Individuality and temporal stability of the human gut microbiome


 

 

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Individuality and temporal 

stability of the human gut 

microbiome 
 

 

Shinichi Sunagawa, Siegfried 

Schloissnig, Manimozhiyan 

Arumugam, Kristoffer Forslund, 

Makedonka Mitreva, Julien Tap, 

Ana Zhu, Alison Waller, Daniel R. 

Mende, Jens Roat Kultima, John 

Martin, Karthik Kota, Shamil R. 

Sunyaev, Athanasios Typas, 

George M. Weinstock, Peer Bork 
 

 
European Molecular Biology Laboratory, 
Heidelberg, Germany 

 

Vol. 2, Suppl. (2013)   |   ISSN 2166-7403 (online)     

DOI 10.5195/cajgh.2013.120   |   http://cajgh.pitt.edu 

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SUNAGAWA 

 

 

This work is licensed under a Creative Commons Attribution 3.0 United States License. 

 

This journal is published by the University Library System of the University of Pittsburgh as part  

of its D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press. 

 

Central Asian Journal of Global Health 

Volume 2, Suppl. (2013)  |  ISSN 2166-7403 (online) |  DOI 10.5195/cajgh.2013.120 |  http://cajgh.pitt.edu 

  

 

Abstract 

Introduction: The breakthrough of next generation sequencing-technologies has enabled large-scale studies of natural microbial 

communities and the 16S rRNA genes have been widely used as a phylogenetic marker to study community structure. However, 

major limitations of this approach are that neither strain-level resolution nor genomic context of microorganisms can be provided. 

This information, however, is crucial to answer fundamental questions about the temporal stability and distinctiveness of natural 

microbial communities.  

 

Material and methods: We developed a methodological framework for metagenomic single nucleotide polymorphism (SNP) 

variation analysis and applied it to publicly available data from 252 human fecal samples from 207 European and North 

American individuals. We further analyzed samples from 43 healthy subjects that were sampled at least twice over time intervals 

of up to one year and measured population similarities of dominant gut species. 

 

Results: We detected 10.3 million SNPs in 101 species, which nearly amounts to the number identified in more than 1,000 

humans. 

 

Conclusion: The most striking result was that host-specific strains appear to be retained over long time periods. This indicates 

that individual-specific strains are not easily exchanged with the environment and furthermore, that an individuals appear to have 

a unique metagenomic genotype. This, in turn, is linked to implications for human gut physiology, such as the stability of 

antibiotic resistance potential.  

Keywords: gut microbiome, genotype, antibiotic resistance 

 

 

 

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