Microarray based characterization of the human microbial flora.

摘要

The human gastrointestinal (GI) tract is host to a remarkably dense and complex microbial ecosystem---the nearly 1012 microbes per milliliter of luminal content comprise an estimated 500-1000 bacterial species. In humans and other animals, the gut microbiota carries out a number of important functions for its host, including nutrient processing, protection against pathogens, and education of the immune system. Because of its incredible diversity, the huge range of abundances of the resident species, and our inability to culture many of these species, the GI microbiota is challenging to study. Previously, no method has been available for reliably quantifying the rare and abundant components of complex microbial mixtures in a high throughput way. Consequently, we have a poor understanding of many fundamental aspects of the human-microbe relationship. The process by which the newborn gastrointestinal tract progresses from sterility at birth to a mature microbial ecosystem within the first year of life is particularly important and poorly understood. In order to enable investigation of this and other questions in microbial ecology, we developed a novel small subunit ribosomal DNA microarray-based approach for systematic, quantitative characterization of complex microbial populations. After extensive testing and optimization, we were able to reliably detect and quantify microbial species in complex mixtures at relative abundances of 0.1%. We then developed a second generation microarray designed to give nearly comprehensive coverage of all known SSU rDNA species, and used this microarray to characterize the process of colonization of the neonatal GI tract. In a study of fourteen healthy babies from birth to approximately one year of age, we observed a high degree of variability in microbial flora during the first several months of life, and a steady progression towards a generic adult-like flora. In addition, in both babies and adults some individual patterns of bacterial colonization persisted for periods of months to more than a year. Despite its diversity, the colonization process appears to be highly deterministic, and potentially traceable to distinct genetic and environmental factors as evidenced by the observation that a pair of fraternal twins had remarkably similar temporal profiles.