The development of novel bioinformatics tools has allowed for researchers to glean increasing amounts of information from next generation sequencing of 16S rRNA gene data. Current methods of sequence analysis have been limited to taxonomic identity up to genera or operational taxonomic units (OTUs). However, within these taxonomic classifications, numerous species can reside and play key roles in health and disease. One example of this can be seen within the oral microbiome where numerous Streptococci species cohabitate and are functionally diverse while sharing similar 16S rRNA sequences that are not distinguished between in routine taxonomic classification.
This week’s journal club at 3:30pm on Friday, July 31st at West End pub will discuss “Oligotyping Analysis of the Human Oral Microbiome” by Eren et al. This publication demonstrates the usage of oligotyping, a supervised computational approach designed to provide increased taxonomic resolution in the oral microbiome (such as distinguishing between the aforementioned Streptococci), to achieve a better understanding of the human microbiome.
I look forward to discussing:
- Their results on the spatial location of various oligotypes
- The application of oligotyping to other microbiome data
- Limitations of oligotyping
Relevant/ Related Publications:
For the original methods paper on oligotyping, click here.
For information on minimal entropy decomposition, or MED (‘unsupervised oligotyping’), click here.