Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

TitleOrganismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.
Publication TypeJournal Article
Year of Publication2010
AuthorsTurnbaugh, PJ, Quince, C, Faith, JJ, McHardy, AC, Yatsunenko, T, Niazi, F, Affourtit, J, Egholm, M, Henrissat, B, Knight, R, Gordon, JI
JournalProc Natl Acad Sci U S A
Volume107
Issue16
Pagination7503-8
Date Published2010 Apr 20
ISSN1091-6490
KeywordsAdult, Algorithms, Bacteria, Carbohydrates, Feces, Female, Gastrointestinal Tract, Genetic Variation, Humans, Male, Models, Genetic, Obesity, Phylogeny, RNA, Ribosomal, 16S, Transcription, Genetic, Twins, Monozygotic
Abstract

We deeply sampled the organismal, genetic, and transcriptional diversity in fecal samples collected from a monozygotic (MZ) twin pair and compared the results to 1,095 communities from the gut and other body habitats of related and unrelated individuals. Using a new scheme for noise reduction in pyrosequencing data, we estimated the total diversity of species-level bacterial phylotypes in the 1.2-1.5 million bacterial 16S rRNA reads obtained from each deeply sampled cotwin to be approximately 800 (35.9%, 49.1% detected in both). A combined 1.1 million read 16S rRNA dataset representing 281 shallowly sequenced fecal samples from 54 twin pairs and their mothers contained an estimated 4,018 species-level phylotypes, with each sample having a unique species assemblage (53.4 +/- 0.6% and 50.3 +/- 0.5% overlap with the deeply sampled cotwins). Of the 134 phylotypes with a relative abundance of >0.1% in the combined dataset, only 37 appeared in >50% of the samples, with one phylotype in the Lachnospiraceae family present in 99%. Nongut communities had significantly reduced overlap with the deeply sequenced twins' fecal microbiota (18.3 +/- 0.3%, 15.3 +/- 0.3%). The MZ cotwins' fecal DNA was deeply sequenced (3.8-6.3 Gbp/sample) and assembled reads were assigned to 25 genus-level phylogenetic bins. Only 17% of the genes in these bins were shared between the cotwins. Bins exhibited differences in their degree of sequence variation, gene content including the repertoire of carbohydrate active enzymes present within and between twins (e.g., predicted cellulases, dockerins), and transcriptional activities. These results provide an expanded perspective about features that make each of us unique life forms and directions for future characterization of our gut ecosystems.

DOI10.1073/pnas.1002355107
Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID20363958
PubMed Central IDPMC2867707
Grant ListDK70977 / DK / NIDDK NIH HHS / United States
DK78669 / DK / NIDDK NIH HHS / United States
R01 DK070977 / DK / NIDDK NIH HHS / United States
/ / Howard Hughes Medical Institute / United States