbial flora.

Jejunal inflammatory cytokines, barrier proteins and microbiome-metabolome responses to early supplementary feeding of Bamei suckling piglets

BACKGROUND

Dietary intervention has been reported to improve intestinal health. The intestinal microbiota of newborn animals plays a fundamental role in the development of intestinal function and the innate immune system. However, little is currently known about dietary interventions in the gut microbiota and barrier function of livestock, especially suckling Bamei piglets. To this end, we studied the effect of early dietary supplementation on intestinal bacterial communities and intestinal barrier function in piglets.

RESULTS

10 purebred Bamei sows were randomly allocated into two groups. In group one, the piglets received a supplementary milk replacer on day 7 of age, whereas the other control group was allowed sow's milk alone. At 21 days, 18 and 17, respectively, piglets in each group of average weight were randomly selected and sacrificed. Tissue and digesta samples were collected from the jejunum to evaluate differences in the microbiome-metabolome and the mRNA expression of inflammatory cytokines (TLR4, TNFα and IL-8) and barrier proteins (ZO-1, Occludin and Claudin-1). Sequencing of 16S rRNA revealed that ES improved the gut microbiome composition of Bamei suckling piglets. The relative abundances of some bacterial species such as Lactobacillales, Romboutsia, Actinobacillus, Bacteroides were significantly reduced in the ES group. Metabolomics analysis indicated that 23 compounds were enriched and 35 compounds decreased in the ES group. And correlation analysis demonstrated that some gut bacterial genera were highly correlated with altered gut microbiota-related metabolites. Meanwhile, ES of Bamei suckling piglets altered the gene expression of inflammatory cytokine and barrier protein in the jejunum.

CONCLUSIONS

In summary, these results provide important insights on the relationships between jejunal microbiota and related metabolites, and jejunal barrier function during the early life of Bamei suckling piglets.

A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents

Understanding oral microbiota programming attracts increasing interest due to its importance for oral health and potential associations with systemic diseases. Here the oral microbiota was longitudinally characterized in children from 2 days (n = 206) to 5 years of age and in young adults (n = 175) by sequencing of the v3-v4 region of the 16S rRNA gene from saliva extracted DNA. Alpha diversity increased by age, with 2-day- and 3-month-old infants in one sub-group, and 18-month- and 3-year-old children in another. Firmicutes decreased up to 3 years of age, whereas Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria abundances increased. Abiotrophia, Actinomyces, Capnocytophaga, Corynebacterium, Fusobacterium, Kingella, Leptotrichia, Neisseria and Porphyromonas appeared from 18-months of age. This was paralleled by expansions in the core microbiome that continued up to adulthood. The age-related microbiota transformation was paralleled by functional alterations, e.g., changed metabolic pathways that reflected e.g., breastfeeding and increasing proportions of anaerobic species. Oral microbiotas differed by feeding mode and weakly by mode of delivery, but not gender, pacifier use or cleaning method or probiotic intake. The study shows that the saliva microbiota is diverse 2 days after birth and under transformation up to 5 years of age and beyond, with fluctuations possibly reflecting age-related environmental influences.

Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula

Mother’s milk is the best choice for infants nutrition, however when it is not available or insufficient to satisfy the needs of the infant, formula is proposed as an effective substitute. Here, we report the results of a randomized controlled clinical trial (NCT03637894) designed to evaluate the effects of two different dietary regimens (standard formula and Lactobacillus paracasei CBA L74-fermented formula) versus breastfeeding (reference group) on immune defense mechanisms (primary endpoint: secretory IgA, antimicrobial peptides), the microbiota and its metabolome (secondary outcomes), in healthy full term infants according to the type of delivery (n = 13/group). We show that the fermented formula, safe and well tolerated, induces an increase in secretory IgA (but not in antimicrobial peptides) and reduces the diversity of the microbiota, similarly, but not as much as, breastmilk. Metabolome analysis allowed us to distinguish subjects based on their dietary regimen and mode of delivery. Together, these results suggest that a fermented formula favors the maturation of the immune system, microbiota and metabolome.

Milk breastfeeding and prebiotic-supplemented formulas have varying effects on the infant gut microbiome. Here, in a randomized controlled clinical trial, the authors investigate the effects of a Lactobacillus paracasei-fermented formula on the immune defense mechanisms, microbiota and its metabolome in full term infants.

Comparing Gut Microbiome in Mothers' Own Breast Milk- and Formula-Fed Moderate-Late Preterm Infants

Gut microbiome plays an important role in adult human health and diseases. However, how nutritional factors shape the initial colonization of gut bacteria in infants, especially in preterm infants, is still not completely known. In this study, we compared the effects of feeding with mothers' own breast milk (MBM) and formula on the initial composition and gene expression of gut bacteria in moderate-late preterm infants. Fecal samples were collected from ten formula-fed and ten MBM healthy infants born between 32 and 37 weeks' gestation after they reached full-volume enteral feedings. Total DNAs were extracted from fecal samples for amplicon sequencing of 16S ribosomal RNA (rRNA) gene and total RNA with rRNA depletion for metatranscriptome RNA-Seq 16S rRNA gene amplicon sequencing results showed that the alpha-diversity was similar between the MBM- and formula-fed preterm infants, but the beta-diversity showed a significant difference in composition (p = 0.002). The most abundant taxa were Veillonella (18.4%) and Escherichia/Shigella (15.2%) in MBM infants, whereas the most abundant taxa of formula-fed infants were Streptococcus (18.6%) and Klebsiella (17.4%). The genera Propionibacterium, Streptococcus, and Finegoldia and order Clostridiales had significantly higher relative abundance in the MBM group than the formula group, whereas bacteria under family Enterobacteriaceae, genera Enterococcus and Veillonella, and class Bacilli were more abundant in the formula group. In general, microbiomes from both diet groups exhibited high functional levels of catalytic activity and metabolic processing when analyzed for gene ontology using a comparative metatranscriptome approach. Statistically, the microbial genes in the MBM group had an upregulation in expression related to glycine reductase, periplasmic acid stress response in Enterobacteria, acid resistance mechanisms, and L-fucose utilization. In contrast, the formula-fed group had upregulations in genes associated with methionine and valine degradation functions. Our data suggest that the nutritional source plays a role in shaping the moderate-late preterm gut microbiome as evidenced by the differences in bacterial composition and gene expression profiles in the fecal samples. The MBM group enriched Propionibacterium. Glycine reductase was highly upregulated in the microbiota from MBM along with the upregulated acid stress tolerance genes, suggesting that the intensity of fermentation process was enhanced.

Breastfeeding may have a long-term effect on oral microbiota: results from the Fin-HIT cohort

BACKGROUND

Breastfeeding contributes to gastrointestinal microbiota colonization in early life, but its long-term impact is inconclusive. We aimed to evaluate whether the type of feeding during the first six months of life was associated with oral microbiota in adolescence.

METHODS

This is a cross-sectional sub-study using baseline information of 423 adolescents from the Finnish Health in Teens (Fin-HIT) cohort. Type of feeding was recalled by parents and dichotomized as (i) No infant formula; (ii) Infant formula (breastmilk + formula or only formula). Saliva microbiota was analysed using 16S rRNA (V3-V4) sequencing. Alpha diversity and beta diversity were compared between feeding type groups using ANCOVA and PERMANOVA, respectively. Differential bacteria abundance was tested using appropriate general linear models.

RESULTS

Mean age and body mass index were 11.7 years and 18.0 kg/m2, respectively. The No formula group contained 41% of the participants. Firmicutes (51.0%), Bacteroidetes (19.1%), and Proteobacteria (16.3%) were the most abundant phyla among all participants. Alpha and beta diversity indices did not differ between the two feeding groups. Three Operational Taxonomic Units (OTUs) belonging to Eubacteria and Veillonella genera (phylum Firmicutes) were more abundant in the No formula than in the Infant formula group (log2fold changes/ p - values - 0.920/ < 0.001, - 0.328/ 0.001, - 0.577/ 0.004).

CONCLUSION

Differences exist in abundances of some OTUs in adolescence according to feeding type during the first six months of life, but our findings do not support diversity and overall oral microbiota composition in adolescents being affected by early feeding type.

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type

The microbiome is a new frontier for building predictors of human phenotypes. However, machine learning in the microbiome is fraught with issues of reproducibility, driven in large part by the wide range of analytic models and metagenomic data types available. We aimed to build robust metagenomic predictors of host phenotype by comparing prediction performances and biological interpretation across 8 machine learning methods and 4 different types of metagenomic data. Using 1,570 samples from 300 infants, we fit 7,865 models for 6 host phenotypes. We demonstrate the dependence of accuracy on algorithm choice and feature definition in microbiome data and propose a framework for building microbiome-derived indicators of host phenotype. We additionally identify biological features predictive of age, sex, breastfeeding status, historical antibiotic usage, country of origin, and delivery type. Our complete results can be viewed at http://apps.chiragjpgroup.org/ubiome_predictions/.

Distinct Gut Microbiota and Metabolite Profiles Induced by Different Feeding Methods in Healthy Chinese Infants

Human milk is closely correlated with infant gut microbiota and is important for infant development. However, most infants receive exclusively insufficient breast milk, and the discordance between effects of commercial formula and human milk exists. To elucidate the differences induced by various feeding methods, we determined microbiota and metabolites composition in fecal samples from 77 healthy infants in Northeast China and identified the differences in various feeding methods. Bacterial 16S rRNA gene sequence analysis demonstrated that the fecal samples of exclusively breastfed (BF) infants were abundant in Bifidobacterium and Lactobacillus; the mixed-fed (MF) infants had the highest abundance of Veillonella and Klebsiella; the exclusively formula-fed (FF) infants were enriched in Bacteroides and Blautia; and the complementary food-fed (CF) infants were associated with higher relative abundance of Lachnoclostridium and Akkermansia. Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics data revealed that the fecal samples of BF infants had the highest abundance of dl-citrulline, threonine, l-proline, l-glutamine, guanine, and l-arginine; the MF infants were abundant in d-maltose, stearidonic acid, capric acid, and myristic acid; the FF infants were enriched in itaconic acid, 4-pyridoxic acid, prostaglandin B2, thymine, dl-α-hydroxybutyric acid, and orotic acid; and the CF infants were associated with higher relative abundance of taurine, l-tyrosine, adenine, and uric acid. Furthermore, compared with the BF infants, the MF and FF infants were more abundant in fatty acid biosynthesis. Collectively, these findings will provide probable explanations for some of the risks and benefits related to infant feeding methods and will support a theoretical basis for the development of infant formula.

Development of the Microbiota and Associations With Birth Mode, Diet, and Atopic Disorders in a Longitudinal Analysis of Stool Samples, Collected From Infancy Through Early Childhood

BACKGROUND & AIMS

Establishment of the gastrointestinal microbiota during infancy affects immune system development and oral tolerance induction. Perturbations in the microbiome during this period can contribute to development of immune-mediated diseases. We monitored microbiota maturation and associations with subsequent development of allergies in infants and children.

METHODS

We collected 1453 stool samples, at 5, 13, 21, and 31 weeks postpartum (infants), and once at school age (6-11 years), from 440 children (49.3% girls, 24.8% born by cesarean delivery; all children except for 6 were breastfed for varying durations; median 40 weeks; interquartile range, 30-53 weeks). Microbiota were analyzed by amplicon sequencing. Children were followed through 3 years of age for development of atopic dermatitis; data on allergic sensitization and asthma were collected when children were school age.

RESULTS

Diversity of fecal microbiota, assessed by Shannon index, did not differ significantly among children from 5 through 13 weeks after birth, but thereafter gradually increased to 21 and 31 weeks. Most bacteria within the Bacteroidetes and Proteobacteria phyla were already present at 5 weeks after birth, whereas many bacteria of the Firmicutes phylum were acquired at later times in infancy. At school age, many new Actinobacteria, Firmicutes, and Bacteroidetes bacterial taxa emerged. The largest increase in microbial diversity occurred after 31 weeks. Vaginal, compared with cesarean delivery, was most strongly associated with an enrichment of Bacteroides species at 5 weeks through 31 weeks. From 13 weeks onward, diet became the most important determinant of microbiota composition; cessation of breastfeeding, rather than solid food introduction, was associated with changes. For example, Bifidobacteria, staphylococci, and streptococci significantly decreased on cessation of breastfeeding, whereas bacteria within the Lachnospiraceae family (Pseudobutyrivibrio, Lachnobacterium, Roseburia, and Blautia) increased. When we adjusted for confounding factors, we found fecal microbiota composition to be associated with development of atopic dermatitis, allergic sensitization, and asthma. Members of the Lachnospiraceae family, as well as the genera Faecalibacterium and Dialister, were associated with a reduced risk of atopy.

CONCLUSIONS

In a longitudinal study of fecal microbiota of children from 5 weeks through 6 to 11 years, we tracked changes in diversity and composition associated with the development of allergies and asthma.