title: A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.
abstract: Recent analyses of human-associated bacterial diversity have categorized individuals into 'enterotypes' or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we recommend that multiple approaches be used and compared when testing for enterotypes.
authors: Department of Microbiology, Cornell University, Ithaca, New York, United States of America.
authors: Omry
authors: O
authors: Koren
authors: Dan
authors: D
authors: Knights
authors: Antonio
authors: A
authors: Gonzalez
authors: Levi
authors: L
authors: Waldron
authors: Nicola
authors: N
authors: Segata
authors: Rob
authors: R
authors: Knight
authors: Curtis
authors: C
authors: Huttenhower
authors: Ruth E
authors: RE
authors: Ley
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D044822:Biodiversity; D006801:Humans; D054892:Metagenome; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S