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Modern microbiologists are learning \u201csystem thinking\u201d and \u201cholism.\u201d Such an approach is changing our understanding of microbial physiology and our ability to diagnose\/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name \u201cdental plaque,\u201d oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. 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