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Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method
Örebro University, School of Medical Sciences.
Örebro University, School of Medical Sciences.ORCID iD: 0000-0003-3887-9519
Örebro University, School of Medical Sciences.ORCID iD: 0000-0002-0362-0008
Örebro University, School of Medical Sciences.ORCID iD: 0000-0002-8391-1576
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2019 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 9, article id e0222171Article in journal (Refereed) Published
Abstract [en]

The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles. Modern approaches employ whole genome shotgun next-generation sequencing as the basis for these analyses. Sequencing depth as well as choice of next-generation sequencing data analysis method constitute two main interacting methodological factors for such an approach. In this study, we used 200 million sequence read pairs from one fecal sample for comparing different taxonomy classification methods, using default and custom-made reference databases, at different sequencing depths. A mock community data set with known composition was used for validating the classification methods. Results suggest that sequencing beyond 60 million read pairs does not seem to improve classification. The phylogeny prediction pattern, when using the default databases and the consensus database, appeared to be similar for all three methods. Moreover, these methods predicted rather different species. We conclude that the choice of sequencing depth and classification method has important implications for taxonomy composition prediction. A multi-method-consensus approach for robust gut microbiota NGS analysis is recommended.

Place, publisher, year, edition, pages
PLOS , 2019. Vol. 14, no 9, article id e0222171
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Bioinformatics and Systems Biology
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URN: urn:nbn:se:oru:diva-76641DOI: 10.1371/journal.pone.0222171PubMedID: 31527871OAI: oai:DiVA.org:oru-76641DiVA, id: diva2:1353747
Available from: 2019-09-24 Created: 2019-09-24 Last updated: 2019-12-20Bibliographically approved

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Rajan, Sukithar K.Lindqvist, Carl MårtenBrummer, Robert JanSchoultz, IdaRepsilber, Dirk

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