Fetal exposures and perinatal influences on the stool microbiota of premature infants

Sociodemographic Factors and Intestinal Microbiome Development in Preterm, Very Low Birth Weight Infants

OBJECTIVE

 Preterm very low birth weight (VLBW) infants are at risk for intestinal morbidities and dysbiotic development of the intestinal microbiome. Despite the influence of sociodemographic factors on premature infant health outcomes, whether they shape the intestinal microbiome early in life is not clear. The objective was to explore the associations between race, sex, and socioeconomic status and the intestinal microbiome of VLBW infants during the first 4 weeks of life.

STUDY DESIGN

 This was a secondary analysis of data from an ongoing randomized trial of 79 infants ≤30 weeks' gestation and ≤1,500 g. Stool samples were collected at week 1 through week 4, frozen to -80°C and analyzed by 16S rRNA sequencing of the V4 region using Illumina MiSeq. Reads were analyzed to measure α and β diversity as well as relative abundance of bacteria in the intestinal microbiome.

RESULTS

 Of the 79 infants, 63 had at least one sample available. Twenty-three (37%) of infants were African American, 30 (48%) were male, and 44 (71%) had Medicaid insurance. There were no statistically significant (<0.05) differences in α diversity or β diversity, and the differential abundance analysis suggests limited patterns of distinction in the intestinal microbiome between non-African American and African American infants, male and female infants, and infants with maternal private or Medicaid insurance.

CONCLUSION

 Our results suggest race, sex, and socioeconomic status shape colonization of specific microorganisms to a limited extent. Future studies should confirm these findings and determine clinical relevance through further study of differentially abundant microorganisms and additional factors contributing to colonization patterns.

KEY POINTS

· Diversity of the gut microbiome was similar between infants of varying race, sex, and socioeconomic status.. · We observed sociodemographic-linked differences in colonization of individual taxa.. · Further study is required to confirm these results and the clinical relevance of these findings..

Determinants of microbial colonization in the premature gut

Abnormal microbial colonization in the gut at an early stage of life affects growth, development, and health, resulting in short- and long-term adverse effects. Microbial colonization patterns of preterm infants differ from those of full-term infants in that preterm babies and their mothers have more complicated prenatal and postnatal medical conditions. Maternal complications, antibiotic exposure, delivery mode, feeding type, and the use of probiotics may significantly shape the gut microbiota of preterm infants at an early stage of life; however, these influences subside with age. Although some factors and processes are difficult to intervene in or avoid, understanding the potential factors and determinants will help in developing timely strategies for a healthy gut microbiota in preterm infants. This review discusses potential determinants of gut microbial colonization in preterm infants and their underlying mechanisms.

Increased antibiotic exposure in early life is associated with adverse outcomes in very low birth weight infants

BACKGROUND

The use of antibiotics in the early lives of premature infants may alter the microbiota and influence their clinical outcomes. However, whether the administration of probiotics can influence these outcomes remains unknown. In our study, probiotics were routinely administered unless contraindicated. We explored whether increased antibiotic exposure with the routine use of probiotics was associated with necrotizing enterocolitis (NEC) or bronchopulmonary dysplasia (BPD).

METHODS

A retrospective cohort study was conducted, enrolling very low birth weight (VLBW) infants admitted between January 1, 2016, and March 31, 2020, to a medical center. Days of antibiotic exposure in the first 14 days of life were recorded. The primary outcomes were NEC and BPD. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were calculated using multivariable regression analyses to assess risk factors.

RESULTS

Of 185 VLBW infants admitted to the medical center, 132 met the inclusion criteria. Each additional day of antibiotic treatment was associated with increased odds of NEC (aOR, 1.278; 95% CI, 1.025-1.593) and BPD (aOR, 1.630; 95% CI, 1.233-2.156). The association remained in the NEC analysis after adjustment for probiotic use.

CONCLUSION

Increased antibiotic exposure in the early lives of VLBW infants was associated with increased risks of NEC and BPD. The probiotics did not influence the outcomes. Our findings suggest that clinicians should be alerted to the adverse outcomes of antibiotic use in infants with VLBWs.

Dominant bacteria and influencing factors of early intestinal colonization in very low birth weight infants: A prospective cohort study

Background

The intestine of newborns is colonized by bacteria immediately after birth. This study explored dominant bacteria and influencing factors of early intestinal colonization in the early life of very low birth weight infants (VLBWI).

Methods

We enrolled 81 VLBWI and collected anal swabs at 24 h, 7th, 14th and 21st day after birth. We conducted bacterial culture for anal swabs, then selected the colony with obvious growth advantages in the plate for further culture and identification. Afterward, we analyzed the distribution and influencing factors of intestinal dominant microbiota combined with clinical data.

Results

A total of 300 specimens were collected, of which 62.67% (188/300) had obvious dominant bacteria, including 29.26% (55/188) Gram‐positive bacteria and 70.74% (133/188) Gram‐negative bacteria. The top five bacteria with the highest detection rates were Klebsiella pneumoniae, Escherichia coli, Enterococcus faecium, Enterococcus faecalis and Serratia marcescens. Meconium‐stained amniotic fluid and chorioamnionitis were correlated with intestinal bacterial colonization within 24 h of birth. Mechanical ventilation and antibiotics were independent risk factors affecting colonization. Nosocomial infection of K. pneumoniae and S. marcescens were associated with intestinal colonization. The colonization rates of K. pneumoniae, E. coli, E. faecium, and E. faecalis increased with the birth time.

Conclusions

The colonization rate in the early life of VLBWI increased over time and the predominant bacteria were Gram‐negative bacteria. Meconium‐stained amniotic fluid and chorioamnionitis affect intestinal colonization in early life. Mechanical ventilation and antibiotics were independent risk factors for intestinal bacterial colonization. The nosocomial infection of some bacteria was significantly related to intestinal colonization.

A systematic review of the factors influencing microbial colonization of the preterm infant gut

Prematurity coupled with the necessary clinical management of preterm (PT) infants introduces multiple factors that can interfere with microbial colonization. This study aimed to review the perinatal, physiological, pharmacological, dietary, and environmental factors associated with gut microbiota of PT infants. A total of 587 articles were retrieved from a search of multiple databases. Sixty studies were included in the review after removing duplicates and articles that did not meet the inclusion criteria. Review of this literature revealed that evidence converged on the effect of postnatal age, mode of delivery, use of antibiotics, and consumption of human milk in the composition of gut microbiota of PT infants. Less evidence was found for associations with race, sex, use of different fortifiers, macronutrients, and other medications. Future studies with rich metadata are needed to further explore the impact of the PT exposome on the development of the microbiota in this high-risk population.

To Probiotic or Not to Probiotic: A Metagenomic Comparison of the Discharge Gut Microbiome of Infants Supplemented With Probiotics in NICU and Those Who Are Not

BACKGROUND

Preterm birth is associated with the development of both acute and chronic disease, and the disruption of normal gut microbiome development. Recent studies have sought to both characterize and understand the links between disease and the microbiome. Probiotic treatment may correct for these microbial imbalances and, in turn, mitigate disease. However, the criteria for probiotic supplementation in NICU's in North Queensland, Australia limits its usage to the most premature (<32 weeks gestation) and small for gestational age infants (<1,500 g). Here we use a combination of amplicon and shotgun metagenomic sequencing to compare the gut microbiome of infants who fulfill the criteria for probiotic-treatment and those who do not. The aims of this study were to determine if probiotic-supplemented preterm infants have significantly different taxonomic and functional profiles when compared to non-supplemented preterm infants at discharge.

METHODS

Preterm infants were recruited in North Queensland, Australia, with fecal samples collected just prior to discharge (36 ± 0.5 weeks gestation), to capture potential changes that could be probiotic induced. All samples underwent 16S rRNA gene amplicon sequencing, with a subset also used for shotgun metagenomics. Mixed effects models were used to assess the effect of probiotics on alpha diversity, beta diversity and taxonomic abundance, whilst accounting for other known covariates.

RESULTS

Mixed effects modeling demonstrated that probiotic treatment had a significant effect on overall community composition (beta diversity), characterized by greater alpha diversity and differing abundances of several taxa, including Bifidobacterium and Lactobacillus, in supplemented infants.

CONCLUSION

Late preterm-infants who go without probiotic-supplementation may be missing out on stabilizing-effects provided through increased alpha diversity and the presence of commensal microbes, via the use of probiotic-treatment. These findings suggest that late-preterm infants may benefit from probiotic supplementation. More research is needed to both understand the consequences of the differences observed and the long-term effects of this probiotic-treatment.

The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge

BACKGROUND

Preterm birth is associated with the development of acute and chronic disease, potentially, through the disruption of normal gut microbiome development. Probiotics may correct for microbial imbalances and mitigate disease risk. Here, we used amplicon sequencing to characterise the gut microbiome of probiotic-treated premature infants. We aimed to identify and understand variation in bacterial gut flora from admission to discharge and in association with clinical variables.

METHODS

Infants born <32 weeks gestation and <1500 g, and who received probiotic treatment, were recruited in North Queensland Australia. Meconium and faecal samples were collected at admission and discharge. All samples underwent 16S rRNA short amplicon sequencing, and subsequently, a combination of univariate and multivariate analyses.

RESULTS

71 admission and 63 discharge samples were collected. Univariate analyses showed significant changes in the gut flora from admission to discharge. Mixed-effects modelling showed significantly lower alpha diversity in infants diagnosed with either sepsis or retinopathy of prematurity (ROP) and those fed formula. In addition, chorioamnionitis, preeclampsia, sepsis, necrotising enterocolitis and ROP were also all associated with the differential abundance of several taxa.

CONCLUSIONS

The lower microbial diversity seen in infants with diagnosed disorders or formula-fed, as well as differing abundances of several taxa across multiple variables, highlights the role of the microbiome in the development of health and disease. This study supports the need for promoting healthy microbiome development in preterm neonates.

IMPACT

Low diversity and differing taxonomic abundances in preterm gut microbiota demonstrated in formula-fed infants and those identified with postnatal conditions, as well as differences in taxonomy associated with preeclampsia and chorioamnionitis, reinforcing the association of the microbiome composition changes due to maternal and infant disease. The largest study exploring an association between the preterm infant microbiome and ROP. A novel association between the preterm infant gut microbiome and preeclampsia in a unique cohort of very-premature probiotic-supplemented infants.

Clinical implications of preterm infant gut microbiome development

Perturbations to the infant gut microbiome during the first weeks to months of life affect growth, development and health. In particular, assembly of an altered intestinal microbiota during infant development results in an increased risk of immune and metabolic diseases that can persist into childhood and potentially into adulthood. Most research into gut microbiome development has focused on full-term babies, but health-related outcomes are also important for preterm babies. The systemic physiological immaturity of very preterm gestation babies (born earlier than 32 weeks gestation) results in numerous other microbiome-organ interactions, the mechanisms of which have yet to be fully elucidated or in some cases even considered. In this Perspective, we compare assembly of the intestinal microbiome in preterm and term infants. We focus in particular on the clinical implications of preterm infant gut microbiome composition and discuss the prospects for microbiome diagnostics and interventions to improve the health of preterm babies.

Use of Antibiotic Treatment in Pregnancy and the Risk of Several Neonatal Outcomes: A Population-Based Study

BACKGROUND

Limited evidence is available on the safety and efficacy of antimicrobials during pregnancy, with even less according to the trimester of their use.

OBJECTIVE

This study aimed to evaluate the association between exposure to antibiotics therapy (AT) during pregnancy and short-term neonatal outcomes.

METHODS

We considered 773,237 deliveries that occurred between 2007-2017 in the Lombardy region of Italy. We evaluated the risk of neonatal outcomes among infants that were born to mothers who underwent AT during pregnancy. The odds ratios and the hazard ratios, with the 95% confidence intervals, were estimated respectively for early (first/second trimester) and late (third trimester) exposure. The propensity score was used to account for potential confounders. We also performed subgroup analysis for the class of AT.

RESULTS

We identified 132,024 and 76,921 singletons that were exposed to AT during early and late pregnancy, respectively. Infants born to mothers with early exposure had 17, 11, and 16% increased risk of preterm birth, low birth weight, and low Apgar score, respectively. Infants that were exposed in late pregnancy had 25, 11, and 13% increased risk of preterm birth, low birth weight, and low Apgar score, respectively. The results were consistent in the subgroup analysis.

CONCLUSION

Our results suggested an increased risk of several neonatal outcomes in women exposed to ATs during pregnancy, albeit we were not able to assess to what extent the observed effects were due to the infection itself. To reduce the risk of neonatal outcomes, women that are prescribed AT during pregnancy should be closely monitored.

Postnatal age is strongly correlated with the early development of the gut microbiome in preterm infants

BACKGROUND

The gut microbiome plays a potential role in clinical events in preterm infants and may affect their lateral development. Understanding the initial colonization of microbes in the gut, their early dynamic changes, and the major factors correlated with these changes would provide crucial information about the developmental process in early life.

METHODS

The present study enrolled 151 preterm infants and examined the longitudinal dynamics of their fecal microbiome profiles during the period of hospitalization using 16S ribosomal RNA gene sequencing. Random forest modeling was used to predict postnatal age (Age), postmenstrual age (PMA), and gestational age (GA), using gut microbiome features.

RESULTS

Principal coordinate analysis revealed that the gut microbiome of the preterm infants displayed an obvious time-dependent change pattern, which showed the strongest association with Age, followed by PMA, and a much weaker association with (GA). Random forest modeling further evidenced the time-dependent change pattern, with the Pearson's correlation coefficients between the actual values and the gut microbiome-predicted values being 0.68, 0.53, and 0.38 for postnatal, postmenstrual, and gestational age, respectively. The microbiome dynamism could be further divided into four Age stages, each with its own characteristic microbial taxa. The first 1-4 days (T1 stage) represented the meconium microbiome, with colonization of a high diversity of microbes before or during delivery. During 5-15 days (T2 stage), the gut microbiome of the preterm infants underwent a rapid turnover, in which microbial diversity declined, and stabilized afterward. Enterobacteriaceae, Enterococcaceae, Streptococcaceae, Staphylococcaceae, and Clostridiaceae were the major classes in the gut microbiome in the lateral stages of development (T3-T4 stage).

CONCLUSIONS

Postnatal age, rather than the gestational age, is significantly correlated with the gut microbiome of preterm infants, suggesting that clinical interventions contribute more to the early dynamics of gut microbiome in preterm infants than the natural development of the gut.

Methods for exploring the faecal microbiome of premature infants: a review

The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.

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.

Exploring the Role of Gut Bacteria in Health and Disease in Preterm Neonates

The mortality rate of very preterm infants with birth weight <1500 g is as high as 15%. The survivors till discharge have a high incidence of significant morbidity, which includes necrotising enterocolitis (NEC), early-onset neonatal sepsis (EONS) and late-onset neonatal sepsis (LONS). More than 25% of preterm births are associated with microbial invasion of amniotic cavity. The preterm gut microbiome subsequently undergoes an early disruption before achieving bacterial maturation. It is postulated that bacterial gut colonisation at birth and postnatal intestinal dysbacteriosis precede the development of NEC and LONS in very preterm infants. In fact, bacterial colonization patterns in preterm infants greatly differ from term infants due to maternal chorioamnionitis, gestational age, delivery method, feeding type, antibiotic exposure and the environment factor in neonatal intensive care unit (NICU). In this regard, this review provides an overview on the gut bacteria in preterm neonates' meconium and stool. More than 50% of preterm meconium contains bacteria and the proportion increases with lower gestational age. Researchers revealed that the gut bacterial diversity is reduced in preterm infants at risk for LONS and NEC. Nevertheless, the association between gut dysbacteriosis and NEC is inconclusive with regards to relative bacteria abundance and between-sample beta diversity indices. With most studies show a disruption of the Proteobacteria and Firmicutes preceding the NEC. Hence, this review sheds light on whether gut bacteria at birth either alone or in combination with postnatal gut dysbacteriosis are associated with mortality and the morbidity of LONS and NEC in very preterm infants.

Considering the Microbiome in Stress-Related and Neurodevelopmental Trajectories to Schizophrenia

Early life adversity and prenatal stress are consistently associated with an increased risk for schizophrenia, although the exact pathogenic mechanisms linking the exposures with the disease remain elusive. Our previous view of the HPA stress axis as an elegant but simple negative feedback loop, orchestrating adaptation to stressors among the hypothalamus, pituitary, and adrenal glands, needs to be updated. Research in the last two decades shows that important bidirectional signaling between the HPA axis and intestinal mucosa modulates brain function and neurochemistry, including effects on glucocorticoid hormones and brain-derived neurotrophic factor (BDNF). The intestinal microbiome in earliest life, which is seeded by the vaginal microbiome during delivery, programs the development of the HPA axis in a critical developmental window, determining stress sensitivity and HPA function as well as immune system development. The crosstalk between the HPA and the Microbiome Gut Brain Axis (MGBA) is particularly high in the hippocampus, the most consistently disrupted neural region in persons with schizophrenia. Animal models suggest that the MGBA remains influential on behavior and physiology across developmental stages, including the perinatal window, early childhood, adolescence, and young adulthood. Understanding the role of the microbiome on critical risk related stressors may enhance or transform of understanding of the origins of schizophrenia and offer new approaches to increase resilience against stress effects for preventing and treating schizophrenia.

Early Life Risk Factors in Pediatric EoE: Could We Prevent This Modern Disease?

Eosinophilic esophagitis (EoE) is a chronic antigen-mediated inflammatory disease that affects the esophagus. In the last 20 years, a large number of epidemiological studies showed a significant increase in the incidence and prevalence of EoE, especially in developed countries. This phenomenon might correlate to the overall increase in pediatric allergic diseases or might be a result of improved medical awareness and knowledge through modern diagnostic instruments. Since 1993, when EoE was first recognized as a distinct clinical entity, several signs of progress in the pathophysiology of EoE were achieved. However, a few studies reported data on early risk factors for pediatric EoE and how these factors may interfere with genes. Currently, the most defined risk factors for EoE are male sex, Caucasian race, and atopic comorbidities. Other putative risk factors may include alterations in epithelial barrier function and fibrous remodeling, esophageal dysbiosis, variation in the nature and timing of oral antigen exposure, and early prescription of proton pump inhibitors and antibiotics. Notably, the timing and nature of food antigen exposure may be fundamental in inducing or reversing immune tolerance, but no studies are reported. This review summarized the current evidence on the risk factors that might contribute to the increasing development of EoE, focusing on the possible preventive role of early interventions.

Determinants of the Very Low-Birth-Weight Infant's Intestinal Microbiome: A Systematic Review

The intestinal microbiome is the genetic material from microorganisms residing in the intestinal tract. Very low-birth-weight infants (VLBW; birth weight ≤1500 g) are a physiologically compromised population undergoing a unique period of initial intestinal microbiome establishment. Evidence supports a connection between the intestinal microbiome and gastrointestinal illness that disproportionately affects VLBW infants. Necrotizing enterocolitis, an inflammatory and often necrotic condition of the intestine, and late-onset sepsis, a bloodstream infection occurring after 3 days of life, are thought to be associated with delayed or abnormal intestinal microbiome development. Here, we review the determinants, or factors, that influence the VLBW infant's intestinal microbiome and discuss clinical implications. PubMed, Web of Science, EMBASE, and CINAHL were systematically searched for publications addressing factors with the potential to affect the intestinal microbiome of VLBW infants. Results indicate that infant's age and weight, mode of delivery, antibiotic exposure, medication use, feeding regime, environment, and perinatal-/infant-associated factors may be important determinants of the microbiome in this vulnerable population. Clinicians have opportunities to support positive development of the VLBW infant's intestinal microbiome through antibiotic stewardship, support of human milk feeding, and hygienic care practices.

Microbiome as an Immunological Modifier

Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.

The microbiota composition of the offspring of patients with gestational diabetes mellitus (GDM)

The microbiota composition of the offspring of women with gestational diabetes mellitus (GDM), a common pregnancy complication, is still little known. We investigated whether the GDM offspring gut microbiota composition is associated with the maternal nutritional habits, metabolic variables or pregnancy outcomes. Furthermore, we compared the GDM offspring microbiota to the microbiota of normoglycemic-mother offspring. Fecal samples of 29 GDM infants were collected during the first week of life and assessed by 16S amplicon-based sequencing. The offspring’s microbiota showed significantly lower α-diversity than the corresponding mothers. Earlier maternal nutritional habits were more strongly associated with the offspring microbiota (maternal oligosaccharide positively with infant Ruminococcus, maternal saturated fat intake inversely with infant Rikenellaceae and Ruminococcus) than last-trimester maternal habits. Principal coordinate analysis showed a separation of the infant microbiota according to the type of feeding (breastfeeding vs formula-feeding), displaying in breast-fed infants a higher abundance of Bifidobacterium. A few Bacteroides and Blautia oligotypes were shared by the GDM mothers and their offspring, suggesting a maternal microbial imprinting. Finally, GDM infants showed higher relative abundance of pro-inflammatory taxa than infants from healthy women. In conclusion, many maternal conditions impact on the microbiota composition of GDM offspring whose microbiota showed increased abundance of pro-inflammatory taxa.

Bacterial Baptism: Scientific, Medical, and Regulatory Issues Raised by Vaginal Seeding of C-Section-Born Babies

Several lines of evidence suggest that children born via Cesarean section (C-section) are at greater risk for adverse health outcomes including allergies, asthma and obesity. Vaginal seeding is a medical procedure in which infants born by C-section are swabbed immediately after birth with vaginal secretions from the mother. This procedure has been proposed as a way to transfer the mother's vaginal microbiome to the child, thereby restoring the natural exposure that occurs during vaginal birth that is interrupted in the case of babies born via C-section. Preliminary evidence indicates partial restoration of microbes. However, there is insufficient evidence to determine the health benefits of the procedure. Several studies, including trial, are currently underway. At the same time, in the clinic setting, doctors are increasingly being asked to by expectant mothers to have their babies seeded. This article reports on the current research on this procedure and the issues it raises for regulators, researchers, physicians, and patients.

Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study

OBJECTIVE

To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.

DESIGN

Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).

SETTINGS

Rural New Hampshire, USA.

POPULATION OR SAMPLE

Two hundred and sixty-six full-term infants from the NHBCS.

METHODS

Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.

EXPOSURES

Maternal exposure to antibiotics during labour and delivery.

MAIN OUTCOME MEASURE

Taxonomic and functional profiles of faecal samples.

RESULTS

Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin-only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi-class group experienced a significantly higher increase in Veillonella dispar.

CONCLUSIONS

Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa.

TWEETABLE ABSTRACT

Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.

The role of antimicrobial treatment during pregnancy on the neonatal gut microbiome and the development of atopy, asthma, allergy and obesity in childhood

INTRODUCTION

The use of antibiotics prenatally, during pregnancy, or neonatally may have adverse effects on the neonatal gut microbiome, and adversely affect the development of the infant immune system, leading to childhood atopy, asthma, allergy and obesity.

AREAS COVERED

Vaginal eubiosis and dysbiosis from molecular-based, cultivation-independent techniques, and how this affects the neonatal gut microbiome and early development of the immune system, the association between maternal antibiotics and the beneficial role of vitamin D in the development of atopy, asthma, allergy and obesity, efforts to reduce the use of antibiotics in pregnancy and therapeutic interventions such as vaginal 'seeding', probiotics, breastfeeding and neonatal dietary supplementation.

EXPERT OPINION

Currently available research gives insufficient attention to confounding variables. There remains uncertainty as to whether it is relevant that the mother suffered from the same condition as the purported infant outcome variable, for which she may have received antibiotics. In most studies, there is a lack of control for the number of antibiotic courses administered, the timing of use, the use of broad spectrum or narrow range antibiotics, the indication for antibiotics, the dose-dependent nature of the effect, the class of antibiotics used, or a varying degree of risk.

Characterization of the bacterial microbiome in first-pass meconium using propidium monoazide (PMA) to exclude nonviable bacterial DNA

Numerous studies have reported bacterial DNA in first-pass meconium samples, suggesting that the human gut microbiome is seeded prior to birth. However, these studies have not been able to discriminate between DNA from living bacterial cells, DNA from dead bacterial cells or cell-free DNA. Here we have used propidium monoazide (PMA) together with 16S rRNA gene sequencing to determine whether there are intact bacterial cells in the fetal gut. DNA was extracted from first-pass meconium (n = 5) and subjected to 16S rRNA gene sequencing with/without PMA treatment. All meconium samples, regardless of PMA treatment, contained detectable levels of bacterial DNA; however, treatment with PMA prior to DNA extraction decreased the DNA yield by approximately 20%. PMA-treated meconium samples did not differ significantly from untreated samples in terms of observed number of OTUs (P = 0·945); although they did differ taxonomically, with around one quarter of OTUs identified in untreated samples only, suggesting that they have originated from cell-free/nonviable DNA. The mean Sørensen coefficient for treated vs untreated samples was 0·527. Our findings suggest that the fetal gut is seeded with intact bacterial cells prior to birth. This is an important finding, as exposure to live bacteria during gestation might have a significant impact on the developing fetus. SIGNIFICANCE AND IMPACT OF THE STUDY: DNA-based microbiome studies performed using 16S rRNA gene sequencing are limited by their inability to discriminate between live bacterial cells, dead bacterial cells and cell-free DNA. Here we use propidium monoazide (PMA) to exclude nonviable bacteria from microbiome analysis of first-pass meconium samples and thereby reveal that the majority of the purported fetal gut microbiome is from intact bacterial cells. This work demonstrates the importance of excluding nonviable bacteria when analysing the microbial community in low-biomass samples such as meconium.

Association between the intestinal microbiota and allergic sensitization, eczema, and asthma: A systematic review

The intestinal microbiota plays an important role in development of the immune system and regulation of immune responses. This review summarizes the association between the intestinal microbiota and the development of allergic sensitization, eczema, and asthma in neonates and children. Overall, a greater relative abundance of Bacteroidaceae, Clostridiaceae, and Enterobacteriaceae and a lower relative abundance of Bifidobacteriaceae and Lactobacillaceae is associated with the development of allergic sensitization, eczema, or asthma. Reduced bacterial diversity can be associated with the development of allergic disease. The association between the composition of the intestinal microbiota and the development of allergic disease or asthma is less consistent in older children than in neonates, suggesting that early-life microbial exposure plays a more important role. Inconsistencies in the results reported from different studies might partly be explained by heterogeneity in design, study populations, diagnostic criteria, microbiota analysis methods, and reporting on different taxonomic levels. Larger studies that better account for antenatal and postnatal factors will further help determine specific microbial intestinal signatures associated with increased risk of allergy and asthma. This will enable the early identification of infants at high risk and facilitate novel strategies and interventions to prevent and treat these conditions, including modifying the intestinal microbiota early in life.

Factors Influencing the Intestinal Microbiome During the First Year of Life

The intestinal microbiome plays a crucial role in the development of the immune system and regulation of immune responses. Many factors influence the composition of the infant intestinal microbiome and therefore the development and function of the immune system. This, in turn, may alter the risk of subsequent allergies, autoimmune diseases and other adverse health outcomes. Here, we review factors that influence the composition of the intestinal microbiome during the first year of life, including birth location, gestational age, delivery mode, feeding method, hospitalization, antibiotic or probiotic intake and living conditions. Understanding how the early intestinal microbiome is established and how this is perturbed provides many opportunities for interventions to improve health.

Development of the Gut Microbiome in Children, and Lifetime Implications for Obesity and Cardiometabolic Disease

Emerging evidence suggests that microbiome composition and function is associated with development of obesity and metabolic disease. Microbial colonization expands rapidly following birth, and microbiome composition is particularly variable during infancy. Factors that influence the formation of the gut microbiome during infancy and childhood may have a significant impact on development of obesity and metabolic dysfunction, with life-long consequences. In this review, we examine the determinants of gut microbiome composition during infancy and childhood, and evaluate the potential impact on obesity and cardiometabolic risk.

The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth

BACKGROUND

The impact of degree of prematurity at birth on premature infant gut microbiota has not been extensively studied in comparison to term infants in large cohorts.

METHODS

To determine the effect of gestational age at birth and postnatal exposures on gut bacterial colonization in infants, we analyzed 65 stool samples from 17 premature infants in the neonatal intensive care unit, as well as 13 samples from 13 mostly moderate-to-late premature infants and 189 samples from 176 term infants in the New Hampshire Birth Cohort Study. Gut colonization patterns were determined with 16S rDNA microbiome profiling.

RESULTS

Gut bacterial alpha-diversity differed between premature and term infants at 6 weeks of age, after adjusting for exposures (p = 0.027). Alpha-diversity varied between extremely premature (<28 weeks gestation) and very premature infants (≥28 but <32 weeks, p = 0.011), as well as between extremely and moderate-to-late premature infants (≥32 and <37 weeks, p = 0.004). Newborn antibiotic use among premature infants was associated with lower Bifidobacterium and Bacteroides abundance (p = 0.015 and p = 0.041).

CONCLUSION

Gestational age at birth and early antibiotic exposure have significant effects on the premature infant gut microbiota.

Environmental factors and eosinophilic esophagitis

The incidence and prevalence of eosinophilic esophagitis (EoE) have markedly increased over the past 2 decades, outpacing increased detection of the disease. Although genetic susceptibility markers for EoE have begun to be elucidated, the rate at which EoE has increased in incidence suggests environmental factors predominate. Despite many advances in understanding of the pathogenesis of EoE, the cause of EoE is unknown. This article reviews the emerging data related to environmental risk factors for EoE. Many of these environmental factors are rooted in the theoretical framework of the hygiene hypothesis, specifically mediation of disease development through dysbiosis. Other hypotheses are based on associations that have been observed in studies of non-EoE allergic disease. We describe the evidence that early-life exposures, including antibiotic use, acid suppression, and cesarean delivery, can increase the risk of disease. We also describe the evidence that infectious agents, such as Helicobacter pylori, are inversely associated with disease. Current evidence on geographic risk factors, such as population density, climate zone, and seasonality, is reviewed. We also describe behavioral factors that have been evaluated. Limitations of the existing research are discussed, and recommendations for future areas of research, including assessment of gene-environment interaction, are presented.

Bacterial DNA is present in the fetal intestine and overlaps with that in the placenta in mice

Bacterial DNA has been reported in the placenta and amniotic fluid by several independent groups of investigators. However, it's taxonomic overlap with fetal and maternal bacterial DNA in different sites has been poorly characterized. Here, we determined the presence of bacterial DNA in the intestines and placentas of fetal mice at gestational day 17 (n = 13). These were compared to newborn intestines (n = 15), maternal sites (mouth, n = 6; vagina, n = 6; colon, n = 7; feces, n = 8), and negative controls to rule out contamination. The V4 region of the bacterial 16S rRNA gene indicated a pattern of bacterial DNA in fetal intestine similar to placenta but with higher phylogenetic diversity than placenta or newborn intestine. Firmicutes were the most frequently assignable phylum. SourceTracker analysis suggested the placenta as the most commonly identifiable origin for fetal bacterial DNA, but also over 75% of fetal gut genera overlapped with maternal oral and vaginal taxa but not with maternal or newborn feces. These data provide evidence for the presence of bacterial DNA in the mouse fetus.

The potential of gut microbiota and fecal volatile organic compounds analysis as early diagnostic biomarker for necrotizing enterocolitis and sepsis in preterm infants

Although the exact pathophysiological mechanisms of both necrotizing enterocolitis (NEC) and late-onset sepsis (LOS) in preterm infants are yet to be elucidated, evidence is emerging that the gut microbiota plays a key role in their pathophysiology. Areas covered: In this review, initial microbial colonization and factors influencing microbiota composition are discussed. For both NEC and LOS, an overview of studies investigating preclinical alterations in gut microbiota composition and fecal volatile organic compounds (VOCs) is provided. Fecal VOCs are considered to reflect not only gut microbiota composition, but also their metabolic activity and concurrent interaction with the host. Expert review: Heterogeneity in study protocols and applied analytical techniques hampers reliable comparison between outcomes of different microbiota studies, limiting the ability to draw firm conclusions. This dilemma is illustrated by the finding that study results often cannot be reproduced, or even contradict each other. A NEC- and sepsis specific microbial or metabolic signature has not yet been discovered. Identification of 'disease-specific' VOCs and microbiota composition may increase understanding on pathophysiological mechanisms and may allow for development of an accurate screening tool, opening avenues towards timely identification and initiation of targeted treatment for preterm infants at increased risk for NEC and sepsis.

Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units

Background

To explore the influences of prenatal antibiotic exposure, the intensity of prenatal and postnatal antibiotic exposure on gut microbiota of preterm infants and whether gut microbiota and drug resistant strains in the neonatal intensive care unit (NICU) over a defined period are related.

Methods

Among 28 preterm infants, there were two groups, the PAT (prenatal antibiotic therapy) group (12 cases), and the PAF (prenatal antibiotic free) group (12 cases). Fecal samples from both groups were collected on days 7 and 14. According to the time of prenatal and postnatal antibiotic exposure, cases were divided into two groups, H (high) group (11 cases) and L (low) group (11 cases), and fecal samples on day 14 were collected. Genomic DNA was extracted from the fecal samples and was subjected to high throughput 16S rRNA amplicon sequencing. Bioinformatics methods were used to analyze the sequencing results.

Results

Prenatal and postnatal antibiotic exposure exercised influence on the early establishment of intestinal microflora of preterm infants. Bacteroidetes decreased significantly in the PAT group (p < 0.05). The number of Bifidobacterium significantly decreased in the PAT group and H group (p < 0.05). The early gut microbiota of preterm infants with prenatal and postnatal antibiotic exposure was similar to resistant bacteria in NICU during the same period.

Conclusion

Prenatal and postnatal antibiotic exposure may affect the composition of early gut microbiota in preterm infants. Antibiotic-resistant bacteria in NICU may play a role in reshaping the early gut microbiota of preterm infants with prenatal and postnatal antibiotic exposure.

Electronic supplementary material

The online version of this article (10.1186/s12941-018-0264-y) contains supplementary material, which is available to authorized users.

Independent of Birth Mode or Gestational Age, Very-Low-Birth-Weight Infants Fed Their Mothers' Milk Rapidly Develop Personalized Microbiotas Low in Bifidobacterium

Background

Very-low-birth-weight (VLBW; born weighing <1500 g) infant feeding with mother's own milk (mother's milk) is associated with numerous beneficial health outcomes. Several interventions, including the prophylactic use of probiotics, are being adopted to promote a gastrointestinal microbiota favorable to the gut health of VLBW infants. An improved understanding of the microbiota that results from mother's milk feeding would therefore facilitate progress in this field.

Objective

A preplanned primary objective of this research was to characterize the development of the gut microbiota in exclusively mother's milk-fed VLBW infants and describe the reference taxonomic profile that results from mother's milk feeding.

Methods

In this prospective longitudinal cohort study, we collected weekly stool samples from exclusively mother's milk-fed VLBW infants admitted to Mount Sinai Hospital and profiled their gastrointestinal microbiota development from birth (primary outcome of stool collection). In total, we profiled 231 stools from 54 exclusively mother's milk-fed VLBW infants with the use of V6-16S ribosomal RNA gene sequencing.

Results

Bacterial evenness, but not bacterial richness, increased over time in VLBW infants (P < 0.001). Bifidobacterium relative abundances were consistently low in all microbiotas at all time points (<0.5% in 97% of samples). VLBW infant microbiotas did not cluster by birth mode, gestational age, or weeks after birth and instead clustered as a function of patient identity (R2 = 0.51, P < 0.001).

Conclusions

Exclusively mother's milk-fed VLBW infants rapidly develop personalized gut microbiotas that show increasing evenness and are seemingly unaffected by birth mode or gestational age at birth. The benefits from mother's milk feeding are likely modulated through microbes or pathways that are not dependent on Bifidobacterium because these microbes are present at low levels in VLBW infants. These results help define a reference VLBW infant microbiota profile derived from mother's milk, the optimal source of nutrition for these infants. This trial was registered at ISRCTN (http://www.isrctn.com/) as ISRCTN35317141.

Maternal microbiomes in preterm birth: Recent progress and analytical pipelines

Worldwide, 10% of babies are born preterm, defined as birth before 37 weeks' gestation. We have had little success in developing strategies to prevent preterm births, the majority of which are due to infection or are idiopathic. An emerging hypothesis is that the maternal microbiome-the bacteria that inhabit the mother's body and play vital functions in normal health-contributes to the etiology of preterm birth. Here, we highlight the latest data revealing correlations between preterm birth and maternal intestinal, vaginal, cervical, and placental microbiomes. Additionally, we describe the most commonly used comparative microbiome analysis methods and highlight important issues to consider when conducting such studies.

Early microbiota, antibiotics and health

The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance. Exposure to antibiotics, either prenatally or postnatally, is common in early life mainly due to the use of intrapartum prophylaxis or to the administration of antibiotics in C-section deliveries. However, we are still far from understanding the impact of early antibiotics and their long-term effects. Increased risk of non-communicable diseases, such as allergies or obesity, has been observed in individuals exposed to antibiotics during early infancy. Moreover, the impact of antibiotics on the establishment of the infant gut resistome, and on the role of the microbiota as a reservoir of resistance genes, should be evaluated in the context of the problems associated with the increasing number of antibiotic resistant pathogenic strains. In this article, we review and discuss the above-mentioned issues with the aim of encouraging debate on the actions needed for understanding the impact of early life antibiotics upon human microbiota and health and for developing strategies aimed at minimizing this impact.

Planting the seed: Origins, composition, and postnatal health significance of the fetal gastrointestinal microbiota

It has long been assumed that establishment of the fetal microbiome commences with the birthing process. However, recent studies have found bacterial DNA in umbilical cord blood, placenta, amniotic fluid, meconium, and fetal membranes in healthy normal pregnancies, leading to suggestions that the seeding of the fetal microbiome may commence in utero long before delivery. The origins of the microbiota of the fetal gastrointestinal (GI) tract have not yet been conclusively determined, although bacterial translocation from the maternal circulation, or ascension from the vagina, are both likely to be contributing pathways. Mother-to-child efflux of bacteria during pregnancy has the potential to markedly influence postnatal health, as the composition of gut microbiota determines production of important metabolites which are absorbed systemically and which modify immune function and development. Hence, the importance of understanding the colonization of the fetal GI microbiome is becoming clear, although few studies have investigated the origins, dynamics, and timing of the fetal microbiome. This is the topic of this review. By gaining a deeper understanding of the mechanisms underpinning fetal microbiome seeding, strategies may be developed to optimize fetal immune development and reduce the risk of adverse health and developmental outcomes.

Antibiotic use during pregnancy: how bad is it?

BACKGROUND

Our microbial companions (the "microbiota") are extremely important for the preservation of human health. Although changes in bacterial communities (dysbiosis) are commonly associated with disease, such changes have also been described in healthy pregnancies, where the microbiome plays an essential role in maternal and child health outcomes, including normal immune and metabolic function in later life. Nevertheless, this new understanding of the importance of the microbiome has not yet influenced contemporary clinical practice regarding antibiotic use during pregnancy.

DISCUSSION

Antibiotic treatment during pregnancy is widespread in Western countries, and accounts for 80 % of prescribed medications in pregnancy. However, antibiotic treatment, while at times lifesaving, can also have detrimental consequences. A single course of antibiotics perturbs bacterial communities, with evidence that the microbial ecosystem does not return completely to baseline following treatment. Antibiotics in pregnancy should be used only when indicated, choosing those with the narrowest range possible. Bacteria are essential for normal human development and, while antibiotic treatment during pregnancy has an important role in controlling and preventing infections, it may have undesired effects regarding the maternal and fetoplacental microbiomes. We expect that microbiota manipulation in pregnancy, through the use of probiotics and fecal microbiota transplantation, will be the subject of increasing clinical interest.

Assessing Early Life Factors for Eosinophilic Esophagitis: Lessons From Other Allergic Diseases

OPINION STATEMENT

Few studies have been conducted to investigate possible early life determinants for eosinophilic esophagitis. An improved understanding of the etiologic factors implicated in disease development would further elucidate possible disease pathogenesis, inform therapeutic targets for disease treatment, and identify possible modifiable factors for disease prevention in genetically susceptible individuals. Although eosinophilic esophagitis is increasing in incidence and prevalence, the disease remains relatively rare, posing challenges for studying etiologic factors in disease development. Eosinophilic esophagitis is believed to be antigen-mediated, and most patients with EoE have concomitant atopic disease. In recent years, the evolution of our understanding of possible etiologic mechanisms in allergic disease has been informed by our understanding of how early life perturbations can lead to dysbiosis in the colonization of the microflora in the gastrointestinal tract and subsequent dysregulated immune development. Perturbations include factors such as antibiotic use, including prenatal, intra-antepartum, and infancy use of antibiotics, Cesarean delivery, preterm delivery, and neonatal intensive care admission. This article provides a review of these recent developments, as they relate to atopic disease, to inform future directions in the study of early life etiologic factors in the development of eosinophilic esophagitis.

Working group reports: evaluation of the evidence to support practice guidelines for nutritional care of preterm infants-the Pre-B Project

The "Evaluation of the Evidence to Support Practice Guidelines for the Nutritional Care of Preterm Infants: The Pre-B Project" is the first phase in a process to present the current state of knowledge and to support the development of evidence-informed guidance for the nutritional care of preterm and high-risk newborn infants. The future systematic reviews that will ultimately provide the underpinning for guideline development will be conducted by the Academy of Nutrition and Dietetics' Evidence Analysis Library (EAL). To accomplish the objectives of this first phase, the Pre-B Project organizers established 4 working groups (WGs) to address the following themes: 1) nutrient specifications for preterm infants, 2) clinical and practical issues in enteral feeding of preterm infants, 3) gastrointestinal and surgical issues, and 4) current standards of infant feeding. Each WG was asked to 1) develop a series of topics relevant to their respective themes, 2) identify questions for which there is sufficient evidence to support a systematic review process conducted by the EAL, and 3) develop a research agenda to address priority gaps in our understanding of the role of nutrition in health and development of preterm/neonatal intensive care unit infants. This article is a summary of the reports from the 4 Pre-B WGs.