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Study Description

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 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 Type: Case-Control
  • Number of study subjects that have individual level data available through Authorized Access: 44

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

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 (108 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.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
16S rRNA Roche 454 GS FLX Titanium N/A N/A
Study History

This study is part of the NIH Road Map Human Microbiome Project. The first subject was enrolled on August 2009. There are currently 26 Pediatric IBS (PIBS) and 22 Pediatric Control (PCtrl) enrolled. 4 PIBS have been excluded by the time of the study description submittal. We have collected 36 PIBS and 33 PCtrl samples. 61 samples have been extracted thus far for 16S rRNA gene sequencing (454), Phylochip, and qPCR analysis. Data analysis has been completed for 46 samples representing 21 PCtrl and 25 PIBS. These 46 samples have been sequenced (454) and analyzed by phylochip and qPCR. 15 samples are currently in the pipeline for 16S rRNA gene sequencing and PhyloChip hybridization. 7 samples are currently in the pipeline for DNA extraction.

Selected publications
Diseases/Traits Related to Study (MESH terms)
Authorized Data Access Requests
Study Attribution
  • Principal Investigator
    • James Versalovic, MD, PhD. Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
  • Funding Source
    • 1UH2DK083990-01. 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.
    • Delphine Saulnier, PhD. Baylor College of Medicine, Houston, TX, USA
  • Data Analyst, Bioinformatician, Biostatistician
    • Toni-Ann Mistretta, PhD. Baylor College of Medicine, Houston, TX, USA
  • Bioinformatician, Data Analyst, Pipeline Development
    • Kevin Riehle, 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
  • Database Design and Management, Data Analyst
    • Sabeen Raza, MS. 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 (Responsible for PhyloChip Analysis)
    • Susan Lynch, PhD. University of California San Francisco, San Francisco, CA, USA
    • Debasmita Mandal, PhD. University of California San Francisco, San Francisco, CA, USA
  • Other Collaborator (Sample Preparation for Sequencing)
    • Tulin Ayvaz. Baylor College of Medicine, Houston, TX, USA