Scratching the surface of the rare biosphere with ribosomal sequence tag primers

FEMS Microbiology Letters
Josh D NeufeldWilliam W Mohn

Abstract

Increasingly large datasets of 16S rRNA gene sequences reveal new information about the extent of microbial diversity and the surprising extent of the rare biosphere. Currently, many of the largest datasets are represented by short and variable ribosomal sequence tags (RSTs) that are limited in their ability to accurately assign sequences to broad-scale phylogenetic trees. In this study, we selected 30 rare RSTs from existing sequence datasets and designed primers to amplify c. 1400 bases of the 16S rRNA gene to determine whether these sequences were represented by existing databases or if they might reveal new lineages within the Bacteria. Approximately one-third of the RST primers successfully amplified longer portions of these low-abundance 16S rRNA genes in a specific manner. Subsequent phylogenetic analysis demonstrated that most of these sequences were (1) distantly related to existing cultivated microorganisms and (2) closely related to uncultivated clone sequences that were recently deposited in GenBank. The presence of so many recently collected 16S rRNA gene reference sequences in existing databases suggests that progress is being made quickly towards a microbial census, one which has begun scratching the surface of t...Continue Reading

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Citations

Jul 14, 2012·The ISME Journal·Michael D J LynchJosh D Neufeld
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·William J BrazeltonJohn A Baross
Mar 3, 2010·PLoS Computational Biology·John C WooleyIddo Friedberg
Mar 3, 2015·Nature Reviews. Microbiology·Michael D J Lynch, Josh D Neufeld
Apr 19, 2015·Applied and Environmental Microbiology·Yan YanJohannes A van Veen
Mar 7, 2020·Frontiers in Microbiology·Francisco PascoalRodrigo Costa

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