Evaluation of Skin, Colonic, and Oral Microbiome and Effect of Time and Antibiotic Treatment on Organism Diversity at Each Site

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Read our disclaimer for details. Identifier: NCT01143571
Recruitment Status : Completed
First Posted : June 14, 2010
Last Update Posted : March 14, 2018
Information provided by (Responsible Party):
National Institutes of Health Clinical Center (CC) ( National Cancer Institute (NCI) )

Brief Summary:


  • Most studies of infectious agents have focused on specific microbes, such as human papillomaviruses and cervical cancer, and the hepatitis B and C virus and liver cancer. The skin and many internal areas (including the mouth and the gastrointestinal tract) also contain large numbers of naturally occurring microbes, but these areas have not received as much study.
  • Some of the infectious agents that naturally reside in the body may have an effect on health. The study of naturally occurring microbes in the human body is a new area of research, and much remains to be learned regarding the extent and pattern of their appearance and appropriate techniques for testing them.
  • Researchers are interested in collecting human samples from areas known to contain naturally occurring microbes. These samples will provide baseline information for further studies.


- To collect a set of study samples from individuals who have applied to participate in a study assessing the relationship among the bacteria H. pylori, peptic ulcer disease, and gastric cancer.


- Individuals between the ages of 21 and 65 who are participating in the clinical trial entitled A Phase III Randomized Trial of Three Antibiotic Regimens to Eradicate Helicobacter Pylori.


  • Researchers will collect oral (saliva), colonic, and skin swab samples from study participants who tested positive for the presence of the H. pylori bacteria. These samples will be collected at the three study visits (enrollment, 6 weeks, and 1 year).
  • Researchers will also collect samples from people who applied for the clinical trial but did not test positive for H. pylori. These samples will be collected at the enrollment visit and 1 year later.
  • Blood samples will be collected at each study visit.

Condition or disease
BMI General Demographics Characteristics

Detailed Description:

The study of infectious agents and their role in disease is not new. Most efforts in this area have focused on specific agents, such as human papillomaviruses and cervical cancer, Helicobacter pylori (HP) and gastric diseases and carcinoma, hepatitis B and C virus and liver cancer, to name a few. The body s skin and mucosal surface s play host to microbial communities (the microbiome) whose membership outnumbers our own somatic and germ cells by an order of magnitude or more. The skin, oral, and gastrointestinal (GI) tract are all densely colonized surfaces . Recent technological advances, however, have made exploration of the microbiome, an understudied area, feasible. It is reasonable to hypothesize that some of the infectious agents that naturally reside in the body may impact health, or that perhaps the balance between the various micro-organisms has an effect on health. This new field of study has much promise that could lead to important new discoveries of how infectious agents are associated with disease and how environmental (e.g., diet) and host responses (e.g., immune response and genetics) to these agents determine chronic patterns of colonization and subsequent disease risk.

However, because the study of the human microbiome is a new area of research, much remains to be learned regarding: a) the extent and pattern of the microbiome at various sites, b) determinants of these patterns (e.g., consistency over time), and c) optimal assay techniques.

Prior to launching large-scale epidemiological studies to evaluate the association between microbiome and disease (including cancer), it is crucial to conduct well-designed, systematic, methodological studies to address some of the issues listed above. These methodological studies will begin to provide the baseline information that could be used to plan for, and conduct disease association studies.

We propose to initiate a study to collect oral, skin, vaginal (only women), penile (men only) and colonic samples at enrollment and again 6 months later on up to 150 individuals. Our objectives are:

  1. To evaluate the microbiome heterogeneity between individuals across specimen types - colonic/oral/skin/vaginal/penile.
  2. To evaluate the microbiome heterogeneity within individuals (over time and across specimen types - colonic/oral/skin/vaginal/penile).
  3. To evaluate the effect of self-reported antibiotic treatment on the oral, colonic, skin, penile and vaginal microbiomes diversity and richness.
  4. To evaluate the associations between colonic microbiome and gastrointestinal symptom disorders (assessed by the Rome III questionnaire - a detailed diagnostic questionnaire for adult functional gastrointestinal disorder), inflammatory markers (initially using measures of C-reactive protein (CRP)), and demographic factors.
  5. To evaluate the reproducibility of assays used to measure the microbiota and compare the diversity and abundance determined by the different assays.

Study Type : Observational
Estimated Enrollment : 200 participants
Observational Model: Ecologic or Community
Time Perspective: Prospective
Official Title: Evaluation of Skin, Colonic and Oral Microbiota and Effect of Time and Antibiotic Treatment on Organism Diversity at Each Site
Study Start Date : November 20, 2009

Resource links provided by the National Library of Medicine

MedlinePlus related topics: Antibiotics
U.S. FDA Resources

Information from the National Library of Medicine

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Ages Eligible for Study:   18 Years to 100 Years   (Adult, Senior)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No

Individuals who meet the age criteria of 18 years and older and are interested in the study will be asked to provide written informed consent. Participants must be willing to reside in the study area for the study duration (6 months). Those individuals with any known medical conditions that may limit life expectancy in the short term (including but not limited to: congestive heart failure, renal failure, prior malignancy, or any other chronic disease that limits functional status to the extent that the individual cannot perform light work or the usual activities of daily self care) are ineligible for inclusion in the study. Female participants must not be pregnant.

Individuals who report recent antibiotic use will be deferred and enrolled after they have been at least 6 weeks without antibiotic use.

In Hojancha, region of Guanacaste, Costa Rica, where our study will be conducted, a population based census was completed in March 2009 and will serve as the basis for enrollment, allowing for recruitment of a representative sample of the population. The same census was used to identify participants for another study in the same area. Therefore, because we will use the same census, we will exclude participants that were enrolled in the other study. Eligible participants must be willing to return for one follow-up visit: 6 months after the initial enrollment visit and willing to allow submission of blood for assays of serum immune markers, host genetic susceptibility and environmental factors, and to provide consent for use of the specimens.

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its identifier (NCT number): NCT01143571

Costa Rica
Proyecto Epidemiologico in Hohancha
Hojancha, Costa Rica
Sponsors and Collaborators
National Cancer Institute (NCI)
Principal Investigator: Emily J Vogtmann, Ph.D. National Cancer Institute (NCI)

Responsible Party: National Cancer Institute (NCI) Identifier: NCT01143571     History of Changes
Other Study ID Numbers: 999910018
First Posted: June 14, 2010    Key Record Dates
Last Update Posted: March 14, 2018
Last Verified: July 5, 2017

Keywords provided by National Institutes of Health Clinical Center (CC) ( National Cancer Institute (NCI) ):

Additional relevant MeSH terms:
Anti-Bacterial Agents
Anti-Infective Agents