Keywords
microbiota - gastrointestinal - allergy - asthma - immune
Human infants are born with a naive and immature immune system. The maturation of
immune system during infancy is evidenced by an induction of a pathogen-specific immune
response while maintaining immunological tolerance to dietary components and commensal
microbes.[1] The gastrointestinal tract is the largest immunological tissue in human body and
is colonized with a complex microbial community that induce regulatory T cells (Th3
and Th1 cells) via production of suppressive cytokines, transforming growth factor-β
(TGF-β), and/or interleukin-10 (IL-10), which help to guide a balanced T helper 1
(Th1) and T helper 2 (Th2) response.[1]
[2] Failure to develop a balance between immune tolerance and active immune response
is hypothesized to contribute to immune-related disorders, such as allergy (Th2 mediated)
and inflammatory bowel disease (IBD) (Th1 mediated).[3]
[4] In addition, the gut microbiota also stimulates mucosal IgA secretion, produces
antibacterial substances, and enhances tight junction of the intestinal barrier, which
protect against pathogen invasion in the gut.[5] Thus, cross talk between intestinal epithelium cells and resident microbiota promotes
the immune homeostasis and maturation.[6]
Colonization of the infant gut is initially dominated by facultative anaerobes, such
as enterobacteria, enterococci, lactobacilli, and streptococci, followed by anaerobic
microbes, such as Bacteroides, bifidobacteria, clostridia, and eubacteria.[7] By 1 year of age, the infant gut microbiota resembles a complex adult-like pattern.[8] Development of infant gut microbiota is influenced by prenatal exposure; gestational
age; mode of delivery; feeding type; pre-, pro-, and antibiotic use; and host genetics.
Alteration of gut microbiota by environmental factors may contribute to the development
of immune-related disorders in genetically susceptible infants.[9]
[10] Herein, the environment factors influencing the gut microbiota development ([Fig. 1]) and the relationship between the gut microbiota and immune-related diseases in
childhood ([Fig. 2] and [Table 1]) will be reviewed. In addition, the potential for prevention and intervention of
several important diseases that develop in early life by pre/probiotics supplementation
will be presented.
Table 1
Associations between gut microbiota changes and immune-mediated disorders in childhood
|
Immune-mediated disorders
|
Change in gut microbiota
|
|
Asthma
|
↑ Clostridium difficile
[72]
↑ Bacteroides fragilis subgroup and Clostridium coccoides subcluster XIVa[76]
|
|
Eczema
|
↓ Bacterial diversity[91]
[92]
[93]
↑ B. pseudocatenulatum, Escherichia coli, and C. difficile
[72]
[90]
|
|
Food allergy (cow milk allergy)
|
↑ Total and anaerobic bacteria and ↓ yeast count[100]
↑ C. coccoides group and Atopobium cluster[101]
↑ Bacterial metabolic products, e.g., butyric acid and BCFA[101]
|
|
NEC
|
↑ γ-Proteobacteria and ↓ Firmicutes[32]
↑ Citrobacter-like sequences and Enterococcus-like sequences[110]
Enterobacter associated with NEC[112]
No significant differences between NEC and control[111]
|
|
IBD
|
↑ Aerobic and facultative anaerobic bacteria[118]
↑ γ-Proteobacteria,[117] e.g., adhesive-invasive E. coli
[119]
↓ Clostridia, e.g., Faecalibacterium, Bacteroides, e.g., B. vulgatus and bifidobacteria[115]
[116]
[118]
|
|
IBS
|
↑ γ-Proteobacteria, Haemophilus, and Dorea
[130]
↓ Eubacterium and Anaerovorax
[130]
↑ Veillonella, Prevotella, Lactobacillus, and Parasporobacterium in children with IBS-D[131]
↓ Bifidobacterium and Verrucomicrobium in children with IBS-D[131]
|
Abbreviations: IBD, inflammatory bowel disease; IBS, irritable bowel syndrome; IBS-D,
diarrhea-predominant irritable bowel syndrome; NEC, necrotizing enterocolitis; BCFA,
branched-chain fatty acids.
Figure 1 Factors influencing the development of gut microbiota in early infancy.
Figure 2 Impact of environmental factors on the colonization of gut microbiota and immune-related
disorders. Abbreviations: IBD, inflammatory bowel diseases; IBS, irritable bowel syndrome;
NEC, necrotizing enterocolitis.
Factors Influencing the Development of the Gut Microbiota
Factors Influencing the Development of the Gut Microbiota
Prenatal Exposure
It is commonly stated that newborns are born with a sterile gastrointestinal tract,
and are rapidly colonized by microbes obtained from their mothers and the surrounding
environment during and after birth.[7] However, as early as 1936, Snyder isolated bacteria, such as Lactobacillus acidophilus, Streptococcus pyogenes, and S. mitis, from the first meconium sample of 3 out of 29 infants within 30-minute after delivery.[11] Recently, the presence of bacterial isolates and/or DNA, such as lactic acid bacteria,
Enterococcus, Staphylococcus, and Bifidobacterium, has been documented in meconium,[12] amniotic fluid,[13]
[14] fetal membranes,[15] umbilical cord blood,[16] and placenta[17]
[18] of the healthy mothers and infants, without any clinical signs of infection or inflammation.
These findings suggest that fetuses are not sterile and that prenatal transmission
of bacteria from mother to fetus exists in healthy pregnancies.[12]
[19]
Although the mechanism of transfer in humans is still unclear, a genetically labeled
Enterococcus faecium strain orally inoculated to pregnant mice was detected in amniotic fluid and in meconium
of the pups,[12]
[16] indicating that maternal gut microbes might be the origin of the first colonizers
in fetal gut.[12] Additionally, dendritic cells in Peyer patches penetrate the junctions between gut
epithelial M cells to directly take up bacteria from maternal gut lumen, and then
enter into the lymphatic and blood circulation. Once in the circulation, the bacteria
may be transferred to the fetus cross placental barrier, and initiate the first colonization
of fetal gut.[19]
[20] Furthermore, other studies found that bacteria in the maternal mouth could reach
the amniotic fluid via the bloodstream, particularly in the presence of gingivitis
or periodontitis during pregnancy.[21] Taken together, these studies support the concept that the maternal microbiota seeds
prenatal colonization of the human infant gut, which may stimulate the fetal intestinal
mucosal immune system in utero.[20]
[22]
Gestational Age
Postconceptional age at delivery is another factor affecting infant gut microbial
colonization. The gut microbiota of preterm infants is often colonized more slowly,
has higher interindividual variability and lower diversity than that of healthy full-term
infants.[23]
[24] The early colonizers in preterm infant gut are often potential pathogens, such as
Escherichia coli, Streptococcus, Enterococcus, Staphylococcus, Klebsiella, and Clostridium species.[23]
[25]
[26]
[27] The beneficial bacteria, for example, Bifidobacterium and Lactobacillus, which are commonly found in healthy full-term infants, were rarely detected or were
present at low numbers in the stool of preterm infants.[25]
[26]
[28] The delayed colonization and reduced diversity of gut microbiota in preterm infants
might be due to the aseptic environment, the neonatal intensive care unit, and delayed
oral feeding.[29]
[30] In addition, the extensive use of antibiotics in preterm infants may also be an
important factor causing the disturbance of gut microbiota,[26]
[29] and may consequently lead the preterm infant to be more susceptible to gastrointestinal
disorders and disease, such as necrotizing enterocolitis (NEC).[31]
[32]
Delivery Mode
How an infant is delivered is also associated with the early colonization of microbiota.
A recent study compared the fecal microbiota of newborn infants within 24 hours of
delivery with the microbiota of their mother' skin, oral mucosa, and vagina by 16S
rDNA pyrosequencing[33] and showed that the fecal bacterial composition of vaginally delivered (VD) infants
was most similar to that of vaginal communities of the mothers, with Lactobacillus, Prevotella, and Atopobium spp. predominating. In contrast, the fecal bacterial composition of cesarean delivery
(CsD) infants was most similar to the maternal skin, with an abundance of Staphylococcus and Corynebacterium. Thus, initial colonization is determined to a large extent by the first abundant
microbes that an infant counters, from maternal vagina, feces, or skin. In addition,
the microbiota of CsD infants is less diverse than that of VD infants at 3 days of
age.[34] There was an absence of Bifidobacterium spp. in the stool of CsD infants, whereas VD infant stool was predominated by Bifidobacterium longum and B. catenulatum.[34] In another study, CsD infants had lower numbers of Bifidobacterium and Bacteroides fragilis group, and were more often colonized with Clostridium difficile compared with VD infants.[35] Although differences in early microbiota between CsD and VD infants are well documented,
the long-term impact of early colonization on subsequent childhood immune development
and disease outcomes are not fully understood and shown to be investigated in a long-term
prospective cohort study.
Diet
Feeding mode is one of the most important determinants of gut microbial diversity;
however, its impact on the infant microbiota is often contradictory. Many studies
have shown that breastfed (BF) infants are colonized mainly by Bifidobacterium, while formula-fed (FF) infants harbor a more diverse microbiota, including Bacteroides, clostridia, Enterococcus, and Enterobacteriaceae in addition to Bifidobacterium.[36]
[37] Other studies have shown that Bifidobacterium are found equally often and in similar counts in BF and FF infants.[38] These inconsistencies may arise from the different analytical approaches used in
enumerating the microbiota or the variability in the composition of the human milk
and infant formula that the infants are consuming and geographically distinct infant
groups.
Differences in microbial diversity between BF and FF infants may reflect the prebiotic
effects of the large quantity of structurally diverse human milk oligosaccharides
(HMO),[39] which are negligible in bovine milk and infant formula.[40] The HMO can function as prebiotics to stimulate the growth of specific gut bacteria,
including Bifidobacterium and Bacteroides species in vitro.[41]
[42] Moreover, human milk contains bacteria such as Staphylococcus, Streptococcus, Bifidobacterium, and Lactobacillus
[43] that may serve as a diverse and continuous source of live microbes for the infant
gut.
Introduction of solid food causes rapid and sustained alterations in the gut microbiota
of infants. Koenig et al catalogued the gut microbiome of one infant over 2.5-year
period by 16S rDNA pyrosequencing and found that introduction of table foods to the
diet of the BF infant at approximately 5 months of age induced a sustained increase
in the abundance of Bacteroidetes.[44] Fallani et al examined the composition of fecal microbiota of 531 infants before
weaning and 4 weeks after the introduction of first solid food by fluorescence in
situ hybridization (FISH) and reported that weaning significantly increased the proportion
of Clostridium coccoides and C. leptum groups but decreased Bifidobacterium, Enterobacteria, C. perfringens, and C. difficile.[45]
Pre-, Pro-, and Antibiotics
The composition of the infant's gut microbiota can be influenced by the use of prebiotics,
probiotics, and antibiotics. A prebiotic is defined as “a selectively fermented ingredient
that results in specific changes, in the composition and/or activity of the gastrointestinal
microbiota, thus conferring benefit(s) upon host health.”[46] Several groups have reported that supplementation of infant formula with prebiotics
affected the composition of the gut microbiota.[47]
[48]
[49] For example, infants fed an infant formula containing a combination of 90% short-chain
galactooligosaccharides (scGOS) and 10% long-chain fructooligosaccharides (lcFOS)
had increased fecal bifidobacteria and lactobacilli counts.[47]
[49] Investigations into the effect of prebiotic supplementation during pregnancy on
the composition of neonatal microbiota are rare. In a randomized, double-bind, placebo-controlled
trail, supplementation of 9 g/d scGOS and lcFOS (9:1 ratio) to mothers in the last
trimester of pregnancy resulted in an increase in the relative abundances of bifidobacteria
and lactobacilli in the maternal gut, with no effect on the gut microbiota of their
offspring.[50] A limitation of the study was that only bifidobacteria and lactobacilli were investigated,
and the impact of maternal prebiotic treatment on other bacteria remained unknown.
Furthermore, the authors did not separate BF from FF infants; therefore, the lack
of effect of the prebiotic supplementation to the mother on infant stool could be
due to the HMO consumed by the BF infants.
According to FAO/WHO,[51] probiotics are “live microorganisms which, when consumed in adequate amounts, confer
a health benefit on the host.” A recent Finnish study investigated probiotic administration
to the mother on the infant's microbiota at 6 months of age using FISH and quantitative
PCR (qPCR).[52] The gut microbiota of BF infants whose mothers received Lactobacillus rhamnosus LPR together with B. longum BL999 for 2 months before and 2 months after delivery had higher abundance of lactobacilli,
enterococci and lower counts of Bifidobacterium compared with infants of mothers receiving a placebo treatment. When the same probiotic
combination was administered directly to German FF infants for 4 months, the effect
of the probiotics on microbiota composition was minor; however, Bifidobacterium bifidum count was lowered compared with the placebo group, which is consistent with the previous
study.
In contrast, antibiotics exert detrimental effects on infant microbiota composition.
Using terminal restriction fragment length polymorphism (T-RFLP) analysis and qPCR,
Tanaka et al[53] monitored the impact of cephalexin exposure in the first 4 days of life on the development
of intestinal microbiota. Cephalexin-treated infants had reduced overall diversity,
with a specific reduction of Bifidobacterium and overgrowth of Enterococcus and Enterobacteriaceae in the first month of life compared with untreated infants.[53] Whether antibiotic administration to the mother affects the microbiota of their
infant has also been studied. If a mother was treated with ampicillin and gentamicin
within 48 hours of birth, her infant had a higher proportion of Proteobacteria and
a lower proportion of Actinobacteria and genus Lactobacillus 4 weeks after the cessation of treatment compared with infants of untreated mothers.
Importantly, the Proteobacteria level remained elevated in the infants of treated
mothers 8 weeks posttreatment, suggesting long-term effects on microbial populations.[54]
Host Genetics
The earliest study to show a relationship between host genotype and gut microbiota
in children was conducted in 1983 using cultivation-dependent methods, and found that
the fecal microbiota of monozygotic (MZ) twin siblings was more similar than that
of dizygotic (DZ) twin siblings.[55] Later studies revealed higher similarity of gut microbiota in MZ twins than in DZ
twins and/or unrelated individuals.[56]
[57] Palmer et al also found that the gut microbiota was more similar in DZ twins than
in unrelated children at any stage of development over the first year of life.[8] In contrast, Turnbaugh et al reported that the similarity of fecal microbiota in
MZ twin pairs was not different from that in DZ twin pairs as assessed by next generation16S
rDNA pyrosequencing.[58] Although the results of twins studies appear equivocal, other studies have confirmed
that the gut microbiota of genetically related children is more similar than those
of unrelated individuals,[8]
[56]
[58] indicating that host genetics must play an important role in the selection and colonization
of gut microbes in humans.
Clear evidence linking host genetics and the microbiota has been obtained in mice.
Work in a mouse advanced intercross line originating from a cross between C57BL/6J
and an ICR-derived outbred line mice demonstrated a relationship between host genetics
and the “core measurable microbiota (CMM)” of 64 conserved taxonomic groups that varied
quantitatively across most animals.[59] Testing of the CMM abundances for cosegregation with 530 fully informative single
nucleotide polymorphism (SNP) markers identified 18 host quantitative trait loci (QTL)
that showed significant or suggestive genome-wide linkage with relative abundances
of specific microbial taxa. Some of the loci controlled individual microbial species,
several controlled groups of related taxa, and others had putative pleiotropic effects
on groups of distantly related organisms. Recently, the same group showed that microbial
diversity was influenced by both environmental and host genetic factors and was associated
with several polygenic diseases in BXD recombinant inbred mice.[60] The gut microbial composition differed among BXD strains and linkage analysis defined
QTLs that were either restricted to a particular taxon or that influenced the variation
of taxa across phyla. A QTL region on chromosome 4 that overlapped several interferon
genes modulated the population of Bacteroides, and potentially Bacteroidetes and Firmicutes—the predominant BXD gut phyla. Irak4,
a signaling molecule in the Toll-like receptor pathways, was a candidate for the QTL
on chromosome15 that modulated Rikenellaceae, whereas TGF-β3, a cytokine that modulates intestinal barrier function and tolerance
to commensal bacteria, overlapped a QTL on chromosome 12 that influenced Prevotellaceae. These findings provide clear evidence for the importance of host genetics in shaping
microbiome diversity and contribute to our understanding of the host factors that
govern the assemblages of gut microbiota associated with complex diseases in mice.
Interaction between the Gut Microbiota, Immunity, and Immune-Related Disorders
Interaction between the Gut Microbiota, Immunity, and Immune-Related Disorders
The gut microbiota plays important roles in shaping the immune system during infancy.
The commensal microbes and their products interact with immune cells to create and
maintain host tolerance and influence both innate and adaptive immune response.[61]
[62]
[63] Mounting evidence shows that dysbiosis is associated with the development of immune-mediated
diseases, such as allergy, irritable bowel syndrome (IBS), NEC, and IBD.
Allergic Diseases
The prevalence of allergic diseases has been increasing in industrialized countries
over the past few decades.[64]
[65] The dichotomy in the rate of allergic diseases between industrialized and developing
countries suggests that environmental changes associated with a western lifestyle
are the major factor in the development of allergic diseases.[66]
[67] In 1988, Strachan first introduced the “hygiene hypothesis,” which states that lack
of early microbial exposure increases susceptibility to allergic diseases by suppressing
natural development of the immune system.[68] Numerous epidemiologic and clinical studies have demonstrated that the composition
of the gut microbiota differs between allergic and nonallergic children, even before
the emergence of symptoms.[69]
[70]
[71]
[72] Gut microbes induce regulatory T cells that influence Th1 and Th2 balance and help
prevent aberrant immune response.[73] Therefore, an alternative hypothesis, that is, the “microbiota hypothesis,” has
been generated, which proposes that alteration of the gut microbiota due to antibiotic
use, diet, or lifestyle changes disrupts the normal microbially mediated mechanisms
of immunological tolerance, leading to an increase in the incidence of allergic diseases
including asthma, eczema, and food allergy in later childhood.[74]
[75]
Asthma, a chronic inflammatory disorder of the airway, is often thought to be caused
by a combination of genetic and environmental factors. A prospective birth cohort
study that analyzed nearly 1,000 infants reported that differences in gut microbiota
in the first month of life was predictive of subsequent development of recurrent wheeze
at 2 years of age, and C. difficile was particularly associated with the increase of asthma.[72] In another study, Vael et al identified B. fragilis subgroup and C. coccoides subcluster XIVa in the gut microbiota of infants as early indicators of risk of asthma
later in life.[76]
There is growing interest in exploring which environmental exposures influence the
development of asthma via modulation of gut microbiota. For example, CsD infants had
a higher risk of asthma compared with VD infants,[77]
[78] and were more frequently colonized by the asthma-associated pathogen, C. difficile.[35] van Nimwegen et al, who first explored the delivery mode–gut microbiota–asthma pathway
confirmed that the effect of CsD on asthma development was mediated by C. difficile in the gut.[79] Use of antibiotics in early life is another factor associated with the increased
risk for wheeze or asthma,[80]
[81] apparently by suppressing commensal gut bacteria and causing the growth of pathogens,
for example, C. difficile. In mice, Vancomycin in early life disrupted the microbiota and enhanced susceptibility
to ovalbumin-induced asthma.[82] In contrast to the adverse effect of CsD and antibiotics on gut microbiota and asthma,
breastfeeding favors beneficial bacteria colonization in the infant gut, for example,
Bifidobacterium, and protects against asthma in later childhood.[83]
[84] However, the protection afforded by breastfeeding was not observed in infants whose
mother has atopic diseases.[85]
[86] One possible reason may be related to low amount of bifidobacteria in the breast
milk of allergic mothers, which may have caused their infants to concurrently have
lower counts of bifidobacteria in the gut,[87] and possibly greater susceptibility to asthma in later childhood.
Eczema (atopic dermatitis) is a chronic, inflammatory skin diseases, affecting at
least 10% of U.S. children, and its prevalence has increased over the past a few decades.[88]
[89] A study performed in the Netherlands with 957 infants documented that E. coli and C. difficile in feces at 1 month of age was associated with higher risk of developing eczema,[72] while Gore et al compared Bifidobacterium spp. in the feces of infants at 3 to 6 months of age and showed that B. pseudocatenulatum was more commonly detected in the feces of children with eczema.[90] Using temperature gradient gel electrophoresis and T-RFLP, Wang et al examined overall
patterns of fecal microbial colonization in healthy (n = 20) and atopic (n = 15) infants and found that infants who developed eczema had significantly lower
fecal bacterial diversity at 1 week of age than infants who remained healthy for 18
months.[91] Others have confirmed that a less diverse intestinal microbiota in early life was
associated with an increased risk of eczema.[92]
[93] Thus, diversity of the gut microbiota in early childhood may be more important than
an altered prevalence of particular bacterial species for the increasing incidence
of eczema. Recently, studies have investigated the association between environmental
factors that influences the colonization of microbiota and eczema. For example, a
multicenter, multicountry cross-sectional study (Phase III of ISAAC) of 193,412 children
showed an association between antibiotic use in the first year of life and symptoms
of eczema in 6- and 7-year-old children.[94] The impact of feeding mode on the development of eczema was also studied, but the
results are controversial. Several studies showed exclusive breastfeeding for at least
3 months protected against the development of eczema in infants with a family history
of atopy.[95]
[96] Other studies have not found a protective role of breastfeeding and some found that
breastfeeding increased the risk of eczema.[97]
[98]
Food allergy is defined as an adverse immune reaction to a food protein, such as those
found in milk, egg, and wheat, which causes dermatitis, gastrointestinal, and respiratory
disorders.[99] Several studies have shown an association between altered gut microbiota and the
development of food allergy. A prospective study that compared the fecal microbiota
of children immediately after diagnosis of cow milk allergy found higher amounts of
total and anaerobic bacteria and lower yeast counts[100] compared with healthy children. Furthermore, using FISH combined with flow cytometry,
the same group found that the amount of C. coccoides group and Atopobium cluster and bacterial metabolic products, butyrate and branched-chain fatty acids,
were higher in children with cow milk allergy compared with healthy infants.[101] In addition, a germfree (GF) mouse model of cow milk allergy revealed that GF mice
were more responsive than conventional mice to oral sensitization and challenge with
β-lactoglobulin,[102] while GF mice colonized with an infant fecal microbiota, which was dominated by
Bifidobacterium and Bacteroides, were protected against cow milk allergy via the mechanism of increasing foxp3 gene
expression, which is the master regulatory molecule in Treg cell function.[103] It has been proposed that changes in gut microbiota resulting from CsD might correlate
to the increased risk of developing food allergy in children. Some studies found that
CsD children have a higher risk of food allergy,[61]
[104] while other studies did not detect significant association between delivery mode
and prevalence of food allergy[105] in offspring of atopic mothers.[106]
[107] Thus, the impact of CsD and other environmental factors on gut microbiota and food
allergy should be further investigated in prospective trials.
Necrotizing Enterocolitis
NEC is a major cause of morbidity and mortality in low-birth-weight infants, afflicting
7% of infants weighing less that 1,500 g, with a mortality rate of 20 to 30%.[108] Preterm delivery is the main risk factor for NEC, presumably due to immaturity of
gastrointestinal motility, barrier function, and immune defense. Enteral feeding with
infant formula constitutes another important risk factor, whereas breast milk is protective
against NEC.[108]
[109] The gut bacteria have been shown to be causative for NEC in animal models and dysbiosis
is associative with NEC in preterm infants.[32]
[110]
[111]
[112] Although several bacteria, viruses, and fungi have been found to cause NEC in human
and animal studies, no single change or even pattern of change in the gut microbiota
has been consistently identified as a risk factor for NEC.[108] Even investigations conducted by the same research group using the same sequencing
approach (454 pyrosequencing) have shown differences in the microbial signatures associated
with NEC. For example, Mshvildadze et al detected Citrobacter-like sequences only in cases with NEC and an increased frequency of Enterococcus-like sequences in cases with Klebsiella in control subjects.[110] However, in a subsequent publication,[32] one of the bacterial signatures detected more frequently in NEC cases matched closest
to γ-Proteobacteria and the same Citrobacter-like sequences were not detected in infants with NEC. In a prospective single-center
case–control study, Norman et al mapped the bacterial composition of fecal samples
from 20 extremely preterm infants (10 NEC and 10 matched healthy controls). No significant
differences were observed between NEC and controls; however, a higher Bacillales and
Enterobacteriaceae relative abundance was detected at early time points in infants who developed NEC,
while healthy controls were more dominated by Enterococcus.[111] Stewart et al found that bacterial community structures in infants with NEC and
late onset sepsis differed from healthy preterm infants. The presence of Enterobacteria
and Staphylococcus was associated with the development of NEC and late onset sepsis, respectively.[112] Differences in these studies are likely due to the fact that NEC represents a clinical
scenario that can arise from several bacterial etiologies that can vary among neonatal
intensive care unit and that most studies involved a limited number of subjects (6–40
cases and controls). Overall, the clinical evidence suggests that NEC does not result
from growth of a single causative pathogen, but rather that the disease results from
a generalized disturbance of normal colonization patterns in the developing gut.[108] However, findings of prospective studies documented detectable changes in the microbiota
of infants before the onset of NEC.[32]
[112] Mai et al found phyla-level shifts in fecal microbial signatures of infants who
developed NEC that occurred between 1 week and 3 days before the diagnosis of NEC.[32] Using principal coordination analysis to study bacterial community structure, Stewart
et al demonstrated that profiles from healthy infants were distributed separately
from those infants with NEC and/or late onset sepsis, and samples collected before
NEC onset also showed a distinct cluster.[112] These findings suggest that bacterial changes may trigger alterations in host immunity
and/or barrier function that subsequently lead to the clinical signs and symptoms
of NEC.
Inflammatory Bowel Disease
IBDs, including Crohn disease (CD) and ulcerative colitis (UC), are chronic inflammation
of the small bowel and/or colon leading to recurrent diarrhea and abdominal pain.
Complex interactions between host genetics, mucosal immune system, and enteric microbes
are thought to underlie the development of IBD.[113] Differences in the composition of the gut microbiota between IBD patients and healthy
control have been shown, leading to the hypothesis that dysbiosis could contribute
to the etiology and pathogenesis of IBD.[114] Two studies comparing the fecal microbiota of children with CD and UC with healthy
controls using culture-based methods, combined with qPCR and T-RFLP, found that the
overall fecal microbiota diversity was reduced in CD patients, with specific reductions
in the number of commensal bacteria, such as Faecalibacterium, Bacteroides and bifidobacteria, and increased number of E. coli compared with healthy children. No major changes were detected in UC patients, except
for a decrease in bifidobacteria in the active state of UC.[115]
[116] Recently, Michail et al confirmed these results in patients with severe UC. The
fecal microbial diversity was lower in UC children with a reduction in clostridia
and an increase in γ-Proteobacteria compared with healthy controls.[117] Several studies have examined the mucosal-associated microbiota in subjects with
IBD and also showed similar results. Conte et al found a higher number of aerobic
and facultative anaerobic bacteria in ileal, cecal, and rectal biopsies from children
with IBD and a decrease in Bacteroides vulgatus.[118] Negroni et al also detected two adhesive-invasive E. coli strains in the inflamed tissues of children with IBD, further supporting their role
in the pathogenesis of IBD.[119] Several environmental factors may contribute to the risk of IBD in childhood. A
Danish national cohort study showed that CsD was associated with increased risk of
IBD at age 0 to 14 years,[120] while a German case–control study including 2,000 children and young adolescents
did not find any association between delivery mode and IBD.[121] In terms of early nutrition, two systemic reviews using meta-analysis showed that
breastfeeding was associated with lower risk of UC and CD in childhood.[122]
[123] In contrast, antibiotic use in early life has been shown to associate with a high
risk of IBD development,[124]
[125]
[126] although most studies found an association with antibiotic use only in children
with CD, not in UC children.[125]
[126]
[127] For additional information on the influence of environmental factors on the development
of pediatric IBD, readers are referred to a recent review by Aujnarain et al.[128]
Irritable Bowel Syndrome
IBS is a functional bowel disorder characterized by abdominal pain or discomfort that
is associated with altered bowel habit.[129] The pathophysiology of IBS is poorly understood; however, changes in the composition
of gut microbiota have been linked to IBS.[130]
[131] Saulnier et al compared fecal microbiota of patients with IBS and healthy controls
by 16S rDNA pyrosequencing and microarray, and reported that children with IBS had
a greater abundance of the class γ-Proteobacteria compared with controls. Furthermore,
genera of Haemophilus and Dorea were increased, while Eubacterium and Anaerovorax were reduced in IBS children.[130] Rigsbee et al investigated the fecal microbiota of children with diarrhea-predominant
IBS. Compared with healthy subjects, higher levels of Veillonella, Prevotella, Lactobacillus, and Parasporobacterium and lower levels of Bifidobacterium and Verrucomicrobium were found in children with IBS.[131] Few studies have examined the link between environmental factors that impacts the
colonization of microbiota and IBS; however, a prospective community-based study found
that subjects who were given a course of antibiotics were more than three times as
likely to report more functional bowel symptoms 4 months later than nonantibiotic-treated
controls.[132]
Prebiotics and Probiotics on the Prevention and Treatment of Immune-Related Disease
Prebiotics and Probiotics on the Prevention and Treatment of Immune-Related Disease
Allergic Disease
The literature surrounding probiotics and allergic diseases is equivocal, which may
be related to considerable variations in the probiotic strains used, daily doses administered,
and the timing of administration.[133] Several meta-analyses have evaluated probiotics for prevention of eczema in children,
and most of studies involved combined pre- and postnatal treatment.[133]
[134] The majority of combined pre- and postnatal studies demonstrated that probiotics
reduced incidence of eczema during first 2 years of life, but a few studies found
that probiotics had no beneficial effect on eczema.[133] Most studies examining either prenatal or postnatal probiotic treatment found no
eczema-preventative effect,[135]
[136]
[137] except one study that reported a reduced incidence of eczema after postnatal treatment
with L. paracasei F19.[138] Several studies showed that administration of probiotics was associated with reduced
eczema severity (SCORing Atopic Dermatitis, SCORAD) in children with eczema[139]
[140]; however, other studies did not show any effect of probiotics on the incidence or
severity of eczema.[141]
A few studies investigated the role of probiotics on asthma and most of these reported
that probiotics had no effect on the prevention or treatment of asthma/wheezing during
first 2 years of life.[134] Clinical trials of probiotics for the treatment of food allergy are limited and
no protective effect has thus far been reported.[133] A meta-analysis that reviewed the effect of prebiotics given to infants for the
prevention of eczema and asthma reported a significant reduction in eczema and asthma
in infants at high risk of allergy up to 2 years of age; however, no protective effect
was found when children were not selected for allergy risk.[142] Thus, future randomized, controlled, double-blind studies to examine the efficacy
of probiotics for both prevention and treatment of food allergies are warranted.
Inflammatory Bowel Diseases
Probiotics have been used in the treatment of IBD in children; however, their efficacy
is inconsistent. In a small, open-label pilot study, Gupta et al showed that Lactobacillus GG (LGG) administered to children with mildly to moderately active, but stable, CD
improved gut barrier function and clinical status.[143] However, in a later randomized clinical trial, administration of LGG to children
with CD in remission for 2 years did not show any efficacy of LGG compared with placebo
treatment.[144] Studies conducted on the effects of probiotics in CD in adults have also shown negative
results.[145]
[146]
In contrast, the efficacy of probiotics in UC seems to be better than in CD. Miele
et al[147] conducted the first pediatric randomized, placebo-controlled trial in which children
with a newly diagnosed UC received either a highly concentrated mixture of probiotic
bacterial strains (VSL#3 containing L. paracasei, L. plantarum, L. acidophilus, L. delbrueckii subsp. bulgaricus, B. longum, B. breve, B. infantis, and Streptococcus salivarius subsp. thermophiles) or a placebo in conjunction with concomitant steroid induction and mesalamine maintenance
treatment. Children treated with VSL#3 had a significantly higher rate of remission
and a lower incidence of relapse within 1 year of follow-up compared with the placebo
group.[147] The efficacy of VSL#3 in inducing/maintaining the UC remission was also confirmed
by an open-label pilot study in children[148] and in clinical trials in adults.[149]
[150] In addition to oral administration, rectal infusion of L. reuteri in children with active distal UC reduced mucosal inflammation and changed mucosal
cytokine expression.[151] Thus, a consensus for “Probiotic Use-2011 update” recommended the use of probiotics,
such as VSL#3, for maintaining remission of UC,[152] while there is no basis for recommending the use of probiotics in CD.[153]
A few pilot studies have examined the use of prebiotics, such as inulin,[154] germinated barley foodstuff,[155] and FOS[156] in the treatment of IBD in adults and showed similarly positive results; however,
no study in children has been reported and the efficacy of prebiotics remains to be
further investigated in clinical trials.
Irritable Bowel Syndrome
The effect of probiotics on the treatment of IBS in adults has been studied extensively,
but data in children are limited and the results are inconsistent.[157]
[158] Several reports indicated that probiotic treatment had no effect on global symptoms
of IBS in children[159]; however, recent studies demonstrated improvement of symptoms following probiotics.[160]
[161] For example, in a randomized, double-blind, placebo-controlled trial in 141 children
with IBS or functional pain, LGG significantly reduced the frequency and severity
of abdominal pain in children with IBS.[160] In contrast to probiotics, few studies investigated prebiotics on IBS[158] and to our knowledge, no data in children were reported. Several studies suggested
that supplementation of low dose of prebiotics, for example, FOS or GOS, may be effective,
while high doses may have a negative impact on symptoms. A recent study advised that
reducing intake of fermentable carbohydrates, including FOS and GOS, may actually
improve symptom in IBS.[162]
Necrotizing Enterocolitis
Probiotic use to reduce NEC has been the subject of several recent reviews.[163]
[164]
[165] A 2011 Cochrane review based on 16 trials (2,842 infants) concluded that enteral
probiotic supplementation to preterm infants less than 2,500 g birth weight significantly
reduced the incidence of severe NEC (stage II or more) and mortality.[163] Based on the 2011 Cochrane review, the American Pediatric Surgical Association Outcomes
and Clinical trial Committee advised the use of probiotics to decrease the incidence
of NEC.[164] However, recently published clinical guidelines from the American Society for Parenteral
and Enteral Nutrition did not support the use of probiotics in infants at risk for
NEC, and suggested that further studies are necessary to determine the most effective
type(s) of probiotic, effective dosage, and duration of treatment.[165] Studies of prebiotics on the prevention of NEC are rare, and, to the best of our
knowledge, there is no clinical evidence supporting the use of prebiotics to prevent
NEC.[166]
[167]
Conclusions and Future Needs
Conclusions and Future Needs
Accumulating evidence provides strong associations between the gut microbiota, dysregulation
of mucosal and systemic immune function, and increased risk of immune-related diseases
in children. However, these relationships are multifaceted and are mediated through
a complex interaction between the child's genetic background, which dictates the child's
risk for developing the disorder and the composition of his/her microbiota and pre-,
peri-, and postnatal environmental factors. Most of these environmental factors are
amenable to clinical intervention, for example, reducing preterm births, CsD, and
the use of antibiotics and promoting breastfeeding and potentially pre- and probiotics.
However, to maximize the clinical benefit, a richer understanding of the causal relationships
among these factors and the incidence and severity of the immune-related disease is
needed.
In general, a reduction in overall bacterial diversity, reduced abundance of commensal
bacteria, and increased abundance of potentially pathogenic bacteria has been associated
with the immune-related disorders reviewed herein. In some cases, specific bacteria
have been identified in cases versus controls ([Table 1]); however, there is a lack of consistency between studies, which may be attributable
to the small numbers of subjects included in most studies, differences in analytical
approaches; even among 16s rDNA-based approaches (qPCR, DGGE, T-RFLP, 454 Pyrosequencing)
and between Pyrosequencing and next generation sequencing technologies. To better
define the role of the microbiota, researchers are encouraged to work together in
multicenter prospective trials and to incorporate randomized, placebo-controlled,
double-blind study design into future clinical interventions, testing the efficacy
of pre- and probiotic interventions. In addition, future investigations should extend
beyond descriptions of the composition of the fecal microbiota to incorporate metagenomic
and metatranscriptomic analyses, which will provide insight into microbial metabolism.
Investigations into the gut virome and fungiome may also provide unique insights into
the additional aspects of dysbiosis, underlying disease onset and severity. Additionally,
coordinate analysis of host–microbe interactions are needed in both health and disease.
For example, using exfoliated epithelial cells, recent work in our laboratory has
shown relationship between host intestinal gene expression[168] and bacterial metagenome virulence factors in BF and FF infants.[169] This noninvasive approach facilitates investigations into host–microbiome interactions
in infants and children and is also amenable to longitudinal studies of cases of chronic
inflammation—for example, relationships between gut gene expression and bacterial
composition and gene expression could be investigated during phases of disease activity
or clinical remission in IBD or responses before and after pre- or probiotic treatments
could be assessed. Finally, based on research in rodent models demonstrating genome-wide
linkage with relative abundances of specific microbial taxa, future research investigating
specific disease-related QTL and the composition of the microbiota are warranted in
children with diseases such as IBD.
