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..
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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.