Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
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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 ~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.
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Human gut microbial composition differs substantially among individuals and depends on age, genetic background, physiological state, microbial interactions, environmental factors, and diet.
“Human studies have unveiled substantial differences in the gut microbial composition among individuals139–141 that depend on age, genetic background, physiological state, microbial interactions, environmental factors, and diet.142–144”
From The Gut Microbiome and the Brain (2014) · cites this paper as [141]
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- Authors
- Turnbaugh, P. J., Quince, C., Faith, J. J., McHardy, A. C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- University of Glasgow (GB)
- Max Planck Society (DE)
- 454 Life Sciences, Branford, CT 06405;
- Centre National de la Recherche Scientifique (FR)
- Howard Hughes Medical Institute (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2010-04-02
- Volume
- 107
- Issue
- 16
- Pages
- 7503-7508
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2867707
- OpenAlex
- W2082464084
- Cited by
- 478
- References
- 16
- Citations by year
- 2026: 3 · 2025: 10 · 2024: 9 · 2023: 16 · 2022: 16 · 2021: 17 · 2020: 24 · 2019: 23 · 2018: 26 · 2017: 32 · 2016: 30 · 2015: 41 · 2014: 53 · 2013: 57 · 2012: 56
- FWCI
- 23.18
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Crohn's and Colitis Foundation
- Engineering and Physical Sciences Research Council (EP/H003851/1)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01DK078669, DK78669, DK 70977, R01DK070977)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- gut microbiota, monozygotic twins, fecal microbiota, bacterial phylotypes, 16S rRNA gene sequencing, metagenome assembly, gene content, carbohydrate-active enzymes, cellulase, dockerin, Lachnospiraceae, microbial diversity, interindividual variability, transcriptional activity
- MeSH terms
- Adult, Algorithms, Bacteria, Carbohydrates, Feces, Female, Humans, Male, Models, Genetic, Obesity, Phylogeny, RNA, Ribosomal, 16S, Transcription, Genetic, Twins, Monozygotic, Genetic Variation, Gastrointestinal Tract
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