Microbiota Of Healthy Children Research Articles

Gut microbiota in chronic liver diseases in children

The impact of gut microbiota on the development of various diseases is of great interest to researchers. However, data on the taxonomic diversity of the intestinal microbiota in chronic liver diseases in children are lacking.Purpose. To study the taxonomic diversity of the fecal microbiota in children with chronic liver diseases in comparison with healthy patients.Material and methods. A metagenomic analysis of the intestinal microbiota of 24 children with chronic liver diseases (mean age 10.3 ± 4.7 years) was carried out with the isolation of the target fragment of the 16S rRNA gene. The group included 18 children with autoimmune liver diseases and 6 children with non-autoimmune liver diseases. The comparison group consisted of fecal samples of 34 apparently healthy children.Results. The conducted study revealed 684 types of microorganisms in the studied samples of patients’ feces. An analysis of the conducted studies showed that fecal samples of healthy children and patients with chronic liver diseases differ in bacterial diversity. The dominant taxa in healthy children were Neisseria flavescens, in patients with chronic liver diseases, the dominant taxa were Bifidobacterium longum, Bifidobacterium adolescentis, Blautia massiliensis. At the same time, Bifidobacterium longum, Bifidobacterium adolescentis, Blautia massiliensis in fecal samples of patients with chronic liver diseases was 8 times as high.Conclusion. Studies have shown differences in the composition of the intestinal microbiota in healthy children and children with chronic liver diseases.

Gut Microbiota in Stunted Children

Stunting is a condition of failure to thrive in children under five which is characterized by a lack of height compared to other children of their age. Although there was a decrease in the proportion of stunting from 37.2% in 2013 to 30.8% in 2018, this figure is still far from the target of WHO, which is 20%. In stunted children, there is a change in the intestinal microbiota which causes disruption of nutrient absorption, leading to malnutrition. The microbiota in healthy children contains many probiotic species such as Bifidobacterium longum and Lactobacillus mucosae, while in stunted children there are many inflammogenic taxa such as the genus Desulfovibrio. the order of Campylobacterales, E. coli, Firmicutes, Proteobacteria, and Bacterioides.

Gut Microbiota Profiles in Children and Adolescents with Psychiatric Disorders.

The aim of our work is to summarize the current state of knowledge on gut microbiota differences in children and adolescents with psychiatric disorders. To find the relevant articles, the PubMed, Web of Science, and Google Scholar databases were searched. Articles in English presenting original data and comparing the composition of gut microbiota in child psychiatric patients with gut microbiota in healthy children and adolescents were selected. Finally, we identified 55 articles eligible for our purpose. The majority of patients with autism spectrum disorders (ASD) were investigated. A smaller number of studies evaluating the gut microbiota in children and adolescents with attention-deficit/hyperactivity disorder (ADHD), Rett syndrome, anorexia nervosa, depressive disorder (DD), and tic disorders were found. The main findings of this research are discussed in our review, focusing on the age-related gut microbiota specificity for psychiatric disorders and the differences between individual diagnosis. To conclude, the gut microbiota in children and adolescents with psychiatric disorders is evidently different from that in controls. The most pronounced differences are seen in children with ASD, less in ADHD. Moreover, the changes are not identical to those in adult psychiatric patients, as Ruminococcus, Turicibacter, and Bilophila were increased in adults, and decreased in children with ASD, and Parabacteroides and Alistipes were more frequently represented in adults, but less frequently represented in children with depression. The available data suggest some genera have a different abundance in individual psychiatric disorders (e.g., Bilophila, Bifidobacterium, Clostridium, Coprococcus, Faecalibacterium, and Ruminococcus), suggesting their importance for the gut–brain axis. Other bacterial genera might be more important for the pathophysiology of specific disorder in children and adolescents, as Akkermansia and Desulfovibrio for ASD, or Romboutsia for DD. Based on the research findings, we assume that gut microbiota corrections have the potential to improve clinical symptoms in psychiatric patients.

Development of the gut microbiota in healthy children in the first ten years of life: associations with internalizing and externalizing behavior

ABSTRACT Background Increasing evidence indicates that psychopathological disorders are associated with the gut microbiota. However, data are largely lacking from long-term longitudinal birth cohorts, especially those comprising low-risk healthy individuals. Therefore, this study aims to describe gut microbiota development in healthy children from birth till age 10 years, as well as to investigate potential associations with internalizing and externalizing behavior. Results Fecal microbial composition of participants in an ongoing longitudinal study (N = 193) was analyzed at 1, 3 and 4 months, and 6 and 10 years of age by 16S ribosomal RNA gene sequencing. Based on these data, three clusters were identified in infancy, two of which were predominated by Bifidobacterium. In childhood, four clusters were observed, two of which increased in prevalence with age. One of the childhood clusters, similar to an enterotype, was highly enriched in genus-level taxon Prevotella_9. Breastfeeding had marked associations with microbiota composition up till age 10, implying an extended role in shaping gut microbial ecology. Microbial clusters were not associated with behavior. However, Prevotella_9 in childhood was positively related to mother-reported externalizing behavior at age 10; this was validated in child reports. Conclusions This study validated previous findings on Bifidobacterium-enriched and -depleted clusters in infancy. Importantly, it also mapped continued development of gut microbiota in middle childhood. Novel associations between gut microbial composition in the first 10 years of life (especially Prevotella_9), and externalizing behavior at age 10 were found. Replications in other cohorts, as well as follow-up assessments, will help determine the significance of these findings.

Gut Microbiota Dysbiosis Associated With Altered Production of Short Chain Fatty Acids in Children With Neurodevelopmental Disorders.

While gut microbiota dysbiosis has been linked with autism, its role in the etiology of other neurodevelopmental disorders (NDD) is largely underexplored. To our knowledge this is the first study to evaluate gut microbiota diversity and composition in 36 children from the Republic of Serbia diagnosed with NDD and 28 healthy children. The results revealed an increased incidence of potentially harmful bacteria, closely related to Clostridium species, in the NDD patient group compared to the Control group: Desulfotomaculum guttoideum (P < 0.01), Intestinibacter bartlettii (P < 0.05), and Romboutsia ilealis (P < 0.001). On the other hand, significantly lower diversity of common commensal bacteria in the NDD group of patients was noticed. Enterococcus faecalis (P < 0.05), Enterococcus gallinarum (P < 0.01), Streptococcus pasteurianus (P < 0.05), Lactobacillus rhamnosus (P < 0.01) and Bifidobacteria sp. were detected in lower numbers of patients or were even absent in some NDD patients. In addition, butyrate-producing bacteria Faecalibacterium prausnitzii (P < 0.01), Butyricicoccus pullicaecorum (P < 0.05), and Eubacterium rectale (P = 0.07) were less frequent in the NDD patient group. In line with that, the levels of fecal short chain fatty acids (SCFAs) were determined. Although significant differences in SCFA levels were not detected between NDD patients and the Control group, a positive correlation was noted between number of rDNA amplicons obtained with universal primers and level of propionic acid, as well as a trend for levels of total SCFAs and butyric acid in the Control group. This correlation is lost in the NDD patient group, indicating that NDD patients' microbiota differs from the microbiota of healthy children in the presence or number of strong SCFA-producing bacteria. According to a range-weighted richness index it was observed that microbial diversity was significantly lower in the NDD patient group. Our study reveals that the intestinal microbiota from NDD patients differs from the microbiota of healthy children. It is hypothesized that early life microbiome might have an impact on GI disturbances and accompanied behavioral problems frequently observed in patients with a broad spectrum of NDD.

The Study of the Nasopharynx Microbiota in Healthy Children of Different Age Groups by Gas Chromatography

The Study of the Nasopharynx Microbiota in Healthy Children of Different Age Groups by Gas Chromatography

The characterization of bacterial communities of oropharynx microbiota in healthy children by combining culture techniques and sequencing of the 16S rRNA gene

The high incidence of bacterial respiratory infections has led to a focus on evaluating the human respiratory microbiome. Studies based on culture-based and molecular methods have shown an increase in the bacterial community that includes the bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria in the oropharynx of healthy individuals. Therefore, recognizing this microbial compound and subsequently identifying those carriers of specific pathogens can be of great help in predicting future infections and their control. In this prospective study, we sought to characterize the bacterial communities of the respiratory microbiome in healthy children aged between 3 and 6 years old by combining both cultural techniques and sequencing of the 16S rRNA gene. Seventy-seven oropharynx samples using Dacron swabs were collected from 77 healthy children in the kindergartens of Ilam, Iran. Bacterial identification was performed by phenotypic methods and in house developed PCR-based sequencing (the V1–V9 hypervariable region of the bacterial 16S ribosomal RNA gene). In total, 346 bacterial isolates were characterized based on phenotypic and sequencing-based molecular methods. The 3 most predominant phyla were Firmicutes (74%), Proteobacteria (22%), and Actinobacteria (4%). At the level of the genus, Staphylococci (coagulase-positive and coagulase-negative) and Streptococci were dominant. Also, the most commonly identified potentially pathogenic colonisers were S. aureus (75%), Enterobacteriaceae spp. (40.1%), and A. baumannii (15.6%). The present study identified 3 phyla and 9 family of bacteria in the oropharyngeal microbiome. Remarkably, the presence of potential pathogenic bacteria in the nasopharynx of healthy children can predispose them to infectious diseases, and also frequent exposure to human respiratory bacterial pathogens are further risk factors.

Maturation of the Oral Microbiome in Caries-Free Toddlers: A Longitudinal Study

Understanding the development of the oral microbiota in healthy children is of great importance to oral and general health. However, limited data exist on a healthy maturation of the oral microbial ecosystem in children. Moreover, the data are biased by mislabeling “caries-free” populations. Therefore, we aimed to characterize the healthy salivary and dental plaque microbiome in young children. Caries-free (ICDAS [International Caries Detection and Assessment System] score 0) children (n = 119) and their primary caregivers were followed from 1 until 4 y of child age. Salivary and dental plaque samples were collected from the children at 3 time points (T1, ~1 y old; T2, ~2.5 y old; and T3, ~4 y old). Only saliva samples were collected from the caregivers. Bacterial V4 16S ribosomal DNA amplicons were sequenced using Illumina MiSeq. The reads were denoised and mapped to the zero-radius operational taxonomic units (zOTUs). Taxonomy was assigned using HOMD. The microbial profiles of children showed significant differences (P = 0.0001) over time. Various taxa increased, including Fusobacterium, Actinomyces, and Corynebacterium, while others showed significant decreases (e.g., Alloprevotella and Capnocytophaga) in their relative abundances over time. Microbial diversity and child-caregiver similarity increased most between 1 and 2.5 y of age while still not reaching the complexity of the caregivers at 4 y of age. The microbiome at 1 y of age differed the most from those at later time points. A single zOTU (Streptococcus) was present in all samples (n = 925) of the study. A large variation in the proportion of shared zOTUs was observed within an individual child over time (2% to 42% of zOTUs in saliva; 2.5% to 38% in dental plaque). These findings indicate that the oral ecosystem of caries-free toddlers is highly heterogeneous and dynamic with substantial changes in microbial composition over time and only few taxa persisting across the 3 y of the study. The salivary microbiome of 4-y-old children is still distinct from that of their caregivers.

Application of culture-based, mass spectrometry and molecular methods to the study of gut microbiota in children

In recent decades, nucleic acid sequencing technologies used for metagenomic analysis have become the main methods for assessing the composition of microbiota. At the same time, the use of novel methods of cultivation and identification of microorganisms in microbiological research led to the renaissance of culture-based technologies, because facilitated the discovery and isolation of both new strains of well-known microorganisms as well as uncultivated and unexplored bacterial taxa. The aim of this study was to evaluate the potential of using the culture-based method for the assessment of the qualitative and quantitative composition of the intestinal microbiota in healthy children. Eleven growth media were inoculated with serial dilutions of stool samples in order to analyze the profile of dominant anaerobic bacteria, as well as aerobic bacteria and fungi in 20 healthy children aged 2–4 years. The identification of microorganisms was performed using MALDI TOF MS and 16S rRNA gene fragment sequencing were used. 1,819 isolated and identified strains belong to 7 phyla, 13 classes, 18 orders, 33 families, 77 genera and 149 species in the Bacteria domain. The Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria phyla were most abundant and frequent. The greatest species diversity (more than 85 species) was found in the Firmicutes phylum. Ten new previously uncharacterized bacterial strains were isolated.

The airway microbiota in early cystic fibrosis lung disease.

Infection plays a critical role in the pathogenesis of cystic fibrosis (CF) lung disease. Over the past two decades, the application of molecular and extended culture-based techniques to microbial analysis has changed our understanding of the lungs in both health and disease. CF lung disease is a polymicrobial disorder, with obligate and facultative anaerobes recovered alongside traditional pathogens in varying proportions, with some differences observed to correlate with disease stage. While healthy lungs are not sterile, differences between the lower airway microbiota of individuals with CF and disease-controls are already apparent in childhood. Understanding the evolution of the CF airway microbiota, and its relationship with clinical treatments and outcome at each disease stage, will improve our understanding of the pathogenesis of CF lung disease and potentially inform clinical management. This review summarizes current knowledge of the early development of the respiratory microbiota in healthy children and then discusses what is known about the airway microbiota in individuals with CF, including how it evolves over time and where future research priorities lie.

P778 Microbial characterization of paediatric inflammatory bowel disease and stratification into disease severity groups

Background: Imbalance in the faecal microbiota with a reduction in biodiversity; dysbiosis, has been identified in inflammatory bowel disease (IBD). Our aim was to study and compare the faecal microbiota in paediatric patients with newly diagnosed untreated IBD with the microbiota of healthy children and paediatric patients with gastrointestinal symptoms but no IBD. We also aimed at studying the microbiota related to IBD subgroups and treatment. Methods: Faecal samples were collected from 235 children and adolescents. Eighty had Crohn's disease (CD), 27 ulcerative colitis (UC) and 3 IBD unclassified, 50 were non-IBD patients and 75 were healthy children between two and 18 years. The microbiota was analysed using a 16s rRNA DNA based test with the GA-map technology, measuring probe signal intensity (PSI) of 54 DNA probes targeting 300 bacteria on different taxonomic levels. Using non-parametric methods, we selected six probes where the PSI was lower in IBD compared to non-IBD patients. For each of these six probes, IBD patients were given 1 point if their PSI was lower than the median PSI value of non-IBD patients. The points were summarized as a Score ranging from 0–6 points. Logistic regression was used to model possible associations between this Score and risk of having IBD. Results: Most bacterial PSI were reduced in IBD and non-IBD patients (p<0.001) compared to healthy controls. IBD patients had reduced abundance of Firmicutes (Eubacterium, p=0.006; Holdemanella, p=0.038), Tenericutes and Bacteroidetes (Parabacteroidetes p=0.02), p=0.002, and Bifidobacterium, p=0.02, compared to the non-IBD patients. CD patients had lower abundance of Mycoplasma (p=0.045) than UC patients. IBD patients with extensive disease (L3/E3) had more Clostridiales (Ruminococcus gnavus), p=0.02, and CD patients with L3 had more Proteobacteria, p=0.04, than patients with limited disease. IBD patients who later received TNF blockers, 64/110, had lower diversity at baseline for Firmicutes, Tenericutes (Mycoplasma, p=0.009), and Bacteroidetes, p=0.015, compared to IBD patients who were treated with conventional medications, 46/110. Patients who reached 3 or more points using the Score were 2.2 times more likely to have IBD compared to non-IBD (OR=2.1, 95% CI 1.1–4.5, p=0.027). Conclusions: Microbiota profiles may be of value for stratification of paediatric IBD into diagnostic and prognostic subgroups. A severe dysbiotic microbiota profile in newly diagnosed IBD is associated with a severe phenotype with more extensive disease and subsequent need of TNF blocker treatment.

Variations of oral fluid microbiota in healthy children and adolescents

The aim of the study was to establish the bacterial and viral associations of saliva and the immune resistance in 127 healthy people of different ages. The analysis sorted out three variants of oral fluid microbiota differing by certain combination of indigenous and facultative microflora. It was found that with age there is a significant increase in the number of adolescents with the third variant of the microbiota, characterized by a decrease in the number of indigenous microflora and increase in opportunistic microorganisms and viruses. With an increase in microecological shifts a tendency to decrease the level of lysozyme, an increase in the number of secretory IgA, accompanied by a decrease in antibody was revealed. It has been shown that bacterial and viral component of the microbiota of the oral fluid are in a dynamic relationship with each other, as well as immune resistance and can serve as an indicator of the health level and the selection criteria at the stages of clinical examination of children and adolescents, with the risk of dental disease.

Disruption of the microbiota across multiple body sites in critically ill children.

BackgroundDespite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets.ResultsBacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1–9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of “dominant” pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient.ConclusionsWe conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0211-0) contains supplementary material, which is available to authorized users.

Microbiota and infant development

Microbiome Malnutrition in children is a persistent challenge that is not always remedied by improvements in nutrition. This is because a characteristic community of gut microbes seems to mediate some of the pathology. Human gut microbes can be transplanted effectively into germ-free mice to recapitulate their associated phenotypes. Using this model, Blanton et al. found that the microbiota of healthy children relieved the harmful effects on growth caused by the microbiota of malnourished children. In infant mammals, chronic undernutrition results in growth hormone resistance and stunting. In mice, Schwarzer et al. showed that strains of Lactobacillus plantarum in the gut microbiota sustained growth hormone activity via signaling pathways in the liver, thus overcoming growth hormone resistance. Together these studies reveal that specific beneficial microbes could potentially be exploited to resolve undernutrition syndromes. Science , this issue p. [10.1126/science.aad3311][1], p. [854][2] [1]: /lookup/doi/10.1126/science.aad3311 [2]: /lookup/doi/10.1126/science.aad8588

Composition and stability of intestinal microbiota of healthy children within a Dutch population.

Numerous diseases linked to microbial imbalance can be traced back to childhood, illustrating the impact of the juvenile microbiota development from infancy toward adulthood. However, knowledge on this subject is currently very limited. The primary aim of this study was to characterize composition and short- and long-term stability of the intestinal microbiota in healthy children. Between November 2011 and June 2014, 61 children 2 to 18 yr of age from different areas in The Netherlands were included and instructed to collect fecal samples weekly, for 6 wk, and a follow-up sample after 18 mo. The intergenic spacer profiling technique (IS-pro) was used to analyze all available fecal samples. Microbial diversity was calculated by the Shannon diversity index and individual compositional stability by comparing all collection time points. Microbial stability varied per phylum (P< 0.0005), declined rapidly in a short time period, and subsequently stabilized on the long run with very gradual variation, leading to an overall compositional stability of 70% on average over a period of 18 mo. Higher species diversity was correlated to a higher overall compositional stability (P< 0.001). We observed an age-independent bacterial shared core consisting of a limited number of species. In conclusion, in this study, we showed that microbial composition stability in children varied per phylum, at both short-term and long-term intervals. Healthy children seem to share a microbiome core consisting of a limited number of species.-De Meij, T. G. J., Budding, A. E., de Groot, E. F. J., Jansen, F. M., Kneepkens, C. M. F., Benninga, M. A., Penders, J., van Bodegraven, A. A., Savelkoul, P. H. M. Composition and stability of intestinal microbiota of healthy children within a Dutch population.

Sa1985 Short-Term and Long-Term Stability of the Intestinal Microbiota in Healthy Children

Sa1985 Short-Term and Long-Term Stability of the Intestinal Microbiota in Healthy Children