The Microbiome and Its Impact on Disease in the Preterm Patient

Gut Dysbiosis in the First-Passed Meconium Microbiomes of Korean Preterm Infants Compared to Full-Term Neonates

Since gestational age (GA) is an important factor influencing the presence of specific microbiomes, we aimed to characterize the core microbiomes of preterm infants compared to full-term (FT) infants. This study investigated the differences in microbiota composition between very preterm (VP), moderate-to-late preterm (MLP), and FT neonates by examining the core microbiomes of a large cohort of Korean neonates. Meconium samples from 310 neonates with a GA range of 22-40 weeks were collected, and 16S rRNA analyses were performed; 97 samples were obtained from the FT, 59 from the VP, and 154 from the MLP group. Firmicutes, Bacteroidetes, and Proteobacteria were the phylum-level core microbiomes. Infants born before 37 weeks showed a disruption in the core microbiomes. At the phylum level, the relative abundance of Bacteroidetes was positively (r = 0.177, p = 0.002) correlated with GA, while that of Proteobacteria was negatively (r = -0.116, p = 0.040) correlated with GA. At the genus level, the relative abundances of Bacteroides and Prevotella were positively correlated with GA (r = 0.157, p = 0.006; r = 0.160, p = 0.005). The meconium of preterm infants exhibited significantly lower α-diversities than that of FT infants. β-diversities did not appear to differ between the groups. Overall, these findings underscore the importance of GA in shaping the early gut microbiome.

Gut acquisition of Extended-spectrum β-lactamases-producing Klebsiella pneumoniae in preterm neonates: Critical role of enteral feeding, and endotracheal tubes in the neonatal intensive care unit (NICU)

BACKGROUND

Klebsiella spp. can colonize the intestine of preterm neonates, and over-growth has been associated with necrotizing enterocolitis, hospital-acquired infections, and late-onset sepsis. This could lead us to suggest that the clinical pertinence of intestinal colonization with ESBL in preterm neonates appears to be important. We conducted this study to characterize the genetic proprieties of ESBL-producing Klebsiella pneumoniae (ESBL-KP) under clinical isolates and to describe the risk factors for the intestinal tract acquisition event during hospitalization.

METHODS

One hundred and thirteen premature infants were recruited from the neonatal intensive care unit (NICU). All newborns are issued from the birth suites of the pregnancy department. Two rectal swabs were planned to define K. Pneumoniae intestinal carriage status. ESBL-KP was confirmed by Brilliance ESBL selective chromogenic Agar. Antimicrobial susceptibility testing including phenotypic testing and genotypic detection of the most commonly described ESBL genes was done. Logistic regression models were performed to find the variables associated with the acquisition event of ESBL-KP.

RESULTS

A total of 62 (54.86%) premature neonates were colonized with ESBL-KP. The rate of blaSHV, blaTEM, blaCTX-M1, blaCTX-M2, blaCTX-M9, and blaOXA-48 genes among the isolates was 82, 48, 93.5, 4.8, 11.2 and 3.22%, respectively. We found that ESBLs K. Pneumoniae isolates were 100% resistant to amoxicillin, clavulanic acid-amoxicillin, cefotaxime, ceftazidime, and gentamicin. The regression model is for a given significant association between the tract intestinal of ESBL-KP acquisition events and the use of enteral tube feeding (OR = 38.46, 95% CI: 7.86-188.20, p-Value: 0.001), and endotracheal tubes (OR = 4.86, 95% CI: 1.37-17.19, p-Value 0.014).

CONCLUSION

Our finding supposes that the enteral feeding tube and endotracheal tube might have a critical role in colonizing the intestinal tract of preterm infants. This highlights the current status of both practices that will require updated procedures in the NICU.

Extremely preterm neonates have more Lactobacillus in meconium than very preterm neonates - the in utero microbial colonization hypothesis

Growing evidence suggests that maternal microbiota can influence the neonates' gut colonization. However, the mechanisms of vertical bacterial transmission remain poorly defined. We believed that the first colonizers of the newborn come from the mother's gut and vagina during pregnancy and that this is independent of the mode of delivery. We conducted an observational longitudinal study to evaluate the link between the maternal gut microbiota and the meconium's microbiota in extremely and very preterm neonates. Bacterial DNA was extracted from samples and specific bacterial groups were quantified by RT-PCR. In this cohort of 117 preterm neonates, we detected bacterial DNA in 88% of meconium samples. Meconium microbiota of neonates born after 28 gestational weeks (very preterm neonates) showed stronger correlations with their mothers' fecal microbiota. However, neonates born before 28 gestational weeks (extremely preterm neonates) had more Lactobacillus - genus that dominated the vaginal microbiota - than very preterm neonates, regardless of the mode of delivery. Collectively, these data support the hypothesis that maternal bacteria from the gut and vagina can play a role in shaping neonates' gut microbiota and that mother-to-infant bacterial transmission is a controlled and time-specific process. ClinicalTrials.gov Identifier: NCT03663556.

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.

The Role of Microbiota in Retinal Disease

The ten years since the first publications on the human microbiome project have brought enormous attention and insight into the role of the human microbiome in health and disease. Connections between populations of microbiota and ocular disease are now being established, and increased accessibility to microbiome research and insights into other diseases is expected to yield enormous information in the coming years. With the characterization of the ocular microbiome, important insights have already been made regarding corneal and conjunctival tissues. Roles for non-ocular microbiomes in complex retinal diseases are now being evaluated. For example, the gut microbiome has been implicated in the pathogenesis of uveitis. This short review will summarize the few studies linking gut or oral microbiota to diabetic retinopathy (DR), glaucoma, and age-related macular degeneration (AMD). We will also conjecture where the most significant findings still remain to be elucidated. Finally, we will propose the gut-retina axis, related but distinct from the gut-brain axis.

Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation

Human milk (HM) is the golden standard for nutrition of newborn infants. Human milk oligosaccharides (HMOs) are abundantly present in HM and exert multiple beneficial functions, such as support of colonization of the gut microbiota, reduction of pathogenic infections and support of immune development. HMO-composition is during lactation continuously adapted by the mother to accommodate the needs of the neonate. Unfortunately, for many valid reasons not all neonates can be fed with HM and are either totally or partly fed with cow-milk derived infant formulas, which do not contain HMOs. These cow-milk formulas are supplemented with non-digestible carbohydrates (NDCs) that have functional effects similar to that of some HMOs, since production of synthetic HMOs is challenging and still very expensive. However, NDCs cannot substitute all HMO functions. More efficacious NDCs may be developed and customized for specific groups of neonates such as pre-matures and allergy prone infants. Here current knowledge of HMO functions in the neonate in view of possible replacement of HMOs by NDCs in infant formulas is reviewed. Furthermore, methods to expedite identification of suitable NDCs and structure/function relationships are reviewed as in vivo studies in babies are impossible.

Influence of Feeding Type on Gut Microbiome Development in Hospitalized Preterm Infants

BACKGROUND

Premature infants have a high risk for dysbiosis of the gut microbiome. Mother's own milk (MOM) has been found to favorably alter gut microbiome composition in infants born at term. Evidence about the influence of feeding type on gut microbial colonization of preterm infants is limited.

OBJECTIVE

The purpose of this study was to explore the effect of feeding types on gut microbial colonization of preterm infants in the neonatal intensive care unit.

METHODS

Thirty-three stable preterm infants were recruited at birth and followed up for the first 30 days of life. Daily feeding information was used to classify infants into six groups (MOM, human donor milk [HDM], Formula, MOM + HDM, MOM + Formula, and HDM + Formula) during postnatal days 0-10, 11-20, and 21-30. Stool samples were collected daily. DNA extracted from stool was used to sequence the 16S rRNA gene. Exploratory data analysis was conducted with a focus on temporal changes of microbial patterns and diversities among infants from different feeding cohorts. Prediction of gut microbial diversity from feeding type was estimated using linear mixed models.

RESULTS

Preterm infants fed MOM (at least 70% of the total diet) had highest abundance of Clostridiales, Lactobacillales, and Bacillales compared to infants in other feeding groups, whereas infants fed primarily HDM or formula had a high abundance of Enterobacteriales compared to infants fed MOM. After controlling for gender, postnatal age, weight, and birth gestational age, the diversity of gut microbiome increased over time and was constantly higher in infants fed MOM relative to infants with other feeding types (p < .01).

DISCUSSION

MOM benefits gut microbiome development of preterm infants, including balanced microbial community pattern and increased microbial diversity in early life.

Establishment and development of the intestinal microbiota of preterm infants in a Lebanese tertiary hospital

The establishment and development of the intestinal microbiota is known to be associated with profound short- and long-term effects on the health of full-term infants (FTI), but studies are just starting for preterm infants (PTI). The data also mostly come from western countries and little information is available for the Middle East. Here, we determined the composition and dynamics of the intestinal microbiota during the first month of life for PTI (n = 66) and FTI (n = 17) in Lebanon. Fecal samples were collected weekly and analyzed by quantitative PCR (q-PCR) and temporal temperature gradient gel electrophoresis (TTGE). We observed differences in the establishment and composition of the intestinal microbiota between the two groups. q-PCR showed that PTI were more highly colonized by Staphylococcus than FTI in the first three weeks of life; whereas FTI were more highly colonized by Clostridium clusters I and XI. At one month of life, PTI were mainly colonized by facultative anaerobes and a few strict anaerobes, such as Clostridium cluster I and Bifidobacterium. The type of feeding and antibiotic treatments significantly affected intestinal colonization. TTGE revealed low species diversity in both groups and high inter-individual variability in PTI. Our findings show that PTI had altered intestinal colonization with a higher occurrence of potential pathogens (Enterobacter, Clostridium sp) than FTI. This suggests the need for intervention strategies for PTI to modulate their intestinal microbiota and promote their health.

Early Gut Colonization of Preterm Infants: Effect of Enteral Feeding Tubes

OBJECTIVE

The aim of the study was to evaluate the potential colonization of nosocomial bacteria in enteral feeding systems and its effect on early gut colonization of preterm neonates.

METHODS

Mother's own milk, donor milk, and preterm formula samples obtained after passing through the external part of the enteral feeding tubes were cultured. In addition, meconium and fecal samples from 26 preterm infants collected at different time points until discharge were cultured. Random amplification polymorphism DNA and pulse field gel electrophoresis were performed to confirm the presence of specific bacterial strains in milk and infant fecal samples.

RESULTS

Approximately 4000 bacterial isolates were identified at the species level. The dominant species in both feces from preterm infants and milk samples were Staphylococcus epidermidis, S aureus, Enterococcus faecalis, E faecium, Serratia marcescens, Klebsiella pneumoniae, and Escherichia coli. All of them were present at high concentrations independently of the feeding mode. Random amplification polymorphism DNA and pulse field gel electrophoresis techniques showed that several bacteria strains were found in both type of samples. Furthermore, scanning electron microscopy revealed the presence of a dense bacterial biofilm in several parts of the feeding tubes and the tube connectors.

CONCLUSIONS

There is a sharing of bacterial strains between the neonates' gastrointestinal microbiota and the feeding tubes used to feed them.

Sialylated galacto-oligosaccharides and 2′-fucosyllactose reduce necrotising enterocolitis in neonatal rats

Necrotising enterocolitis (NEC) is one of the most frequent and fatal intestinal disorders in preterm infants and has very limited treatment options. Breast-fed infants are at a 6–10-fold lower NEC risk than formula-fed infants, and we have previously shown that human milk oligosaccharides (HMO) improved survival and reduced pathology in a rat NEC model. The HMO disialyllacto-N-tetraose (DSLNT) was most effective, and sialylation was shown to be essential for its protective effect. Galacto-oligosaccharides (GOS), currently added to some infant formula, but not containing sialic acid, had no effect. In addition to DSLNT, our previous work also showed that the neutral HMO fraction, which contains high concentrations of 2′-fucosyllactose (2′FL), slightly improved pathology scores. Here, we assessed the in vivo efficacy of 2′FL, as well as of GOS that we enzymatically sialylated (Sia-GOS). Neonatal rats were randomised into the following study groups – dam-fed (DF), formula-fed (FF), FF containing pooled HMO (10 mg/ml), GOS (8 mg/ml), Sia-GOS (500 µm) or 2′FL (2 mg/ml) – and subjected to the established NEC protocol. The DF and HMO groups had the lowest pathology scores with mean values of 0·67 (sd 0·34) and 0·90 (sd 0·47), respectively. The FF group had significantly elevated pathology scores of 2·02 (sd 0·63). Although the addition of GOS to the formula had no protective effect and generated scores of 2·00 (sd 0·63), the addition of Sia-GOS or 2′FL significantly lowered pathology scores to 1·32 (sd 0·56) (P<0·0034) and 1·43 (sd 0·51) (P<0·0040), respectively. The results warrant further studies to investigate the underlying mechanisms and to assess safety and efficacy in human neonates.

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

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

Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung's associated enterocolitis

Next generation sequencing techniques are currently revealing novel insight into the microbiome of the human gut. This new area of research seems especially relevant for neonatal diseases, because the development of the intestinal microbiome already starts in the perinatal period and preterm infants with a still immature gut associated immune system may be harmed by a dysproportional microbial colonization. For most gastrointestinal diseases requiring pediatric surgery there is very limited information about the role of the intestinal microbiome. This review aims to summarize the current knowledge and outline future perspectives for important pathologies like necrotizing enterocolitis (NEC) of the newborn, short bowel syndrome (SBS), and Hirschsprung’s disease associated enterocolitis (HAEC). Only studies applying next generation sequencing techniques to analyze the diversity of the intestinal microbiome were included. In NEC patients intestinal dysbiosis could already be detected prior to any clinical evidence of the disease resulting in a reduction of the bacterial diversity. In SBS patients the diversity seems to be reduced compared to controls. In children with Hirschsprung’s disease the intestinal microbiome differs between those with and without episodes of enterocolitis. One common finding for all three diseases seems to be an overabundance of Proteobacteria. However, most human studies are based on fecal samples and experimental data question whether fecal samples actually represent the microbiome at the site of the diseased bowel and whether the luminal (transient) microbiome compares to the mucosal (resident) microbiome. In conclusion current studies already allow a preliminary understanding of the potential role of the intestinal microbiome in pediatric surgical diseases. Future investigations could clarify the interface between the intestinal epithelium, its immunological competence and mucosal microbiome. Advances in this field may have an impact on the understanding and non-operative treatment of such diseases in infancy.

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.