Bacterial identification and analytic challenges in clinical microbiome studies

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The importance of the human microbiome is rapidly emerging. Our bodies host complex communities of microbes with much greater genetic diversity than our own genome. This complexity is variable across subjects, and there is still much to learn about the processes that drive the establishment and maintenance of these communities.More importantly, these communities fundamentally affect the normal function of our bodies and thus are critical to understand as modifiers of human processes, including disease. The gut is an important interface with the environment and a major source of antigen exposure throughout life. In this issue of the Journal, Abrahamsson et al report on the relationship between bacterial diversity in the gut and the development of IgEpositive atopic eczema in the article entitled ‘‘Low diversity of the gut microbiota in infants with atopic eczema.’’ Three stool samples were available for study from the first year of life from 20 infants with eczema and 20 control subjects with no allergic manifestation before 2 years of age. Infants with eczema had lower stool diversity than control subjects at 1 month. Furthermore, particular subsets of bacteria differed between the groups, suggesting a specific relationship between these organisms and disease. These results are supported by several studies showing relationships between eczema and specific constituents of the infant gut microbiota. However, larger prospective trials have found that no particular bacterial groups were associated with the development of eczema. This might reflect geographic differences that confound larger studies but do not affect more localized recruitment. Resolving the differences between different studies requires consideration of how microbiome studies are analyzed, particularly with respect to feature selection, statistical approaches to higher-dimensional datasets, and taxonomic identification.