The Human Gut Microbiome and Recurrent Abdominal Pain in Children

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, children with functional abdominal pain, and children with abdominal pain and changes in bowel habits (irritable bowel syndrome). Multiple strategies have been deployed to navigate and understand the nature of the intestinal microbiome in childhood. These strategies include 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 are being applied as complementary strategies to gain an understanding of the intestinal microbiome from various perspectives. Data collected and analyzed during the HMP UH2 and UH3 Demo project, from a set of healthy and IBS children may enable the identification of core microbiomes in children in addition to variable components that may distinguish healthy from diseased pediatric states. 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. This study explores the nature of core and variable human microbiomes in pre-adolescent healthy children and children with recurrent abdominal pain.

• Study Design:
  • Metagenomics
• Study Type:
  • Case-Control
• Total number of consented subjects: 69
• Subject Sample Telemetry Report (SSTR)

• BioProject
• PubMed
• Sequence Read Archive
• BioSample
• MeSH
• PMC

Inclusion Criteria:

Children aged 7-12 years of age who either have IBS or FAP or are healthy without complaints (Controls).

IBS:

1. Minimum of 1 healthcare visit for abdominal pain.
2. Minimum number of pain episodes of at least once per month, for three consecutive months within the year prior to enrolling in study.
3. Pain episodes have been severe enough to cause functional impairment; or have prompted medication use; or have been rated moderate to severe (≥ 3/10).
4. Symptoms current.
5. Less than 95th percentile blood pressure for age.

Controls:

1. Asymptomatic with regards to abdominal pain and without significant chronic health issues.
2. Less than 95% blood pressure for age

Exclusion Criteria:

IBS/FAP:

1. Organic disease that accounts for abdominal pain.
2. Child currently taking an anti-inflammatory medication, or if their abdominal pain responded to an anti-inflammatory medication in the past.
3. Child currently taking medication for reflux to which abdominal pain symptoms are responding.
4. Other chronic health condition or chronic illness (except mild intermittent or mild persistent asthma).
5. Cognitive impairment significantly below average age and/or grade level.
6. Vomiting ≥ 2 times per month within 3 months prior to enrolling on study.
7. Unintentional weight loss of ≥ 5% body weight within 3-month period.
8. Females who have menses.
9. Use of the following drugs within the last 6 months: systemic antibiotics, oral, intravenous, intramuscular, nasal or inhaled corticosteroids, cytokines, methotrexate or immunosuppressive cytotoxic agents, or large doses of commercial probiotics (10e8 cfu per day or higher).
10. Major diet change in the past month prior to enrollment (e.g., change to vegetarianism or vice versa; avoidance or inclusion of major food group [fruit, vegetables]). This does not include diet changes related to lactose intolerance.
11. Major surgery including surgery involving the gastrointestinal tract.

Controls:

1. Other chronic illness or health condition or chronic illness (except mild intermittent or mild persistent asthma)
2. Cognitive impairment significantly below average age and/or grade level
3. Child seen a physician more than once in past year for abdominal pain unexplained by common illness (e.g., gastroenteritis)
4. Females who have menses
5. Use of the following drugs within the last 6 months: systemic antibiotics, oral, intravenous, intramuscular, nasal or inhaled corticosteroids, cytokines, methotrexate or immunosuppressive cytotoxic agents, or large doses of commercial probiotics (10e8 cfu per day or higher).
6. Major diet change in the past month prior to enrollment (e.g., change to vegetarianism or vice versa; avoidance or inclusion of major food group [fruit, vegetables]). This does not include diet changes related to lactose intolerance.
7. Major surgery including surgery involving the gastrointestinal tract.
8. Non-English speaking parent or child.

This study is part of the NIH Road Map Human Microbiome Project. The first subject was enrolled on August 2009. The first phase of the study enrolled 26 Pediatric IBS (PIBS) and 22 Pediatric Control (PCtrl) subjects. 4 PIBS dropped out of the study. Multiple samples were collected from some of the subjects at 2-3 month intervals. 22 PCtrl were samples collected as follows: 17 were sampled once (1x), 1 was sampled twice (2x), and 5 were sampled three times (3x). PIBS subjects were collected as follows: 13 - 1x, 3 - 2x, 6 - 3x. Data analysis has been completed for these 71 samples representing 22 PCtrl and 22 PIBS. These 71 samples have been sequenced (454) and analyzed by phylochip (55) and qPCR. The UH3 portion of the study has currently enrolled a total of 1 Pediatric IBS (PIBS), 28 Pediatric Control (PCtrl) and 3 Pediatric FAP (PFAP) subjects. 1 PCtrl and 1 PFAP have been excluded by the time of the study description submittal. Three (3) samples per subject are being collected at 2 month intervals. 19 PCtrl (7 - 1x; 2 - 2x; 10 - 3x), 1 PIBS (1 - 2x) and 2 PFAP (1 - 2x; 1 - 3x) (5 samples) subjects have submitted samples for a total of 49 samples. These samples have been extracted for 16S rRNA gene sequencing (454). Of these, 46 samples have been sequenced and are currently in the pipeline for data analysis. Additional samples are currently being collected and processed and will be submitted for 16S rRNA gene sequencing. Deep 16S rRNA, WGS, and meta-RNA analysis will be performed on samples chosen from the UH3 samples. Sequence data from the UH2 and UH3 samples will be combined and submitted for in-depth analysis.

• Primary Phenotype: Irritable Bowel Syndrome
• Digestive System Diseases
• Abdominal Pain

• Principal Investigator
  • James Versalovic, MD, PhD. Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA.
• Funding Source
  • 1UH3DK083990-02. National Institutes of Health, Bethesda, MD, USA.
• Co-Investigator Clinical
  • Robert J. Shulman, MD. Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA.
• Clinical Research Coordinator III
  • Erica Weidler Baimbridge. Baylor College of Medicine, Houston, TX, USA.
• Clinical Research Coordinator II
  • Michelle Rubio-Gonzales. Baylor College of Medicine, Houston, TX, USA.
• Instructor responsible for sample preparation and logistics, data analysis
  • Jennifer Spinler, PhD. Baylor College of Medicine, Houston, TX, USA.
  • Ruth Ann Luna, PhD. Baylor College of Medicine, Houston, TX, USA.
• Responsible for data analysis, data management and logistics. Biostatistician, Bioinformatician
  • Toni-Ann Mistretta, PhD. Baylor College of Medicine, Houston, TX, USA.
• Instructor responsible for data analysis, WGS, metatranscriptomics analysis development. Bioinformatician
  • Emily B. Hollister, PhD. Baylor College of Medicine, Houston, TX, USA.
• Bioinformatician, Data Analyst, Pipeline Development
  • Kevin Riehle, MS. Baylor College of Medicine, Houston, TX, USA.
• Database design and management, Data Analyst
  • Sabeen Raza, MS. Baylor College of Medicine, Houston, TX, USA.
• Postdoctoral Associate Sample Preparation, qPCR, Data Analysis
  • Maria Alejandra Diaz, PhD. Baylor College of Medicine, Houston, TX, USA.
• Bioinformatician
  • Cristian Coarfa, PhD. Baylor College of Medicine, Houston, TX, USA.
• Other Collaborator Pipeline Development
  • Aleksandar Milosavljevic, PhD. Baylor College of Medicine, Houston, TX, USA.
• Other Collaborator (Clinical)
  • Bruno P. Chumpitazi, MD. Baylor College of Medicine, Houston, TX, USA.
• Other Collaborator (Sequencing)
  • Joe Petrosino, PhD. Baylor College of Medicine, Houston, TX, USA.
  • Sarah Highlander, PhD. Baylor College of Medicine, Houston, TX, USA.
  • Richard Gibbs, PhD. Baylor College of Medicine, Houston, TX, USA.
  • Bonnie P. Youmans. Baylor College of Medicine, Houston, TX, USA.
  • Matthew Clayton Ross. Baylor College of Medicine, Houston, TX, USA.
  • Xiang Qin, PhD. Baylor College of Medicine, Houston, TX, USA.
• Other Collaborator (Sample Preparation for Sequencing)
  • Tulin Ayvaz. Baylor College of Medicine, Houston, TX, USA.