The developing intestinal microbiome and its relationship to health and disease in the neonate

The impact of breastfeeding on the preterm infant's microbiome and metabolome: a pilot study

BACKGROUND

Human milk is unquestionably beneficial for preterm infants. We investigated how the transition from tube to oral/breastfeeding impacts the preterm infants' oral and gut microbiome and metabolome.

METHODS

We analyzed stool, saliva, and milk samples collected from a cohort of preterm infants enrolled in the MAP Study, a prospective observational trial. The microbiome and metabolome of the samples were analyzed from 4 longitudinal sample time points, 2 during tube feeds only and 2 after the initiation of oral/breastfeeding.

RESULTS

We enrolled 11 mother-infant dyads (gestational age = 27.9 (23.4-32.2)) and analyzed a total of 39 stool, 44 saliva, and 43 milk samples over 4 timepoints. In saliva samples, there was a shift towards increased Streptococcus and decreased Staphylococcus after oral feeding/breastfeeding initiation (p < 0.05). Milk sample metabolites were strongly influenced by the route of feeding and milk type (p < 0.05) and represented the pathways of Vitamin E metabolism, Vitamin B12 metabolism, and Tryptophan metabolism.

CONCLUSION

Our analysis demonstrated that the milk and preterm infant's saliva microbiome and metabolome changed over the course of the first four to 5 months of life, coinciding with the initiation of oral/breastfeeds.

IMPACT

The microbiome and metabolome is altered in the infant's saliva but not their stool, and in mother's milk when feeds are transitioned from tube to oral/breastfeeding. We assessed the relationship between the gut and oral microbiome/metabolome with the milk microbiome/metabolome over a longitudinal period of time in preterm babies. Metabolites that changed in the infants saliva after the initiation of oral feeds have the potential to be used as biomarkers for disease risk.

Antibiotics Use and Its Effects on the Establishment of Feeding Tolerance in Preterm Neonates

OBJECTIVE

Antibiotics are one of the most widely used medications in today's neonatal intensive care units. Indiscriminate antibiotic usage persists in preterm newborns who are symptomatic due to factors linked to prematurity rather than being septic. Previous studies in older infants suggest that prior antibiotic administration is associated with possible dysmotility and microbial dysbiosis in the intestinal tract. We hypothesize that early antibiotic administration impacts high-risk preterm infants' tolerance to enteral feeding advancement.

STUDY DESIGN

As part of the Routine Early Antibiotic Use in SymptOmatic Preterm Neonates study, symptomatic preterm newborns without maternal infection risk factors were randomized to receive or not receive antibiotics, with C1 receiving antibiotics and C2 not. Of the 55 newborns that underwent pragmatic randomization, 28 preterm neonates in group C1 received antibiotics.

RESULTS

The premature neonates in the randomized groups who received antibiotics and those who did not showed no differences in sustained feeding tolerance.

CONCLUSION

Our investigation of the risk of feeding issues in babies who get antibiotics early in life revealed no differences between neonates who received antibiotics and those who did not when the randomized controlled trial data alone was reviewed. Given the sample sizes, it is uncertain if the preceding analysis is powerful enough to detect differences (a significant percentage of neonates who were randomly assigned to NOT get antibiotics subsequently received early treatment due to changing clinical conditions). This affirms the requirement for a meticulously designed prospective randomized study.

KEY POINTS

· Defining feeding tolerance for the first time in neonates.. · Patients from the REASON trial were evaluated.. · Preterm neonates were the focus of this study..

Effects of Sublingual Colostrum Application on Oral and Intestinal Flora of Extremely Low Birth Weight Infants

BACKGROUND

The aim of this study is to analyze the effects of colostrum application on the establishment of normal flora in the intestinal tracts and oral cavities of extremely low birth weight infants (ELBWI).

METHODS

A prospective cohort study design was adopted following the STROBE guidelines (Supplementary File 1). Colostrum was administered immediately after obtaining maternal breast milk using a special sterile cotton swab. There were no specific treatments for infants who did not receive colostrum. This experiment was completed on day 5 post-birth and the patients were divided into the colostrum and control groups, corresponding to whether or not colostrum was administered. Throat swabs and stool samples were collected on days 1 and 5 post-birth.

RESULTS

Using the conventional bacteria cultivation technique, the detection rate of bacteria in 98 cases of meconium at birth was 15.31%. On day 5, the detection rates of Staphylococcus in the colostrum and control groups were 36.54% and 34.78%, with no significant difference between them (P = 0.856), and that of Enterococcus was 26.92% and 13.04%, respectively, with no statistically significant difference (P = 0.089). Likewise, at birth, the detection rate of bacteria in 98 cases of throat swabs was 27.55%. On day 5, the detection rate of Streptococcus in the colostrum and control groups was 78.85% and 50.00%, respectively, recording a statistically significant difference this time (P = 0.003).

CONCLUSION

Colostrum application had limited effects on intestinal flora colonization but contributes to physiological oral flora colonization.

The importance of the intestinal microbiota in humans and dogs in the neonatal period

The neonatal period represents a critical stage for the establishment and development of the gut microbiota, which profoundly influences the future health trajectory of individuals. This review examines the importance of intestinal microbiota in humans and dogs, aiming to elucidate the distinct characteristics and variations in the composition between these two species. In humans, the intestinal microbiota contributes to several crucial physiological processes, including digestion, nutrient absorption, immune system development, and modulation of host metabolism. Dysbiosis, an imbalance or disruption of the gut microbial community, has been linked to various disorders, such as inflammatory bowel disease, obesity, and even neurological conditions. Furthermore, recent research has unveiled the profound influence of the gut-brain axis, emphasizing the bidirectional communication between the gut microbiota and the central nervous system, impacting cognitive function and mental health. Similarly, alterations in the canine intestinal microbiota have been associated with gastrointestinal disorders, including chronic enteropathy, such as inflammatory bowel disease, food allergies, and ulcerative histiocytic colitis. However, our understanding of the intricacies and functional significance of the intestinal microbiota in dogs remains limited. Understanding the complex dynamics of the intestinal microbiota in both humans and dogs is crucial for devising effective strategies to promote health and manage disease. Moreover, exploring the similarities and differences in the gut microbial composition between these two species can facilitate translational research, potentially leading to innovative therapeutic interventions and strategies to enhance the well-being of both humans and dogs.

Maternal Folic Acid Supplementation during Pregnancy Prevents Hepatic Steatosis in Male Offspring of Rat Dams Fed High-Fat Diet, Which Is Associated with the Regulation of Gut Microbiota

Maternal dietary patterns during pregnancy have been demonstrated to impact the structure of the gut microbiota in offspring, altering their susceptibility to diseases. This study is designed to elucidate whether the impact of folic acid supplementation during pregnancy on hepatic steatosis in male offspring of rat dams exposed to a high-fat diet (HFD) is related to gut-liver axis homeostasis. In this study, female rats were administered a HFD and simultaneously supplemented with 5 mg/kg folic acid throughout their pregnancy. Histopathological examination showed that folic acid supplementation effectively ameliorated hepatic lipid accumulation and inflammatory infiltrate in male offspring subjected to a maternal HFD. Maternal folic acid supplementation reduced the abundance of Desulfobacterota and the Firmicutes/Bacteroidota (F/B) ratio in male offspring. The expression of tight junction proteins in the colon was significantly upregulated, and the serum LPS level was significantly reduced. Furthermore, there was a notable reduction in the hepatic expression of the TLR4/NF-κB signaling pathway and subsequent inflammatory mediators. Spearman's correlation analysis revealed significant associations between hepatic inflammation-related indices and several gut microbiota, particularly Desulfobacterota and Lactobacillus. With a reduction in hepatic inflammation, the expression of PPAR-α was upregulated, and the expression of SREBP-1c and its downstream lipid metabolism-related genes was downregulated. In summary, folic acid supplementation during pregnancy modulates gut microbiota and enhances intestinal barrier integrity in male offspring of HFD dams. This helps reduce the LPS leakage and suppress the expression of TLR4/NF-κB pathway in the liver, thereby improving lipid metabolism disorders, and alleviating hepatic steatosis.

Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund

A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets, and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of Streptococcus bovis/Streptococcus equinus complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living in a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.

Neonatal sepsis definitions from randomised clinical trials

INTRODUCTION

Neonatal sepsis is a leading cause of infant mortality worldwide with non-specific and varied presentation. We aimed to catalogue the current definitions of neonatal sepsis in published randomised controlled trials (RCTs).

METHOD

A systematic search of the Embase and Cochrane databases was performed for RCTs which explicitly stated a definition for neonatal sepsis. Definitions were sub-divided into five primary criteria for infection (culture, laboratory findings, clinical signs, radiological evidence and risk factors) and stratified by qualifiers (early/late-onset and likelihood of sepsis).

RESULTS

Of 668 papers screened, 80 RCTs were included and 128 individual definitions identified. The single most common definition was neonatal sepsis defined by blood culture alone (n = 35), followed by culture and clinical signs (n = 29), and then laboratory tests/clinical signs (n = 25). Blood culture featured in 83 definitions, laboratory testing featured in 48 definitions while clinical signs and radiology featured in 80 and 8 definitions, respectively.

DISCUSSION

A diverse range of definitions of neonatal sepsis are used and based on microbiological culture, laboratory tests and clinical signs in contrast to adult and paediatric sepsis which use organ dysfunction. An international consensus-based definition of neonatal sepsis could allow meta-analysis and translate results to improve outcomes.

Crucial nuances in understanding (mis)associations between the neonatal microbiome and Cesarean delivery

As rates of Cesarean delivery and common non-communicable disorders (NCDs), such as obesity, metabolic disease, and atopy/asthma, have concomitantly increased in recent decades, investigators have attempted to discern a causal link. One line of research has led to a hypothesis that Cesarean birth disrupts the presumed normal process of colonization of the neonatal microbiome with vaginal microbes, yielding NCDs later in life. However, a direct link between a disrupted microbiota transfer at time of delivery and acute and/or chronic illness in infants born via Cesarean has not been causally established. Microbiota seeding from maternal vaginal or stool sources has been preliminarily evaluated as an intervention designed to compensate for the lack of (or limited) exposure to such sources among Cesarean-delivered neonates. However, to date, clinical trials have yet to show a clear health benefit with neonatal 'vaginal seeding' practices. Until the long-term effects of these microbiome alterations can be fully determined, it is paramount to conduct parallel meaningful and mechanistic-minded interrogations of the impact of clinically modifiable maternal, nutritional, or environmental exposure on the functional microbiome over the duration of pregnancy and lactation to determine their role in the mitigation of childhood and adult NCDs.

Milk fat globule membrane supplementation to obese rats during pregnancy and lactation promotes neurodevelopment in offspring via modulating gut microbiota

Pre-pregnancy obesity and high-fat diet (HFD) during pregnancy and lactation are associated with neurodevelopmental delay in offspring. This study aimed to investigate whether milk fat globule membrane (MFGM) supplementation in obese dams could promote neurodevelopment in offspring. Obese female rats induced by HFD were supplemented with MFGM during pregnancy and lactation. Maternal HFD exposure significantly delayed the maturation of neurological reflexes and inhibited neurogenesis in offspring, which were significantly recovered by maternal MFGM supplementation. Gut microbiota analysis revealed that MFGM supplementation modulated the diversity and composition of gut microbiota in offspring. The abundance of pro-inflammatory bacteria such as Escherichia shigella and Enterococcus were down-regulated, and the abundance of bacteria with anti-inflammatory and anti-obesity functions, such as Akkermansia and Lactobacillus were up-regulated. Furthermore, MFGM alleviated neuroinflammation by decreasing the levels of lipopolysaccharides (LPS) and pro-inflammatory cytokines in the circulation and brain, as well as inhibiting the activation of microglia. Spearman’s correlation analysis suggested that there existed a correlation between gut microbiota and inflammation-related indexes. In conclusion, maternal MFGM supplementation promotes neurodevelopment partly via modulating gut microbiota in offspring.

Bench to bedside - new insights into the pathogenesis of necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is the leading cause of death and disability from gastrointestinal disease in premature infants. Recent discoveries have shed light on a unifying theorem to explain the pathogenesis of NEC, suggesting that specific treatments might finally be forthcoming. A variety of experiments have highlighted how the interaction between bacterial signalling receptors on the premature intestine and an abnormal gut microbiota incites a pro-inflammatory response in the intestinal mucosa and its underlying endothelium that leads to NEC. Central amongst the bacterial signalling receptors implicated in NEC development is the lipopolysaccharide receptor Toll-like receptor 4 (TLR4), which is expressed at higher levels in the premature gut than in the full-term gut. The high prenatal intestinal expression of TLR4 reflects the role of TLR4 in the regulation of normal gut development, and supports additional studies indicating that NEC develops in response to signalling events that occur in utero. This Review provides new evidence explaining the pathogenesis of NEC, explores new findings indicating that NEC development has origins before birth, and discusses future questions and opportunities for discovery in this field.

Variability in the Pre-Analytical Stages Influences Microbiome Laboratory Analyses

Introduction: There are numerous confounding variables in the pre-analytical steps in the analysis of gut microbial composition that affect data consistency and reproducibility. This study compared two DNA extraction methods from the same faecal samples to analyse differences in microbial composition. Methods: DNA was extracted from 20 faecal samples using either (A) chemical/enzymatic heat lysis (lysis buffer, proteinase K, 95 °C + 70 °C) or (B) mechanical and chemical/enzymatic heat lysis (bead-beating, lysis buffer, proteinase K, 65 °C). Gut microbiota was mapped through the 16S rRNA gene (V3−V9) using a set of pre-selected DNA probes targeting >300 bacteria on different taxonomic levels. Apart from the pre-analytical DNA extraction technique, all other parameters including microbial analysis remained the same. Bacterial abundance and deviations in the microbiome were compared between the two methods. Results: Significant variation in bacterial abundance was seen between the different DNA extraction techniques, with a higher yield of species noted in the combined mechanical and heat lysis technique (B). The five predominant bacteria seen in both (A) and (B) were Bacteroidota spp. and Prevotella spp. (p = NS), followed by Bacillota (p = 0.005), Lachhnospiraceae (p = 0.0001), Veillonella spp. (p < 0.0001) and Clostridioides (p < 0.0001). Conclusion: As microbial testing becomes more easily and commercially accessible, a unified international consensus for optimal sampling and DNA isolation procedures must be implemented for robustness and reproducibility of the results.

Long-term impact of pre-incision antibiotics on children born by caesarean section: a longitudinal study based on UK electronic health records

BACKGROUND

Since changes in the national guidance in 2011, prophylactic antibiotics for women undergoing caesarean section are recommended prior to skin incision, rather than after the baby's umbilical cord has been clamped. Evidence from randomised controlled trials conducted outside the UK has shown that this reduces maternal infectious morbidity; however, the prophylactic antibiotics also cross the placenta, meaning that babies are exposed to them around the time of birth. Antibiotics are known to affect the gut microbiota of the babies, but the long-term effects of exposure to high-dose broad-spectrum antibiotics around the time of birth on allergy and immune-related diseases are unknown.

OBJECTIVES

We aimed to examine whether or not in-utero exposure to antibiotics immediately prior to birth compared with no pre-incisional antibiotic exposure increases the risk of (1) asthma and (2) eczema in children born by caesarean section.

DESIGN

This was a controlled interrupted time series study.

SETTING

The study took place in primary and secondary care.

PARTICIPANTS

Children born in the UK during 2006-18 delivered by caesarean section were compared with a control cohort delivered vaginally.

INTERVENTIONS

In-utero exposure to antibiotics immediately prior to birth.

MAIN OUTCOME MEASURES

Asthma and eczema in children in the first 5 years of life. Additional secondary outcomes, including other allergy-related conditions, autoimmune diseases, infections, other immune system-related diseases and neurodevelopmental conditions, were also assessed.

DATA SOURCES

The Health Improvement Network (THIN) and the Clinical Practice Research Datalink (CPRD) primary care databases and the Hospital Episode Statistics (HES) database. Previously published linkage strategies were adapted to link anonymised data on mothers and babies in these databases. Duplicate practices contributing to both THIN and the CPRD databases were removed to create a THIN-CPRD data set.

RESULTS

In the THIN-CPRD and HES data sets, records of 515,945 and 3,945,351 mother-baby pairs were analysed, respectively. The risk of asthma was not significantly higher in children born by caesarean section exposed to pre-incision antibiotics than in children whose mothers received post-cord clamping antibiotics, with an incidence rate ratio of 0.91 (95% confidence interval 0.78 to 1.05) for diagnosis of asthma in primary care and an incidence rate ratio of 1.05 (95% confidence interval 0.99 to 1.11) for asthma resulting in a hospital admission. We also did not find an increased risk of eczema, with an incidence rate ratio of 0.98 (95% confidence interval 0.94 to1.03) and an incidence rate ratio of 0.96 (95% confidence interval 0.71 to 1.29) for diagnosis in primary care and hospital admissions, respectively.

LIMITATIONS

It was not possible to ascertain the exposure to pre-incision antibiotics at an individual level. The maximum follow-up of children was 5 years.

CONCLUSIONS

There was no evidence that the policy change from post-cord clamping to pre-incision prophylactic antibiotics for caesarean sections during 2006-18 had an impact on the incidence of asthma and eczema in early childhood in the UK.

FUTURE WORK

There is a need for further research to investigate if pre-incision antibiotics have any impact on developing asthma and other allergy and immune-related conditions in older children.

STUDY REGISTRATION

This study is registered as researchregistry3736.

FUNDING

This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 26, No. 30. See the NIHR Journals Library website for further project information.

Gut Microbiota as a Potential Predictive Biomarker in Relapsing-Remitting Multiple Sclerosis

BACKGROUND

The influence of the microbiome on neurological diseases has been studied for years. Recent findings have shown a different composition of gut microbiota detected in patients with multiple sclerosis (MS). The role of this dysbiosis is still unknown.

OBJECTIVE

We analyzed the gut microbiota of 15 patients with active relapsing-remitting multiple sclerosis (RRMS), comparing with diet-matched healthy controls.

METHOD

To determine the composition of the gut microbiota, we performed high-throughput sequencing of the 16S ribosomal RNA gene. The specific amplified sequences were in the V3 and V4 regions of the 16S ribosomal RNA gene.

RESULTS

The gut microbiota of RRMS patients differed from healthy controls in the levels of the Lachnospiraceae, Ezakiella, Ruminococcaceae, Hungatella, Roseburia, Clostridium, Shuttleworthia, Poephyromonas, and Bilophila genera. All these genera were included in a logistic regression analysis to determine the sensitivity and the specificity of the test. Finally, the ROC (receiver operating characteristic) and AUC with a 95% CI were calculated and best-matched for Ezakiella (AUC of 75.0 and CI from 60.6 to 89.4) and Bilophila (AUC of 70.2 and CI from 50.1 to 90.4).

CONCLUSIONS

There is a dysbiosis in the gut microbiota of RRMS patients. An analysis of the components of the microbiota suggests the role of some genera as a predictive factor of RRMS prognosis and diagnosis.

Long term impact of prophylactic antibiotic use before incision versus after cord clamping on children born by caesarean section: longitudinal study of UK electronic health records

OBJECTIVE

To investigate the impact on child health up to age 5 years of a policy to use antibiotic prophylaxis for caesarean section before incision compared with after cord clamping.

DESIGN

Observational controlled interrupted time series study.

SETTING

UK primary and secondary care.

PARTICIPANTS

515 945 children born in 2006-18 with linked maternal records and registered with general practices contributing to two UK primary care databases (The Health Improvement Network and Clinical Practice Research Datalink), and 7 147 884 children with linked maternal records in the Hospital Episode Statistics database covering England, of which 3 945 351 were linked to hospitals that reported the year of policy change to administer prophylactic antibiotics for caesarean section before incision rather than after cord clamping.

INTERVENTION

Fetal exposure to antibiotics shortly before birth (using pre-incision antibiotic policy as proxy) compared with no exposure.

MAIN OUTCOME MEASURES

The primary outcomes were incidence rate ratios of asthma and eczema in children born by caesarean section when pre-incision prophylactic antibiotics were recommended compared with those born when antibiotics were administered post-cord clamping, adjusted for temporal changes in the incidence rates in children born vaginally.

RESULTS

Prophylactic antibiotics administered before incision for caesarean section compared with after cord clamping were not associated with a significantly higher risk of asthma (incidence rate ratio 0.91, 95% confidence interval 0.78 to 1.05) or eczema (0.98, 0.94 to 1.03), including asthma and eczema resulting in hospital admission (1.05, 0.99 to 1.11 and 0.96, 0.71 to 1.29, respectively), up to age 5 years.

CONCLUSIONS

This study found no evidence of an association between pre-incision prophylactic antibiotic use and risk of asthma and eczema in early childhood in children born by caesarean section.

Remote Stewardship for Medically Underserved Nurseries: A Stepped-Wedge, Cluster Randomized Study

BACKGROUND AND OBJECTIVES

Antibiotic overuse is associated with adverse neonatal outcomes. Many medically underserved centers lack pediatric antibiotic stewardship program (ASP) support. Telestewardship may mitigate this disparity. Authors of this study aimed to determine the effectiveness and safety of a nursery-specific ASP delivered remotely.

METHODS

Remote ASP was implemented in 8 medically underserved newborn nurseries using a stepped-wedge, cluster-randomized design over 3 years. This included a 15-month baseline period, a 9-month "step-in" period using random nursery order, and a 12-month postintervention period. The program consisted of education, audit, and feedback; and 24/7 infectious diseases provider-to-provider phone consultation availability. Outcomes included each center's volume of antibiotic use and the proportion of infants exposed to any antibiotics. Safety measures included length of stay, transfer to another facility, sepsis, and mortality.

RESULTS

During the study period, there were 9277 infants born (4586 preintervention, 4691 postintervention). Infants exposed to antibiotics declined from 6.2% pre-ASP to 4.2% post-ASP (relative risk 0.68 [95% confidence interval, 0.63% to 0.75%]). Total antibiotic use declined from 117 to 84.1 days of therapy per 1000 patient-days (-28% [95% confidence interval -22% to -34%]. No safety signals were observed. Most provider-to-provider consultations were <5 minutes in duration and occurred during normal business hours.

CONCLUSIONS

The number of infants exposed to antibiotics and total antibiotic use declined in medically underserved nurseries after implementing a remote ASP. No adverse safety events were seen, and the remote ASP time demands were manageable. Remote stewardship may be a safe and effective strategy for optimizing antibiotic use in medically underserved newborn nurseries.

Inflammatory Bowel Disease and Reproductive Health: From Fertility to Pregnancy-A Narrative Review

Despite the fact that knowledge on obstetrical management of Inflammatory Bowel Diseases (IBDs) has greatly improved over the years, many patients still actively avoid pregnancy for fear of adverse maternal or neonatal outcomes, of adverse effects of pregnancy on the disease activity, of eventual IBD inheritance, or of an increased risk of congenital malformations. Indeed, though data prove that fertility is hardly affected by the disease, a reduced birth rate is nevertheless observed in patients with IBD. Misconceptions on the safety of drugs during gestation and breastfeeding may influence patient choice and negatively affect their serenity during pregnancy or lactation. Moreover, physicians often showed concerns about starting IBD medications before and during pregnancy and did not feel adequately trained on the safety of IBD therapies. IBD-expert gastroenterologists and gynecologists should discuss pregnancy and breastfeeding issues with patients when starting or changing medications in order to provide appropriate information; therefore, pre-conception counselling on an individualized basis should be mandatory for all patients of reproductive age to reassure them that maintaining disease remission and balancing the eventual obstetrical risks is possible.

Interpretable prediction of necrotizing enterocolitis from machine learning analysis of premature infant stool microbiota

Background

Necrotizing enterocolitis (NEC) is a common, potentially catastrophic intestinal disease among very low birthweight premature infants. Affecting up to 15% of neonates born weighing less than 1500 g, NEC causes sudden-onset, progressive intestinal inflammation and necrosis, which can lead to significant bowel loss, multi-organ injury, or death. No unifying cause of NEC has been identified, nor is there any reliable biomarker that indicates an individual patient’s risk of the disease. Without a way to predict NEC in advance, the current medical strategy involves close clinical monitoring in an effort to treat babies with NEC as quickly as possible before irrecoverable intestinal damage occurs. In this report, we describe a novel machine learning application for generating dynamic, individualized NEC risk scores based on intestinal microbiota data, which can be determined from sequencing bacterial DNA from otherwise discarded infant stool. A central insight that differentiates our work from past efforts was the recognition that disease prediction from stool microbiota represents a specific subtype of machine learning problem known as multiple instance learning (MIL).

Results

We used a neural network-based MIL architecture, which we tested on independent datasets from two cohorts encompassing 3595 stool samples from 261 at-risk infants. Our report also introduces a new concept called the “growing bag” analysis, which applies MIL over time, allowing incorporation of past data into each new risk calculation. This approach allowed early, accurate NEC prediction, with a mean sensitivity of 86% and specificity of 90%. True-positive NEC predictions occurred an average of 8 days before disease onset. We also demonstrate that an attention-gated mechanism incorporated into our MIL algorithm permits interpretation of NEC risk, identifying several bacterial taxa that past work has associated with NEC, and potentially pointing the way toward new hypotheses about NEC pathogenesis. Our system is flexible, accepting microbiota data generated from targeted 16S or “shotgun” whole-genome DNA sequencing. It performs well in the setting of common, potentially confounding preterm neonatal clinical events such as perinatal cardiopulmonary depression, antibiotic administration, feeding disruptions, or transitions between breast feeding and formula.

Conclusions

We have developed and validated a robust MIL-based system for NEC prediction from harmlessly collected premature infant stool. While this system was developed for NEC prediction, our MIL approach may also be applicable to other diseases characterized by changes in the human microbiota.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04618-w.

Association of Intestinal Microbial Dysbiosis With Chronic Obstructive Pulmonary Disease

Normal gut flora plays various beneficial roles for the human body, including the protection against inflammatory states and mucosal viral infections. It also influences the immune system of the body. The metabolites produced by the gut bacteria control local and other systemic organs' immune functions like the lungs and brain, playing a role in their response to acute and chronic illnesses. Probiotics have shown beneficial effects on lung health. On the contrary, dysbiosis is associated with several diseases, including asthma, chronic bronchitis, emphysema, allergies, and other acute viral infections. By altering the diet of patients with respiratory diseases like patients with chronic obstructive pulmonary diseases (COPD), we may be able to mitigate their conditions. This literature review aims to discuss the mechanisms altering the gastrointestinal flora, the pathophysiology of gut and lung axis, the role of diet in gut microbe health, and the association of COPD with gut dysbiosis and peptic ulcer disease (PUD). We have extracted the data from PubMed and Google Scholar, consisting of review articles, case-control studies, and animal studies. The studies showed an association between gut microbes and different lung diseases. It is found that gut dysbiosis not only disrupts intestinal immunity but may also facilitate the development of COPD. Present studies also show an increased seroprevalence of Helicobacter pylori in patients with COPD. The strategies that can improve lung functions, especially in COPD patients, include prebiotics and probiotic supplementation to a diet more balanced than the current average American diet.

A Pilot Study To Establish an In Vitro Model To Study Premature Intestinal Epithelium and Gut Microbiota Interactions

Intestinal microbiota has emerged as an important player in the health and disease of preterm infants. The interactions between intestinal flora and epithelium can lead to local injury and systemic diseases. A suitable in vitro cell model is needed to enhance our understanding of these interactions. In this study, we exposed fetal epithelial cell cultures (FHs-74 int cells, human, ATCC CCL 241) to sterile fecal filtrates derived from stool collected from preterm infants at <2 and at 3 to 4 weeks of age. We measured the cytokine levels from the culture media after 4, 24, and 48 h of exposure to the fecal filtrates. We analyzed the 16S rRNA V4 gene data of the fecal samples and transcriptome sequencing (RNA-seq) data from the fetal epithelial cells after 48 h of exposure to the same fecal filtrates. The results showed correlations between inflammatory responses (both cytokine levels and gene expression) and the Proteobacteria-to-Firmicutes ratio and between fecal bacterial genera and epithelial apoptosis-related genes. Our in vitro cell model can be further developed and applied to study how the epithelium responds to different microbial flora from preterm infants. Combining immature epithelial cells and preterm infant stool samples into one model allows us to investigate disease processes in preterm infants in a way that had not been previously reported.

IMPORTANCE The gut bacterial flora influences the development of the immune system and long-term health outcomes in preterm infants. Studies of the mechanistic interactions between the gut bacteria and mucosal barrier are limited to clinical observations, animal models, and in vitro cell culture models for this vulnerable population. Most in vitro cell culture models of microbe-host interactions use single organisms or adult origin cell lines. Our study is innovative and significant in that we expose immature epithelial cells derived from fetal tissues to fecal filtrates from eight stool samples from four preterm infants to study the role of intestinal epithelial cells. In addition, we analyzed epithelial gene expression to examine multiple cellular processes simultaneously. This model can be developed into patient-derived two- or three-dimensional cell cultures exposed to their own fecal material to allow better prediction of patient physiological responses to support the growing field of precision medicine.

Acquisition of microbiota according to the type of birth: an integrative review

OBJECTIVE

to analyze scientific evidence regarding the relationship between the type of birth and the microbiota acquired by newborns.

METHOD

this integrative review addresses the role of the type of delivery on newborns' microbial colonization. A search was conducted in the Medical Literature Analysis and Retrieval System Online/PubMed and Virtual Health Library databases using the descriptors provided by Medical Subject Headings (MeSH) and Health Science Descriptors (DeCS).

RESULTS

infants born vaginally presented a greater concentration of Bacteroides, Bifidobacteria, and Lactobacillus in the first days of life and more significant microbial variability in the following weeks. The microbiome of infants born via C-section is similar to the maternal skin and the hospital setting and less diverse, mainly composed of Staphylococcus, Streptococcus, and Clostridium.

CONCLUSION

the maternal vaginal microbiota provides newborns with a greater variety of colonizing microorganisms responsible for boosting and preparing the immune system. Vaginal birth is the ideal birth route, and C-sections should only be performed when there are medical indications.

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study

Fading puppy syndrome (FPS) is a fatal condition in neonatal dogs. Intestinal microbial alterations, although never investigated, may be involved in its pathophysiology. The study examined the occurrence of FPS and its associations with dam, puppy, and husbandry characteristics, compared the intestinal microbial diversity of healthy puppies and those with FPS, and examined whether intestinal microbiomes are predictive of FPS. Day 1 and 8 post-partum (PP) rectal swabs were collected from healthy puppies and puppies which later developed FPS. Microbial compositional structure, including alpha and beta diversities and relative abundance of specific taxa were compared between groups, and microbial data was applied to a machine-learning model to assess the predictive performance of microbial indices of FPS or death. FPS occurred in 22/165 puppies (13%), with a 100% mortality rate. FPS was associated (P < 0.001) with decreased Day 1 PP puppy activity. Day 1 (P = 0.003) and 8 (P = 0.005) PP rectal beta diversities were different in puppies with FPS vs healthy ones. Increased Proteobacteria/Firmicutes ratio, increased relative abundance of Pasteurellaceae, and decreased relative abundance of Clostridia and Enterococcus were associated with FPS. A machine-learning model showed that Day 1 PP rectal microbiome composition accurately predicted FPS-related death. We found that specific rectal microbial phenotypes are associated with FPS, reflecting the significant role of microbiome alterations in this phenomenon. These findings may serve as useful microbial indices for early diagnosis of puppies at risk of FPS and may provide specific therapeutic targets.

Massage therapy in infants and children under 5 years of age: protocol for an overview of systematic reviews

INTRODUCTION

Massage is a popularly used complementary and alternative therapy. Previous randomised controlled trials have examined the effects of massage on children, and several systematic reviews have been conducted to synthesise these data. This study aims to assess and summarise the current evidence from published systematic reviews of controlled clinical trials on the practice of paediatric massage, specifically in infants and children aged < 5 years.

METHODS

The online databases MEDLINE, Embase, Health Technology Assessment Database, Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effects, Allied and Complementary Medicine, China National Knowledge Infrastructure and Wanfang Data will be searched from the inception onwards for evidence of the treatment effects. We will include systematic reviews of randomised control trials evaluating the effects and safety of massage therapy in infants and children aged < 5 years. The primary outcomes will be any physical or psychological outcome, and adverse effects on children. Secondary outcomes will include any physical or psychological outcome on caregivers. Two reviewers will independently screen the articles for inclusion as per the eligibility criteria. They will extract information from the included studies and assess the methodological quality of the included studies. A table will be used to summarise of information of the included studies, which includes the basic information, method and findings. The methodological quality of the included systematic reviews will be assessed by A Measurement Tool to Assess Systematic Reviews version 2 (AMSTAR 2). Extracted data from the included studies will be collected and presented using narrative approach. The pooled effect estimates for meta-analysed outcomes will be extracted when possible. If there is a discrepancy in results of two or more reviews on the same topic, then the causes of such discrepancy will be further explored.

DISCUSSION

This overview of systematic reviews will summarise the current evidence on massage, specifically for infants and children aged < 5 years. We will comprehensively present the positive effects and adverse effects of this intervention. Findings from this overview will be published in a peer-reviewed journal.

SYSTEMATIC REVIEW REGISTRATION

CRD42020186003 .

Coronavirus disease-2019 and the intestinal tract: An overview

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can progress to a severe respiratory and systemic disease named coronavirus disease-2019 (COVID-19). The most common symptoms are fever and respiratory discomfort. Nevertheless, gastrointestinal infections have been reported, with symptoms such as diarrhea, nausea, vomiting, abdominal pain, and lack of appetite. Importantly, SARS-CoV-2 can remain positive in fecal samples after nasopharyngeal clearance. After gastrointestinal SARS-CoV-2 infection and other viral gastrointestinal infections, some patients may develop alterations in the gastrointestinal microbiota. In addition, some COVID-19 patients may receive antibiotics, which may also disturb gastrointestinal homeostasis. In summary, the gastrointestinal system, gut microbiome, and gut-lung axis may represent an important role in the development, severity, and treatment of COVID-19. Therefore, in this review, we explore the current pieces of evidence of COVID-19 gastrointestinal manifestations, possible implications, and interventions.

Copper-induced sublethal effects in Bufo gargarizans tadpoles: growth, intestinal histology and microbial alternations

Copper (Cu) is one of the environmental contaminations which can pose significant risks for organisms. The current study explores the effects of Cu exposure on the growth, intestinal histology and microbial ecology in Bufo gargarizans. The results revealed that 0.5-1 μM Cu exposure induced growth retardation (including reduction of total body length and wet weight) and intestinal histological injury (including disordered enterocyte, changes in the villi and vacuoles) of tadpoles. Also, high-throughput sequencing analysis showed that Cu exposure caused changes in richness, diversity and structure of intestinal microbiota. Moreover, the composition of intestinal microbiota was altered in tadpoles exposed to different concentrations of Cu. At the phylum level, we observed the abundance of proteobacteria was increased, while the abundance of fusobacteria was decreased in the intestinal microbiota of tadpoles exposed to 1 μM Cu. At the genus level, a reduced abundance of kluyvera and aeromonas was observed in the intestinal microbiota of tadpoles under the exposure of 0-0.5 μM Cu. Finally, functional predictions revealed that tadpoles exposed to copper may be at a higher risk of developing metabolic disorders or diseases. Above all, our results will develop a comprehensive view of the Cu exposure in amphibians and will yield a new consideration for sublethal effects of Cu on aquatic organisms.

Term newborns at risk for early-onset neonatal sepsis: Clinical surveillance versus systematic paraclinical test

INTRODUCTION

Early-onset neonatal sepsis is a rare but potentially lethal infection that is very often suspected in daily practice. Previous national guidelines recommended the use of systematic paraclinical tests for healthy term newborns with suspected infection. These guidelines were updated in 2017 by the French Health Authority (Haute Autorité de santé), and promote initial clinical monitoring taking into account the infectious risk level for term and near-term born infants.

OBJECTIVES

To assess the impact of the new recommendations on antibiotic therapy prescription and invasive tests, and on the outcomes of infants born from 36weeks' gestation.

MATERIALS AND METHODS

This study compared the management and the outcome of neonates born from 36weeks' gestation at the level III University Hospital of Nancy, according to their infectious risk level during two periods, before and after the update of national recommendations: from July 1 to December 31, 2017, versus July 1 to December 31, 2018. Data were retrospectively collected from the infants' files. This study compared the number and length of antibiotic treatment and the number of invasive tests, the number of documented infections, the number and length of hospitalization, and mortality between the two periods.

RESULTS

During the first period, among 1248 eligible newborns, 643 presented an infectious risk factor, versus 1152 newborns with 343 having an infectious risk factor during the second period. Antibiotic treatment was initiated for 18 newborns during the first period (1.4%) and for nine during the second (0.8%) (P=0.13). The mean (SD) duration of the antibiotic treatment was longer in the first than in the second period: 6.3±2days vs. 3.1±2.3days (P=0.003). There was no death related to neonatal infection. A total of 1052 blood samples were collected during the first period versus 51 during the second (P<0.01). There was no documented infection. In the first period, there were 18 newborns (1.4%) hospitalized for suspected infection versus nine (0.8%) in the second period (P=0.13). The duration of hospitalization was 5.7±1.7days in the first period versus 5.2±3days in the second (P=0.33).

CONCLUSION

In this study, the application of the new guidelines enabled a reduction of antibiotic exposure and a reduction of invasive tests without additional risk.

Fecal microbiota transplantation for COVID-19; a potential emerging treatment strategy

At the end of 2019, an emerging outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that first reported from Wuhan, China. The first manifestations of patients infected with SARS-CoV-2 was flu-like symptoms, while other type of manifestations, especially gastrointestinal manifestations were discovered recently. As of June 2020, there is no specific drug or treatment strategy for COVID-19, a disease caused by SARS-CoV-2, so different combination of antiviral drugs is currently being used. Gut microbiota mostly consists of four phyla, including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The interaction between gut microbiota and immune system through releasing some cytokines such as IL-1β, IL-2, IL-10, TNF-α, and IFN-γ that play roles in the severity of COVID-19. In this article, a new potential treatment for COVID-19 by fecal microbiota transplantation (FMT) is described. FMT revealed promising results in different diseases, especially recurrent clostridium difficile infection, and it might reduce length of hospital admission and severity of the disease by modification of gut microbiota composition.

The intervention of unique plant polysaccharides - Dietary fiber on depression from the gut-brain axis

As an invisible organ of human body, the gut microbiota plays an important role in human life and has become a hot spot in the field of life science in recent years. Due to the increasing pressure of work and life, people are prone to depression. The in-depth mechanism studies indicated that the gut microbiota could improve the depression symptom through the gut-brain axis (GBA). As unique plant polysaccharides, dietary fiber can effectively modulate the intestinal flora disorders and its crucial role in orchestrating host-microbiota crosstalk has been confirmed. This review highlights the mechanisms that the gut microbiota affects the development of depression through GBA and focuses on dietary fiber intervention on the improvement of intestinal microbiota imbalance, which may provide new ideas for the prevention and treatment of depression.

Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States

This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).

Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes.

IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).

Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition

BACKGROUND

The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term contribution to saliva microbiota. Our objectives were to investigate the long-term impact of AM use on saliva microbiota diversity and composition in preadolescents. We compared the lifetime effects by gender and AMs. We used data from 808 randomly selected children in the Finnish Health In Teens (Fin-HIT) cohort with register-based data on AM purchases from the Social Insurance Institution of Finland. Saliva microbiota was assessed with 16S rRNA (V3-V4) sequencing. The sequences were aligned to the SILVA ribosomal RNA database and classified and counted using the mothur pipeline. Associations between AM use and alpha-diversity (Shannon index) were identified with linear regression, while associations between beta-diversity (Bray-Curtis dissimilarity) and low, medium or high AM use were identified with PERMANOVA.

RESULTS

Of the children, 53.6% were girls and their mean age was 11.7 (0.4) years. On average, the children had 7.4 (ranging from 0 to 41) AM prescriptions during their lifespan. The four most commonly used AMs were amoxicillin (n = 2622, 43.7%), azithromycin (n = 1495, 24.9%), amoxicillin-clavulanate (n = 1123, 18.7%) and phenoxymethylpenicillin (n = 408, 6.8%). A linear inverse association was observed between the use of azithromycin and Shannon index (b - 0.015, p value = 0.002) in all children, the effect was driven by girls (b - 0.032, p value = 0.001), while not present in boys. Dissimilarities were marked between high, medium and low users of all AMs combined, in azithromycin users specifically, and in boys with amoxicillin use. Amoxicillin and amoxicillin-clavulanate use was associated with the largest decrease in abundance of Rikenellaceae. AM use in general and phenoxymethylpenicillin specifically were associated with a decrease of Paludibacter and pathways related to amino acid degradations differed in proportion between high and low AM users.

CONCLUSIONS

A systematic approach utilising reliable registry data on lifetime use of AMs demonstrated long-term effects on saliva microbiota diversity and composition. These effects are gender- and AM-dependent. We found that frequent lifelong use of AMs shifts bacterial profiles years later, which might have unforeseen health impacts in the future. Our findings emphasise a concern for high azithromycin use, which substantially decreases bacterial diversity and affects composition as well. Further studies are needed to determine the clinical implications of our findings. Video Abstract.

Randomized Trial of Amoxicillin for Pneumonia in Pakistan

BACKGROUND

The World Health Organization (WHO) recommends oral amoxicillin for patients who have pneumonia with tachypnea, yet trial data indicate that not using amoxicillin to treat this condition may be noninferior to using amoxicillin.

METHODS

We conducted a double-blind, randomized, placebo-controlled noninferiority trial involving children at primary health care centers in low-income communities in Karachi, Pakistan. Children who were 2 to 59 months of age and who met WHO criteria for nonsevere pneumonia with tachypnea were randomly assigned to a 3-day course of a suspension of amoxicillin (the active control) of 50 mg per milliliter or matched volume of placebo (the test regimen), according to WHO weight bands (500 mg every 12 hours for a weight of 4 to <10 kg, 1000 mg every 12 hours for a weight of 10 to <14 kg, or 1500 mg every 12 hours for a weight of 14 to <20 kg). The primary outcome was treatment failure during the 3-day course of amoxicillin or placebo. The prespecified noninferiority margin was 1.75 percentage points.

RESULTS

From November 9, 2014, through November 30, 2017, a total of 4002 children underwent randomization (1999 in the placebo group and 2003 in the amoxicillin group). In the per-protocol analysis, the incidence of treatment failure was 4.9% among placebo recipients (95 of 1927 children) and 2.6% among amoxicillin recipients (51 of 1929 children) (between-group difference, 2.3 percentage points; 95% confidence interval [CI], 0.9 to 3.7). Results were similar in the intention-to-treat analysis. The presence of fever and wheeze predicted treatment failure. The number needed to treat to prevent one treatment failure was 44 (95% CI, 31 to 80). One patient (<0.1%) in each group died. Relapse occurred in 40 children (2.2%) in the placebo group and in 58 children (3.1%) in the amoxicillin group.

CONCLUSIONS

Among children younger than 5 years of age with nonsevere pneumonia, the frequency of treatment failure was higher in the placebo group than in the amoxicillin group, a difference that did not meet the noninferiority margin for placebo. (Funded by the Joint Global Health Trials Scheme [of the Department for International Development, Medical Research Council, and Wellcome] and others; RETAPP ClinicalTrials.gov number, NCT02372461.).

Variations in early gut microbiome are associated with childhood eczema

We assessed the relationship between gut microbiome profile and childhood eczema in 172 subjects (age < 3 years, healthy group N = 123, eczema group N = 49) utilizing 16S rRNA gene sequencing. Lower relative abundance of Bifidobacterium was shown to be associated with childhood eczema. Considering that developmental and environmental factors could modify the state of children's gut microbiome, we divided the samples into four age groups: 0-0.5 years, 0.5-1 years, 1-2 years and 2-3 years for farther analyses. Data revealed significant inter-group differences between healthy and eczema samples in all age groups, and decreased microbial diversity was most significantly found in children with eczema of age 2-3 years old. Decreased abundance of Bifidobacterium was a major finding in eczema groups from 0.5-3 years compared to the age matched healthy controls, but not significant in children younger than 6 month old. Of note, Bifidobacterium operational taxonomic units were identified by Random Forest with highly predictive power of 0.83 (AUC = 0.83) in ROC analysis, which also confirmed its role as a key genus that is associated with eczema. To verify the sequencing results, we performed quantitative polymerase chain reaction of Bifidobacterium and Bacteroides in the same cohort, and in a new eczema cohort (N = 57) for validation. Significantly, lower Bifidobacterium quantities were found in both eczema groups with an age range of 0.5-3 years. These results suggest variations in early gut microbiome are associated with childhood eczema.

The Neonatal Microbiome and Metagenomics: What Do We Know and What Is the Future?

The human microbiota includes the trillions of microorganisms living in the human body whereas the human microbiome includes the genes and gene products of this microbiota. Bacteria were historically largely considered to be pathogens that inevitably led to human disease. However, because of advances in both cultivation-based methods and the advent of metagenomics, bacteria are now recognized to be largely beneficial commensal organisms and thus, key to normal and healthy human development. This relatively new area of medical research has elucidated insights into diseases such as inflammatory bowel disease and obesity, as well as metabolic and atopic disorders. However, much remains unknown about the complexity of microbe-microbe and microbe-host interactions. Future efforts aimed at answering key questions pertaining to the early establishment of the microbiome, alongside what defines its dysbiosis, will likely lead to long-term health and mitigation of disease. Here, we review the relevant literature pertaining to modulations in the perinatal and neonatal microbiome, the impact of environmental and maternal factors in shaping the neonatal microbiome, and future questions and directions in the exciting emerging arena of metagenomic medicine.

Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants

Rotavirus is the leading cause of childhood deaths due to diarrhea. Although existing oral rotavirus vaccines are highly efficacious in high-income countries, these vaccines have been demonstrated to have decreased efficacy in low- and middle-income countries. A possible explanation for decreased efficacy is the impact of gut microbiota on the enteric immune system's response to vaccination. We analyzed the gut microbiome of 50 children enrolled in a prospective study evaluating response to oral pentavalent rotavirus vaccination (RV5) to assess associations between relative abundance of bacterial taxa and seroconversion following vaccination. Stool samples were taken before the first RV5 dose, and microbiome composition characterized using 16S rRNA amplicon sequencing and Quantitative Insights Into Microbial Ecology software. Relative abundance of bacterial taxa between seroconverters following the first RV5 dose, those with ≥ 4-fold increase in rotavirus-specific IgA titers, and nonseroconverters were compared using the Wilcoxon-Mann-Whitney test. We identified no significant differences in microbiome composition between infants who did and did not respond to vaccination. Infants who responded to vaccination tended to have higher abundance of Proteobacteria and Eggerthella, whereas those who did not respond had higher abundance of Fusobacteria and Enterobacteriaceae; however, these differences were not statistically significant following a multiple comparison correction. This study suggests a limited impact of gut microbial taxa on response to oral rotavirus vaccination among infants; however, additional research is needed to improve our understanding of the impact of gut microbiome on vaccine response, toward a goal of improving vaccine efficacy and rotavirus prevention.

Maternal and Perinatal Factors Associated with the Human Milk Microbiome

Microbes are present in human milk regardless of the mother's health. The origins of the milk microbiota likely include the mother's skin, infant's mouth, and transfer from the maternal gastrointestinal (GI) tract. Prominent bacterial taxa in human milk are Staphylococcus and Streptococcus, but many other genera are also found including anaerobic Lactobacillus, Bifidobacterium, and Bacteroides. The milk microbiome is highly variable and potentially influenced by geographic location, delivery mode, time postpartum, feeding mode, social networks, environment, maternal diet, and milk composition. Mastitis alters the milk microbiome, and the intake of Lactobacilli has shown potential for mastitis treatment and prevention. Although milk and infant fecal microbiomes are different, their variations appear to be related - suggesting that milk is an important contributor of early GI colonization. Nonetheless, nothing is known regarding whether the milk microbiome influences infant health. Further research and clinical interventions are needed to determine if changes in the microbiomes of human milk and infant formula/food impact health.

The role of maternal diet on offspring gut microbiota development: A review

In offspring, an adequate maternal diet is important for neurodevelopment. One mechanism by which maternal diet impacts neurodevelopment is through its dynamic role in the development of the gut microbiota. Communication between the gut, and its associated microbiota, and the brain is facilitated by the vagus nerve, in addition to other routes. Currently, the mechanisms through which maternal diet impacts offspring microbiota development are not well-defined. Therefore, this review aims to investigate the relationship between maternal diet during pregnancy and offspring microbiota development and its impact on neurodevelopment. Both human and animal model studies were reviewed to understand the impact of maternal diet on offspring microbiota development and potential consequences on neurodevelopment. In the period after birth, as reported in both human and model system studies, maternal diet impacts offspring bacterial colonization (e.g., decreased presence of Lactobacillus reuteri as a result of a high-fat maternal diet). It remains unknown whether these changes persist into adulthood and whether they impact vulnerability to disease. Therefore, further long-term studies are required in both human and model systems to study these changes. Our survey of the literature indicates that maternal diet influences early postnatal microbiota development, which in turn, may serve as a mechanism through which maternal diet impacts neurodevelopment.

Microbial Metabolites and Intestinal Stem Cells Tune Intestinal Homeostasis

Microorganisms that colonize the gastrointestinal tract, collectively known as the gut microbiota, are known to produce small molecules and metabolites that significantly contribute to host intestinal development, functions, and homeostasis. Emerging insights from microbiome research reveal that gut microbiota-derived signals and molecules influence another key player maintaining intestinal homeostasis-the intestinal stem cell niche, which regulates epithelial self-renewal. In this review, the literature on gut microbiota-host crosstalk is surveyed, highlighting the effects of gut microbial metabolites on intestinal stem cells. The production of various classes of metabolites, their actions on intestinal stem cells are discussed and, finally, how the production and function of metabolites are modulated by aging and dietary intake is commented upon.

Effects of Labor Epidural Analgesia on Short Term Neonatal Morbidity

BACKGROUND

Epidural Analgesia (EA) is the most effective and most commonly used method for pain relief during labor. Some researchers have observed an association between EA and increased neonatal morbidity. But this observation was not consistent in many other studies.

OBJECTIVES

The primary objective of the study was to examine whether exposure to epidural analgesia increased the risk of NICU admission. The secondary objectives included the risks of clinical chorioamnionitis, instrumental delivery, neonatal depression, respiratory distress, birth trauma, and neonatal seizure during the first 24 hours of life.

METHODS

This was a retrospective cohort study involving 2360 low-risk nulliparous women who delivered at AWH, Qatar, during the two years between January 2016 December and 2017. Short-term neonatal outcomes of the mothers who received EA in active labor were compared with a similar population who did not receive EA. As secondary objectives, labor parameters like maternal temperature elevation, duration of the second stage of labor, and instrumental delivery were compared.

RESULTS

Significantly higher numbers of neonates were admitted to the NICU from the EA group (P<0.001, OR 1.89, 95% CI 1.45 to 2.46). They were more likely to have respiratory distress (P=0.01, OR 1.49, 95% CI 1.07 to 2.07), birth injuries (P=0.02, OR =1.71, 95% CI 1.06 to 2.74), admission temperature>37.5 °C (P=0.04, OR 3.40, 95% CI 1.00 to 11.49), need for oxygen on the first day (P=0.04, OR 1.44, 95% CI 1.01 to 2.07) and receive antibiotics (P<0.001, OR 2.06,95% CI 1.47 to 2.79). There was no difference in the Apgar score at 1 minute (P=0.12), need of resuscitation at birth (P=0.05), neonatal white cell count (P=0.34), platelet count (P=0.38) and C reactive protein (P=0.84). Mothers who received EA had a lengthier second stage (P<0.001), temperature elevation >37.5°C (P<0.001, OR 7.40, 95% CI 3.93 to 13.69) and instrumental delivery (P<0.001, OR 2.13, 95% CI 1.69 to 2.68).

CONCLUSION

EA increases NICU admission, antibiotic exposure, neonatal birth injuries, need for positive pressure ventilation at birth, and respiratory distress in the first 24 hours of life. Mothers on epidural analgesia have prolonged second stage of labor, a higher rate of instrumental delivery, meconium-stained amniotic fluid, fetal distress, and temperature elevation.

Prenatal establishment of the foal gut microbiota: a critique of the in utero colonisation hypothesis

Bacteria colonisation of the foal’s gastrointestinal tract (GIT) is a critical developmental stage, effecting subsequent immunological and health outcomes. It has long been thought that the equine fetus develops in a sterile intrauterine environment and GIT colonisation commences at birth. Research now suggests that bacteria isolated from amniotic fluid are the initial colonisers of the fetal GIT, and exposure to the dam’s microbiota and the external environment during birth provide supplementary colonisation. This in utero colonisation hypothesis has only recently been examined in the horse and microbiota were detected in the amniotic fluid and meconium of healthy equine pregnancies. This review highlights the possible colonisation routes of these bacteria into the fetal compartments and examines their likely origins from the existing maternal microbiome. However, the current data describing the amniotic microbiota of the horse are limited and there is a need for research to fill this gap. Understanding the significance of intrauterine microbes for foal GIT colonisation may provide strategies to improve neonatal health.

Characterization of the gut microbiota of Nicaraguan children in a water insecure context

OBJECTIVES

The gut microbiota varies across human populations. The first years of life are a critical period in its development. While delivery mode and diet contribute to observed variation, the additional contribution of specific environmental factors remains poorly understood. One factor is waterborne enteric pathogen exposure. In this pilot study, we explore the relationship between household water security and the gut microbiota of children.

METHODS

From Nicaraguan households (n = 39), we collected drinking water samples, as well as fecal samples from children aged one month to 5.99 years (n = 53). We tested water samples for total coliforms (CFU/mL) and the presence of common enteric pathogens. Composition and diversity of the gut microbiota were characterized by 16S rRNA sequencing. Households were classified as having drinking water that was "low" (<29 CFU/mL) or "high" (≥29 CFU/mL) in coliforms. We used permutational analyses of variance and Mann-Whitney U-tests to identify differences in the composition and diversity of the gut microbiota of children living in these two home types.

RESULTS

Insecure access led households to store drinking water and 85% tested positive for coliforms. High concentrations of Salmonella and Campylobacter were found in water and fecal samples. Controlling for age, the gut microbiota of children from high coliform homes were compositionally different and less diverse than those from low coliform homes.

CONCLUSIONS

Results indicate that research exploring the ways water insecurity affects human biology should consider the gut microbiome and that investigations of inter-population variation in the gut microbial community of children should consider pathogen exposure and infection.

Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome

INTRODUCTION

The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time.

MATERIALS AND METHODS

Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed.

RESULTS

A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R² = 0.044, p = .002) but later courses did not (R² = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome.

CONCLUSION

Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.

Early initiation of broad-spectrum antibiotics in premature infants

BACKGROUND

Neonatal sepsis remains one of the main reasons for mortality among premature infants, and the early initiation of empirical broad-spectrum antibiotics could increase the risk of complications, including late-onset sepsis. This study aimed to investigate the complications related to the use of empirical broad-spectrum antibiotics in the first week of life.

METHODS

A retrospective study of 365 neonates with gestational age ≤32 weeks and birth weight <1500 g who survived and had no confirmed sepsis in the first week of life from July 2015 to June 2018 was performed in a large tertiary Neonatal Intensive Care Unit. The primary outcome of this study was the incidence of a composite outcome consisting of late-onset sepsis, necrotizing enterocolitis, and mortality. The secondary outcomes were the incidences of late-onset sepsis, necrotizing enterocolitis, bronchopulmonary dysplasia, and infant mortality.

RESULTS

Of the 365 premature infants, 75 (20.5%) received broad-spectrum antibiotics. Multivariate regression analysis revealed that administration of broad-spectrum antibiotics in infants was independently associated with adverse outcomes. The composite outcome (late-onset sepsis, necrotizing enterocolitis, and death) had an odds ratio of 3.03 with 95% confidence interval of 1.41-6.49.

CONCLUSIONS

Administration of empirical broad-spectrum antibiotics in the first week of life is associated with severe adverse outcomes. Thus, the restricted use of broad-spectrum antibiotics in the first week of life is recommended.

Long-term impact of giving antibiotics before skin incision versus after cord clamping on children born by caesarean section: protocol for a longitudinal study based on UK electronic health records

INTRODUCTION

In the UK, about a quarter of women give birth by caesarean section (CS) and are offered prophylactic broad-spectrum antibiotics to reduce the risk of maternal postpartum infection. In 2011, national guidance was changed from recommending antibiotics after the umbilical cord was cut to giving antibiotics prior to skin incision based on evidence that earlier administration reduces maternal infectious morbidity. Although antibiotics cross the placenta, there are no known short-term harms to the baby. This study aims to address the research gap on longer term impact of these antibiotics on child health.

METHODS AND ANALYSIS

A controlled interrupted time series study will use anonymised mother-baby linked routine electronic health records for children born during 2006-2018 recorded in UK primary care (The Health Improvement Network, THIN and Clinical Practice Research Datalink, CPRD) and secondary care (Hospital Episode Statistics, HES) databases. The primary outcomes of interest are asthma and eczema, two common allergy-related diseases in childhood. In-utero exposure to antibiotics immediately prior to CS will be compared with no exposure when given after cord clamping. The risk of outcomes in children delivered by CS will also be compared with a control cohort delivered vaginally to account for time effects. We will use all available data from THIN, CPRD and HES with estimated power of 80% and 90% to detect relative increase in risk of asthma of 16% and 18%, respectively at the 5% significance level.

ETHICS AND DISSEMINATION

Ethical approval has been obtained from the University of Birmingham Ethical Review Committee with scientific approvals obtained from the independent scientific advisory committees from the Medicines and Healthcare products Regulatory Agency for CPRD and the data provider, IQVIA for THIN. The results will be published in peer-reviewed journals, presented at national and international conferences and disseminated to stakeholders.

Matrotrophic viviparity constrains microbiome acquisition during gestation in a live-bearing cockroach, Diploptera punctata

The vertical transmission of microbes from mother to offspring is critical to the survival, development, and health of animals. Invertebrate systems offer unique opportunities to conduct studies on microbiome-development-reproduction dynamics since reproductive modes ranging from oviparity to multiple types of viviparity are found in these animals. One such invertebrate is the live-bearing cockroach, Diploptera punctata. Females carry embryos in their brood sac, which acts as the functional equivalent of the uterus and placenta. In our study, 16S rRNA sequencing was used to characterize maternal and embryonic microbiomes as well as the development of the whole-body microbiome across nymphal development. We identified 50 phyla and 121 classes overall and found that mothers and their developing embryos had significantly different microbial communities. Of particular interest is the notable lack of diversity in the embryonic microbiome, which is comprised exclusively of Blattabacteria, indicating microbial transmission of only this symbiont during gestation. Our analysis of postnatal development reveals that significant amounts of non-Blattabacteria species are not able to colonize newborn D. punctata until melanization, after which the microbial community rapidly and dynamically diversifies. While the role of these microbes during development has not been characterized, Blattabacteria must serve a critical role providing specific micronutrients lacking in milk secretions to the embryos during gestation. This research provides insight into the microbiome development, specifically with relation to viviparity, provisioning of milk-like secretions, and mother-offspring interactions during pregnancy.

Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)

Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease

BACKGROUND

Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete. Infant rhesus macaques (Macaca mulatta) are susceptible to diarrhea making them an ideal model to address this question.

RESULTS

The maturation of the infant rhesus macaque gut microbiome throughout the first 8 months of life occurs in a similar pattern as that described for human infants. Moreover, the microbiome of the captive reared infant rhesus macaque more closely resembles that of human infants in the developing world than in the western world. Importantly, prior to disease onset, the gut microbiome of infants that later develop diarrhea is enriched in pathways of immunomodulatory metabolite synthesis, while those of infants that remain asymptomatic are enriched in pathways for short-chain fatty acid production. We identify Prevotella strains that are more abundant at 1 month in infants that later develop diarrhea. At 8 months, the microbiomes of animals that experience diarrhea show increased abundance of Campylobacter and a reduction in Helicobacter macacae.

CONCLUSION

The composition of the microbial community could provide a phenotypic marker of an infant's susceptibility to diarrheal disease. Given the significant physiological and immunological similarities between human and nonhuman primates, these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.

The Preterm Gut Microbiota: An Inconspicuous Challenge in Nutritional Neonatal Care

The nutritional requirements of preterm infants are unique and challenging to meet in neonatal care, yet crucial for their growth, development and health. Normally, the gut microbiota has distinct metabolic capacities, making their role in metabolism of dietary components indispensable. In preterm infants, variation in microbiota composition is introduced while facing a unique set of environmental conditions. However, the effect of such variation on the microbiota's metabolic capacity and on the preterm infant's growth and development remains unresolved. In this review, we will provide a holistic overview on the development of the preterm gut microbiota and the unique environmental conditions contributing to this, in addition to maturation of the gastrointestinal tract and immune system in preterm infants. The role of prematurity, as well as the role of human milk, in the developmental processes is emphasized. Current research stresses the early life gut microbiota as cornerstone for simultaneous development of the gastrointestinal tract and immune system. Besides that, literature provides clues that prematurity affects growth and development. As such, this review is concluded with our hypothesis that prematurity of the gut microbiota may be an inconspicuous clinical challenge in achieving optimal feeding besides traditional challenges, such as preterm breast milk composition, high nutritional requirements and immaturity of the gastrointestinal tract and immune system. A better understanding of the metabolic capacity of the gut microbiota and its impact on gut and immune maturation in preterm infants could complement current feeding regimens in future neonatal care and thereby facilitate growth, development and health in preterm infants.