Journal article

Expanding the taxonomic range in the fecal metagenome

Theo R Allnutt, Alexandra J Roth-Schulze, Leonard C Harrison

BMC BIOINFORMATICS | BMC | Published : 2021

Abstract

BACKGROUND: Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limited numbers of non-bacterial species in their databases compared to available genomic sequences and their methodologies do not favour classification of rare sequences which may represent only a small fraction of their parent genome. In seeking to optimise identification of non-bacterial species, we evaluated five widely-used metagenome classifier programs (BURST, Kraken2, Centrifuge, MetaPhlAn2 and CCMetagen) for their ability to correctly assign and count simulations of bact..

View full abstract

University of Melbourne Researchers

Grants

Awarded by Leona M. and Harry B. Helmsley Charitable Trust


Awarded by NHMRC Program Grant


Awarded by NHMRC Investigator Grant


Funding Acknowledgements

This work was undertaken within the Environmental Determinants of Islet Autoimmunity (ENDIA) pregnancy-birth cohort study supported by a grant from the Juvenile Diabetes Research Foundation Australia (JDRFA) and Leona M. and Harry B. Helmsley Charitable Trust (3-SRA-2019-899-M-N), a NHMRC Program Grant (LCH 1037321) and a NHMRC Investigator Grant (LCH 1173945). Additional support was provided by the Victorian State Government Operational Infrastructure Support and the NHMRC Research Institute Infrastructure Support Scheme. Funding bodies did not contribute to the design of the study, collection, analysis, interpretation of data, or in writing the manuscript.