The intestinal microbiome and necrotizing enterocolitis

Understanding the Biologic Therapies of Probiotics, Prebiotics, and Synbiotics: Exploring Current Evidence for Use in Premature Infants for the Prevention of Necrotizing Enterocolitis

Necrotizing enterocolitis remains a significant cause of morbidity and mortality in very low-birth-weight infants (<1500 g), with current preventive strategies unclear. Scientific evidence has recently emerged, suggesting that probiotics, prebiotics, and synbiotics may effectively and safely alter the premature intestinal microbiota, enhancing a deficient innate immune response and maturing the intestinal barrier to prevent necrotizing enterocolitis development. Currently, formal recommendations do not support routine use of these dietary supplementations for premature infants. Here, we examine how probiotic, prebiotic, and synbiotic preparations physiologically alter the underdeveloped intestinal microbial environment to potentially reduce necrotizing enterocolitis incidence and discuss current evidence that has examined safety and efficacy factors potentially supporting routine use among the premature infant population.

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

DOI:http://dx.doi.org/10.7554/eLife.05477.001

The spread of potentially harmful bacteria is a major source of disease in patients staying in hospitals. Premature babies—born before 37 weeks of pregnancy—can be particularly vulnerable to these infections because their organs may not yet be fully developed. Also, young babies do not have the fully established populations of beneficial microbes that help to protect us from dangerous bacteria.

Necrotizing enterocolitis—a life-threatening disease that can cause portions of the bowel to die—is mostly seen in extremely premature babies. Although it is not known what causes this serious condition, research has suggested that a contagious microbe may be responsible.

The development of methods that can sequence DNA from whole communities of microbes, known as metagenomics, allows researchers to identify the presence of individual strains of bacteria within these communities. This makes it possible to compare and contrast the strains of bacteria present in both diseased and healthy individuals, to help identify the bacteria responsible for a disease.

Here, Raveh-Sadka et al. used a metagenomics approach to study the communities of microbes present in premature babies in a hospital unit during an outbreak of necrotizing enterocolitis. The study found that very few bacterial strains were present in more than one baby, suggesting that bacterial strains are not readily transferred between the babies while they are in the hospital. Furthermore, Raveh-Sadka et al. reveal that no single bacterial strain was shared among all the babies who developed necrotizing enterocolitis.

These findings indicate that necrotizing enterocolitis is not caused by a single strain of bacterium. Instead, if bacteria do contribute to the disease, it maybe that it is caused by a variety of potentially harmful bacteria colonizing the gut at the cost of beneficial bacteria. In future, better understanding of the barriers that limit the transfer of bacteria between premature babies could help inform efforts to reduce the spread of infections between patients in hospitals.

DOI:http://dx.doi.org/10.7554/eLife.05477.002

Computational Studies of the Intestinal Host-Microbiota Interactome

A large and growing body of research implicates aberrant immune response and compositional shifts of the intestinal microbiota in the pathogenesis of many intestinal disorders. The molecular and physical interaction between the host and the microbiota, known as the host-microbiota interactome, is one of the key drivers in the pathophysiology of many of these disorders. This host-microbiota interactome is a set of dynamic and complex processes, and needs to be treated as a distinct entity and subject for study. Disentangling this complex web of interactions will require novel approaches, using a combination of data-driven bioinformatics with knowledge-driven computational modeling. This review describes the computational approaches for investigating the host-microbiota interactome, with emphasis on the human intestinal tract and innate immunity, and highlights open challenges and existing gaps in the computation methodology for advancing our knowledge about this important facet of human health.

Probiotics (Lactobacillus acidophilus and Bifidobacterium infantis) prevent NEC in VLBW infants fed breast milk but not formula [corrected]

BACKGROUND

Specific probiotics prevent necrotizing enterocolitis (NEC). A mixture of lactobacilli and bifidobacteria (Infloran) was highly effective in Asian very-low-birth-weight (VLBW) infants. We analyzed the effect of Infloran on NEC, NEC severity, and the influence of enteral feedings (breast milk vs. formula) on NEC prevention in a cohort of European VLBW infants.

METHODS

Infloran was implemented for routine use at our department. VLBW infants receiving probiotics were prospectively followed (2010-2012) and compared with historic controls (2008-2009). Data on NEC, neonatal morbidity, feeding tolerance, and descriptive parameters on NEC cases were analyzed.

RESULTS

Infloran had no statistically significant impact on NEC (controls: 24/233 (10.3%); probiotics: 16/230 (7%); P = 0.2). However, NEC was significantly reduced in infants of the probiotics group who were fed any breast milk (20/179 (11.2%) vs. 10/183 (5.5%); P = 0.027), whereas it was ineffective in infants exclusively fed formula (4/54 (7.4%) vs. 6/44 (13.6%); P = 0.345). Occurrence of severe NEC (IIIb), time until full feeds, and gastric residuals were similar.

CONCLUSION

Infloran was of lower efficacy in a European VLBW cohort and showed a reduction of NEC only in infants fed breast milk. Future studies should investigate the influence of feeding formula or breast milk on the effect of probiotics.

Maturation of the enteric mucosal innate immune system during the postnatal period

The innate immune system instructs the host on microbial exposure and infection. This information is critical to mount a protective innate and adaptive host response to microbial challenge, but is also involved in homeostatic and adaptive processes that adjust the organism to meet environmental requirements. This is of particular importance for the neonatal host during the transition from the protected fetal life to the intense and dynamic postnatal interaction with commensal and pathogenic microorganisms. Here, we discuss both adaptive and developmental mechanisms of the mucosal innate immune system that prevent inappropriate stimulation and facilitate establishment of a stable homeostatic host-microbial interaction after birth.

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.

The viability of Lactobacillus fermentum CECT5716 is not essential to exert intestinal anti-inflammatory properties

The viability ofL. fermentumCECT5716 did not affect its immune-modulatory and anti-inflammatory properties.

Fecal short-chain fatty acids of very-low-birth-weight preterm infants fed expressed breast milk or formula

OBJECTIVES

In preterm infants, the metabolic responses of gastrointestinal (GI) bacteria to different diets are poorly understood despite the possible effects on GI health. Therefore, we tested the hypothesis that diet influences bacterial metabolism by measuring short-chain fatty acids (SCFAs) in stool samples from very-low-birth-weight (VLBW) preterm infants without GI disorder as surrogate biomarkers of bacterial metabolism.

METHODS

Ion chromatography was used to measure fecal SCFAs (acetate, formate, propionate, butyrate, and isobutyrate), lactate, and chloride in fresh stool samples collected from 32 preterm infants (without major congenital anomalies, GI disorders, or a recent history of antibiotic administration and on full feed of either expressed maternal breast milk [EBM; n = 13] or a formula for preterm infants [Similac Special Care Formula; preterm formula, PTF; n = 19]).

RESULTS

The mean birth weight was 972 g, the mean gestational age was 27 weeks, and the mean postnatal age at first stool sample was 36 days. When adjusted for gestational age, the stools of EBM infants had higher concentrations (micromoles per gram of stool) of total SCFA (128 vs 68; P = 0.002), acetate (41 vs 13; P = 0.005), propionate (15.1 vs 4.4; P = 0.003), and chloride (21,814 vs 10,652; P = 0.02). Interactions between postnatal age and diet were detected for lactate (P = 0.05), propionate (P = 0.03), and butyrate (P = 0.03).

CONCLUSIONS

Diets fed to VLBW preterm infants influence fecal SCFA profiles, and hence the metabolism of the GI bacteria, and potentially the health of preterm infants. The responses of bacterial metabolism to diet are influenced with postnatal age and gestational age at birth.

Bifidobacterium longum subsp. infantis in experimental necrotizing enterocolitis: alterations in inflammation, innate immune response, and the microbiota

BACKGROUND

Probiotics decrease the risk of necrotizing enterocolitis (NEC). We sought to determine the impact of Bifidobacterium longum subsp. infantis (B. infantis) in the established rat model of NEC.

METHODS

Rat pups delivered 1 d prior to term gestation were assigned to one of three groups: dam fed (DF), formula fed (FF), or fed with formula supplemented with 5 × 10(6) CFU B. infantis per day (FF+Binf). Experimental pups were exposed to hypoxia and cold stress. Ileal tissue was examined for pathology and expression of inflammatory mediators, antimicrobial peptides, and goblet-cell products. Ceca were assessed for bacterial composition by analysis of the 16S rRNA sequence.

RESULTS

Administration of B. infantis significantly reduced the incidence of NEC, decreased expression of Il6, Cxcl1, Tnfa, Il23, and iNOS, and decreased expression of the antimicrobial peptides Reg3b and Reg3g. There was significant microbial heterogeneity both within groups and between experiments. The cecal microbiota was not significantly different between the FF and FF+Binf groups. Bifidobacteria were not detected in the cecum in significant numbers.

CONCLUSION

In the rat model, the inflammation associated with NEC was attenuated by administration of probiotic B. infantis. Dysbiosis was highly variable, precluding determination of the precise role of the microbiota in experimental NEC.

The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood

The microbiota "organ" is the central bioreactor of the gastrointestinal tract, populated by a total of 10(14) bacteria and characterized by a genomic content (microbiome), which represents more than 100 times the human genome. The microbiota plays an important role in child health by acting as a barrier against pathogens and their invasion with a highly dynamic modality, exerting metabolic multistep functions and stimulating the development of the host immune system, through well-organized programming, which influences all of the growth and aging processes. The advent of "omics" technologies (genomics, proteomics, metabolomics), characterized by complex technological platforms and advanced analytical and computational procedures, has opened new avenues to the knowledge of the gut microbiota ecosystem, clarifying some aspects on the establishment of microbial communities that constitute it, their modulation and active interaction with external stimuli as well as food, within the host genetic variability. With a huge interdisciplinary effort and an interface work between basic, translational, and clinical research, microbiologists, specialists in "-omics" disciplines, and clinicians are now clarifying the role of the microbiota in the programming process of several gut-related diseases, from the physiological symbiosis to the microbial dysbiosis stage, through an integrated systems biology approach.

Intestinal alkaline phosphatase is protective to the preterm rat pup intestine

BACKGROUND

Necrotizing enterocolitis (NEC) is the most common surgical emergency in neonates, with a mortality rate between 10 and 50%. The onset of necrotizing enterocolitis is highly variable and associated with numerous risk factors. Prior research has shown that enteral supplementation with intestinal alkaline phosphatase (IAP) decreases the severity of NEC. The aim of this study is to investigate whether IAP is protective to the preterm intestine in the presence of formula feeding and in the absence of NEC.

METHODS

Preterm rat pups were fed formula with or without supplementation with IAP, and intestine was obtained on day of life 3 for analysis of IAP activity, mRNA expression of TNFα, IL-6 and iNOS and permeability and cytokine expression after LPS exposure.

RESULTS

There was no difference in the absolute and intestine specific alkaline phosphatase activity in both groups. Rat pups fed IAP had decreased mRNA expression of the inflammatory cytokines TNFα, IL-6 and iNOS. Pups supplemented with IAP had decreased permeability and inflammatory cytokine expression after exposure to LPS ex vivo when compared to formula fed controls.

CONCLUSIONS

Our results support that IAP is beneficial to preterm intestine and decreases intestinal injury and inflammation caused by LPS.

Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003

In the present study we show that luxS of Bifidobacterium breve UCC2003 is involved in the production of the interspecies signaling molecule autoinducer-2 (AI-2), and that this gene is essential for gastrointestinal colonization of a murine host, while it is also involved in providing protection against Salmonella infection in Caenorhabditis elegans. We demonstrate that a B. breve luxS-insertion mutant is significantly more susceptible to iron chelators than the WT strain and that this sensitivity can be partially reverted in the presence of the AI-2 precursor DPD. Furthermore, we show that several genes of an iron starvation-induced gene cluster, which are downregulated in the luxS-insertion mutant and which encodes a presumed iron-uptake system, are transcriptionally upregulated under in vivo conditions. Mutation of two genes of this cluster in B. breve UCC2003 renders the derived mutant strains sensitive to iron chelators while deficient in their ability to confer gut pathogen protection to Salmonella-infected nematodes. Since a functional luxS gene is present in all tested members of the genus Bifidobacterium, we conclude that bifidobacteria operate a LuxS-mediated system for gut colonization and pathogen protection that is correlated with iron acquisition.

Gut microbiota and allergic disease: new findings

PURPOSE OF REVIEW

Disturbed gut colonization patterns are proposed to be associated with the development of allergic disease.

RECENT FINDINGS

Studies using new systems biology methods confirm previous findings that early environmental exposures, for example cesarean delivery, are associated with disturbed gut colonization patterns and reduced microbial diversity. Low microbial diversity in infancy is also observed to precede onset of allergic disease. In a large population-based cohort study, probiotic consumption in pregnancy was associated with reduced risk of eczema and rhinoconjunctivitis in the child, but not asthma. The association between probiotics and rhinoconjunctivitis appeared stronger if both mother and child (from 6 months) consumed probiotics. Follow-up data from primary prevention studies with probiotics do not support a role for probiotics in asthma prevention. In meta-analyses, both prebiotics (high-risk infants only) and probiotics modestly reduce the eczema risk, but no other allergic manifestations. Their use is not generally recommended for prevention, or treatment, of allergic disease.

SUMMARY

Gut microbial patterns are associated with susceptibility to allergic disease, but the incomplete understanding of what constitutes a healthy gut microbiota that promotes tolerance, remains a challenge. Further understanding of gut microbial functions may pave the way for more effective allergy prevention and treatment strategies.

Predictors of full enteral feeding achievement in very low birth weight infants

BACKGROUND

To elucidate the role of prenatal, neonatal and early postnatal variables in influencing the achievement of full enteral feeding (FEF) in very low birth weight (VLBW) infants and to determine whether neonatal intensive care units (NICUs) differ in this outcome.

METHODS

Population-based retrospective cohort study using data on 1,864 VLBW infants drawn from the "Emilia-Romagna Perinatal Network" Registry from 2004 to 2009. The outcome of interest was time to FEF achievement. Eleven prenatal, neonatal and early postnatal variables and the study NICUs were selected as potential predictors of time to FEF. Parametric survival analysis was used to model time to FEF as a function of the predictors. Marginal effects were used to obtain adjusted estimates of median time to FEF for specific subgroups of infants.

RESULTS

Lower gestational age, exclusive formula feeding, higher CRIB II score, maternal hypertension, cesarean delivery, SGA and PDA predicted delayed FEF. NICUs proved to be heterogeneous in terms of FEF achievement. Newborns with PDA had a 4.2 days longer predicted median time to FEF compared to those without PDA; newborns exclusively formula-fed had a 1.4 days longer time to FEF compared to those fed human milk.

CONCLUSIONS

The results of our study suggest that time to FEF is influenced by clinical variables and NICU-specific practices. Knowledge of the variables associated with delayed/earlier FEF achievement could help in improving specific aspects of routine clinical management of VLBW infants and to reduce practice variability.

External influence of early childhood establishment of gut microbiota and subsequent health implications

Postnatal maturation of immune regulation is largely driven by exposure to microbes. The gastrointestinal tract is the largest source of microbial exposure, as the human gut microbiome contains up to 10(14) bacteria, which is 10 times the number of cells in the human body. Several studies in recent years have shown differences in the composition of the gut microbiota in children who are exposed to different conditions before, during, and early after birth. A number of maternal factors are responsible for the establishment and colonization of gut microbiota in infants, such as the conditions surrounding the prenatal period, time and mode of delivery, diet, mother's age, BMI, smoking status, household milieu, socioeconomic status, breastfeeding and antibiotic use, as well as other environmental factors that have profound effects on the microbiota and on immunoregulation during early life. Early exposures impacting the intestinal microbiota are associated with the development of childhood diseases that may persist to adulthood such as asthma, allergic disorders (atopic dermatitis, rhinitis), chronic immune-mediated inflammatory diseases, type 1 diabetes, obesity, and eczema. This overview highlights some of the exposures during the pre- and postnatal time periods that are key in the colonization and development of the gastrointestinal microbiota of infants as well as some of the diseases or disorders that occur due to the pattern of initial gut colonization.

Bacterial colonization and intestinal mucosal barrier development

The intestinal tract is colonized soon after birth with a variety of ingested environmental and maternal microflora. This process is influenced by many factors including mode of delivery, diet, environment, and the use of antibiotics. Normal intestinal microflora provides protection against infection, ensures tolerance to foods, and contributes to nutrient digestion and energy harvest. In addition, enteral feeding and colonization with the normal commensal flora are necessary for the maintenance of intestinal barrier function and play a vital role in the regulation of intestinal barrier function. Intestinal commensal microorganisms also provide signals that foster normal immune system development and influence the ensuing immune responses. There is increasingly recognition that alterations of the microbial gut flora and associated changes in intestinal barrier function may be related to certain diseases of the gastrointestinal tract. This review summarizes recent advances in understanding the complex ecosystem of intestinal microbiota and its role in regulating intestinal barrier function and a few common pediatric diseases. Disruption in the establishment of a stable normal gut microflora may contribute to the pathogenesis of diseases including inflammatory bowel disease, nosocomial infection, and neonatal necrotizing enterocolitis.

Lactobacillus acidophilus alleviates platelet-activating factor-induced inflammatory responses in human intestinal epithelial cells

Probiotics have been used as alternative prevention and therapy modalities in intestinal inflammatory disorders including inflammatory bowel diseases (IBD) and necrotizing enterocolitis (NEC). Pathophysiology of IBD and NEC includes the production of diverse lipid mediators, including platelet-activating factor (PAF) that mediate inflammatory responses in the disease. PAF is known to activate NF-κB, however, the mechanisms of PAF-induced inflammation are not fully defined. We have recently described a novel PAF-triggered pathway of NF-κB activation and IL-8 production in intestinal epithelial cells (IECs), requiring the pivotal role of the adaptor protein Bcl10 and its interactions with CARMA3 and MALT1. The current studies examined the potential role of the probiotic Lactobacillus acidophilus in reversing the PAF-induced, Bcl10-dependent NF-κB activation and IL-8 production in IECs. PAF treatment (5 µM×24 h) of NCM460 and Caco-2 cells significantly increased nuclear p65 NF-κB levels and IL-8 secretion (2-3-fold, P<0.05), compared to control, which were blocked by pretreatment of the cells for 6 h with L. acidophilus (LA) or its culture supernatant (CS), followed by continued treatments with PAF for 24 h. LA-CS also attenuated PAF-induced increase in Bcl10 mRNA and protein levels and Bcl10 promoter activity. LA-CS did not alter PAF-induced interaction of Bcl10 with CARMA3, but attenuated Bcl10 interaction with MALT1 and also PAF-induced ubiquitination of IKKγ. Efficacy of bacteria-free CS of LA in counteracting PAF-induced inflammatory cascade suggests that soluble factor(s) in the CS of LA mediate these effects. These results define a novel mechanism by which probiotics counteract PAF-induced inflammation in IECs.