%0 Journal Article
%T Direct sequencing of the human microbiome readily reveals community differences
%A Justin Kuczynski
%A Elizabeth K Costello
%A Diana R Nemergut
%A Jesse Zaneveld
%A Christian L Lauber
%A Dan Knights
%A Omry Koren
%A Noah Fierer
%A Scott T Kelley
%A Ruth E Ley
%A Jeffrey I Gordon
%A Rob Knight
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-5-210
%X In the past few years, the availability of improved sequencing methods, including pyrosequencing [1], has revolutionized what we know about the microbes that inhabit our bodies. Although it has been known for decades that our microbial symbionts outnumber our own cellsby about a factor of 10 [2], the differences in the repertoires ofsymbiontsharbored by different healthy individuals, different siteswithin the individual, and by individuals over time are only now coming to light. Initially, it was assumed that a 'core microbiome' existed; that is, that a substantial number of microbial species was shared in each body habitat in all or most humans, and that the genomes of these core species could be used as scaffolds to assemble fragmentary data from short-read shotgun sequencing of microbial community DNA [3].The first three individuals whose gut microbiomes were surveyed using substantial numbers of 16S rRNA genesequences shared few of their species, however [4]. Similarly, observations that a person's left and right hands have only 17% of bacterial species in common, and that two different people's hands share only 13% [5], cast doubt on the concept of a substantial core set of microbial species shared by all or most people. This doubt has been reinforced by recent work that redefines core lineages or genes as 'core' even if shared by relatively few people [6,7]. In fact, on the basis of 16S rRNA geneanalyses we can rule out the possibility that, even within relatively homogeneous small populations of fewer than 100 individuals, everyone's skin-surface communities or gut communities share more than a tiny fraction of species [6-8]. This unanticipated variability in shared community membership, and also in other important aspects of the human microbiome, poses substantial conceptual and computational challenges.Of particular importance for microbiome studies is the following question: what is the effect size? That is, using standard terminology from statistics, how
%U http://genomebiology.com/2010/11/5/210