Investigation of the early intestinal microflora in premature infants with/without necrotizing enterocolitis using two different methods

Reduced Gut Bacterial Diversity in Early Life Predicts Feeding Intolerance in Preterm Neonates

Microbiota plays a crucial role in intestinal maturation in preterm newborns. The clinical manifestation of the immaturity of the gastro-intestinal tract is called feeding intolerance (FI). This condition may resolve spontaneously or dramatically evolve into necrotizing enterocolitis. One of the most challenging tasks for the neonatologist is to identify those neonates that will develop the disease early in order to adequately provide nutrition to these patients, from the very first hours of life. A close interplay between the maturity of the gastro-intestinal tract and gut microbiota has been described; however, in preterm neonates, this relationship is still undefined. We analyzed the bacterial composition of stool samples, collected early in life, from 30 preterm newborns classified as intolerant or tolerant according to the degree of readiness of the gastro-intestinal tract to receive enteral nutrition. The Pielou evenness index was significantly increased in intolerant compared with tolerant newborns. Data corrected for confounding variables confirmed that the occurrence of gut maturation was independently influenced by Pielou evenness at birth. A lower bacterial diversity very early in life is associated with improved feeding tolerance in preterm newborns. The abundance analysis showed that neonates not ready to receive enteral nutrition for feeding intolerance show, after birth, an increased abundance of Proteobacteria, Lachnospiracae, Enterobacter and Acinetobacter. We can argue that those are the taxa that prevent the establishment of pioneer bacteria. A lower alpha-diversity, in the first days of life, may facilitate the seeding of beneficial pioneer bacteria that, in turn, drive healthy microbial colonization during neonatal life.

Source of human milk (mother or donor) is more important than fortifier type (human or bovine) in shaping the preterm infant microbiome

Milk fortifiers help meet the nutritional needs of preterm infants receiving their mother's own milk (MOM) or donor human milk. We conducted a randomized clinical trial (NCT03214822) in 30 very low birth weight premature neonates comparing bovine-derived human milk fortifier (BHMF) versus human-derived fortifier (H2MF). We found that fortifier type does not affect the overall microbiome, although H2MF infants were less often colonized by an unclassified member of Clostridiales Family XI. Secondary analyses show that MOM intake is strongly associated with weight gain and microbiota composition, including Bifidobacterium, Veillonella, and Propionibacterium enrichment. Finally, we show that while oxidative stress (urinary F2-isoprostanes) is not affected by fortifier type or MOM intake, fecal calprotectin is higher in H2MF infants and lower in those consuming more MOM. Overall, the source of human milk (mother versus donor) appears more important than the type of milk fortifier (human versus bovine) in shaping preterm infant gut microbiota.

The effect of probiotics on the clinical status of adult patients with atopic dermatitis: a systematic review

OBJECTIVES

To describe, through a literature review, the results and benefits of oral and topical probiotics for adult patients with atopic dermatitis.

DESIGN

A systematic review of articles published over a 13-year period was conducted to answer the following questions: (1) what information is given in the scientific literature concerning the use of probiotics in adult patients with atopic dermatitis? (2) Was there an improvement in the clinical status of the patients? (3) Was there a change in the microbial profile in patients after using such approaches? (4) Among the probiotics used, which was the most used in adult AD patients? (5) What was the average time of these interventions? (6) What were the outcomes?

RESULTS

Seven studies with different sample sizes, ranging from 16 to 109 patients, were included in this review. These studies were all clinical trials (7/7), and probiotics (7/7) was the model of intervention chosen. Probiotics showed a potential to relieve the symptoms of the study groups with a reduction of pruritus and SCORAD when compared to the placebo groups. However, their effectiveness varied according to the strain, period, and form of administration.

CONCLUSIONS

Many studies have demonstrated that probiotics improve the symptoms of atopic dermatitis and even its prevention. However, there is still much controversy and divergence concerning the real benefits. Despite this, probiotics have demonstrated a fair ability in improving AD adult patients' symptoms in terms of decreasing pruritus and severity related to SCORAD.

A mini-review of advances in intestinal flora and necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a digestive disease that frequently occurs in premature infants with low gestational age and low birth weight, and seriously threatens the life of NEC patients. NEC pathogenesis is recognized to be affected by multiple factors, such as preterm birth, formula feeding, and low birth weight. As a popular object for the past decades, intestinal flora is commonly used in NEC-related studies, and intestinal disorder is considered as a critical risk factor for the occurrence and development of NEC. The colonization of abnormal microbiota into gastrointestinal micro-ecosystem can easily lead to the damage of intestinal mucosal barrier, destruction of immune function, inflammatory reaction, and further the occurrence of NEC. Although it is a low-cost and safe way to prevent and treat the NEC by early intervention of oral probiotics to regulate the intestinal homeostasis, more studies in the future are still encouraged to narrow the gap between theoretical guidance and practical application.

The neonatal microbiome in utero and beyond: perinatal influences and long-term impacts

The neonatal microbiome offers a valuable model for studying the origins of human health and disease. As the field of metagenomics expands, we also increase our understanding of early life influences on its development. In this review we will describe common techniques used to define and measure the microbiome. We will review in utero influences, normal perinatal development, and known risk factors for abnormal neonatal microbiome development. Finally, we will summarize current evidence that links early life microbial impacts on the development of chronic inflammatory diseases, obesity, and atopy.

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.

The effect of early probiotic exposure on the preterm infant gut microbiome development

Premature birth, especially if born before week 32 of gestation, is associated with increased risk of neonatal morbidity and mortality. Prophylactic use of probiotics has been suggested to protect preterm infants via supporting a healthy gut microbiota (GM) development, but the suggested strains and doses vary between studies. In this study, we profiled the GM of 5, 10 and 30-day fecal samples from two cohorts of preterm neonates (born <30 weeks of gestation) recruited in the same neonatal intensive care unit. One cohort (n = 165) was recruited from September 2006 to January 2009 before probiotics were introduced in the clinic. The second cohort (n = 87) was recruited from May 2010 to October 2011 after introducing Lacticaseibacillus rhamnosus GG and Bifidobacterium animalis ssp. lactis BB-12 supplementation policy. Through V3-V4 region 16S rRNA gene amplicon sequencing, a distinct increase of L. rhamnosus and B. animalis was found in the fecal samples of neonates supplemented with probiotics. During the first 30 days of life, the preterm GM went through similarly patterned progression of bacterial populations. Staphylococcus and Weissella dominated in early samples, but was gradually overtaken by Veillonella, Enterococcus and Enterobacteriaceae. Probiotic supplementation was associated with pronounced reduction of Weissella, Veillonella spp. and the opportunistic pathogen Klebsiella. Potential nosocomial pathogens Citrobacter and Chryseobacterium species also gradually phased out. In conclusion, probiotic supplementation to preterm neonates affected gut colonization by certain bacteria, but did not change the overall longitudinal bacterial progression in the neonatal period.Abbreviations: GM: Gut microbiota; ASV: Amplicon sequence variant; NEC: Necrotizing enterocolitis; DOL: Days of life; NICU: Neonatal intensive care unit; ESPGHAN: European Society for Pediatric Gastroenterology, Hepatology and Nutrition; Db-RDA: Distance-based redundancy analysis; PERMANOVA: Permutational multivariate analysis of variance; ANCOM: Analysis of compositions of microbiomes; LGG: Lacticaseibacillus (former Lactobacillus) rhamnosus GG; BB-12: Bifidobacterium animalis ssp. lactis BB-12; DGGE: Denaturing Gradient Gel Electrophoresis.

Incomplete resection of necrotic bowel may increase mortality in infants with necrotizing enterocolitis

BACKGROUND

Infants with advanced necrotizing enterocolitis (NEC) often need surgical resection of necrotic bowel. We hypothesized that incomplete resection of NEC lesions, signified by the detection of necrotic patches in margins of resected bowel loops, results in inferior clinical outcomes.

METHODS

We reviewed the medical records of infants with surgical NEC in the past 15 years for demographic, clinical, and histopathological data. We also developed statistical models to predict mortality and hospital stay.

RESULTS

Ninety infants with surgical NEC had a mean (±standard error) gestational age of 27.3 ± 0.4 weeks, birth weight 1008 ± 48 g, NEC onset at 25.2 ± 2.4 days, and resected bowel length of 29.2 ± 3.2 cm. Seventeen (18.9%) infants who had complete resection of the necrosed bowel had fewer (4; 23.5%) deaths and shorter lengths of hospital stay. In contrast, a group of 73 infants with some necrosis within the margins of resected bowel had significantly more (34; 46.6%) deaths and longer hospital stay. The combination of clinical and histopathological data gave better regression models for mortality and hospital stay.

CONCLUSION

In surgical NEC, incomplete resection of necrotic bowel increased mortality and the duration of hospitalization. Regression models combining clinical and histopathological data were more accurate for mortality and the length of hospital stay.

IMPACT

In infants with surgical NEC, complete resection of necrotic bowel reduced mortality and hospital stay. Regression models combining clinical and histopathological information were superior at predicting mortality and hospital stay than simpler models focusing on either of these two sets of data alone. Prediction of mortality improved with the combination of antenatal steroids, chorioamnionitis, and duration of post-operative ileus, with severity of inflammation and hemorrhages in resected intestine. Length of hospital stay was shorter in infants with higher gestational ages, but longer in those with greater depth of necrosis or needing prolonged parenteral nutrition or supervised feedings.

Clinical determinants of postoperative outcomes in surgical necrotizing enterocolitis

OBJECTIVE

Investigate predictors of postoperative morbidity and mortality in surgical NEC.

STUDY DESIGN

We analyzed the clinical outcomes of infants with surgical NEC from the years 2000-2015.

RESULTS

Ninety infants born at gestation (mean ± standard deviation, SD; standard error of mean, SEM) 27.3 ± 6.6 weeks (SEM ± 0.07 weeks) and weighing 1008 ± 456 g (SEM ± 48 g) developed NEC on 25.2 ± 22.4 days (SEM ± 2.4 days). Average bowel resection was 29.2 ± 30.5 cm (SEM ± 3.2 cm). Postoperative Ileus lasted 16.5 ± 12.2 days (SEM ± 1.3 days), and was significantly longer in infants with higher gestation and birth weight, age at onset of NEC, length of intestinal resection, maternal chorioamnionitis, and need for pressors. Thirty-eight (42.2%) infants died. Mortality was higher at gestation <31 weeks.

CONCLUSION

Gestational age, birth weight, age at NEC onset, and length of resected bowel determined postoperative morbidity and mortality in NEC. Length of hospital stay was affected by above factors, and also the duration of postoperative ileus and parenteral nutrition.

Staphylococcus epidermidis in feedings and feces of preterm neonates

Staphylococcus epidermidis has emerged as the leading agent causing neonatal late-onset sepsis in preterm neonates; although the severity of the episodes caused by this species is often underestimated, it might exert relevant short- and long-term detrimental effects on neonatal outcomes. In this context, the objective of this study was to characterize a collection of S. epidermidis strains obtained from meconium and feces of preterm infants, and to assess the potential role of the enteral feeding tubes as potential reservoirs for this microorganism. A total of 26 preterm infants were enrolled in the study. Meconium and fecal samples were collected weekly during their first month of life (n = 92). Feeding samples were collected after their pass through the enteral feeding tubes (n = 84). S. epidermidis was present in the fecal samples of all the infants in, at least, one sampling time at concentrations ranging from 6.5 to 7.8 log₁₀ CFU/g. Initially, 344 isolates were obtained and pulsed-field gel electrophoresis (PFGE) profiling allowed the reduction of the collection to 101 strains. Among them, multilocus sequence typing (MLST) profiling showed the presence of 32 different sequence types (ST). Globally, most of the STs to hospital-adapted high-risk clones and belonged to clonal complexes (CC) associated to the hospital environment, such as CC2. The virulence gene most commonly detected among the strains was altE. High resistance rates to macrolides and aminoglycosides were detected and 64% of the strains harboured the mecA gene, which was codified in SCCmec types. Our results indicates the existence of a complex and genetically diverse S. epidermidis population in the NICU environment. A better knowledge of S. epidermidis strains may help to devise strategies to avoid their conversion from symbiont to pathobiont microorganisms in the NICUs.

Intestinal dysbiosis and necrotizing enterocolitis: assessment for causality using Bradford Hill criteria

In recent years, several studies have shown that premature infants who develop NEC frequently display enteric dysbiosis with increased Gram-negative bacteria for several days to weeks prior to NEC onset. The importance of these findings, for the possibility of a causal role of these bacteria in NEC pathogenesis, and for potential value of gut dysbiosis as a biomarker of NEC, is well-recognized. In this review, we present current evidence supporting the association between NEC in premature infants and enteric dysbiosis, and its evaluation using the Bradford Hill criteria for causality. To provide an objective appraisal, we developed a novel scoring system for causal inference. Despite important methodological and statistical limitations, there is support for the association from several large studies and a meta-analysis. The association draws strength from strong biological plausibility of a role of Gram-negative bacteria in NEC and from evidence for temporality, that dysbiosis may antedate NEC onset. The weakness of the association is in the low level of consistency across studies, and the lack of specificity of effect. There is a need for an improved definition of dysbiosis, either based on a critical threshold of relative abundances or at higher levels of taxonomic resolution.

Impact of Early Exposure to Cefuroxime on the Composition of the Gut Microbiota in Infants Following Cesarean Delivery

OBJECTIVES

To assess in mothers giving birth by cesarean delivery if prophylactic antibiotics administered either before skin incision or immediately after cutting the umbilical cord influences gut microbiota colonization and antibiotic susceptibility of the gut bacteria in the newborn.

STUDY DESIGN

Forty-two pregnant women scheduled for elective cesarean delivery were recruited at Odense University Hospital, Denmark, and randomly assigned to receive cefuroxime either before skin incision or immediately after the umbilical cord was cut. Fecal samples were collected from all infants at age 10 days and 9 months. Composition of the gut microbiota was determined by 16S ribosomal RNA gene amplicon high-throughput sequencing. Gram-positive cocci and Enterobacteriaceae were isolated and identified before antimicrobial susceptibility tests were performed by disk diffusion.

RESULTS

No clear difference in the composition of the gut microbiota was observed between infants whose mothers received cefuroxime before or after cesarean delivery at neither time point, though surprisingly at 9 months of age, but not at 10 days of age, the number of observed species was higher in infants where mothers received cefuroxime after cord clamping. No differences in antimicrobial susceptibility of Enterobacteriaceae, Enterococcus spp, and Staphylococcus spp were seen at 10 days.

CONCLUSIONS

Timing of cefuroxime administration to mothers undergoing cesarean delivery does not have a major effect on the gut microbiota and bacterial antibiotic resistance traits in infants.

TRIAL REGISTRATION

Clinicaltrials.gov: NCT02072798.

Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

Background

Necrotising enterocolitis (NEC) is a common cause of death in preterm infants and is closely linked to the gut microbiota. Spontaneous intestinal perforation (SIP) also occurs in preterm neonates, but results in lower mortality and less adverse neonatal outcomes than NEC. Existing studies are largely limited to non-invasive stool samples, which may not be reflective of the anatomical site of disease. Therefore, we analysed historical formalin-fixed paraffin-embedded (FFPE) tissue from NEC and SIP preterm infants. A total of 13 NEC and 16 SIP infants were included. Extracted DNA from FFPE tissue blocks underwent 16S rRNA gene sequencing. For a subset of infants, diseased tissue and marginal healthy tissue from the same infant were compared.

Results

Xylene provided a cost and time effective means of deparaffinization. Tissue from the site of disease was highly comparable to adjacent healthier tissue. Comparing only diseased tissue from all infants showed significantly lower Shannon diversity in NEC (P = 0.026). The overall bacterial communities were also significantly different in NEC samples compared to SIP (P = 0.038), and large variability within NEC infants was observed. While no single OTU or genus was significantly associated with NEC or SIP, at the phylum level Proteobacteria (P = 0.045) and Bacteroidetes (P = 0.024) were significantly higher in NEC and SIP infants, respectively.

Conclusions

Existing banks of intestinal FFPE blocks provide a robust and specific sample for profiling the microbiota at the site of disease. We showed preterm infants with NEC have lower diversity and different bacterial communities when compared to SIP controls.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1426-6) contains supplementary material, which is available to authorized users.

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.

The Microbiota of the Extremely Preterm Infant

Colonization of the extremely preterm infant's gastrointestinal tract and skin begins in utero and is influenced by a variety of factors, the most important including gestational age and environmental exposures. The composition of the intestinal and skin microbiota influences the developing innate and adaptive immune responses with short-term and long-term consequences including altered risks for developing necrotizing enterocolitis, sepsis, and a wide variety of microbe-related diseases of children and adults. Alteration of the composition of the microbiota to decrease disease risk is particularly appealing for this ultra-high-risk cohort that is brand new from an evolutionary standpoint.

Mechanisms Affecting the Gut of Preterm Infants in Enteral Feeding Trials

Large randomized controlled trials (RCTs) in preterm infants offer unique opportunities for mechanistic evaluation of the risk factors leading to serious diseases, as well as the actions of interventions designed to prevent them. Necrotizing enterocolitis (NEC) a serious inflammatory gut condition and late-onset sepsis (LOS) are common feeding and nutrition-related problems that may cause death or serious long-term morbidity and are key outcomes in two current UK National Institutes for Health Research (NIHR) trials. Speed of increasing milk feeds trial (SIFT) randomized preterm infants to different rates of increases in milk feeds with a primary outcome of survival without disability at 2 years corrected age. Enteral lactoferrin in neonates (ELFIN) randomizes infants to supplemental enteral lactoferrin or placebo with a primary outcome of LOS. This is a protocol for the mechanisms affecting the gut of preterm infants in enteral feeding trials (MAGPIE) study and is funded by the UK NIHR Efficacy and Mechanistic Evaluation programme. MAGPIE will recruit ~480 preterm infants who were enrolled in SIFT or ELFIN. Participation in MAGPIE does not change the main trial protocols and uses non-invasive sampling of stool and urine, along with any residual resected gut tissue if infants required surgery. Trial interventions may involve effects on gut microbes, metabolites (e.g., short-chain fatty acids), and aspects of host immune function. Current hypotheses suggest that NEC and/or LOS are due to a dysregulated immune system in the context of gut dysbiosis, but mechanisms have not been systematically studied within large RCTs. Microbiomic analysis will use next-generation sequencing, and metabolites will be assessed by mass spectrometry to detect volatile organic and other compounds produced by microbes or the host. We will explore differences between disease cases and controls, as well as exploring the actions of trial interventions. Impacts of this research are multiple: translation of knowledge of mechanisms promoting gut health may explain outcomes or suggest alternate strategies to improve health. Results may identify new non-invasive diagnostic or monitoring techniques, preventative or treatment strategies for NEC or LOS, or provide data useful for risk stratification in future studies. Mechanistic evaluation might be especially informative where there are not clear effects on the primary outcome (ISRCTN 12554594).

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

BACKGROUND

Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack power and have reported inconsistent results.

METHODS AND RESULTS

Our objectives were to perform a systematic review and meta-analyses of stool microbiome profiles in preterm infants to discern and describe microbial dysbiosis prior to the onset of NEC and to explore heterogeneity among studies. We searched MEDLINE, PubMed, CINAHL, and conference abstracts from the proceedings of Pediatric Academic Societies and reference lists of relevant identified articles in April 2016. Studies comparing the intestinal microbiome in preterm infants who developed NEC to those of controls, using culture-independent molecular techniques and reported α and β-diversity metrics, and microbial profiles were included. In addition, 16S ribosomal ribonucleic acid (rRNA) sequence data with clinical meta-data were requested from the authors of included studies or searched in public data repositories. We reprocessed the 16S rRNA sequence data through a uniform analysis pipeline, which were then synthesized by meta-analysis. We included 14 studies in this review, and data from eight studies were available for quantitative synthesis (106 NEC cases, 278 controls, 2944 samples). The age of NEC onset was at a mean ± SD of 30.1 ± 2.4 weeks post-conception (n = 61). Fecal microbiome from preterm infants with NEC had increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes prior to NEC onset. Alpha- or beta-diversity indices in preterm infants with NEC were not consistently different from controls, but we found differences in taxonomic profiles related to antibiotic exposure, formula feeding, and mode of delivery. Exploring heterogeneity revealed differences in microbial profiles by study and the target region of the 16S rRNA gene (V1-V3 or V3-V5).

CONCLUSIONS

Microbial dysbiosis preceding NEC in preterm infants is characterized by increased relative abundances of Proteobacteria and decreased relative abundances of Firmicutes and Bacteroidetes. Microbiome optimization may provide a novel strategy for preventing NEC.

The influence of probiotics for preterm neonates on the incidence of atopic dermatitis-results from a historically controlled cohort study

Probiotic supplementation is a promising preventive strategy for atopic dermatitis (AD). To help clarifying the significance of timing with respect to prevention of AD, we here evaluate the benefit of prophylactic use of probiotic supplementation in neonates younger than 30 weeks of gestation. Preterm children from the Department of Neonatology, Rigshospitalet, Denmark from two different admission periods were included in a historically controlled cohort study. Neonates from January 2007 to February 2010, not treated with and neonates from March 2010 to February 2013 treated with probiotic were enrolled. Main outcome was prevalence of AD, and secondary outcomes were use of topical corticosteroids, and number of skin-related visits to GPs and dermatologists. 527 preterm neonates were included in the study, 249 treated and 278 not treated with probiotics. Response rate for the two cohorts was 76.7 and 77.7% respectively. The prevalence of AD was similar in the two groups (20.9% in the probiotic treated group versus 17.1% in the not treated group, p = 0.33). No significant differences were found between the groups with respect to treatment with topical corticosteroids, or visits at GPs or dermatologist. We found no indication that probiotics may prevent AD when administered to neonates <30 gestation weeks from birth until discharge home. Factors influencing the early maturation of the immune system have been assumed to be of particular importance in atopic dermatitis, and hence, our unique cohorts contribute information on how probiotic supplementation may affect the extremely immature immune systems of preterm infants.

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

BACKGROUND

The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease.

RESULTS

A core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1-5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6.

CONCLUSIONS

This is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.

Cesarean section changes neonatal gut colonization

BACKGROUND

Delivery by means of cesarean section has been associated with increased risk of childhood immune-mediated diseases, suggesting a role of early bacterial colonization patterns for immune maturation.

OBJECTIVE

We sought to describe the influence of delivery method on gut and airway colonization patterns in the first year of life in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) birth cohort.

METHODS

Seven hundred children from the COPSAC2010 birth cohort participated in this analysis. Fecal samples were collected at age 1 week, 1 month, and 1 year, and hypopharyngeal aspirates were collected at age 1 week, 1 month, and 3 months and cultured for bacteria. Detailed information on delivery method, intrapartum antibiotics, and lifestyle factors was obtained by personal interviews.

RESULTS

Seventy-eight percent of the children were born by means of natural delivery, 12% by means of emergency cesarean section, and 9% by means of elective cesarean section. Birth by means of cesarean section was significantly associated with colonization of the intestinal tract by Citrobacter freundii, Clostridium species, Enterobacter cloacae, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella pneumoniae, and Staphylococcus aureus at age 1 week, whereas colonization by Escherichia coli was associated with natural birth. At age 1 month, these differences were less prominent, and at age 1 year, they were not apparent, which was confirmed by means of multivariate data-driven partial least squares analyses. The initial airway microbiota was unaffected by birth method.

CONCLUSION

Delivery by means of cesarean section was associated with early colonization patterns of the neonatal gut but not of the airways. The differences normalized within the first year of life. We speculate that microbial derangements, as indicated in our study, can demonstrate a possible link between delivery by means of cesarean section and immune-mediated disease.

An Integrated Review of Intestinal Microbiota in the Very Premature Infant

BACKGROUND

The intestinal microbiota is important for optimal intestinal function and protection against infection. Disruption of the intestinal microbiota has been linked to necrotizing enterocolitis (NEC) and late-onset sepsis (LOS).

OBJECTIVES

To determine what is known about the intestinal microbiota of very premature infants. We describe the relationship of the intestinal microbiota to NEC and LOS and provide an overview of the effect of environmental factors.

METHODS

A review was conducted using PubMed/MEDLINE from 2008 to 2015 to examine what is currently known about the intestinal microbiota of very premature infants.

DISCUSSION

The intestinal bacteria are low in diversity and generally contain a predominance of potentially pathogenic bacteria. Evidence suggests that these bacteria play a role in NEC as well as LOS through translocation. Environmental factors such as mode of delivery, use of antibiotics, and type of feeding may also contribute to the development of the intestinal microbiota.

Preterm gut microbiota and metabolome following discharge from intensive care

The development of the preterm gut microbiome is important for immediate and longer-term health following birth. We aimed to determine if modifications to the preterm gut on the neonatal intensive care unit (NICU) impacted the gut microbiota and metabolome long-term. Stool samples were collected from 29 infants ages 1-3 years post discharge (PD) from a single NICU. Additional NICU samples were included from 14/29 infants. Being diagnosed with disease or receiving increased antibiotics while on the NICU did not significantly impact the microbiome PD. Significant decreases in common NICU organisms including K. oxytoca and E. faecalis and increases in common adult organisms including Akkermansia sp., Blautia sp., and Bacteroides sp. and significantly different Shannon diversity was shown between NICU and PD samples. The metabolome increased in complexity, but while PD samples had unique bacterial profiles we observed comparable metabolomic profiles. The preterm gut microbiome is able to develop complexity comparable to healthy term infants despite limited environmental exposures, high levels of antibiotic administration, and of the presence of serious disease. Further work is needed to establish the direct effect of weaning as a key event in promoting future gut health.

Application of Laser Capture Microdissection and 16S rRNA Gene Polymerase Chain Reaction in the Analysis of Bacteria Colonizing the Intestinal Tissue of Neonates With Necrotizing Enterocolitis

BACKGROUND

Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in newborns. However, the pathogenesis of NEC remains unclear because most bacterial characterizations of alleged pathogens have been performed via the analysis of human fecal samples and experimental animal studies. The objective is to investigate the microbial composition of NEC using inflamed intestinal tissue surgically removed from neonates diagnosed with NEC (n = 18).

METHODS

We obtained intestinal tissues via a combination of laser capture microdissection and Gram staining, which was used to mark individual bacteria. Tissues with congenital intestinal atresia (n = 7) served as control specimens. An analysis of the 16S rRNA of each sample was performed via polymerase chain reaction-denaturing gradient gel electrophoresis.

RESULTS

Numerous bacteria were observed in the inflamed intestinal wall tissue samples obtained from neonates with NEC following Gram staining and examination under an optical microscope. The total number of types detected by polymerase chain reaction-denaturing gradient gel electrophoresis was 12.17 ± 2.83 per infant with NEC, whereas only 2.57 ± 1.81 types were detected in each infant with congenital intestinal atresia. Proteobacteria had the highest constituent ratio (188 of 285) of all detected clone sequences in the NEC group. Additionally, Pseudomonas sp., Acinetobacter sp., Klebsiella sp., Clostridium sp., Ochrobactrum sp. and Arcobacter sp. were detected only in the NEC group.

CONCLUSIONS

The combination of Gram staining and laser capture microdissection was a reliable method to obtain and prepare tissue samples for processing. NEC was associated with multiple species of bacteria, and microflora within the disease-affected sites may be relatively specific and stable. Proteobacteria demonstrated the highest constituent ratio. Our observations warrant closer examination of the 6 bacterial genera that were only detected in NEC, particularly Clostridium sp., which may be closely correlated with pneumatosis intestinalis.

Probiotic administration can prevent necrotizing enterocolitis in preterm infants: A meta-analysis

PURPOSE

Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in preterm infants, affecting ~6-7% of very-low-birth-weight (VLBW) infants. Early intervention and aggressive treatment has improved clinical outcomes, but considerable morbidity continues to accrue to NEC survivors. This meta-analysis examines the impact of probiotics on the incidence of NEC and complications among VLBW infants.

METHODS

A comprehensive literature search for all published randomized control trials (RCTs) assessing the use of probiotics to prevent NEC in VLBW infants was conducted using PubMed, Cochrane Central Registry of Controlled Trials, and Google Scholar (1966-2014). The incidences of NEC, sepsis, overall mortality, and time to reach full enteral feeds were analyzed.

RESULTS

20 RCTs involving 5982 preterm VLBW infants were analyzed. Risk of NEC was reduced by 49.1% (RR=0.509; 95% CI, 0.385-0.672; p<0.001), and overall mortality by 26.9% among infants receiving probiotics (RR=0.731; 95% CI, 0.577-0.926; p=0.009). An 8.1% reduction in sepsis was also observed in infants receiving probiotics (RR=0.919; 95% CI, 0.823-1.027; p=0.137). Time to reach full enteral feeds was reduced by 1.2 days among infants receiving probiotics (MD: -1.217; 95% CI, -2.151 to -0.283; p=0.011).

CONCLUSION

The use of probiotic supplementation in preterm VLBW infants is associated with a significant reduction in the risk of NEC and overall mortality. Additional studies are required to determine the optimal genus, species, and dose of probiotic.

Alterations in platelet-derived growth factor expression in the pathophysiology of necrotizing enterocolitis

BACKGROUND

Necrotizing enterocolitis (NEC) involves impaired ileal blood flow due to alterations in vascular tone control and intestinal angiogenesis. Platelet-derived growth factor (PDGF) is a mediator of normal angiogenesis in intestinal epithelium. We hypothesized that gene dysregulation during experimental NEC results in altered PDGF expression.

METHODS

Sprague-Dawley rats were randomized to groups by litter. Controls were delivered vaginally and dam-fed. NEC groups were delivered prematurely by cesarean section and subjected to an established NEC protocol. Ileum was obtained at 0, 12, 24, 48, 72, and 96 h of life from all animals (N = 108 animals). Western blot analysis was carried out for every time point, and samples were evaluated by immunohistochemistry. Antibodies against PDGF-A, PDGF-B, and their receptors, PDGFR-α and PDGFR-β, were used. Statistical analysis was performed using two-way analysis of variance with a priori P < 0.05.

RESULTS

Ileal PDGF-A concentration was higher in controls versus NEC from 24-96 h of life. Its receptor, PDGFR-α, was low in concentration in both groups at all time points. PDGF-B concentration was increased in controls at 24 and 72 h of life but decreased at the 48-h mark. Its receptor, PDGFR-β, was also low in both groups at 12 and 24 h but increased in controls at 48 and 72 h.

CONCLUSIONS

These data support our hypothesis that PDGF and PDGF receptor expression are altered in experimental NEC. Dysregulation of PDGF during intestinal maturation could contribute to the development of NEC. Further investigation into this pathway could yield new therapeutic targets for this devastating disease.

The neonatal bowel microbiome in health and infection

PURPOSE OF REVIEW

In newborns, interactions between the host and the microbiome operate synergistically, modulating host immune function and shaping the microbiome. Next generation molecular sequencing methodologies in tandem with modeling complex communities allow insights into the role of the microbiome in health and disease states. Infection-related disease states in which dysbiosis is integral include late-onset sepsis (LOS) and necrotizing enterocolitis (NEC), which still cause deaths and morbidity. Understanding microbiomic interactions may lead to alternative prevention, monitoring or treatment strategies, and modulation of long-term health outcomes especially in the preterm population. Recent studies have advanced understanding of the microbiome in NEC and LOS.

RECENT FINDINGS

Mechanisms of host-microbiome interaction have been demonstrated. Patterns of microbiomic change in association with NEC and LOS have been observed, with community changes dominated by Proteobacteria and Firmicutes appearing to precede NEC, and very early microbiomic signatures influencing LOS. Data on viral and fungal elements are emerging.

SUMMARY

Greater understanding of the neonatal bowel microbiome may allow tailored clinical practice and therapeutic intervention. Data handling and interpretation is challenging. Mechanistic studies of clinical interventions that affect the gut microbiome are important next steps.

The human neonatal gut microbiome: a brief review

The field of genomics has expanded into subspecialties such as metagenomics over the course of the last decade and a half. The development of massively parallel sequencing capabilities has allowed for increasingly detailed study of the genome of the human microbiome, the microbial super organ that resides symbiotically within the mucosal tissues and integumentary system of the human host. The gut microbiome, and particularly the study of its origins in neonates, has become subtopics of great interest within the field of genomics. This brief review seeks to summarize recent literature regarding the origins and establishment of the neonatal gut microbiome, beginning in utero, and how it is affected by neonatal nutritional status (breastfed versus formula fed) and gestational age (term versus preterm). We also explore the role of dysbiosis, a perturbation within the fragile ecosystem of the microbiome, and its role in the origin of select pathologic states, specifically, obesity and necrotizing enterocolitis (NEC) in preterm infants. We discuss the evidence supporting enteral pre- and pro-biotic supplementation of commensal organisms such as Bifidobacterium and Lactobacillus in the neonatal period, and their role in the prevention and amelioration of NEC in premature infants. Finally, we review directions to consider for further research to promote human health within this field.

Bacterial and fungal viability in the preterm gut: NEC and sepsis

BACKGROUND AND AIMS

Evidence suggests that microbial communities in the preterm gut may influence the development of necrotising enterocolitis (NEC) and sepsis. Existing data often neglect fungi and whether bacteria were metabolically active or not. We sought to characterise the bacterial and fungal stool flora of preterm neonates and organism viability and evaluate any associations with NEC and sepsis.

PATIENTS

136 stools from 32 patients (<32 weeks gestation) were collected between birth and day 95. Seven infants developed NEC and 13 sepsis.

METHODS

Stools were analysed by PCR-DGGE for assessment of the total bacterial and fungal communities by analysis of 16S rRNA and 28S rRNA, respectively. In 65 samples (25 infants), the viable (RNA) bacterial and fungal communities were analysed. Analyses were performed to examine the possible effects of demographic or treatment related factors and the development of NEC or sepsis.

RESULTS

80 (66 viable) bacterial species were identified overall and 12 fungal (none viable). Total bacterial communities significantly differed between healthy infants and those with NEC or sepsis, with Sphingomonas spp. significantly associated with NEC. Significant drivers of community structure differed based on either total or viable analysis. Antifungal prophylaxis was associated with altered bacterial community and a reduction in bacterial richness was observed in week 4, correlating with high antibiotic exposure.

CONCLUSIONS

Total and viable communities differ in preterm infants, and non-viable fungal species are present in infants on fungal prophylaxis. Exploration of viability and non-bacterial contributors to the total community may increase understanding of NEC and sepsis.

Systemic inflammation associated with severe intestinal injury in extremely low gestational age newborns

To define the role of systemic inflammation in infants with intestinal perforation (IP) and necrotizing enterocolitis (NEC), we measured 25 blood protein concentrations on days 1, 7 and 14 in 939 infants born before 28 weeks' gestation. On days 7 and 14, infants with NEC had elevated levels of C-reactive protein (CRP), serum amyloid A (SAA), IL-6 and IL-8. Infants with IP had elevated levels of CRP and insulin growth factor binding protein-1 on day 7 and elevated CRP, SAA, TNF-receptor-2 and matrix metalloproteinase-9 levels on day 14. A better understanding of systemic inflammation might help prevent and treat these disorders.

The role of the intestinal microbiota in the pathogenesis of necrotizing enterocolitis

Development of necrotizing enterocolitis (NEC) requires a susceptible host, typically a premature infant or an infant with congenital heart disease, enteral feedings and bacterial colonization. Although there is little doubt that microbes are critically involved in the pathogenesis of NEC, the identity of specific causative pathogens remains elusive. Unlike established normal adult gut microbiota, which is quite complex, uniform, and stable, early postnatal bacterial populations are simple, diverse, and fluid. These properties complicate studies aimed at elucidating characteristics of the gut microbiome that may play a role in the pathogenesis of NEC. A broad variety of bacterial, viral, and fungal species have been implicated in both clinical and experimental NEC. Frequently, however, the same species have also been found in physiologically matched healthy individuals. Clustered outbreaks of NEC, in which the same strain of a suspected pathogen is detected in several patients suggest, but do not prove, a causative relationship between the specific pathogen and the disease. Studies in Cronobacter sakazakii, the best characterized NEC pathogen, have demonstrated that virulence is not a property of a bacterial species as a whole, but rather a characteristic of certain strains, which may explain why the same species can be pathogenic or non-pathogenic. The fact that a given microbe may be innocuous in a full-term, yet pathogenic in a pre-term infant has led to the idea of opportunistic pathogens in NEC. Progress in understanding the infectious nature of NEC may require identifying specific pathogenic strains and unambiguously establishing their virulence in animal models.

A clinical perspective of necrotizing enterocolitis: past, present, and future

Necrotizing enterocolitis (NEC) primarily affects premature infants. It is less common in term and late preterm infants. The age of onset is inversely related to the postmenstrual age at birth. In term infants, NEC is commonly associated with congenital heart diseases. NEC has also been associated with other anomalies. More than 85% of all NEC cases occur in very low birth weight infants or in very premature infants. Despite incremental advances in our understanding of the clinical presentation and pathophysiology of NEC, universal prevention of this disease continues to elude us even in the twenty-first century.

Intestinal microbial profiles in extremely preterm infants with and without necrotizing enterocolitis

AIM

Necrotizing enterocolitis (NEC) represents one of the gravest complications in premature infants. The suggested role of intestinal microbiota in the development of NEC needs to be elucidated.

METHODS

This prospective single-centre case-control study applied barcoded pyrosequencing to map the bacterial composition of faecal samples from extremely preterm infants. Ten patients were diagnosed with NEC and matched to healthy controls with regard to sex, gestational age and mode of delivery prior to analysis of the samples.

RESULTS

Enterococcus, Bacillales and Enterobacteriaceae dominated the flora. Although not statistically significant, a high relative abundance of Bacillales and Enterobacteriaceae was detected at early time points in patients developing NEC, while healthy controls had a microbiota more dominated by Enterococcus. A low diversity of intestinal microbial flora was found without any differences between NEC patients and controls. In 16 healthy controls, Firmicutes (Enterococcus and Bacillales) dominated the faecal flora during the first weeks after birth and were then succeeded by Enterobacteriaceae.

CONCLUSION

No significant differences in the composition of intestinal microbiota of patients developing NEC were detected; however, some findings need to be scrutinized in subsequent studies.

Functions of intestinal microflora in children

PURPOSE OF REVIEW

This review discusses the structural composition of intestinal microbiota, the functional relationship between the latter and the host, and the role of abnormal microflora in chronic diseases.

RECENT FINDINGS

A more complete view of the gut microbiota is being developed following the Human Microbiome Project. The microflora in children is plastic, susceptible to changes in response to diet modifications, antibiotic treatment and other events, providing the opportunity to study its functional role. Increasing evidence highlights the role of nutrition in the age-related development of microflora. Eubiosis, that is, a normal microflora structure, provides protection against infections, educates the immune system, ensures tolerance to foods, and contributes to nutrient digestion and energy harvest. Changes in microflora, consisting in the overpresence of harmful species or underpresence of commensal species, or dysbiosis produce dysfunctions, such as intestinal inflammation or dysmotility. Moreover abnormal pattern of microflora have been consistently detected in specific diseases.

SUMMARY

A relationship exists between eubiosis and functions and conversely between dysbiosis and dysfunctions or even diseases. Abnormalities in microflora composition may trigger or contribute to specific diseases. This raises the hypothesis to target microflora in order to restore eubiosis through the use of antibiotics, probiotics or nutrients.