Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework

PeerJ

article

Gemma Henderson¹  Pelin Yilmaz²  Sandeep Kumar¹  Robert J. Forster³  William J. Kelly¹  Sinead C. Leahy¹  Le Luo Guan⁴  Peter H. Janssen¹ 

[1] Grasslands Research Centre, AgResearch;Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology;Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada;Department of Agricultural, Food and Nutritional Science, University of Alberta

关键词: Rumen bacteria;    16S rRNA genes;    Taxonomic assignment;    Next generation sequencing;    Working taxonomic framework;    SILVA;   

DOI  :  10.7717/peerj.6496

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.

【 授权许可】

CC BY