The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7–12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA). Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity. Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.
Historically, the gold standard for diagnosing small intestinal bacterial overgrowth (SIBO) has been quantitative culture of jejunal aspirate. However this test is costly and invasive. More commonly in clinical practice the glucose hydrogen breath test (GHBT) is used. We aimed to determine which clinical features and baseline laboratory investigations indicate a high likelihood of SIBO as defined by positive GHBT.
Methods
We undertook a retrospective analysis of records for all patients referred for GHBT at a single teaching hospital over a 13-year period 1998–2010. Data collected included age, sex, baseline and peak hydrogen levels, previous surgical procedures, comorbidities, haemoglobin levels, vitamin B12, folate, ferritin and albumin levels. A positive result was a rise in hydrogen of at least 20 ppm, or methane of 12 ppm, over the baseline for each gas.
Results
447 patients were identified (120 male, median age 56 years, range 17–90). Overall 84/447 (18.8%) of tests were positive. The patient characteristics associated with a positive result were concurrent use of proton pump inhibitor (PPI) (p=0.0005), previous partial gastrectomy (p<0.0001), previous right hemicolectomy (p=0.0004), and age over 75 tears p<0.0001. The laboratory investigations predictive of a positive result were low vitamin B12 (p=0.02) and low albumin <30 g/dl (p=0.03).
Conclusion
This is the largest single centre study of factors predictive of SIBO as defined by positive GHBT. Use of proton pump inhibitor, partial gastrectomy, right hemicolectomy, age over 75 years, low vitamin B12 and low albumin were predictive of SIBO.
Abstract This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS). Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain. 3. Perform functional gut metagenomics by evaluation of whole community gene expression profiles and discovery of disease-specific pathway signatures. Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies included 454 pyrosequencing-based strategies to sequence 16S rRNA genes and understand the detailed composition of microbes in healthy and disease groups. Microarray-based hybridization with the PhyloChip and quantitative real-time PCR (qPCR) probes were applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 Demo project, from a set of healthy and IBS children (7-12 yo) may enable the identification of core microbiomes in children, in addition to variable components that may distinguish healthy from diseased pediatric states. Twenty-two children with IBS and twenty-two healthy children were enrolled and analyzed in the UH2 phase of this study. The planned enrollment targets for the UH2/3 phases include 50 healthy children, 50 children with FAP and 50 children with IBS (minimum of 3 time points per child). We are currently analyzing the dataset for the presence of disease-specific signatures in the human microbiome, and correlating these microbial signatures with pediatric health or IBS disease status in addition to IBS subtype (e.g., diarrhea-vs constipation-predominant). In the next phase, whole genome shotgun sequencing and metatranscriptomics will be performed with a subset of children in each group. This study explores the nature of core and variable human microbiome in pre-adolescent healthy children and children with IBS.
KEGG pathways differing in the functional metagenomic profiles of GI communities from healthy children and adults. Between-group differences were evaluated with Whiteâ s non-parametric t-tests and Storeyâ s false discovery rate corrections. (TIF 15.5 kb)
A prospective, placebo-controlled, triple blind clinical trial was carried out in Pakistan to determine the effect of Lactobacillus GG on the course of acute diarrhea in hospitalized children. Forty children (mean age, 13 months) were enrolled and after rehydration received either oral Lactobacillus GG (n = 21) or placebo (n = 19) twice daily for 2 days, in addition to the usual diet. The clinical course of diarrhea was followed during the treatment period. Features on admission into the study groups were similar and were characterized by severe diarrhea, malnutrition and inappropriate management before presentation. Response was evident on Day 2 when the frequency of both vomiting and diarrhea was less in the Lactobacillus group. In those who had presented with acute nonbloody diarrhea (n = 32), the percentage of children with persistent watery diarrhea at 48 hours was significantly less in the Lactobacillus group: 31% vs. 75% (P < 0.01). No significant difference was observed by 48 hours in those presenting with bloody diarrhea. The relevance of this finding to the management of diarrhea in the tropics is discussed.
Small intestine bacterial overgrowth (SIBO) has been proposed as a cause of altered small bowel motility both in irritable bowel syndrome (IBS) and coeliac disease. The glucose hydrogen breath test (GHBT) is most commonly used in practice to diagnose SIBO. The aim of this study was to assess the prevalence of SIBO using GHBT in coeliac disease and IBS.
Methods
Group A comprised patients with biopsy-proven, untreated coeliac disease (n=44, 14 male, median age 47 y, range 18–75). Group B comprised patients with IBS (n=207, 55 male, median age 53 y, range 17–90). Group C comprised controls (n=47, 9 male, median age 58 years, range 20–74). All had GHBT performed on a normal, gluten containing diet. In the coeliac group this was repeated after a median of 180 days on a gluten-free diet (GFD). None had antibiotics in the 4 weeks prior to testing. A positive result was a rise in hydrogen of at least 20 ppm, or methane of 12 ppm, over the baseline for each gas.
Results
6/44 (13.6%) with coeliac disease had a positive result. 30/207 (14.5%) patients with IBS had a positive breath test. 1/47 (2.1%) controls tested positive. Patients with coeliac disease (p=0.05) and IBS (p=0.02) were significantly more likely than controls to have a positive GHBT. In the coeliac group positive GHBT was associated with male sex but no other features. There were no associated features in groups B and C. Patients with coeliac disease had lower baseline hydrogen levels (9.4 ppm±8) compared with IBS patients (13.4 ppm±13.7) (p=0.07) and controls (16.6 ppm±18.0) (p=0.025). In the coeliac group 4/6 with a positive result had a significant rise in methane but not hydrogen. At repeat testing all four were persistently methane positive but the absolute peak methane levels had fallen from a mean of 64 ppm to a mean of 49 ppm. Only one coeliac subject had a positive GHBT that normalised on GFD.
Conclusion
The prevalence of SIBO diagnosed by GHBT is similar in IBS and coeliac disease. SIBO is significantly more common in IBS and coeliac disease than in controls. The prevalence of SIBO in coeliac disease may not vary between treated and untreated disease. Despite this increased prevalence of SIBO in coeliac disease and IBS, the failure of prevalence to fall following GFD may suggest that neurodysmotility is not the method for symptoms in these patients.
This project explores the nature of the human intestinal microbiome in healthy children and children with recurrent abdominal pain. The overall goal is to obtain a robust knowledge base of the intestinal microbiome in children without evidence of pain or gastrointestinal disease and in those with recurrent abdominal pain (functional abdominal pain (FAP) and FAP associated with changes in bowel habits, i.e., irritable bowel syndrome or IBS). Specific aims include: 1. Characterize the composition of the gut microbiome in healthy children by DNA sequencing. 2. Determine the presence of disease-specific organism signatures of variable gut microbiomes in children with recurrent abdominal pain. 3. Perform functional gut metagenomics by evaluation of whole community gene expression profiles and discovery of disease-specific pathway signatures. Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies included 454 pyrosequencing-based strategies to sequence 16S rRNA genes and understand the detailed composition of microbes in healthy and disease groups. Microarray-based hybridization with the PhyloChip and quantitative real-time PCR (qPCR) probes were applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 Demo project, from a set of healthy and IBS children (7-12 yo) may enable the identification of core microbiomes in children, in addition to variable components that may distinguish healthy from diseased pediatric states. Twenty-two children with IBS and twenty-two healthy children were enrolled and analyzed in the UH2 phase of this study. The planned enrollment targets for the UH2/3 phases include 50 healthy children, 50 children with FAP and 50 children with IBS (minimum of 3 time points per child). We are currently analyzing the dataset for the presence of disease-specific signatures in the human microbiome, and correlating these microbial signatures with pediatric health or IBS disease status in addition to IBS subtype (e.g., diarrhea-vs constipation-predominant). In the next phase, whole genome shotgun sequencing and metatranscriptomics will be performed with a subset of children in each group. This study explores the nature of core and variable human microbiome in pre-adolescent healthy children and children with IBS.
Hybrid de novo assembly of Illumina/Nanopore sequence data produced complete circular sequences of the chromosome and a plasmid for the multidrug-resistant Pseudomonas aeruginosa Houston-1 strain. This provides a high-quality representative sequence for a lineage endemic to a pediatric cystic fibrosis care center at Texas Children's Hospital.
