In a nutshell, oligotyping is a novel computational method that can help microbial ecologists to investigate concealed diversity at an extremely precise level within their closely related organisms by utilizing very subtle variations among 16S Ribosomal RNA gene pyro-tag sequences.
With the availability and affordability of massively parallel high-throughput sequencing technologies it is now possible to collect vast amounts of sequence data that cover a great deal of bacterial diversity within an environmental sample. However, due to the nature of pyrosequencing, sequences do contain biologically irrelevant random sequencing errors, rendering them imprecise and noisy for inferring diversity at a very high-resolution using canonical computational approaches.
Oligotyping utilizes Shannon entropy as a measure to identify subtle nucleotide variation, and has been useful at revealing various ecological patterns to provide insight to answer different questions.
This web site is dedicated to explain all steps of the oligotyping pipeline, while trying to explore and explain various caveats and potential benefits of using it.
Frequently asked questions:
A success story with Gardnerella vaginalis:
Oligotyping pipeline tutorial:
Contact for questions:
meren [at] mbl.edu
Various Studies Used Oligotyping
- “A single genus in the gut microbiome reflects host preference and specificity“, 2014, The ISME Journal.
- “Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities“, 2014, mBio Journal.
- “Host-specificity among abundant and rare taxa in the sponge microbiome“, 2014, The ISME Journal.
- “Sewage reflects the distribution of human faecal Lachnospiraceae“, 2013, Environmental Microbiology.
- “Eukaryotic diversity at pH extremes“, 2013, Frontiers in Microbiology.
- “Exploring the Diversity of Gardnerella vaginalis in the Genitourinary Tract Microbiota of Monogamous Couples Through Subtle Nucleotide Variation“, 2011, PLOS ONE.