Paper Info
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.
Year
DOI
Venue
2013
10.1371/journal.pcbi.1002863
PLOS COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
microbiology,biology,computational biology
Shotgun sequencing,Human Microbiome Project,Biology,Microbiome,Metagenomics,Enterotype,Bioinformatics,Cluster analysis,Human microbiome,Sequence analysis
Journal
Volume
Issue
ISSN
9
1
1553-7358
Citations 
PageRank 
References 
20
1.69
0
Authors
8
Name
Order
Citations
PageRank
Omry Koren1201.69
Dan Knights2403.73
Antonio Gonzalez3201.69
Levi Waldron4516.96
Nicola Segata523424.61
Rob Knight636626.19
Curtis Huttenhower743830.18
Ruth E Ley8202.03