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Research Article

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

  • Les Dethlefsen,

    Affiliations: Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America, Department of Medicine, Stanford University, Stanford, California, United States of America

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  • Sue Huse,

    Affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America

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  • Mitchell L Sogin,

    Affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America

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  • David A Relman mail

    To whom correspondence should be addressed. E-mail: relman@stanford.edu

    Affiliations: Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America, Department of Medicine, Stanford University, Stanford, California, United States of America, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America

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  • Published: November 18, 2008
  • DOI: 10.1371/journal.pbio.0060280

Reader Comments (2)

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Intragenomic 16S rRNA heterogeneity

Posted by plosbiology on 07 May 2009 at 22:27 GMT

Author: Francisco Rodriguez-Valera
Position: Professor of Microbiology
Institution: Universidad MIguel Hernandez, Alicante, Spain
E-mail: frvalera@umh.es
Submitted Date: November 19, 2008
Published Date: November 27, 2008
This comment was originally posted as a “Reader Response” on the publication date indicated above. All Reader Responses are now available as comments.

The issue of the intercistronic (intragenomic if you wish) heterogeneity that affects the ribosomal operons is not addressed in this kind of studies. It is a well known fact that most bacterial cells containing more than one ribosomal operon have different versions of the 16S rRNA sequence. Furthermore, variability is often concentrated in the stem loops of the highly variable regions amplified in the pyrosequencing approach . But in any case it is quite common that different copies could diverge as much as 2% overall, in some cases much more. So we have to consider the possibility that one single natural bacterial clone contains several diverse 16S rRNA sequences (not to mention a strain or a species). The paradigm of - one 16S sequence represents one OTU - is basically flawed, regardless of the similarity range selected to define it.

No competing interests declared.